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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Oncol.</journal-id>
<journal-title>Frontiers in Oncology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Oncol.</abbrev-journal-title>
<issn pub-type="epub">2234-943X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fonc.2024.1337954</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Oncology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>
<italic>IKZF1<sup>plus</sup>
</italic> is a frequent biomarker of adverse prognosis in Mexican pediatric patients with B-acute lymphoblastic leukemia</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>Garcia-Solorio</surname>
<given-names>Joaquin</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2248800"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
<role content-type="https://credit.niso.org/contributor-roles/visualization/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
<role content-type="https://credit.niso.org/contributor-roles/project-administration/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/formal-analysis/"/>
<role content-type="https://credit.niso.org/contributor-roles/data-curation/"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
</contrib>
<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>N&#xfa;&#xf1;ez-Enriquez</surname>
<given-names>Juan Carlos</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/980779"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
<role content-type="https://credit.niso.org/contributor-roles/project-administration/"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/funding-acquisition/"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jim&#xe9;nez-Olivares</surname>
<given-names>Marco</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1076375"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Flores-Lujano</surname>
<given-names>Janet</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1012962"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Flores-Espino</surname>
<given-names>Fernanda</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Molina-Garay</surname>
<given-names>Carolina</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/926133"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Cervera</surname>
<given-names>Alejandra</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1296283"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Casique-Aguirre</surname>
<given-names>Diana</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1058835"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Pe&#xf1;aloza-Gonzalez</surname>
<given-names>Jos&#xe9; Gabriel</given-names>
</name>
<xref ref-type="aff" rid="aff6">
<sup>6</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1789726"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ba&#xf1;os-Lara</surname>
<given-names>Ma. Del Roc&#xed;o</given-names>
</name>
<xref ref-type="aff" rid="aff7">
<sup>7</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1395782"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Garc&#xed;a-Soto</surname>
<given-names>&#xc1;ngel</given-names>
</name>
<xref ref-type="aff" rid="aff8">
<sup>8</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2576582"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Galv&#xe1;n-D&#xed;az</surname>
<given-names>C&#xe9;sar Alejandro</given-names>
</name>
<xref ref-type="aff" rid="aff9">
<sup>9</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/673231"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Olaya-Vargas</surname>
<given-names>Alberto</given-names>
</name>
<xref ref-type="aff" rid="aff9">
<sup>9</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2482365"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Aguilar</surname>
<given-names>Hilario Flores</given-names>
</name>
<xref ref-type="aff" rid="aff10">
<sup>10</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1077010"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mata-Rocha</surname>
<given-names>Minerva</given-names>
</name>
<xref ref-type="aff" rid="aff11">
<sup>11</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/635440"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Garrido-Hern&#xe1;ndez</surname>
<given-names>Miguel &#xc1;ngel</given-names>
</name>
<xref ref-type="aff" rid="aff12">
<sup>12</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2532451"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sol&#xed;s-Poblano</surname>
<given-names>Juan Carlos</given-names>
</name>
<xref ref-type="aff" rid="aff13">
<sup>13</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Luna-Silva</surname>
<given-names>Nuria Citlalli</given-names>
</name>
<xref ref-type="aff" rid="aff14">
<sup>14</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Cano-Cuapio</surname>
<given-names>Lena Sarahi</given-names>
</name>
<xref ref-type="aff" rid="aff15">
<sup>15</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Aristil-Chery</surname>
<given-names>Pierre Mitchel</given-names>
</name>
<xref ref-type="aff" rid="aff16">
<sup>16</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Herrera-Quezada</surname>
<given-names>Fernando</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Carrillo-Sanchez</surname>
<given-names>Karol</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1076365"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mu&#xf1;oz-Rivas</surname>
<given-names>Anallely</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1076499"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Flores-Lagunes</surname>
<given-names>Luis Leonardo</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mendoza-Caamal</surname>
<given-names>Elvia Cristina</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1798824"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Villegas-Torres</surname>
<given-names>Beatriz Eugenia</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/997900"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Gonz&#xe1;lez-Osnaya</surname>
<given-names>Vincent</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1909360"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jim&#xe9;nez-Hern&#xe1;ndez</surname>
<given-names>Elva</given-names>
</name>
<xref ref-type="aff" rid="aff17">
<sup>17</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/382198"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Torres-Nava</surname>
<given-names>Jos&#xe9; Refugio</given-names>
</name>
<xref ref-type="aff" rid="aff17">
<sup>17</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1889152"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mart&#xed;n-Trejo</surname>
<given-names>Jorge Alfonso</given-names>
</name>
<xref ref-type="aff" rid="aff18">
<sup>18</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Guti&#xe9;rrez-Rivera</surname>
<given-names>Mar&#xed;a de Lourdes</given-names>
</name>
<xref ref-type="aff" rid="aff19">
<sup>19</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1480059"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Espinosa-Elizondo</surname>
<given-names>Rosa Martha</given-names>
</name>
<xref ref-type="aff" rid="aff20">
<sup>20</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1889111"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Merino-Pasaye</surname>
<given-names>Laura Elizabeth</given-names>
</name>
<xref ref-type="aff" rid="aff21">
<sup>21</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>P&#xe9;rez-Sald&#xed;var</surname>
<given-names>Mar&#xed;a Luisa</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1077194"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jim&#xe9;nez-Morales</surname>
<given-names>Silvia</given-names>
</name>
<xref ref-type="aff" rid="aff22">
<sup>22</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/959423"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Curiel-Quesada</surname>
<given-names>Everardo</given-names>
</name>
<xref ref-type="aff" rid="aff23">
<sup>23</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/379833"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Rosas-Vargas</surname>
<given-names>Hayde&#xe9;</given-names>
</name>
<xref ref-type="aff" rid="aff11">
<sup>11</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1076385"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Mej&#xed;a-Arangure</surname>
<given-names>Juan Manuel</given-names>
</name>
<xref ref-type="aff" rid="aff24">
<sup>24</sup>
</xref>
<xref ref-type="aff" rid="aff25">
<sup>25</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/758647"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
<role content-type="https://credit.niso.org/contributor-roles/funding-acquisition/"/>
<role content-type="https://credit.niso.org/contributor-roles/formal-analysis/"/>
<role content-type="https://credit.niso.org/contributor-roles/data-curation/"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Alaez-Verson</surname>
<given-names>Carmen</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/933719"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
<role content-type="https://credit.niso.org/contributor-roles/visualization/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
<role content-type="https://credit.niso.org/contributor-roles/project-administration/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/funding-acquisition/"/>
<role content-type="https://credit.niso.org/contributor-roles/formal-analysis/"/>
<role content-type="https://credit.niso.org/contributor-roles/data-curation/"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Laboratorio de Diagn&#xf3;stico Gen&#xf3;mico, Instituto Nacional de Medicina Gen&#xf3;mica (INMEGEN)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Unidad de Investigaci&#xf3;n M&#xe9;dica en Epidemiolog&#xed;a Cl&#xed;nica, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatr&#xed;a, Centro M&#xe9;dico Nacional (CMN) Siglo XXI, Instituto Mexicano del Seguro Social (IMSS)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Subdirecci&#xf3;n de Gen&#xf3;mica Poblacional, Instituto Nacional de Medicina Genomica (INMEGEN)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>Laboratorio de Cit&#xf3;mica del C&#xe1;ncer Infantil, Centro de Investigaci&#xf3;n Biom&#xe9;dica de Oriente, Instituto Mexicano del Seguro Social, Delegaci&#xf3;n Puebla</institution>, <addr-line>Puebla</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff5">
<sup>5</sup>
<institution>Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCYT)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff6">
<sup>6</sup>
<institution>Servicio de Onco-Pediatr&#xed;a, Hospital Ju&#xe1;rez de M&#xe9;xico, Secretar&#xed;a de Salud (SSA)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff7">
<sup>7</sup>
<institution>Centro de Investigaci&#xf3;n Oncol&#xf3;gica Una Nueva Esperanza, Universidad Popular Aut&#xf3;noma del Estado de Puebla</institution>, <addr-line>Puebla</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff8">
<sup>8</sup>
<institution>Hospital General Centro M&#xe9;dico La Raza, Instituto Mexicano del Seguro Social (IMSS)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff9">
<sup>9</sup>
<institution>Departamento de Oncologia, Instituto Nacional de Pediatr&#xed;a (INP)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff10">
<sup>10</sup>
<institution>Departamento de Inmunogenetica, Instituto de Diagnostico y Referencia Epidemiologicos (InDRE)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff11">
<sup>11</sup>
<institution>Unidad de Investigaci&#xf3;n M&#xe9;dica en Gen&#xe9;tica Humana, Hospital de Pediatr&#xed;a, CMN Siglo XXI, Instituto Mexicano del Seguro Social (IMSS)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff12">
<sup>12</sup>
<institution>Servicio de Oncohematolog&#xed;a Pedi&#xe1;trica, Hospital para el Ni&#xf1;o Poblano, Secretar&#xed;a de Salud (SS)</institution>, <addr-line>Puebla</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff13">
<sup>13</sup>
<institution>Servicio de Oncohematolog&#xed;a Pedi&#xe1;trica, Instituto Mexicano del Seguro (IMSS) Unidad M&#xe9;dica de Alta Especialidad (UMAE) Centro M&#xe9;dico Nacional (CMN) Hospital de Especialidades Dr. Manuel &#xc1;vila Camacho</institution>, <addr-line>Puebla</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff14">
<sup>14</sup>
<institution>Servicio de Hemato-Oncolog&#xed;a Pedi&#xe1;trica, Hospital de la Ni&#xf1;ez Oaxaque&#xf1;a "Dr. Guillermo Z&#xe1;rate Mijangos", Secretaria de Salud y Servicios de Salud Oaxaca (SSO)</institution>, <addr-line>Oaxaca</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff15">
<sup>15</sup>
<institution>Hospital Infantil de Tlaxcala, Servicio de Oncolog&#xed;a Pedi&#xe1;trica</institution>, <addr-line>Tlaxcala</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff16">
<sup>16</sup>
<institution>Instituto de Seguridad y Servicios Sociales de los Trabajadores al Servicio de los Poderes del Estado (ISSSTE) de Puebla, Departamento de Ense&#xf1;anza e Investigaci&#xf3;</institution>, <addr-line>Puebla</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff17">
<sup>17</sup>
<institution>Servicio de Oncolog&#xed;a, Hospital Pedi&#xe1;trico Moctezuma, Secretar&#xed;a de Salud de la Ciudad de M&#xe9;xico (SSCDMX)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff18">
<sup>18</sup>
<institution>Servicio de Hematolog&#xed;a, Centro M&#xe9;dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad M&#xe9;dica de Alta Especialidad (UMAE) Hospital de Pediatr&#xed;a &#x201c;Dr. Silvestre Frenk Freund&#x201d;</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff19">
<sup>19</sup>
<institution>Servicio de Oncolog&#xed;a, Centro M&#xe9;dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad M&#xe9;dica de Alta Especialidad (UMAE) Hospital de Pediatr&#xed;a &#x201c;Dr. Silvestre Frenk Freund&#x201d;</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff20">
<sup>20</sup>
<institution>Servicio de Hematolog&#xed;a Pedi&#xe1;trica, Hospital General de M&#xe9;xico, Secretar&#xed;a de Salud (SSA)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff21">
<sup>21</sup>
<institution>Servicio de Hematolog&#xed;a Pedi&#xe1;trica, Centro M&#xe9;dico Nacional (CMN) &#x201c;20 de Noviembre&#x201d;, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff22">
<sup>22</sup>
<institution>Laboratorio de Medicina de Precisi&#xf3;n, Instituto Nacional de Medicina Gen&#xf3;mica (INMEGEN)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff23">
<sup>23</sup>
<institution>Departamento de Bioqu&#xed;mica, Escuela Nacional de Ciencias Biol&#xf3;gicas, Instituto Politecnico Nacional (IPN)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff24">
<sup>24</sup>
<institution>Laboratorio de Gen&#xf3;mica Funcional del C&#xe1;ncer, Instituto Nacional de Medicina Gen&#xf3;mica (INMEGEN)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<aff id="aff25">
<sup>25</sup>
<institution>Facultad de Medicina, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (UNAM)</institution>, <addr-line>Mexico City</addr-line>, <country>Mexico</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Michele Redell, Baylor College of Medicine, United States</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Jose Manuel Vagace Valero, University Hospital of Badajoz, Spain</p>
<p>Adolfo Martinez, General Hospital of Mexico, Mexico</p>
<p>Kristen Kurtz, Baylor College of Medicine, United States</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Juan Manuel Mej&#xed;a-Arangure, <email xlink:href="mailto:jmejia@inmegen.gob.mx">jmejia@inmegen.gob.mx</email>; Carmen Alaez-Verson, <email xlink:href="mailto:calaez@inmegen.gob.mx">calaez@inmegen.gob.mx</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors have contributed equally to this work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>03</day>
<month>04</month>
<year>2024</year>
</pub-date>
<pub-date pub-type="collection">
<year>2024</year>
</pub-date>
<volume>14</volume>
<elocation-id>1337954</elocation-id>
<history>
<date date-type="received">
<day>13</day>
<month>11</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>29</day>
<month>02</month>
<year>2024</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2024 Garcia-Solorio, N&#xfa;&#xf1;ez-Enriquez, Jim&#xe9;nez-Olivares, Flores-Lujano, Flores-Espino, Molina-Garay, Cervera, Casique-Aguirre, Pe&#xf1;aloza-Gonzalez, Ba&#xf1;os-Lara, Garc&#xed;a-Soto, Galv&#xe1;n-D&#xed;az, Olaya-Vargas, Aguilar, Mata-Rocha, Garrido-Hern&#xe1;ndez, Sol&#xed;s-Poblano, Luna-Silva, Cano-Cuapio, Aristil-Chery, Herrera-Quezada, Carrillo-Sanchez, Mu&#xf1;oz-Rivas, Flores-Lagunes, Mendoza-Caamal, Villegas-Torres, Gonz&#xe1;lez-Osnaya, Jim&#xe9;nez-Hern&#xe1;ndez, Torres-Nava, Mart&#xed;n-Trejo, Guti&#xe9;rrez-Rivera, Espinosa-Elizondo, Merino-Pasaye, P&#xe9;rez-Sald&#xed;var, Jim&#xe9;nez-Morales, Curiel-Quesada, Rosas-Vargas, Mej&#xed;a-Arangure and Alaez-Verson</copyright-statement>
<copyright-year>2024</copyright-year>
<copyright-holder>Garcia-Solorio, N&#xfa;&#xf1;ez-Enriquez, Jim&#xe9;nez-Olivares, Flores-Lujano, Flores-Espino, Molina-Garay, Cervera, Casique-Aguirre, Pe&#xf1;aloza-Gonzalez, Ba&#xf1;os-Lara, Garc&#xed;a-Soto, Galv&#xe1;n-D&#xed;az, Olaya-Vargas, Aguilar, Mata-Rocha, Garrido-Hern&#xe1;ndez, Sol&#xed;s-Poblano, Luna-Silva, Cano-Cuapio, Aristil-Chery, Herrera-Quezada, Carrillo-Sanchez, Mu&#xf1;oz-Rivas, Flores-Lagunes, Mendoza-Caamal, Villegas-Torres, Gonz&#xe1;lez-Osnaya, Jim&#xe9;nez-Hern&#xe1;ndez, Torres-Nava, Mart&#xed;n-Trejo, Guti&#xe9;rrez-Rivera, Espinosa-Elizondo, Merino-Pasaye, P&#xe9;rez-Sald&#xed;var, Jim&#xe9;nez-Morales, Curiel-Quesada, Rosas-Vargas, Mej&#xed;a-Arangure and Alaez-Verson</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<sec>
<title>Background</title>
<p>Recurrent genetic alterations contributing to leukemogenesis have been identified in pediatric B-cell Acute Lymphoblastic Leukemia (B-ALL), and some are useful for refining classification, prognosis, and treatment selection. <italic>IKZF1<sup>plus</sup>
</italic> is a complex biomarker associated with a poor prognosis. It is characterized by <italic>IKZF1</italic> deletion coexisting with <italic>PAX5</italic>, <italic>CDKN2A/2B</italic>, or PAR1 region deletions. The mutational spectrum and clinical impact of these alterations have scarcely been explored in Mexican pediatric patients with B-ALL. Here, we report the frequency of the <italic>IKZF1<sup>plus</sup>
</italic> profile and the mutational spectrum of <italic>IKZF1, PAX5, CDKN2A/2B</italic>, and <italic>ERG</italic> genes and evaluate their impact on overall survival (OS) in a group of patients with B-ALL.</p>
</sec>
<sec>
<title>Methods</title>
<p>A total of 206 pediatric patients with <italic>de novo</italic> B-ALL were included. DNA was obtained from bone marrow samples at diagnosis before treatment initiation. A custom-designed next-generation sequencing panel was used for mutational analysis. Kaplan-Meier analysis was used for OS estimation.</p>
</sec>
<sec>
<title>Results</title>
<p>We identified the <italic>IKZF1<sup>plus</sup>
</italic> profile in 21.8% of patients, which was higher than that previously reported in other studies. A significantly older age (<italic>p=0.04</italic>), a trend toward high-risk stratification (<italic>p=0.06</italic>), and a decrease in 5-year Overall Survival (OS) (<italic>p=0.009</italic>) were observed, although heterogeneous treatment protocols in our cohort would have impacted OS. A mutation frequency higher than that reported was found for <italic>IKZF1</italic> (35.9%) and <italic>CDKN2A/2B</italic> (35.9%) but lower for <italic>PAX5</italic> (26.6%). <italic>IKZF1<sup>MUT</sup>
</italic> group was older at diagnosis (<italic>p=0.0002</italic>), and most of them were classified as high-risk (73.8%, <italic>p=0.02</italic>), while patients with <italic>CDKN2A/2B<sup>MUT</sup>
</italic> had a higher leukocyte count (<italic>p=0.01</italic>) and a tendency toward a higher percentage of blasts (98.6%, &gt;50% blasts, <italic>p=0.05</italic>) than the non-mutated patients. A decrease in OS was found in <italic>IKZF1<sup>MUT</sup>
</italic> and <italic>CDKN2A/2B<sup>MUT</sup>
</italic> patients, but the significance was lost after <italic>IKZF1<sup>plus</sup>
</italic> was removed.</p>
</sec>
<sec>
<title>Discussion</title>
<p>Our findings demonstrated that Mexican patients with B-ALL have a higher prevalence of genetic markers associated with poor outcomes. Incorporating genomic methodologies into the diagnostic process, a significant unmet need in low- and mid-income countries, will allow a comprehensive identification of relevant alterations, improving disease classification, treatment selection, and the general outcome.</p>
</sec>
</abstract>
<kwd-group>
<kwd>
<italic>IKZF1<sup>plus</sup>
</italic>
</kwd>
<kwd>
<italic>IKZF1</italic> gene mutation</kwd>
<kwd>
<italic>CDKN2A/2B</italic> gene mutation</kwd>
<kwd>
<italic>PAX5</italic> gene mutation</kwd>
<kwd>PAR1 deletions</kwd>
<kwd>pediatric B-ALL</kwd>
<kwd>overall survival</kwd>
</kwd-group>    <contract-num rid="cn001">303082, 303019, 302994</contract-num>    <contract-sponsor id="cn001">Consejo Nacional de Ciencia y Tecnolog&#xed;a<named-content content-type="fundref-id">10.13039/501100003141</named-content>
</contract-sponsor>
<counts>
<fig-count count="3"/>
<table-count count="3"/>
<equation-count count="0"/>
<ref-count count="65"/>
<page-count count="14"/>
<word-count count="7157"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Hematologic Malignancies</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<label>1</label>
<title>Introduction</title>
<p>Genomic and transcriptomic analyses performed on large cohorts of pediatric and adult B-ALL patients have identified recurrent genetic alterations and expression signatures that contribute to leukemogenesis. Some of these have clinical utility as biomarkers for refining disease classification and treatment selection. The last WHO classification for B-lymphoblastic leukemia/lymphoma comprises 13 subtypes, depending on the specific genetic alterations acquired in the leukemic cells (<xref ref-type="bibr" rid="B1">1</xref>). In addition to gene fusion information, specific treatment protocols currently incorporate a combined evaluation of copy number alterations (CNAs) in the selected genes. CNAs affecting one or more genes related to cell differentiation, cell cycle control, and apoptosis have been identified in approximately 71% of pediatric B-ALL cases (<xref ref-type="bibr" rid="B2">2</xref>). Some CNA combinations, such as the <italic>IKZF1<sup>plus</sup>
</italic> profile, have been identified as adverse modifiers of childhood B-ALL prognosis (<xref ref-type="bibr" rid="B3">3</xref>).</p>
<p>
<italic>IKZF1<sup>plus</sup>
</italic> is a high-risk category identified by Stanulla M et&#xa0;al. (<xref ref-type="bibr" rid="B3">3</xref>) in a cohort of 991 patients with B-ALL enrolled in the International Multicenter Trial AIEOP-BFM ALL 2000. <italic>IKZF1<sup>plus</sup>
</italic> was defined as &#x201c;deletion of <italic>IKZF1</italic> that co-occurred with at least one additional deletion in <italic>CDKN2A, CDKN2B</italic> (homozygous deletion only), <italic>PAX5</italic>, or PAR1 in the absence of <italic>ERG</italic> deletion&#x201d;. The PAR1 region (pseudoautosomal region 1) is located in Xp22 and Yp11 and comprises the <italic>CRLF2</italic>, <italic>CSF2RA</italic>, and <italic>IL3RA</italic> genes. Patients with deletions affecting <italic>ERG</italic> were excluded from the <italic>IKZF1<sup>plus</sup>
</italic> group. <italic>IKZF1<sup>plus</sup>
</italic> was associated with a very poor prognosis in B-ALL patients with detectable minimal residual disease (MRD) (<xref ref-type="bibr" rid="B3">3</xref>). Following the initial report, several other studies have confirmed that this subgroup of patients had inferior outcomes (<xref ref-type="bibr" rid="B4">4</xref>&#x2013;<xref ref-type="bibr" rid="B7">7</xref>).</p>
<p>
<italic>IKZF1</italic> encodes Ikaros, a zinc-finger transcription factor required for the development of all lymphoid lineages. Deletions (<italic>IKZF1<sup>DEL</sup>
</italic>) and small mutations in this gene lead to the acquisition of a stem cell-like phenotype by haploinsufficiency and loss of DNA-binding capacity (<xref ref-type="bibr" rid="B8">8</xref>). These alterations have been reported to be independent biomarkers of adverse prognoses (<xref ref-type="bibr" rid="B9">9</xref>&#x2013;<xref ref-type="bibr" rid="B11">11</xref>). Deletions in the <italic>ERG</italic> gene (<italic>ERG<sup>DEL</sup>
</italic>) can suppress this negative outcome, whereas JAK-STAT activation enhances this adverse effect (<xref ref-type="bibr" rid="B12">12</xref>, <xref ref-type="bibr" rid="B13">13</xref>). These findings support the importance of evaluating the mutational profiles of several genes rather than specific alterations in isolated genes for more accurate risk stratification.</p>
<p>
<italic>CDKN2A</italic> and <italic>CDKN2B</italic> (<italic>CDKN2A/2B</italic>) are tumor suppressor genes located on chromosome 9p21 and encode three key cell cycle regulators, p16INK4A and p14ARF, encoded by the alternative readings of <italic>CDKN2A</italic>, and p15INK4B, encoded by <italic>CDKN2B</italic> (<xref ref-type="bibr" rid="B14">14</xref>). <italic>CDKN2A/2B</italic> deletions (<italic>CDKN2A/2B<sup>DEL</sup>
</italic>) have been detected in approximately 20&#x2013;25% of pediatric patients with B-ALL (<xref ref-type="bibr" rid="B15">15</xref>). It has been suggested that inactivation of <italic>CDKN2A/2B</italic> is a secondary cooperative event that plays an essential role in leukemogenesis, cell cycle regulation, chemosensitivity, and apoptosis (<xref ref-type="bibr" rid="B14">14</xref>). The contribution of this alteration to prognosis is controversial. Some studies support that <italic>CDKN2A/2B<sup>DEL</sup>
</italic>, especially in the case of biallelic status, is associated with inferior outcomes in B-ALL (<xref ref-type="bibr" rid="B16">16</xref>&#x2013;<xref ref-type="bibr" rid="B18">18</xref>), while others claim that this alteration is not a poor prognostic factor in childhood B-ALL (<xref ref-type="bibr" rid="B14">14</xref>, <xref ref-type="bibr" rid="B19">19</xref>).</p>
<p>
<italic>PAX5</italic> encodes a transcription factor that participates in the development of normal B cells and in maintaining cell identity by repressing the signature genes of other lineages during differentiation (<xref ref-type="bibr" rid="B20">20</xref>). <italic>PAX5</italic> is found in a physiological complex with <italic>IKZF1</italic> and <italic>RUNX1</italic> (<xref ref-type="bibr" rid="B21">21</xref>). Somatic or germline alterations that deregulate <italic>PAX5</italic> activity may lead to B cell malignancies (<xref ref-type="bibr" rid="B22">22</xref>). <italic>PAX5</italic> alterations include deletions (<italic>PAX5<sup>DEL</sup>
</italic>), focal intragenic amplifications (<italic>PAX5<sup>igAMP</sup>
</italic>), translocations with various partners, or point mutations. All these were identified in B-ALL at different frequencies (<xref ref-type="bibr" rid="B23">23</xref>). Alterations in <italic>PAX5</italic> have been associated with inferior outcomes (<xref ref-type="bibr" rid="B2">2</xref>), which are worse when <italic>IKZF1</italic> deletion is present (<xref ref-type="bibr" rid="B24">24</xref>).</p>
<p>The frequency of alterations, mutational spectrum, and clinical impact of <italic>IKZF1, PAX5, CDKN2A/2B</italic>, <italic>ERG</italic> gene mutations, and the <italic>IKZF1<sup>plus</sup>
</italic> profile have not been extensively explored in Mexican pediatric B-ALL patients. A better understanding of genomic alterations occurring in B-ALL pediatric leukemia and their clinical impact is crucial for Hispanic populations such as Mexicans. High incidence rates of childhood acute leukemia have been consistently observed in the Mexican population (55.0 cases per million children under 15 years of age) (<xref ref-type="bibr" rid="B25">25</xref>&#x2013;<xref ref-type="bibr" rid="B27">27</xref>). Additionally, mortality and morbidity rates are higher than those in high-income countries, particularly as a consequence of deaths related to refractory disease and treatment-related toxicity (<xref ref-type="bibr" rid="B28">28</xref>, <xref ref-type="bibr" rid="B29">29</xref>). The identification of clinically relevant genetic alterations may contribute to more effective and personalized treatment options for these patients, potentially improving their outcomes while minimizing unnecessary treatment-related side effects and costs. Genomic alterations play a significant role in determining disease evolution and the response of cancer cells to specific treatments (<xref ref-type="bibr" rid="B30">30</xref>). Genetic data from ethnically diverse populations would help obtain a more comprehensive understanding of leukemia subtypes and treatment responses across diverse populations.</p>
<p>This study aimed to identify the frequency and heterogeneity of the <italic>IKZF1<sup>plus</sup>
</italic> profile and mutational spectrum of <italic>IKZF1, PAX5, CDKN2A/2B</italic>, and <italic>ERG</italic> in a cohort of 206 Mexican pediatric patients with <italic>de novo</italic> B-ALL. The clinical impact on overall survival was also evaluated for the analyzed genes and <italic>IKZF1<sup>plus</sup>
</italic> profile.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<label>2</label>
<title>Materials and methods</title>
<sec id="s2_1">
<label>2.1</label>
<title>Population</title>
<p>This analysis included 206 <italic>de novo</italic> B-ALL pediatric Mexican patients from 10 different states of Mexico (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;1A</bold>
</xref> displays the number of patients by state). Patients were treated at 18 public health institutions (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;1B</bold>
</xref>). The diagnosis was established between January 2018 and April 2023 by pediatric hematologists/oncologists according to clinical features: cell morphology, immunophenotype, and genetics, as defined by the 2008 WHO classification of lymphoid neoplasms (<xref ref-type="bibr" rid="B31">31</xref>). The patients had a range of 0 to 17 years, and only 3 of them were younger than one year. The risk classification was established as defined by the Children&#x2019;s Oncology Group (COG) and the National Cancer Institute (NCI) (<xref ref-type="bibr" rid="B32">32</xref>). The presence of at least one of the following clinical features was considered as high-risk: age at diagnosis &#x2265;10 years, WBC counts higher than 5x10<sup>4</sup> count/&#xb5;L, positive minimal residual disease (MRD) on day 28, presence of nervous system infiltration, treatment failure response, and identification of any high-risk gene fusion (when that information was available). Cytogenetic results were unavailable for most patients. Before treatment initiation, 3&#x2013;5 mL of bone marrow was collected into EDTA tubes at their respective medical institutions and sent to the Laboratory of Genomic Diagnosis at INMEGEN. Clinical data were collected from medical charts, including the child&#x2019;s sex, age, white blood cell count in the peripheral blood, and percentage of blasts in the bone marrow at diagnosis and treatment protocol. The median follow-up of these patients was 1.4 years.</p>
</sec>
<sec id="s2_2">
<label>2.2</label>
<title>Nucleic acid extraction and quantification</title>
<p>DNA was isolated using the Maxwell&#xae; RSC Instrument (Promega Corporation, Madison, WI, USA). DNA concentration and quality were evaluated using a NanoDrop&#xae; 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) and a Qubit&#xae; 4 Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA).</p>
</sec>
<sec id="s2_3">
<label>2.3</label>
<title>Next-generation sequencing (Targeted DNAseq) and bioinformatics</title>
<p>A customized panel was designed to identify genetic alterations in <italic>CDKN2A</italic>, <italic>CDKN2B</italic>, <italic>PAX5</italic>, <italic>ERG</italic>, and <italic>IKZF1</italic>. Panel synthesis was performed using an Archer Dx (ArcherDX, Inc., Boulder, CO, USA). Library preparation was performed following the manufacturer&#x2019;s instructions. Libraries were sequenced on the NextSeq 500/550 using the High Output Sequencing Reagent Kit v2.5 (300 cycles) (Illumina, Inc., San Diego, CA, USA). Bioinformatics analysis was performed using the Archer Suite Analysis v5.1.3 software (ArcherDX, Inc., Boulder, CO, USA) using the human reference genome GRCh37.p13/hg19. The bioinformatics pipeline allowed the identification of single nucleotide variations, small insertions/deletions, copy number alterations (CNAs), and structural variations (SV) (this last only for the <italic>IKZF1</italic> gene). According to the Archer Dx bioinformatics pipeline (ArcherDX, Inc., Boulder, CO, USA), SV occurs when individual reads contain nucleotide sequences that are aligned to different genome regions. The length of the SV was determined by observing the breakpoint positions of the partners identified in the event and subtracting the differences in their genomic positions (User Manual Archer Analysis 6.0 CS001). Mutations were considered if the variant allele fraction (VAF) was &#x2265; 5%. A minimum 500x-fold depth coverage was required for all targeted regions in the panel.</p>
</sec>
<sec id="s2_4">
<label>2.4</label>
<title>Multiplex ligation-dependent probe amplification</title>
<p>NGS-predicted <italic>IKZF1, CDKN2A/2B</italic>, and <italic>PAX5</italic> deletions were confirmed by MLPA using SALSA Probemix P335 (ALL-IKZF1) according to the manufacturer&#x2019;s protocol (Holland, Amsterdam, Netherlands). This probe also allowed for the identification of PAR1 deletions, as described previously (<xref ref-type="bibr" rid="B3">3</xref>). The P327 iAMP21-ERG probe mix was used to confirm ERG deletions. Fragment separation was performed on a 3500 Genetic Analyzer (Thermo Fisher Scientific Inc., Waltham, MA, USA). The raw data files were imported and analyzed using Coffalyser.Net&#x2122; software (MRC Holland, Amsterdam, Netherlands).</p>
</sec>
<sec id="s2_5">
<label>2.5</label>
<title>
<italic>IKZF1<sup>plu</sup>
</italic>
<sup>s</sup> profile definition</title>
<p>The <italic>IKZF1<sup>plu</sup>
</italic>
<sup>s</sup> profile was defined based on the <italic>Stanulla et&#xa0;al., 2018</italic> report (<xref ref-type="bibr" rid="B3">3</xref>). Briefly, the patient was considered <italic>IKZF1<sup>plus</sup>
</italic> positive if <italic>IKZF1<sup>DEL</sup>
</italic> co-occurred with <italic>CDKN2A<sup>DEL</sup>
</italic>, <italic>CDKN2B<sup>DEL</sup>
</italic> (homozygous deletion only), <italic>PAX5<sup>DEL</sup>
</italic>, or pseudoautosomal region 1 (PAR1) deletion. As it has been reported that <italic>ERG<sup>DEL</sup>
</italic> mitigates the adverse prognosis associated with <italic>IKZF1</italic> deletions (<xref ref-type="bibr" rid="B12">12</xref>), patients with <italic>ERG<sup>DEL</sup>
</italic> were excluded from the <italic>IKZF1<sup>plus</sup>
</italic> group. The <italic>NO-IKZF1<sup>plus</sup>
</italic> group included any other patient, regardless of whether they were <italic>IKZF1<sup>MUT</sup>
</italic> or <italic>IKZF1<sup>WT</sup>
</italic>.</p>
</sec>
<sec id="s2_6">
<label>2.6</label>
<title>Statistical analysis</title>
<p>Measures of central tendency were used to describe continuous variables related to the patient&#x2019;s clinical and demographic features. The &#x3c7;&#xb2; test or Fisher&#x2019;s exact test was used to assess the relationship between categorical variables. In contrast, the nonparametric Mann&#x2013;Whitney U test was used to analyze the association between continuous variables, where p &lt;0.05 was considered statistically significant. OS was estimated using the Kaplan-Meier method. The log-rank test was used to evaluate the differences between survival distributions with a 95% confidence interval (CI). The Cox regression model was used to perform a multivariate analysis, with adjustments made for other risk factors such as sex, age at diagnosis, WBC count, percentage of blast cells, and risk stratification at diagnosis. OS was calculated from the day of diagnosis until either the last follow-up or death from any cause. Patients who did not experience any event were censored at the last follow-up visit. Those who did not attend the follow-up were censored at the date of the last known contact. Statistical calculations were performed using the RStudio software version 4.3.1, and the data were visualized using the ggplot2 package version 3.4.3.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<label>3</label>
<title>Results</title>
<p>The clinical features of the study population are summarized in <xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>. Most patients (63.2%) were classified as high-risk. The most frequent high-risk features were age at diagnosis &lt; 1 or &#x2265; 10 years, WBC counts higher than 5x10<sup>4</sup> count/&#xb5;L, followed by positive minimal residual disease (MRD) on day 28. The remaining patients were classified as having a standard risk.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Clinical features of the analyzed population.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="center">Characteristic</th>
<th valign="top" align="center">N (%)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">
<bold>Sex</bold>
</td>
<td valign="middle" align="center">
<bold>N=206</bold>
</td>
</tr>
<tr>
<td valign="middle" align="center">Male</td>
<td valign="middle" align="center">110 (53.4%)</td>
</tr>
<tr>
<td valign="middle" align="center">Female</td>
<td valign="middle" align="center">96 (46.6%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>Age at diagnosis</bold>
<break/>
<bold>Mean 7.9 &#xb1; 4.8 (0-17 years)</bold>
</td>
<td valign="middle" align="center">
<bold>N=185</bold>
</td>
</tr>
<tr>
<td valign="middle" align="center">&lt; 10</td>
<td valign="middle" align="center">114 (61.6%)</td>
</tr>
<tr>
<td valign="middle" align="center">&#x2265; 10</td>
<td valign="middle" align="center">71 (38.4%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>WBC at Diagnosis (count/&#xb5;L)</bold>
</td>
<td valign="middle" align="center">
<bold>N=185</bold>
</td>
</tr>
<tr>
<td valign="middle" align="center">&lt; 10,000</td>
<td valign="middle" align="center">82 (44.3%)</td>
</tr>
<tr>
<td valign="middle" align="center">10,000 to &lt; 20,000</td>
<td valign="middle" align="center">36 (19.5%)</td>
</tr>
<tr>
<td valign="middle" align="center">20,000 &lt; 100,000</td>
<td valign="middle" align="center">53 (28.6%)</td>
</tr>
<tr>
<td valign="middle" align="center">&#x2265; 100000</td>
<td valign="middle" align="center">14 (7.6%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>% of blasts at diagnosis in bone marrow</bold>
</td>
<td valign="middle" align="center">
<bold>N=185</bold>
</td>
</tr>
<tr>
<td valign="middle" align="center">20% to 50%</td>
<td valign="middle" align="center">14 (7.6%)</td>
</tr>
<tr>
<td valign="middle" align="center">&#x2265; 50%</td>
<td valign="middle" align="center">171 (92.4%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>Risk classification at diagnosis</bold>
</td>
<td valign="middle" align="center">
<bold>N=182</bold>
</td>
</tr>
<tr>
<td valign="middle" align="center">Standard</td>
<td valign="middle" align="center">67 (36.8%)</td>
</tr>
<tr>
<td valign="middle" align="center">High Risk</td>
<td valign="middle" align="center">115 (63.2%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>High-risk criteria</bold>
</td>
<td valign="middle" align="center">
<bold>N (%)*</bold>
</td>
</tr>
<tr>
<td valign="middle" align="left">Age<break/>WBC Count<break/>Positive MRD<break/>Extramedullary disease<break/>Steroid pretretment<break/>Positive BCR::ABL1<break/>Hypodiploidy<break/>Immunophenotype<break/>Not Specified</td>
<td valign="top" align="center">58 (50.43%)<break/>34 (29.6%)<break/>13 (11.3%)<break/>12 (10.4%)<break/>8 (6.9%)<break/>6 (5.2%)<break/>4 (3.5%)<break/>3 (2.6%)<break/>4 (3.5%)</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>WBC, white blood cell count; N, patients with available data for each category.</p>
</fn>
<fn>
<p>*Percentage of patients who met each high-risk criterion was calculated considering N=115 classified as &#x201c;high-risk&#x201d;, several patients had more than one, therefore percentage added&gt;100%.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>This group of patients was treated using six different protocols, depending on the medical preferences and institutional resources available in each case. The number of patients per treatment protocol is presented in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;2</bold>
</xref>.</p>
<sec id="s3_1">
<label>3.1</label>
<title>Frequency of <italic>IKZF1<sup>plus</sup>
</italic> profile in B-ALL Mexican pediatric patients</title>
<p>The <italic>IKZF1<sup>plus</sup>
</italic> profile was present in 21.8% (45/206) of the evaluated patients. Gene deletion combinations within the <italic>IKZF1<sup>plus</sup>
</italic> group are shown in <xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>. In our series, three patients were excluded from the <italic>IKZF1<sup>plus</sup>
</italic> profile because of <italic>ERG<sup>DEL</sup>
</italic>.</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Frequency of the different gene-deletion combinations conforming to the <italic>IKZF <sup>plus</sup>
</italic> profile.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="center"/>
<th valign="middle" align="center">
<italic>CDKN2A/2B</italic>
</th>
<th valign="middle" align="center">
<italic>PAX5</italic>
</th>
<th valign="middle" align="center">
<italic>PAR1</italic>
</th>
<th valign="middle" align="center">N (%)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" rowspan="7" align="center">
<bold>
<italic>IKZF1<sup>DEL</sup>
</italic>
</bold>
</td>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">15 (33.3%)</td>
</tr>
<tr>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">13 (28.9%)</td>
</tr>
<tr>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">7 (15.6%)</td>
</tr>
<tr>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">5 (11.1%)</td>
</tr>
<tr>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">NEG</td>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">4 (8.9%)</td>
</tr>
<tr>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">DEL</td>
<td valign="middle" align="center">1 (2.2%)</td>
</tr>
<tr>
<td valign="middle" colspan="3" align="center">
<italic>Total with IKZF1<sup>plus</sup>
</italic>
</td>
<td valign="middle" align="center">
<italic>45/206, (21.8%)</italic>
</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>N, patients in each category.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3_2">
<label>3.2</label>
<title>Clinical impact and overall survival analysis of the <italic>IKZF1<sup>plus</sup>
</italic> profile</title>
<p>The patients were stratified according to the presence of <italic>IKZF1<sup>plus,</sup>
</italic> and the clinical feature distribution was evaluated between the groups (<xref ref-type="table" rid="T3">
<bold>Table&#xa0;3</bold>
</xref>). Age at diagnosis showed significant differences between the groups, with patients with <italic>IKZF1<sup>plus</sup>
</italic> being older (<italic>p=0.04</italic>). Additionally, a trend toward higher risk classification was observed within the <italic>IKZF1<sup>plus</sup>
</italic> group. No significant differences were found in sex distribution, percentage of bone marrow blasts, or WBC count at diagnosis between the two groups.</p>
<table-wrap id="T3" position="float">
<label>Table&#xa0;3</label>
<caption>
<p>Clinical features of patients with the <italic>IKZF1<sup>plus</sup>
</italic> profile.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="center">Characteristics</th>
<th valign="top" align="center">
<italic>IKZF1<sup>plus</sup>
</italic>
</th>
<th valign="top" align="center">
<italic>NO IKZF1<sup>plus</sup>
</italic>
</th>
<th valign="top" align="center">OR<break/>CI 95%</th>
<th valign="top" align="center">*p value</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">
<bold>Sex</bold>
</td>
<td valign="middle" align="center">
<bold>N=45</bold>
</td>
<td valign="middle" align="center">
<bold>N=161</bold>
</td>
<td valign="middle" align="center"/>
<td valign="middle" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">Male</td>
<td valign="middle" align="center">28 (62.2%)</td>
<td valign="middle" align="center">84 (52.2%)</td>
<td valign="middle" rowspan="2" align="center">1.5098<break/>0.7669 to 2.9723</td>
<td valign="middle" rowspan="2" align="center">0.23</td>
</tr>
<tr>
<td valign="middle" align="center">Female</td>
<td valign="middle" align="center">17 (37.8%)</td>
<td valign="middle" align="center">77 (47.8%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>Age at diagnosis</bold>
</td>
<td valign="middle" align="center">
<bold>N=38</bold>
</td>
<td valign="middle" align="center">
<bold>N=149</bold>
</td>
<td valign="middle" align="center"/>
<td valign="middle" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">&lt; 10</td>
<td valign="middle" align="center">18 (47.4%)</td>
<td valign="middle" align="center">97 (65.1%)</td>
<td valign="middle" rowspan="2" align="center">2.0726<break/>1.0085 to 0.42598</td>
<td valign="middle" rowspan="2" align="center">0.04</td>
</tr>
<tr>
<td valign="middle" align="center">&#x2265; 10</td>
<td valign="middle" align="center">20 (52.6%)</td>
<td valign="middle" align="center">52 (34.9%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>WBC at diagnosis</bold>
</td>
<td valign="middle" align="center">
<bold>N=38</bold>
</td>
<td valign="middle" align="center">
<bold>N=147</bold>
</td>
<td valign="middle" align="center"/>
<td valign="middle" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">&lt; 10,000</td>
<td valign="middle" align="center">15 (39.5%)</td>
<td valign="middle" align="center">67 (45.6%)</td>
<td valign="middle" align="center"/>
<td valign="middle" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">10,000 to &lt; 20,000</td>
<td valign="middle" align="center">6 (15.7%)</td>
<td valign="middle" align="center">29 (19.7%)</td>
<td valign="middle" align="center">0.9241<break/>0.3259 to 2.6203</td>
<td valign="middle" align="center">0.82</td>
</tr>
<tr>
<td valign="middle" align="center">20,000 &lt; 100,000</td>
<td valign="middle" align="center">14 (36.8%)</td>
<td valign="middle" align="center">39 (26.5%)</td>
<td valign="middle" align="center">1.6034<break/>0.7002 to 3.6715</td>
<td valign="middle" align="center">0.26</td>
</tr>
<tr>
<td valign="middle" align="center">&#x2265; 100000</td>
<td valign="middle" align="center">3 (8%)</td>
<td valign="middle" align="center">12 (8.2%)</td>
<td valign="middle" align="center">1.1167<break/>0.2799 to 4.4543</td>
<td valign="middle" align="center">0.87</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>% of blasts at diagnosis in bone marrow</bold>
</td>
<td valign="middle" align="center">
<bold>N=38</bold>
</td>
<td valign="middle" align="center">
<bold>N=147</bold>
</td>
<td valign="middle" align="center"/>
<td valign="middle" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">20% to 50%</td>
<td valign="middle" align="center">0 (0%)</td>
<td valign="middle" align="center">13 (8.8%)</td>
<td valign="middle" rowspan="2" align="center">7.7286<break/>0.4491 to 132.9930</td>
<td valign="middle" rowspan="2" align="center">0.15</td>
</tr>
<tr>
<td valign="middle" align="center">&#x2265; 50%</td>
<td valign="middle" align="center">38 (100%)</td>
<td valign="middle" align="center">134 (91.2%)</td>
</tr>
<tr>
<td valign="middle" align="center">
<bold>Risk classification at Diagnosis</bold>
</td>
<td valign="middle" align="center">
<bold>N=38</bold>
</td>
<td valign="middle" align="center">
<bold>N=144</bold>
</td>
<td valign="middle" align="center"/>
<td valign="middle" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">Standard</td>
<td valign="middle" align="center">9 (23.7%)</td>
<td valign="middle" align="center">58 (40.3%)</td>
<td valign="middle" rowspan="2" align="center">2.1731<break/>0.9584 to 4.9275</td>
<td valign="middle" rowspan="2" align="center">0.06</td>
</tr>
<tr>
<td valign="top" align="center">High Risk</td>
<td valign="top" align="center">29 (76.3%)</td>
<td valign="top" align="center">86 (59.7%)</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>*Fisher&#x2019;s exact or chi-square test; OR, Odds Ratio; CI, Confidence interval; N, number of patients with available data for each category; WBC, white blood cell count.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>The impact of <italic>IKZF1<sup>plus</sup>
</italic> on OS at five years was evaluated in 168 patients for whom information for OS calculation was available (35 <italic>IKZF1<sup>plus</sup>
</italic> vs. 133 <italic>NO-IKZF1<sup>plus</sup>
</italic>). The <italic>IKZF1<sup>plus</sup>
</italic> group showed significantly reduced OS at 5 years compared to the <italic>NO-IKZF1<sup>plus</sup>
</italic> group (<italic>p=0.009</italic>, <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). A significantly worse OS was also observed for the high-risk-<italic>IKZF1<sup>plus</sup>
</italic>-positive subgroup when patients were stratified by the <italic>IKZF1<sup>plus</sup>
</italic> status and the risk category (<italic>p=0.02</italic>, <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>).</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Overall survival curves at five years of <italic>IKZF1<sup>plus</sup>
</italic> were estimated with the Kaplan&#x2013;Meier method. <bold>(A)</bold> Decreased OS in patients with <italic>IKZF1<sup>plus</sup>
</italic> (blue) versus <italic>NO-IKZF1<sup>plus</sup>
</italic> (yellow). <bold>(B)</bold> Overall survival curves stratified according to <italic>IKZF1<sup>plus</sup>
</italic> status and risk classification at diagnosis. The lowest OS was observed in the high-risk <italic>IKZF1<sup>plus</sup>
</italic> positive group. Standard-risk <italic>NO-IKZF1<sup>plus</sup>
</italic> patients (navy blue), high-risk <italic>NO-IKZF1<sup>plus</sup>
</italic> patients (light blue), high-risk <italic>IKZF1<sup>plus</sup>
</italic> (gray), standard-risk <italic>IKZF1<sup>plus</sup>
</italic> (yellow).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-14-1337954-g001.tif"/>
</fig>
<p>We conducted a Cox regression multivariate analysis to examine the impact of the <italic>IKZF1<sup>plus</sup>
</italic> profile, taking into account additional clinical factors such as patient age, sex, white blood cell count, percentage of blast cells, and the risk classification at the time of diagnosis. The analysis revealed that having the <italic>IKZF1<sup>plus</sup>
</italic> profile significantly increases the risk of death by 3.7 times (HR = 3.7227, p = 0.02), highlighting its role as an independent poor outcome-predicting factor. The other variables included in the model did not demonstrate a statistically significant effect on the outcome.</p>
</sec>
<sec id="s3_3">
<label>3.3</label>
<title>Mutational profiles of <italic>IKZF1</italic>, <italic>PAX5</italic>, <italic>CDKN2A</italic>, <italic>CDKN2B</italic>, <italic>ERG</italic> genes and PAR1 regions in Mexican patients with B-ALL</title>
<p>The types of mutations identified in each gene and their frequencies are shown in <xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2</bold>
</xref>. <italic>IKZF1</italic> was altered (<italic>IKZF1<sup>MUT</sup>
</italic>) in 35.9% (74/206) of patients studied (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;3</bold>
</xref> for sequence mutations and <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;4</bold>
</xref> for CNAs). Deletions were the most common alterations, representing 86.5% (64/74) of positive cases. Deletion affecting exons 4&#x2013;7 (IK6 isoform) was the most common (39%, 25/64), followed by complete gene deletion (31.2%, 20/64). Moreover, a deletion spanning exons 1&#x2013;8 was present in 7.9% (5/64) of cases (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>). SV was also detected in 54.7% of the patients with deletions. In contrast, only SVs were identified in seven individuals; interestingly, in six of them, the VAF was &lt; 10%.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Frequency and type of mutations identified for <italic>IKZF1</italic>, <italic>CDKN2A/2B</italic>, <italic>PAX5</italic>, and <italic>ERG</italic> genes. For <italic>IKZF1</italic>, CNAs concomitant (red) with SV (green) were identified in some patients (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;4</bold>
</xref>); these patients were counted only in the CNA_del group in this figure. The PAR1 region was not included because only deletions can be detected by MLPA.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-14-1337954-g002.tif"/>
</fig>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Schematic representation of the mutational profile identified in the <italic>IKZF</italic>1, <italic>PAX5</italic>, <italic>CDKN2A</italic>, <italic>CDKN2B</italic>, and <italic>ERG</italic> genes. Coding exons and the corresponding protein domain are shown for each gene. Red lines indicate the deleted region, and the percentage (right side) represents the proportion of cases with deletions. The remaining percentage corresponds to deleted regions with lower frequencies (not represented in the Figure). The complete deletion information is available in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;4</bold>
</xref>. <bold>(A)</bold> <italic>IKZF1</italic>; NM_006060, <bold>(B)</bold> <italic>PAX5</italic>; NM_016734.2, the yellow line represents regions with <italic>PAX5<sup>igAMP</sup>
</italic>, <bold>(C)</bold> <italic>CDKN2A</italic>; NM_000077, <bold>(D)</bold> <italic>CDKN2B</italic>; NM_004936, <bold>(E)</bold> <italic>ERG</italic>; NM_004449. Chromosome figures were taken from NCBI Bookshelf ID: NBK22266.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-14-1337954-g003.tif"/>
</fig>
<p>Sequence mutations were identified in 9 cases; in six of them, a concomitant deletion or SV was also present. Ten mutations were identified in nine cases: four missense mutations, four nonsense mutations, and two frameshift mutations, most of which were located in the DNA-binding domain coding region. In two patients, p.Asn159Tyr (N159Y) was identified without additional <italic>IKZF1</italic> alterations.</p>
<p>At least one <italic>PAX5</italic> alteration (<italic>PAX5<sup>MUT</sup>
</italic>) was identified in 26.6% (55/206) of patients (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Tables&#xa0;3, 4</bold>
</xref>). These include CNAs caused by complete or partial gene deletions, gains, and small sequence mutations. <italic>PAX5<sup>DEL</sup>
</italic> was the most common alteration, representing 75% (41/55) of <italic>PAX5<sup>MUT</sup>
</italic>. In most cases, 63.4% (26/41), several exons were deleted, most commonly from exon 2 to 5 or from exon 2 to 6 (14%, 6/41 of each). In two cases, only one exon was deleted (exon 1 or exon 7). The whole gene (exons 1-10) was deleted in 36.6% (15/41) of cases. <italic>PAX5<sup>igAMP</sup>
</italic> was identified in four patients; in two of them, additional genetic material was present in exons 2-5, one in exon 5, and one in the whole gene (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>; <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;4</bold>
</xref>).</p>
<p>A total of 17 <italic>PAX5</italic> sequence mutations were identified in 15 patients: four nonsense mutations, five missense mutations [one p.Pro80Arg (P80R)], seven frameshifts, and one intronic variant (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;3</bold>
</xref>). In eight of them, a second alteration in <italic>PAX5</italic> was also present: four deletions, two sequence mutations, and two gains of material in <italic>PAX5</italic>.</p>
<p>
<italic>CDKN2A<sup>DEL</sup>
</italic> was identified in 35.92% (74/206) of the cases; in most cases (65/74), <italic>CDKN2B</italic> was entirely or partially deleted (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3C, D</bold>
</xref>). <italic>CDKN2A</italic> homozygous deletion was observed in 40 patients; in 30 of them, <italic>CDKN2B</italic> also showed homozygous deletion. The most frequent <italic>CDKN2A<sup>DEL</sup>
</italic> comprised exons 1 to 3 and was identified in 85.1% (63/74) of the patients, followed by the deletion of exon 1, which was identified in 14.9% (11/74) of <italic>CDKN2A<sup>DEL</sup>
</italic> patients. For <italic>CDKN2B</italic>, exon 1 and 2 deletions were identified in 87.7% (57/65), followed by exon 2 deletion in 12.3% (8/65) of the <italic>CDKN2B-</italic>positive cases (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;4</bold>
</xref>). In six cases, sequence variants were identified in <italic>CDKN2A</italic> (four cases) and <italic>CDKN2B</italic> (two cases) (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;3</bold>
</xref>).</p>
<p>
<italic>ERG<sup>MUT</sup>
</italic> was identified in 8.7% (18/206) of cases (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Tables&#xa0;3, 4</bold>
</xref>). Among the <italic>ERG<sup>DEL</sup>
</italic> patients (13/18), involved various exons. These deletions affect the region expanding exons 2 to 11, encoding the <italic>ERG</italic> protein&#x2019;s pointed domain (PNT) or alternative domain (AD) of the ERG protein. Sequencing variants were identified in five cases, three of which were located in the erythroblast transformation-specific domain (Ets) of the protein (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3E</bold>
</xref>, <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;3</bold>
</xref>).</p>
<p>Deletion of the PAR1 region was assessed by MLPA in patients with <italic>IKZF1<sup>DEL</sup>
</italic>. We identified only ten patients with PAR1 deletions (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;4</bold>
</xref>).</p>
</sec>
<sec id="s3_4">
<label>3.4</label>
<title>Clinical impact and overall survival analysis of patients with <italic>IKZF1</italic>, <italic>PAX5</italic>, <italic>CDKN2A/2B</italic>, and <italic>ERG</italic> mutations</title>
<p>Sex distribution, age at diagnosis, WBC count at diagnosis, percentage of blasts, and risk assignment were compared between patients positive and negative for <italic>IKZF1</italic>, <italic>PAX5</italic>, <italic>CDKN2A/2B</italic>, and <italic>ERG</italic> mutations (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Tables&#xa0;5A&#x2013;D</bold>
</xref>). The frequency of high-risk patients and of those older than 10 years at diagnosis was significantly higher in the <italic>IKZF1<sup>MUT</sup>
</italic> group (<italic>p=0.02</italic> and <italic>p=0.002</italic>, respectively). A higher proportion (37.7%) of patients with <italic>CDKN2A/2B<sup>MUT</sup>
</italic> had a WBC count in the range of 20,000&#x2013;100,000 cells than <italic>CDKN2A/2B<sup>NEG</sup>
</italic> patients (22.4%) (<italic>p=0.01</italic>). Additionally, a significantly higher proportion of patients had &gt; 50% blasts at diagnosis in the CDKN<italic>2A/2B<sup>MUT</sup>
</italic> (98.6%) group than in the <italic>CDKN2A/2B<sup>NEG</sup>
</italic> group (89.7%) (<italic>p=0.05</italic>) (<xref ref-type="supplementary-material" rid="SM2">
<bold>Supplementary Table&#xa0;5B</bold>
</xref>). In the case of <italic>PAX5<sup>MUT</sup>
</italic>, a higher percentage of cases was associated with high-risk classification at diagnosis, but the difference was not statistically significant (<italic>p=0.06</italic>).</p>
<p>A significant decrease in OS was observed in the <italic>IKZF1<sup>MUT</sup>
</italic> (<italic>p=0.02</italic>) (<xref ref-type="supplementary-material" rid="SM2">
<bold>Supplementary Figure&#xa0;1A</bold>
</xref>) and <italic>CDKN2A/2B<sup>MUT</sup>
</italic> (<italic>p=0.006</italic>) (<xref ref-type="supplementary-material" rid="SM2">
<bold>Supplementary Figure&#xa0;1B</bold>
</xref>) groups. Significant differences (<italic>p=0.02</italic>) in OS were identified between the homozygous <italic>CDKN2A<sup>MUT</sup>
</italic> and heterozygous <italic>CDKN2A<sup>MUT</sup>
</italic> vs. <italic>CDKN2A<sup>NEG</sup>
</italic> patients. (<xref ref-type="supplementary-material" rid="SM2">
<bold>Supplementary Figure&#xa0;1C</bold>
</xref>). No significant effect on OS was observed for <italic>PAX5<sup>MUT</sup>
</italic> or <italic>ERG<sup>MUT</sup>
</italic> (<xref ref-type="supplementary-material" rid="SM2">
<bold>Supplementary Figures&#xa0;1D, E</bold>
</xref>).</p>
<p>To determine whether the observed negative impact of <italic>CDKN2A/2B<sup>MUT</sup>
</italic> and <italic>IKZF1<sup>MUT</sup>
</italic> mutations on OS was conferred by <italic>IKZF1<sup>plus</sup>
</italic>-positive patients in both groups, we excluded <italic>IKZF1<sup>plus</sup>
</italic> patients from the OS analysis. After eliminating these patients, no significant differences in OS were observed between the <italic>CDKN2A/2B<sup>MUT</sup>
</italic> or <italic>IKZF1<sup>MUT</sup>
</italic> groups and those without mutations in these genes (<xref ref-type="supplementary-material" rid="SM2">
<bold>Supplementary Figures&#xa0;2A, B</bold>
</xref>).</p>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<p>To the best of our knowledge, this is the first study to evaluate the frequency, heterogeneity, and clinical impact of the <italic>IKZF1<sup>plus</sup>
</italic> profile in an unselected group of Mexican pediatric patients with B-ALL. We also report the comprehensive mutational spectrum of <italic>IKZF1</italic>, <italic>PAX5</italic>, <italic>CDKN2A/2B</italic>, and <italic>ERG</italic> genes present at diagnosis in these patients. In contrast to most published studies that used MLPA to evaluate deletions in <italic>IKZF1</italic>, <italic>PAX5</italic>, <italic>CDKN2A/2B</italic>, and <italic>ERG</italic> genes related to the <italic>IKZF1<sup>plus</sup>
</italic> profile, we used a custom-designed panel based on NGS. The bioinformatics algorithm allows the simultaneous evaluation of CNA (gain or deletions) with higher sensitivity than MLPA and of the sequence mutations present in at least 5% of the cells.</p>
<p>The frequency of <italic>IKZF1<sup>plus</sup>
</italic> was higher (21.8%) than that reported in previous studies that analyzed patients of European ethnicities. Examples include Stanulla et&#xa0;al. (6%) (<xref ref-type="bibr" rid="B3">3</xref>), Braun et&#xa0;al. (2%) (<xref ref-type="bibr" rid="B4">4</xref>), Kicinski et&#xa0;al. (6%) (<xref ref-type="bibr" rid="B33">33</xref>), and Schwab et&#xa0;al. (13%) (<xref ref-type="bibr" rid="B34">34</xref>). Although few studies have been performed in Latin American populations, the frequencies are also lower than those detected in Argentina (9.2%) (<xref ref-type="bibr" rid="B5">5</xref>) and Brazil (11%, including pediatric and adult patients) (<xref ref-type="bibr" rid="B35">35</xref>). Using NGS, a more sensitive analysis methodology may have contributed to the higher frequency observed in our study. MLPA can only detect alterations if present in at least 25% of cells but fails to detect alterations when present in a smaller fraction of malignant cells, such as a subclone.</p>
<p>The two most frequent combinations, representing approximately 70% of the <italic>IKZF1<sup>plus</sup>
</italic>-positive cases, comprised the simultaneous deletion of <italic>IKZF1</italic>-<italic>CDKN2A/2B</italic> or <italic>IKZF1</italic>-<italic>CDKN2A/2B</italic>-<italic>PAX5</italic>, similar to the results observed in other series (<xref ref-type="bibr" rid="B4">4</xref>). The high frequency of these two combinations is unsurprising given that <italic>CDKN2A/2B<sup>DEL</sup>
</italic> is the most recurrently reported CNA in B-ALL, and frequently, the deletion also removes <italic>PAX5</italic>, which is located close to the <italic>CDKN2A/2B</italic> complex.</p>
<p>Because gene fusion information and iAMP21 were available for these patients (personal communication, the fusion data are being prepared for publication), we correlated the distribution of <italic>IKZF1<sup>plus</sup>
</italic> with these alterations. The <italic>BCR::ABL1</italic> fusion group had the highest proportion of <italic>IKZF1<sup>plus</sup>
</italic>-positive patients (66.7%), followed by the iAMP21 (50%) and Ph-like groups (47%). <italic>IKZF1<sup>plus</sup>
</italic> was also present in cases without these alterations but in a much lower proportion (13.7%)<italic>. IKZF1<sup>plus</sup>
</italic> was not identified in the <italic>ETV6::RUNX1, TCF3::PBX1, PAX5::ETV6, DUX4, or MEFD2</italic> rearranged group of patients. The <italic>IKZF1<sup>plus</sup>
</italic> molecular profile was associated with older age at diagnosis (52.6% &#x2265; 10 years in the <italic>IKZF1<sup>plus</sup>
</italic> group vs. 34.9% in the <italic>NO-IKZF1<sup>plus</sup>
</italic> cases, <italic>p=0.04</italic>) and high-risk classification at diagnosis (76.3% of <italic>IKZF1<sup>plus</sup>
</italic> were classified as high-risk, <italic>p=0.06</italic>), similar to previous findings (<xref ref-type="bibr" rid="B3">3</xref>, <xref ref-type="bibr" rid="B36">36</xref>).</p>
<p>According to our results, <italic>IKZF1<sup>plus</sup>
</italic> had a significantly negative effect on OS. Similar results were reported by Crepinsek et&#xa0;al., who showed that the <italic>IKZF1<sup>plus</sup>
</italic> subgroup had the lowest OS compared with <italic>IKFZ1<sup>MUT</sup>
</italic> patients or <italic>IKZF1<sup>WT</sup>
</italic> (<xref ref-type="bibr" rid="B36">36</xref>). The decline in OS observed in our patients was especially pronounced for <italic>IKZF1<sup>plus</sup>
</italic> patients classified as high-risk at diagnosis compared with <italic>IKZF1<sup>plus</sup>
</italic> standard-risk patients. In most studies, the negative prognostic impact of <italic>IKZF1<sup>plus</sup>
</italic> on disease-free survival (DFS) was found to be limited to the subgroup of patients with positive MRD after induction (<xref ref-type="bibr" rid="B4">4</xref>, <xref ref-type="bibr" rid="B33">33</xref>). The effect of <italic>IKZF1<sup>plus</sup>
</italic> on DFS was not evaluated in our patients because the MRD information was not available. However, a more recent study that included 1,200 patients reported no statistically significant association between <italic>IKZF1<sup>plus</sup>
</italic> and DFS (<xref ref-type="bibr" rid="B33">33</xref>).</p>
<sec id="s4_1">
<label>4.1</label>
<title>Mutational profile of <italic>IKZF1</italic>, <italic>PAX5</italic>, <italic>CDKN2A</italic>, <italic>CDKN2B</italic>, <italic>ERG</italic> genes and PAR1 region in Mexican patients with B-ALL</title>
<p>The frequency of <italic>IKZF1<sup>MUT</sup>
</italic> in this cohort (35.9%) was higher than that reported for Mexican patients. Ay&#xf3;n-Perez et&#xa0;al. found that 20.6% (36 cases) (<xref ref-type="bibr" rid="B37">37</xref>), while Rosales-Rodr&#xed;guez et&#xa0;al. (<xref ref-type="bibr" rid="B38">38</xref>) detected 27% (63 cases) both using MLPA. The frequency of <italic>IKZF1<sup>MUT</sup>
</italic> in our study was still higher (31.1%) than previously reported in Mexicans if only the deletions were considered in the <italic>IKZF1<sup>MUT</sup>
</italic> count. <italic>IKZF1<sup>MUT</sup>
</italic> frequencies in other populations were also lower: American (28.6%) (<xref ref-type="bibr" rid="B9">9</xref>), Brazilian (19.3%) (<xref ref-type="bibr" rid="B39">39</xref>), and Argentinian (9.2%) (<xref ref-type="bibr" rid="B5">5</xref>). The differences in the sensitivity of the methodology contributed to the increased frequency detected in our study. In most previous reports, MLPA was used; therefore, SV present in a low proportion could not be observed. In fact, seven patients in our study had SV with a VAF &lt; 10%; concomitant deletion was not detected in these patients. Therefore, they would have been considered &#x201c;negative&#x201d; if MLPA had been used as the detection method.</p>
<p>In most patients with <italic>IKZF1<sup>DEL</sup>
</italic>, deletion of exons 4&#x2013;7, which encode the dominant negative IK6 isoform, was identified. Whole gene deletion, resulting in the loss of expression of the wild-type allele, was the second most frequent deletion. Four patients showed deletions in the noncoding exon 1. Deletions involving the 5&#x2019; region of <italic>IKZF1</italic> also result in haploinsufficiency owing to a significant reduction in <italic>IKZF1</italic> mRNA expression (<xref ref-type="bibr" rid="B40">40</xref>). <italic>IKZF1</italic> is intolerant to variants that cause loss of function, according to the constraint metrics obtained from the gnomAD exome database (<xref ref-type="bibr" rid="B41">41</xref>).</p>
<p>The <italic>IKZF1</italic>
<sup>N159Y</sup> mutation was present in less than 1% of our cases (two cases, 0.9%), and a similar low frequency was found in an analysis of 1988 pediatric B-ALL cases (0.4%) (<xref ref-type="bibr" rid="B42">42</xref>). No other <italic>IKZF1</italic> alterations were present in these two patients, suggesting retention of the non-mutated <italic>IKZF1</italic> allele, as previously reported in this subgroup of patients (<xref ref-type="bibr" rid="B42">42</xref>). This mutation is located inside the DNA-binding domain and induces nuclear mislocalization and intercellular adhesion. The transcriptomic profile of the <italic>IKZF1</italic>
<sup>N159Y</sup> positives was different from that observed in other patients with alterations in <italic>IKZF1</italic>, suggesting that <italic>IKZF1</italic>
<sup>N159Y</sup> could define a new subtype of B-ALL (<xref ref-type="bibr" rid="B42">42</xref>). The upregulation of genes involved in oncogenesis, chromatin remodeling, and signaling has been identified in patients with <italic>IKZF1</italic>
<sup>N159Y</sup> (<xref ref-type="bibr" rid="B43">43</xref>).</p>
<p>
<italic>IKZF1<sup>DEL</sup>
</italic> was associated with older age at diagnosis, which is in accordance with the results of previous studies (<xref ref-type="bibr" rid="B9">9</xref>, <xref ref-type="bibr" rid="B44">44</xref>). <italic>IKZF1<sup>DEL</sup>
</italic> was associated with poor outcomes in several studies (<xref ref-type="bibr" rid="B9">9</xref>&#x2013;<xref ref-type="bibr" rid="B11">11</xref>). In our patients, a significant decrease in OS was also observed for <italic>IKZF1<sup>MUT</sup>
</italic> (<italic>p=0.02</italic>). Still, it seems to have been mainly contributed by the <italic>IKZF1<sup>plus</sup>
</italic> patients present in the <italic>IKZF1<sup>MUT</sup>
</italic> group since significance was lost after removing the <italic>IKZF1<sup>plus</sup>
</italic> patients. In previous reports, the contribution of <italic>IKZF1<sup>plus</sup>
</italic> to the poor outcome observed with <italic>IKZF1<sup>MUT</sup>
</italic> was not independently evaluated.</p>
<p>
<italic>PAX5<sup>MUT</sup>
</italic> was less frequent in Mexican patients than in other ethnic groups. <italic>PAX5<sup>MUT</sup>
</italic> has been found in approximately one-third of non-Hispanic B-ALL pediatric cases, according to studies performed in the USA and Netherlands (<xref ref-type="bibr" rid="B9">9</xref>, <xref ref-type="bibr" rid="B45">45</xref>). In this study, the proportion of <italic>PAX5<sup>MUT</sup>
</italic> was only 26.6%, considering all alterations (deletions, gain, and small sequence mutations). The frequency of <italic>PAX5</italic> fusion-positive patients increased to only 27.7%, which is still lower than that reported in other studies (<xref ref-type="bibr" rid="B46">46</xref>). A previous study in Mexican patients found that 15.9% <italic>PAX5<sup>DEL</sup>
</italic> by MLPA (<xref ref-type="bibr" rid="B38">38</xref>) was lower than that reported in Brazilians (25.2%) using the same methodology (<xref ref-type="bibr" rid="B39">39</xref>).</p>
<p>Monoallelic deletions affecting the paired domain were the most frequently identified <italic>PAX5</italic> alterations, similar to the findings in other groups (<xref ref-type="bibr" rid="B9">9</xref>, <xref ref-type="bibr" rid="B45">45</xref>). They involve small portions of the gene or cause whole-gene loss, impairing the DNA-binding capacity of the PAX5 protein. Mouse models have shown that haploinsufficiency of Pax5, caused by monoallelic deletion, confers susceptibility to B-cell transformation. However, other oncogenic events that act synergistically are required for leukemic transformation (<xref ref-type="bibr" rid="B47">47</xref>). In our cohort, <italic>PAX5<sup>DEL</sup>
</italic> was concomitant with the BCR::ABL1, Ph-like-related fusions, and <italic>EBF1</italic> mutations. The activation of STAT5 and mutations in <italic>EBF1, JAK3</italic>, and <italic>BCR::ABL1</italic> have also been identified as cooperative events in <italic>PAX5<sup>DEL</sup>
</italic> mice (<xref ref-type="bibr" rid="B48">48</xref>, <xref ref-type="bibr" rid="B49">49</xref>).</p>
<p>Extra copies of <italic>PAX5</italic> regions were identified in four cases, representing 1.9% of the total and 7.4% of the <italic>PAX5</italic>-positive group. An extra chromosome 9 would be present in one of them, as the other genes in chromosome 9 included in the NGS panel also showed more than two copies. No cytogenetic data were available for this patient to confirm the presence of extra Chr 9. <italic>PAX5<sup>igAMP</sup>
</italic> was the most likely alteration in the three other patients, with a gain in genetic material observed for the exons encoding the DNA-binding and octapeptide domains, as reported previously (<xref ref-type="bibr" rid="B50">50</xref>).</p>
<p>
<italic>PAX5<sup>igAMP</sup>
</italic> has been associated with male sex, age at diagnosis older than ten years, and high-risk stratification. This alteration is frequently associated with <italic>CDKN2A/2B<sup>DEL</sup>
</italic> (82%), and appears to be mutually exclusive with other significant risk-stratifying genetic lesions (<xref ref-type="bibr" rid="B50">50</xref>). Despite the small number of patients with <italic>PAX5<sup>igAMP</sup>
</italic> in our analysis (3 cases), the clinical features were similar to those reported: three were males, 2/3 were older than ten years, and 1/3 had nine years; all were classified as high-risk at diagnosis. <italic>CDKN2A/2B<sup>DEL</sup>
</italic> was present in all cases, and <italic>BCR::ABL1</italic> was the only fusion identified (one case). Although the functional consequences of amplification have not yet been established, it has been suggested that increased copies of the DNA-binding region may alter binding to PAX5 target genes, leading to dysregulated B-cell differentiation and transformation (<xref ref-type="bibr" rid="B51">51</xref>). <italic>PAX5<sup>igAMP</sup>
</italic> was associated with a high incidence of relapse (<xref ref-type="bibr" rid="B50">50</xref>). We did not evaluate the impact of <italic>PAX5<sup>igAMP</sup>
</italic> on OS because of the small number of patients.</p>
<p>It has been suggested that some sequencing mutations may serve as initiating rather than secondary cooperative events in leukemogenesis (<xref ref-type="bibr" rid="B42">42</xref>). <italic>PAX5</italic> point mutations have been identified in 7&#x2013;10% of pediatric cases of B-ALL, similar to the frequency in our patients (7.3%), being the second most common <italic>PAX5</italic> type of alteration. Fourteen mutations were identified, mainly located in the paired or transactivating domains. The most common consequence was the loss of function due to a frameshift or premature stop codon (7/14). Only seven of them have been previously reported in the COSMIC database (as of October 2023), and two previously described cases were recurrent in our patients: p.Ala322ArgfsTer19 (three cases) and p.Trp358Ter (two cases), both of which affect the transactivation domain. The frequency of <italic>PAX5<sup>P80R</sup>
</italic> in our cases was lower than that previously reported. Only one case (0.5%) was identified, in contrast to the 2&#x2013;6% observed in other studies (<xref ref-type="bibr" rid="B42">42</xref>, <xref ref-type="bibr" rid="B52">52</xref>&#x2013;<xref ref-type="bibr" rid="B54">54</xref>). In accordance with previous observations, this case was negative for fusions or iAMP21 and had an additional <italic>PAX5</italic> loss-of-function mutation affecting the other allele. Mart&#xed;nez-Anaya et&#xa0;al. reported <italic>PAX5<sup>P80R</sup>
</italic> in 1.4% of the patients; however, only Ph-like Mexican pediatric patients were analyzed (<xref ref-type="bibr" rid="B55">55</xref>). In seven cases with sequence mutations, both <italic>PAX5</italic> copies were affected, with a deletion, gain, or a second point mutation in the other allele.</p>
<p>
<italic>PAX5</italic> alterations can function as cooperative events or germline-initiating genetic lesions in B-ALL patients (<xref ref-type="bibr" rid="B23">23</xref>). In most of our cases, the VAF of <italic>PAX5</italic> sequence mutations was lower than expected, considering the percentage of blast cells present in the bone marrow sample analyzed, suggesting that <italic>PAX5</italic> sequence mutations are secondary events that occur only in a subpopulation of malignant cells. Additionally, none of the sequencing mutations identified in our study has been reported as germline variants according to the HGMD professional database (as of October 2023) or had a VAF suggesting a germline origin.</p>
<p>As observed in another series of B-ALL patients, <italic>CDKN2A/2B<sup>DEL</sup>
</italic> was the most frequently identified CNA (35.9%) in Mexican patients. Homozygous deletion of both genes occurred in a high proportion of the cases (40.5%). As previously reported, none of the patients had <italic>CDKN2B<sup>DEL</sup>
</italic> without <italic>CDKN2A<sup>DEL</sup>
</italic> (<xref ref-type="bibr" rid="B3">3</xref>). The frequency of <italic>CDKN2A/2B<sup>DEL</sup>
</italic> was higher than that reported by Rosales-Rodr&#xed;guez et&#xa0;al. (31.7%) in Mexican patients (<xref ref-type="bibr" rid="B38">38</xref>). Lower frequencies have also been reported in other Latin American and Asian populations, including Colombia (25%) (<xref ref-type="bibr" rid="B56">56</xref>), Brazil (31.8%) (<xref ref-type="bibr" rid="B39">39</xref>), China (20.2%) (<xref ref-type="bibr" rid="B15">15</xref>), and India (19.8%) (<xref ref-type="bibr" rid="B57">57</xref>). In our study, <italic>CDKN2A/2B<sup>DEL</sup>
</italic> was associated with higher blast counts at diagnosis and high-risk features. Most patients with this alteration were classified as high-risk, although the difference was not statistically significant.</p>
<p>Sequence variants of <italic>CDKN2A/2B</italic>, including <italic>CDKN2A</italic> (1.9%) and <italic>CDKN2B</italic> (0.97%), occur in a very low proportion of patients with B-ALL. Three <italic>CDKN2A</italic> sequence variants, p.Ile49Thr, p.Val51ProfsTer89, and c.151-6_151delinsC, had a VAF close to 50% and were classified as likely pathogenic according to ACMG criteria (<xref ref-type="bibr" rid="B58">58</xref>). However, p.Ile49Thr is probably of germline origin since it has been previously identified in the Latino population database (f=0.00451, 1456/34586, gnomAD exomes database, as of October 2023). Although it is listed in ClinVar (ID 127523) with conflicting classifications (pathogenic vs. uncertain significance), functional studies support its role in pathogenicity (<xref ref-type="bibr" rid="B59">59</xref>). However, this effect appears more moderate than other known pathogenic variants of <italic>CDKN2A</italic> (<xref ref-type="bibr" rid="B60">60</xref>). The variant has been reported to be pathogenic in families with melanoma and pancreatic cancer (<xref ref-type="bibr" rid="B60">60</xref>). It has been identified several times in Mexican women with breast cancer who fulfill genetic risk criteria. Ten patients with cancer carrying this variant, identified in our laboratory, reported no family history of leukemia or other hematological malignancies during routine evaluation for cancer predisposition syndromes. No history of cancer was present in the family of the B-ALL patient carriers of this variant. The variant p.Val51ProfsTer89 produces a loss of function due to a frameshift, and c.151-6_151delinsC is a deletion insertion that affects the canonical splicing site in exon two and may cause nonsense-mediated decay. These variants are not listed in the HGMD or ClinVar databases (as of October 2023), are absent from population databases, and have not been reported as germline variants in cancer syndromes. None of the patients had a family history of cancer. As DNA obtained from non-hematopoietic tissue was unavailable, variants&#x2019; germline or somatic origins could not be clarified.</p>
<p>
<italic>CDKN2B</italic> p.Asn44Ser was identified in two cases, with a VAF of approximately 50%. It is classified as having uncertain significance according to ACMG and has not been reported as a somatic mutation. It has a low frequency in Latino individuals. (f=0.0121%, 4/33098, gnomAD exomes, as of August 2023), and was absent from the Mexican database incorporated into the Franklin By Genoox platform (470 individuals). The allele frequency in our cohort of B-ALL patients was significantly higher than in gnomAD patients (0.4% in B-ALL vs. 0.0121% in gnomAD exomes, X<sup>2</sup> = 22, <italic>p=2.7E-06</italic>). As both patients were from Oaxaca State, we can speculate that this variant could be frequent in this region of Mexico. However, a possible association with an increased risk of leukemia development cannot be ruled out without further investigation.</p>
<p>OS was significantly decreased (<italic>p=0.006</italic>) in the <italic>CDKN2A/2B<sup>MUT</sup>
</italic> group, but similar to what happened for the decreased OS in the <italic>IKZF1<sup>DEL</sup>
</italic> group, the significance was lost after removing the <italic>IKZF1<sup>plus</sup>
</italic> patients. <italic>CDKN2A/2B<sup>DEL</sup>
</italic> has been correlated with inferior 3-year event-free survival and 3-year OS rates in B-ALL patients (<xref ref-type="bibr" rid="B15">15</xref>). Other researchers have concluded that <italic>CDKN2A/2B<sup>DEL</sup>
</italic> is associated with an increased probability of relapse and death (<xref ref-type="bibr" rid="B17">17</xref>, <xref ref-type="bibr" rid="B57">57</xref>, <xref ref-type="bibr" rid="B61">61</xref>, <xref ref-type="bibr" rid="B62">62</xref>), but the contribution of <italic>IKZF1<sup>plus</sup>
</italic> patients to these outcomes has not been evaluated.</p>
<p>No conclusive data exist regarding the contribution of <italic>CDKN2A/2A<sup>DEL</sup>
</italic> heterozygous or homozygous status. In our study, <italic>CDKN2A/2B<sup>DEL</sup>
</italic> heterozygous patients showed a significant decrease in OS (<italic>p=0.02</italic>) compared with homozygous and wild-type patients. However, Feng et&#xa0;al. (<xref ref-type="bibr" rid="B15">15</xref>) showed that patients with biallelic deletions had a worse 3-year EFS than those without. However, other authors have reported that homozygous <italic>CDKN2A/2B<sup>DEL</sup>
</italic> is not associated with poor prognosis in childhood B-ALL (<xref ref-type="bibr" rid="B63">63</xref>).</p>
<p>In our cohort, somatic mutations in <italic>ERG</italic> were identified in 8.7% of patients, with most presenting deletions (72.2% of the <italic>ERG<sup>MUT</sup>
</italic> cases) that affect one or more exons encoding the <italic>ERG</italic> protein&#x2019;s pointed domain of the ERG protein or the alternative domain. All sequence variants identified in <italic>ERG</italic> are probably somatic, considering the VAF, and are located mainly in the erythroblast transformation-specific domain. According to the COSMIC database (as of October 2023), these domains are reported to be mutated in hematopoietic neoplasms.</p>
<p>Patients with <italic>ERG<sup>MUT</sup>
</italic> had better OS, although statistical significance was not reached because of the small sample size. None of the patients with <italic>ERG<sup>DEL</sup>
</italic> experienced mortality, supporting the reported association between <italic>ERG<sup>DEL</sup>
</italic> and favorable outcomes (<xref ref-type="bibr" rid="B12">12</xref>, <xref ref-type="bibr" rid="B13">13</xref>).</p>
<p>The present study has several limitations that must be considered when interpreting the results. It was a multicenter retrospective analysis of a heterogeneous group of patients. Treatment protocol and hospital-related factors would have influenced OS. The patients were treated according to six protocols, the only target therapy available was imatinib, and it was used only in the BCR::ABL1 positive patients. Due to the lack of molecular testing, Ph-like patients were not identified and did not receive target therapy, which would affect their OS. Economic resources and hospital infrastructure may vary among the 18 hospitals where the patients were treated. Cytogenetic/FISH characterization and MRD determination are not routinely performed in all Mexican public institutions, and this information was unavailable for these patients. Despite being one of the most extensive series evaluating molecular alterations in pediatric B-ALL, the number of patients is still small, and clinical information was not available for 100% of the patients; thus, it reduces the statistical power to detect additional differences in the distribution of clinical features between mutation-positive and mutation-negative patients or between subgroups of <italic>IKZF1<sup>plus</sup>
</italic> patients or to evaluate the impact of specific mutations on OS. Finally, additional biological and socioeconomic factors that were not assessed in the present study could have contributed to the poor patient outcomes.</p>
</sec>
</sec>
<sec id="s5" sec-type="conclusions">
<label>5</label>
<title>Conclusion</title>
<p>This study is the first to evaluate the prevalence and impact of the <italic>IKZF1<sup>plus</sup>
</italic> profile on OS in Mexican pediatric patients with B-ALL using NGS. Our results showed a higher frequency than previously reported and a significantly lower OS in patients with this alteration. Our results support the notion that a high frequency of genetic markers related to poor outcomes is present in Mexican patients at the time of diagnosis. The interplay between adverse genetic features and socioeconomic challenges contributes to the higher mortality and morbidity observed in pediatric B-ALL patients in our country (<xref ref-type="bibr" rid="B64">64</xref>, <xref ref-type="bibr" rid="B65">65</xref>). The incorporation of genomic methodologies into the diagnosis process of B-ALL, a significant unmet need in low- and mid-income countries, will allow the comprehensive identification of clinically relevant alterations, improving disease classification, treatment selection, and probably the general outcome.</p>
</sec>
<sec id="s6" sec-type="data-availability">
<title>Data availability statement</title>
<p>The data presented in this study are deposited in online repository of National Center for Biotechnology Information, ClinVar, accession number SUB13858637.</p>
</sec>
<sec id="s7" sec-type="ethics-statement">
<title>Ethics statement</title>
<p>The studies involving humans were approved by Comisi&#xf3;n Nacional de Investigaci&#xf3;n Cient&#xed;fica del Instituto Mexicano del Seguro Social (IMSS) (Number of document R-2020-785-022. The studies were conducted in accordance with the local legislation and institutional requirements. Written informed consent for participation in this study was provided by the participants&#x2019; legal guardians/next of kin.</p>
</sec>
<sec id="s8" sec-type="author-contributions">
<title>Author contributions</title>
<p>JGS, JCNE, JMMA, and CAV carried out the conceptualization, data curation, formal analysis, funding acquisition, investigation, methodology, project administration, resources, software, supervision, validation, and visualization. MJO, FFE, CMG, AC, KCS, AMR, LLFL, ECMC, BEVT, VGO, ECQ, HFA, and JMMA provided technical support in methodology. JCNE, JFL, DCA, JGPG, EJH, MRBL, JRTN, AGS, JAMT, CAGD, MLGR, AOV, RMEE, LEMP, MLPS, MMR, MAGH, JCSP, NCLS, LSCC, PMAC, HRV, SJM, and FHQ provided resources such as study materials and clinical data. JGS and CAV undertook writing &#x2013; original draft and writing &#x2013; review &amp; editing. Final approval of the manuscript was provided by all authors, who were accountable for all aspects of the work. JGS and JCNE share equal contributions, whereas JMMA and CAV are corresponding authors.</p>
</sec>
</body>
<back>
<sec id="s9" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCYT) grants: &#x201c;Pronaii Leucemia Infantil, Proyecto Nacional de Investigaci&#xf3;n e Incidencia &#x201c;: FORDECYT-PRONACES/303082/2019 and FORDECYT-PRONACES/303019/2019, FORDECYT-PRONACES/302994/2019, &#x201c;Fondo Sectorial de Investigaci&#xf3;n en Salud y Seguridad Social SS/IMSS/ISSSTE-CONACYT &#x201c;000000000273210 and Frontera de la Ciencia CF-2023-G-1399. JG-S received a fellowship from CONAHCYT (CVU 1042482).</p>
</sec>
<ack>
<title>Acknowledgments</title>
<p>The authors would like to thank the patients and their families for cooperating with this study.</p>
</ack>
<sec id="s10" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
<p>The reviewer, AM, declared a shared affiliation with the author RE-E to the handling editor at the time of review.</p>
</sec>
<sec id="s11" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s12" sec-type="supplementary-material">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fonc.2024.1337954/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fonc.2024.1337954/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet_1.xlsx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/>
<supplementary-material xlink:href="DataSheet_2.docx" id="SM2" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document"/>
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