Journal
LEUKEMIA
Volume 36, Issue 6, Pages 1492-1498Publisher
SPRINGERNATURE
DOI: 10.1038/s41375-022-01547-8
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Funding
- American Lebanese Syrian Associated Charities of SJCRH
- American Society of Hematology Scholar Award
- Leukemia & Lymphoma Society's Career Development Program Special Fellow
- NIH/NCI K99/R00 Award [CA241297]
- NCI Outstanding Investigator Award [R35 CA197695]
- National Institute of General Medical Sciences [P50 GM115279]
- NCI [P30 CA021765]
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In this study, the authors describe a method called RNAseqCNV for detecting CNVs from RNA-seq data. They used models based on gene expression and minor allele frequency to accurately classify CNVs in ALL and AML. The results showed that RNAseqCNV outperforms other algorithms in detecting CNVs in the ALL dataset and the calls were highly concordant with DNA-based CNV results.
Transcriptome sequencing (RNA-seq) is widely used to detect gene rearrangements and quantitate gene expression in acute lymphoblastic leukemia (ALL), but its utility and accuracy in identifying copy number variations (CNVs) has not been well described. CNV information inferred from RNA-seq can be highly informative to guide disease classification and risk stratification in ALL due to the high incidence of aneuploid subtypes within this disease. Here we describe RNAseqCNV, a method to detect large scale CNVs from RNA-seq data. We used models based on normalized gene expression and minor allele frequency to classify arm level CNVs with high accuracy in ALL (99.1% overall and 98.3% for non-diploid chromosome arms, respectively), and the models were further validated with excellent performance in acute myeloid leukemia (accuracy 99.8% overall and 99.4% for non-diploid chromosome arms). RNAseqCNV outperforms alternative RNA-seq based algorithms in calling CNVs in the ALL dataset, especially in samples with a high proportion of CNVs. The CNV calls were highly concordant with DNA-based CNV results and more reliable than conventional cytogenetic-based karyotypes. RNAseqCNV provides a method to robustly identify copy number alterations in the absence of DNA-based analyses, further enhancing the utility of RNA-seq to classify ALL subtype.
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