title: Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.
abstract: The identification of specific genetic alterations as key oncogenic drivers and the development of targeted therapies are together transforming clinical oncology and creating a pressing need for increased breadth and throughput of clinical genotyping. Next-generation sequencing assays allow the efficient and unbiased detection of clinically actionable mutations. To enable precision oncology in patients with solid tumors, we developed Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a hybridization capture-based next-generation sequencing assay for targeted deep sequencing of all exons and selected introns of 341 key cancer genes in formalin-fixed, paraffin-embedded tumors. Barcoded libraries from patient-matched tumor and normal samples were captured, sequenced, and subjected to a custom analysis pipeline to identify somatic mutations. Sensitivity, specificity, reproducibility of MSK-IMPACT were assessed through extensive analytical validation. We tested 284 tumor samples with previously known point mutations and insertions/deletions in 47 exons of 19 cancer genes. All known variants were accurately detected, and there was high reproducibility of inter- and intrarun replicates. The detection limit for low-frequency variants was approximately 2% for hotspot mutations and 5% for nonhotspot mutations. Copy number alterations and structural rearrangements were also reliably detected. MSK-IMPACT profiles oncogenic DNA alterations in clinical solid tumor samples with high accuracy and sensitivity. Paired analysis of tumors and patient-matched normal samples enables unambiguous detection of somatic mutations to guide treatment decisions.
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Donavan T
authors: DT
authors: Cheng
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Talia N
authors: TN
authors: Mitchell
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Ahmet
authors: A
authors: Zehir
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Ronak H
authors: RH
authors: Shah
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Ryma
authors: R
authors: Benayed
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Aijazuddin
authors: A
authors: Syed
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Raghu
authors: R
authors: Chandramohan
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Zhen Yu
authors: ZY
authors: Liu
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Helen H
authors: HH
authors: Won
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Sasinya N
authors: SN
authors: Scott
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: A Rose
authors: AR
authors: Brannon
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Catherine
authors: C
authors: O'Reilly
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Justyna
authors: J
authors: Sadowska
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Jacklyn
authors: J
authors: Casanova
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Angela
authors: A
authors: Yannes
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Jaclyn F
authors: JF
authors: Hechtman
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Jinjuan
authors: J
authors: Yao
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Wei
authors: W
authors: Song
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Dara S
authors: DS
authors: Ross
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Alifya
authors: A
authors: Oultache
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Snjezana
authors: S
authors: Dogan
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Laetitia
authors: L
authors: Borsu
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Meera
authors: M
authors: Hameed
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Khedoudja
authors: K
authors: Nafa
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Maria E
authors: ME
authors: Arcila
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
authors: Marc
authors: M
authors: Ladanyi
authors: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Electronic address: bergerm1@mskcc.org.
authors: Michael F
authors: MF
authors: Berger
mesh_terms: D004247:DNA / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding; D015203:Reproducibility of Results
chemical_list: D004247:DNA