Multi-Cohort Transcriptomic Subtyping of B-Cell Acute Lymphoblastic Leukemia

International Journal of Molecular Sciences

Deborah L. White¹  Jacqueline Rehn¹  David Yeung¹  Ville-Petteri Mäkinen²  James Breen³ 

[1] Blood Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia;Computational and Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia;Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;

关键词: acute lymphoblastic leukemia;    RNA-seq;    confounder adjustment;    machine learning;   

DOI  :  10.3390/ijms23094574

来源: DOAJ

【 摘 要 】

RNA sequencing provides a snapshot of the functional consequences of genomic lesions that drive acute lymphoblastic leukemia (ALL). The aims of this study were to elucidate diagnostic associations (via machine learning) between mRNA-seq profiles, independently verify ALL lesions and develop easy-to-interpret transcriptome-wide biomarkers for ALL subtyping in the clinical setting. A training dataset of 1279 ALL patients from six North American cohorts was used for developing machine learning models. Results were validated in 767 patients from Australia with a quality control dataset across 31 tissues from 1160 non-ALL donors. A novel batch correction method was introduced and applied to adjust for cohort differences. Out of 18,503 genes with usable expression, 11,830 (64%) were confounded by cohort effects and excluded. Six ALL subtypes (ETV6::RUNX1, KMT2A, DUX4, PAX5 P80R, TCF3::PBX1, ZNF384) that covered 32% of patients were robustly detected by mRNA-seq (positive predictive value ≥ 87%). Five other frequent subtypes (CRLF2, hypodiploid, hyperdiploid, PAX5 alterations and Ph-positive) were distinguishable in 40% of patients at lower accuracy (52% ≤ positive predictive value ≤ 73%). Based on these findings, we introduce the Allspice R package to predict ALL subtypes and driver genes from unadjusted mRNA-seq read counts as encountered in real-world settings. Two examples of Allspice applied to previously unseen ALL patient samples with atypical lesions are included.

【 授权许可】

Unknown