{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T00:04:26Z","timestamp":1775174666570,"version":"3.50.1"},"reference-count":39,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["23-25-00490"],"award-info":[{"award-number":["23-25-00490"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Chromosomal microarray analysis (CMA) was performed for 40 patients with B-ALL undergoing treatment according to the ALL-2016 protocol to investigate the copy number alterations (CNAs) and copy neutral loss of heterozygosity (cnLOH) associated with minimal residual disease (MRD)-positive remission. Aberrations involving over 20,000 genes were identified, and a random forest approach was applied to isolate a subset of genes whose CNAs and cnLOH are significantly associated with poor therapeutic response. We have assembled the triple matched healthy population data and used that data as a reference, but not as a matched control. We identified a recurrent cluster of cnLOH in the 19q13.2\u201319q13.31 region, significantly enriched in MRD-positive patients (70% vs. 47% in the reference group vs. 16% in MRD-negative patients). This region includes the pregnancy-specific glycoprotein (PSG) gene family and the oncogene ERF, suggesting a potential role in leukemic persistence and treatment resistance. Additionally, we observed significant deletions involving 7p22.3 and 16q13, often as part of large-scale losses affecting almost the entire chromosomes 7 and 16, indicative of global chromosomal instability. These findings highlight specific genomic regions potentially involved in therapy resistance and may contribute to improved risk stratification in B-ALL. Our findings emphasize the value of high-resolution CMA in diagnostics and risk stratification and suggest that PSG genes and other candidate genes could serve as biomarkers for predicting treatment outcomes.<\/jats:p>","DOI":"10.3390\/ijms26157437","type":"journal-article","created":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T15:56:16Z","timestamp":1754409376000},"page":"7437","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["PSG and Other Candidate Genes as Potential Biomarkers of Therapy Resistance in B-ALL: Insights from Chromosomal Microarray Analysis and Machine Learning"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-0323-1493","authenticated-orcid":false,"given":"Valeriya","family":"Surimova","sequence":"first","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"},{"name":"Intelligent Systems in Management and Automation Department, Moscow Technical University of Communications and Informatics, 111024 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2957-1619","authenticated-orcid":false,"given":"Natalya","family":"Risinskaya","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekaterina","family":"Kotova","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdulpatakh","family":"Abdulpatakhov","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anastasia","family":"Vasileva","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8044-598X","authenticated-orcid":false,"given":"Yulia","family":"Chabaeva","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sofia","family":"Starchenko","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9969-8482","authenticated-orcid":false,"given":"Olga","family":"Aleshina","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolay","family":"Kapranov","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irina","family":"Galtseva","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alina","family":"Ponomareva","sequence":"additional","affiliation":[{"name":"\u201cGenomed\u201d Laboratory of Molecular Pathology, 115419 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilya","family":"Kanivets","sequence":"additional","affiliation":[{"name":"\u201cGenomed\u201d Laboratory of Molecular Pathology, 115419 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergey","family":"Korostelev","sequence":"additional","affiliation":[{"name":"\u201cGenomed\u201d Laboratory of Molecular Pathology, 115419 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6288-7570","authenticated-orcid":false,"given":"Sergey","family":"Kulikov","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9463-9187","authenticated-orcid":false,"given":"Andrey","family":"Sudarikov","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Parovichnikova","sequence":"additional","affiliation":[{"name":"National Medical Research Center for Hematology, 125167 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"460","DOI":"10.35754\/0234-5730-2022-67-4-460-477","article-title":"Comparison of the treatment results in adult patients with acute Ph-negative lymphoblastic leukemia on protocols of the Russian multicenter studies ALL-2009 and ALL-2016","volume":"67","author":"Parovichnikova","year":"2022","journal-title":"Russ. 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