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• W2186615354 abstract "Background: Rapid advancements in cancer genomics and therapeutics are driving the use of targeted therapies to improve patient outcomes based on the genomic alterations driving an individual patient’s disease. We developed a novel, CLIA-certified NGS-based assay designed to provide targeted assessment of the genomic landscape of hematologic malignancies (HM) with high accuracy in a clinically relevant timeframe. Methods: DNA and RNA were successfully extracted from 350/362 (96%) specimens from 319 patients, including 20 ALL, 83 AML, 53 CLL, 57 DLBCL, 48 MDS, 32 MPN and 57 multiple myeloma samples. Adaptor ligated sequencing libraries were captured by solution hybridization using a custom bait-set targeting 374 cancer-related genes a by DNA-seq, and 258 frequently- rearranged genes by RNA-seq. All captured libraries were sequenced to high depth in a CLIA- certified laboratory (Foundation Medicine), averaging 590x for DNA and >20M total pairs for RNA, to enable accurate detection of substitutions, indels, CNAs and gene fusions. Results: A total of 885 alterations were identified (3.1 alterations per sample), including 555 base substitutions, 213 indels, 36 splice mutations, 51 CNAs and 36 fusions/rearrangements from the 317/350 (91%) of the samples successfully sequenced. The most frequent alterations across all HM included mutations in TP53 (9%), ASXL1, KRAS, NRAS, IDH2, TET2, SF3B1, JAK2, MLL2, DNMT3A, RUNX1, and SRSF2 (2-5% each); FLT3 ITDs (2%); MLL PTDs (1%); homozygous loss of CDKN2A/B (3%); and focal amplification of REL (1%). Rearrangements in BCL2/6, MYC, MLL, MLL2, NOTCH2, ABL1 and ETV6 were identified using DNA and RNA targeted sequencing, demonstrating the ability of this platform to reliably identify gene fusions with immediate clinical relevance. Comparison of detected alterations to previous molecular testing for JAK2, NPM1, IDH2, FLT3 and CEBPA in MPN/AML samples demonstrated 97% sensitivity. In 28 cases of CLL, there was 100% concordance between cytogenetic/FISH gene amplification results and copy number status identified by the targeted NGS-based assay. Conclusions: We have developed a sensitive, high throughput assay to detect somatic alterations in hundreds of genes known to be deregulated in hematologic malignancies. We demonstrate that targeted DNA and RNA sequencing can be used to identify all classes of genomic alterations in genes known to be therapeutic targets in a broad spectrum of hematologic malignancies." @default.
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• W2186615354 date "2013-01-01" @default.
• W2186615354 modified "2023-09-27" @default.
• W2186615354 title "Comprehensive genomic profiling of hematologic malignancies by a clinical next generation sequencing-based assay" @default.
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