{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T19:33:12Z","timestamp":1783625592608,"version":"3.55.0"},"reference-count":39,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2021,5,17]],"date-time":"2021-05-17T00:00:00Z","timestamp":1621209600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007903","name":"Bloodwise","doi-asserted-by":"publisher","award":["15036"],"award-info":[{"award-number":["15036"]}],"id":[{"id":"10.13039\/501100007903","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["C27995\/A21019"],"award-info":[{"award-number":["C27995\/A21019"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001273","name":"CHILDREN with CANCER UK","doi-asserted-by":"publisher","award":["17\u2010242"],"award-info":[{"award-number":["17\u2010242"]}],"id":[{"id":"10.13039\/501100001273","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012295","name":"NIHR Newcastle Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012295","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Genes Chromosomes &amp; Cancer"],"published-print":{"date-parts":[[2021,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Low hypodiploidy (30\u201339 chromosomes) is one of the most prevalent genetic subtypes among adults with ALL and is associated with a very poor outcome. Low hypodiploid clones can often undergo a chromosomal doubling generating a near\u2010triploid clone (60\u201378 chromosomes). When cytogenetic techniques detect a near triploid clone, a diagnostic challenge may ensue in differentiating presumed duplicated low hypodiploidy from good risk high hyperdiploid ALL (51\u201367 chromosomes). We used single\u2010nucleotide polymorphism (SNP) arrays to analyze low hypodiploid\/near triploid (HoTr) (<jats:italic>n<\/jats:italic>\u00a0=\u200948) and high hyperdiploid (HeH) (<jats:italic>n<\/jats:italic>\u00a0=\u200940) cases. In addition to standard analysis, we derived log2 ratios for entire chromosomes enabling us to analyze the cohort using machine\u2010learning techniques. Low hypodiploid and near triploid cases clustered together and separately from high hyperdiploid samples. Using these approaches, we also identified three cases with 50\u201360 chromosomes, originally called as HeH, which were, in fact, HoTr and two cases incorrectly called as HoTr. <jats:italic>TP53<\/jats:italic> mutation analysis supported the new classification of all cases tested. Next, we constructed a classification and regression tree model for predicting ploidy status with chromosomes 1, 7, and 14 being the key discriminators. The classifier correctly identified 47\/50 (94%) HoTr cases. We validated the classifier using an independent cohort of 44 cases where it correctly called 7\/7 (100%) low hypodiploid cases. The results of this study suggest that HoTr is more frequent among older adults with ALL than previously estimated and that SNP array analysis should accompany cytogenetics where possible. The classifier can assist where SNP array patterns are challenging to interpret.<\/jats:p>","DOI":"10.1002\/gcc.22956","type":"journal-article","created":{"date-parts":[[2021,5,3]],"date-time":"2021-05-03T08:39:13Z","timestamp":1620031153000},"page":"604-615","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Single nucleotide polymorphism array\u2010based signature of low hypodiploidy in acute lymphoblastic leukemia"],"prefix":"10.1002","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8536-5428","authenticated-orcid":false,"given":"Thomas","family":"Creasey","sequence":"first","affiliation":[{"name":"Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amir","family":"Enshaei","sequence":"additional","affiliation":[{"name":"Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karin","family":"Nebral","sequence":"additional","affiliation":[{"name":"Department of Clinical Genetics Children's Cancer Research Institute  Vienna Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Schwab","sequence":"additional","affiliation":[{"name":"Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Watts","sequence":"additional","affiliation":[{"name":"Northern Genetics Service The Newcastle\u2010upon\u2010Tyne Hospitals NHS Foundation Trust, Institute of Genetic Medicine, International Centre for Life  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gavin","family":"Cuthbert","sequence":"additional","affiliation":[{"name":"Northern Genetics Service The Newcastle\u2010upon\u2010Tyne Hospitals NHS Foundation Trust, Institute of Genetic Medicine, International Centre for Life  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajay","family":"Vora","sequence":"additional","affiliation":[{"name":"Haematology and Oncology Department Great Ormond Street Hospital  London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Moppett","sequence":"additional","affiliation":[{"name":"Paediatric Haematology Department Bristol Royal Hospital for Children  Bristol UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0526-6794","authenticated-orcid":false,"given":"Christine J.","family":"Harrison","sequence":"additional","affiliation":[{"name":"Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adele K.","family":"Fielding","sequence":"additional","affiliation":[{"name":"Department of Haematology UCL Cancer Institute  London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oskar A.","family":"Haas","sequence":"additional","affiliation":[{"name":"Department of Clinical Genetics Children's Cancer Research Institute  Vienna Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony V.","family":"Moorman","sequence":"additional","affiliation":[{"name":"Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute Newcastle University  Newcastle upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,5,17]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrclinonc.2015.38"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2006-10-051912"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2019-123642"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.2017.74.0449"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2141.2004.04948.x"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.18.00822"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cancergen.2019.07.009"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(10)70066-8"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2016-10-743765"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2009-07-232124"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2019-124395"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2003-04-1299"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/leu.2012.227"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2532"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a026286"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1177\/1947601911413466"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.22163"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.6000"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cancergen.2014.11.003"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2016.03.004"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.22350"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2013.129"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-10-2900"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12308-013-0189-5"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1006981107"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2141.2001.02643.x"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2013.02.003"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.2174\/15680096113139990089"},{"key":"e_1_2_9_30_1","unstructured":"R Core Team.R: A language and environment for statistical computing. R Foundation for Statistical Computing Vienna Austria.2020.https:\/\/www.R-project.org\/."},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw313"},{"key":"e_1_2_9_32_1","unstructured":"RomanskiP KotthoffL.FSelector: selecting attributes. R package version 0.31.2018."},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0974-4"},{"key":"e_1_2_9_34_1","unstructured":"TherneauT AtkinsonB.Rpart: recursive partitioning and regression trees. R package version 4.1\u201315;2019."},{"key":"e_1_2_9_35_1","doi-asserted-by":"crossref","unstructured":"KuhnM.Building Predictive Models in R Using the caret Package.2008;28(5):26.","DOI":"10.18637\/jss.v028.i05"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1015"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/leu.2013.379"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn624"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1009843107"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrc3257"}],"updated-by":[{"DOI":"10.1002\/gcc.23021","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2022,1,7]],"date-time":"2022-01-07T00:00:00Z","timestamp":1641513600000}}],"container-title":["Genes, Chromosomes and Cancer"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/gcc.22956","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/gcc.22956","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/gcc.22956","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T17:07:28Z","timestamp":1693242448000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/gcc.22956"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,17]]},"references-count":39,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2021,9]]}},"alternative-id":["10.1002\/gcc.22956"],"URL":"https:\/\/doi.org\/10.1002\/gcc.22956","archive":["Portico"],"relation":{"correction":[{"id-type":"doi","id":"10.1002\/gcc.23021","asserted-by":"object"}]},"ISSN":["1045-2257","1098-2264"],"issn-type":[{"value":"1045-2257","type":"print"},{"value":"1098-2264","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,17]]},"assertion":[{"value":"2020-10-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-04-26","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-05-17","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}