Journal article
ALLSorts: an RNA-Seq subtype classifier for B-cell acute lymphoblastic leukemia
B Schmidt, LM Brown, GL Ryland, A Lonsdale, HJ Kosasih, LE Ludlow, IJ Majewski, P Blombery, PG Ekert, NM Davidson, A Oshlack
Blood Advances | ELSEVIER | Published : 2022
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Subtypes within B-ALL are distinguished by characteristic structural variants and mutations, which in some instances strongly correlate with responses to treatment. The World Health Organisation (WHO) recognises seven distinct classifications, or subtypes, as of 2016. However, recent studies have demonstrated that B-ALL can be segmented into 23 subtypes based on a combination of genomic features and gene expression profiles. A method to identify a patient's subtype would have clear utility. Despite this, no publically available classification methods using RNA-Seq exist for this purpose. Here we present ALLSorts..
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Awarded by Murdoch Children's Research Institute
Funding Acknowledgements
Tumor samples and coded data were supplied by the Children's Cancer Centre Tissue Bank at the Murdoch Children's Research Institute and The Royal Children's Hospital (www.mcri.edu.au/childrenscancercentretissuebank).Establishment and running of the Children's Cancer Centre Tissue Bank is made possible through generous support by Cancer In Kids @ RCH, The Royal Children's Hospital Foundation, and the Murdoch Children's Research Institute. Raw gene expression counts for B-ALL tumor samples used for analysis in this study were obtained from St. Jude Cloud (https://www.stjude.cloud), which is a publicly accessible pediatric genomic data resource requiring approval for controlled data access. The authors acknowledge the support of the SCOR Grant (7015-18) from the Lymphoma and Leukemia Society and of Perpetual Trustees and the Samuel Nissen Foundation. This work was supported by grants from the Wilson Centre for Lymphoma Genomics and the Snowdome Foundation. This work was funded by National Health and Medical Research Council project grant GNT1140626.