Batch effect detection and network analysis in BCR/ABL-independent CML imatinib resistance Public Deposited

Due to the complexity of BCR/ABL-independent TKI resistance, a central question is whether relapse acts through the canonical BCR/ABL CML pathways seen in dependent cases, or through a di˙erent set of genes and pathways. To answer this question, both RNA-seq and Whole Exome Sequencing data was collected and analyzed as part of a large retrospective study of CML patients with acquired resistance to imatinib and other related TKI inhibitors. RNA-seq and Whole Exome sequencing are both next generation sequencing approaches which allow for the high-throughput, cost-e˙ective characterization of an individual’s entire mRNA transcript profile (RNAseq) or protein coding region of the genome (WES)[15]. This study was comprised of 244 samples (123 WES, 121 RNAseq) collected from seven di˙erent clinical locations across the United States and Europe. These samples represented 130 unique patients, 70 of which had samples collected for both data types, 36 for WES only, and 24 for RNAseq only.

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