MSK-IMPACT panel (generic)

Overview

Generic slug for MSK-IMPACT, the Memorial Sloan Kettering matched tumor/normal hybridization-capture targeted DNA sequencing assay. Specific cBioPortal panel versions are tracked separately as [IMPACT341](../methods/IMPACT341.md), [IMPACT410](../methods/IMPACT410.md), [IMPACT468](../methods/IMPACT468.md), and [IMPACT505](../methods/IMPACT505.md). Used here when papers refer to MSK-IMPACT without specifying a panel era.

Used by

  • PMID:36493333 — used to profile a retrospective MSK cohort of appendiceal adenocarcinoma patients (April 2015–October 2020). Matched tumor/normal hybridization-capture NGS, with oncogenic/actionable variants annotated via OncoKB and clonality assessed with FACETS, defined three molecular MAAP subtypes (RAS-mut, GNAS-mut, TP53-mut predominant) associated with OS, peritoneal tumor burden, and chemotherapy response PMID:36493333.
  • PMID:37084736 — used to profile 2,532 LUAD specimens from 2,309 MSK patients for the metastatic organotropism study; an additional WES subcohort supported mutational signature analysis. Identified TP53/SMARCA4/CDKN2A inactivation as correlated with site-specific shorter time to metastasis, and showed only ~4% of metastases harbored actionable alterations not present in the matched primary PMID:37084736.
  • PMID:37682528 — used to sequence 1,507 urothelial carcinoma tumors from 1,421 MSK patients (BLCA/UTUC), defining the landscape of FGFR3 alterations across NMIBC, MIBC, UTUC, and metastatic disease, and documenting 26% primary/metastasis FGFR3 discordance in paired samples PMID:37682528.
  • PMID:37910594 — 468-gene targeted hybrid-capture NGS applied to 73/128 patients with IDH-mutant Grade 2 glioma with tissue available, identifying TERT promoter mutations (100%), CIC (42%) and FUBP1 (24%) in 1p19q codeleted tumors and TP53 (94%) and ATRX (77%) in 1p19q intact tumors; CDKN2A/B homozygous deletion defined molecular grade-high tumors with ~2x faster tumor volume growth rate PMID:37910594.
  • PMID:39506116 — MSK-IMPACT targeted panel sequencing of 24,950 MSK patients across NSCLC, BRCA, COADREAD, PRAD, and PAAD formed the genomic backbone of the MSK-CHORD clinicogenomic dataset; enabled discovery of SETD2 driver mutations in 3% of LUAD as a biomarker of longer OS, lower CNS metastasis, and improved immune checkpoint blockade response PMID:39506116.
  • PMID:37477937 — MSK-IMPACT sequencing contributed to the cohort analysis PMID:37477937.
  • PMID:38147626 — MSK-IMPACT sequencing contributed to the cohort analysis PMID:38147626.
  • PMID:38864854 — MSK-IMPACT sequencing contributed to the cohort analysis PMID:38864854.
  • PMID:38995739 — referenced alongside the heme-focused MSK-HemePACT panel in the phase I/II ibrutinib trial in r/r CNS lymphoma; an independent cohort of 177 MSK PCNSL patients treated with standard of care was used to show TBL1XR1 status was not prognostic under SOC, supporting its predictive (rather than prognostic) role for ibrutinib benefit PMID:38995739.
  • PMID:39214094 — applied to 397/1,360 resected PAAD patients in the MSK pancreas_msk_2024 cohort with no selection criteria, producing driver-gene and KRAS-allele calls that underpinned the stage I KRASG12R enrichment and allele-specific outcome findings; authors explicitly note that CDKN2A/B deep deletions were under-detected by IMPACT and excluded from their main analyses PMID:39214094.
  • PMID:39289779 — FDA-authorized MSK-IMPACT (IMPACT468 n=274, IMPACT505 n=733) applied to cfDNA from 1,007 CSF samples from 711 patients with CNS tumors; detected somatic alterations in 53% of samples from patients with documented CNS disease (specificity 100%); ctDNA positivity associated with HR 3.23 for death (p<0.001) PMID:39289779.
  • PMID:39746944 — MSK-IMPACT (including IMPACT468) used as the primary sequencing platform for MiMSI training (n=741) and prospective cohort (n=5,037 and n=45,112); microsatellite loci from 1,755 IMPACT-covered microsatellite sites were used to train the deep MIL classifier; MiMSI reduced the indeterminate MSI call rate from 3.8% to 0.47% across 45,112 samples PMID:39746944.
  • PMID:39753968 — FDA-authorized MSK-IMPACT applied to 2,336 PAAD patients (median 606× depth); four panel generations (IMPACT341 n=17, IMPACT410 n=438, IMPACT468 n=1,536, IMPACT505 n=345); enabled definition of three genomic PDAC subtypes (KRAS-mutant 95%, other-MAPK-mutant 3%, MAPK-WT 2%) and KRAS mutant-allele dosage prognostic analyses PMID:39753968.
  • PMID:40256659 — MSK-IMPACT applied to matched archival tumor tissue from 107 of 201 mUC patients in the CALGB 90601 trial; 57.1% of DDR alterations concordant between cfDNA and matched tumor; cfDNA numerically detected higher rates of PIK3CA, RB1, ERCC2, BRAF, and KRAS alterations than matched tumor PMID:40256659.
  • PMID:37643132 — MSK-IMPACT (341, 410, or 468 genes, avg 648x coverage) used to sequence 177 CESC patients; actionability annotated via OncoKB v3.1.4 PMID:37643132.
  • PMID:37651310 — MSK-IMPACT (341–505 gene panel, tumor-normal, FDA-authorized) used to sequence 1,882 endometrial carcinoma patients; genetic ancestry inferred from IMPACT data; copy number analysis performed with FACETS PMID:37651310.
  • PMID:37699004 — MSK-IMPACT (IMPACT505, up to 505 genes) used to sequence 902/1,123 esophagogastric cancer patients; germline analysis performed with a 76–88-gene MSK-IMPACT panel PMID:37699004.
  • PMID:37730754 — MSK-IMPACT used to sequence MSK cohort (n=20) of relapsed/metastatic rhabdomyosarcoma patients PMID:37730754.
  • PMID:38488807 — MSK-IMPACT (341–505 genes) used to profile 195 STLMS and 238 ULMS cases; longitudinal subset of 18 STLMS and 15 ULMS patients had sequential tumors sequenced PMID:38488807.
  • PMID:38630790 — MSK-IMPACT used to profile 290 diffuse pleural mesothelioma (PLMESO) patients; 210 (72%) had sufficient tumor purity for FACETS LOH analysis PMID:38630790.
  • PMID:38653864 — MSK-IMPACT used for MSI/TMB assessment in 35 patients with dMMR/MSI-H/hypermutated gynecologic cancers on nivolumab phase 2 trial PMID:38653864.
  • PMID:38758238 — MSK-IMPACT used to sequence all pituitary neuroendocrine tumors; retrospective cohort (n=26) also underwent WES for USP8 mutation detection PMID:38758238.
  • PMID:38922339 — 97,024 samples from 69,337 patients sequenced via MSK-IMPACT, MSK-ACCESS, and MSK-Fusion between January 2014 and November 2022; identified 212 patients with oncogenic BRAF fusions across 52 histologies PMID:38922339.
  • PMID:38949888 — 3,244 prostate cancer tumors from 2,257 patients sequenced using MSK-IMPACT targeted NGS panel; WES performed on 48 tumor samples via recapture of MSK-IMPACT libraries PMID:38949888.
  • PMID:35764743 — MSK-IMPACT targeted clinical sequencing used to infer HRD status for 130 MSKCC HGSOC patients with research consent; variant significance annotated via OncoKB and Hotspot; high-confidence COSMIC SBS3 detected in 48 and low-confidence in 30 patients; HRD status combined with histopathological and radiological features in the multimodal late-fusion prognostic model PMID:35764743.
  • Used to sequence 103 GIST patients (341, 410, or 505 gene panels) and 499 tumor-normal pairs at MSKCC; ESMO-recommended VAF thresholds (>30% SNVs, >20% indels) correctly distinguished germline from somatic P/LP variants PMID:36593350
  • Applied to 1,313 bladder urothelial carcinoma patients at MSK (2014-2021); mean TMB 11.7 in primary vs 11.2 in metastatic tumors (Wilcoxon p=0.1); 23% of actionable mutations (FGFR3, PIK3CA, TSC1, ERBB2) discordant between primary-metastasis pairs PMID:36543146
  • IMPACT468 (468-gene panel) applied to 42 treatment-naive HGSOC patients; validation cohort of 1,298 HGSOC patients used to confirm clonal 6p HLA LOH frequency (31% in BRCA1-mutant cases) PMID:36517593
  • Used alongside Guardant360 CDx and MSK-ACCESS for sequencing KRASG12C-mutant colorectal cancer cell lines, PDX, and tissue samples to characterize acquired resistance mechanisms to combined KRAS/EGFR inhibition PMID:36355783
  • Used to profile 244 GBC samples (233 patients) at MSK with 341–505 gene panel versions (median coverage 634X), identifying actionable alterations in 35% of patients PMID:36228155
  • Used for genomic profiling in a 247-patient NSCLC cohort treated with PD-(L)1 blockade; TMB from MSK-IMPACT achieved AUC = 0.61 alone vs AUC = 0.80 for the full multimodal DyAM model PMID:36038778
  • Targeted hybrid-capture sequencing of 279 cancer-associated genes (Illumina HiSeq 2000, mean depth 442×, ≥100× at 97% of targeted exons) used on 12 paired SCCOHT tumor/normal samples, identifying biallelic SMARCA4 inactivating mutations in 100% of cases PMID:24658004
  • Capture-based MSK-IMPACT sequencing of 109 high-grade urothelial bladder carcinomas (blca_mskcc_solit_2014) at mean 579x coverage across targeted exons; detected mutations in 240 genes with 23 mutated in ≥5% of cases; PIK3CA mutation associated with improved post-cystectomy recurrence-free survival PMID:25092538
  • Custom 230-gene targeted capture panel (mean coverage 692×) applied to 69 matched CRC primary/metastasis trios; demonstrated 100% concordance of KRAS/NRAS/BRAF and 93% overall concordance for recurrent driver mutations. PMID:25164765
  • Used in MPNST validation cohort (37 FFPE MPNSTs and 7 neurofibromas from 32 NF1 patients); targeted hybrid-capture panel including NF1, SUZ12, EED, CDKN2A, TP53 confirmed PRC2 alterations in 70–90% of MPNSTs PMID:25240281
  • MSK-IMPACT targeted sequencing panel applied to >650 pancreatic ductal adenocarcinoma samples to profile somatic mutations and copy-number alterations PMID:26278805
  • Used as the 341-gene IMPACT341 targeted-capture NGS panel (mean depth 584x tumor / 236x normal; 739x for ATCs) to sequence 117 advanced thyroid tumors (84 PDTC, 33 ATC) at MSKCC; detected TP53, TERT, SWI/SNF, and HMT mutations at 2-3x higher frequency than WES due to deep coverage. PMID:26878173
  • Used as the CLIA-certified MSK-IMPACT 341-gene panel to profile 6 plasmacytoid-variant bladder tumors in a prospective clinical cohort at MSKCC; identified CDH1 truncating mutations in all 6 plasmacytoid cases and 0/56 urothelial NOS cases. PMID:26901067
  • MSK-IMPACT 410-gene panel (IMPACT410) applied to 151 advanced head and neck tumors at MSK; CLIA-approved, median coverage 600x; guided therapy in 21/151 (14%) patients and 13/53 (25%) HNSC cases PMID:27442865
  • MSK-IMPACT 410-gene targeted exon-capture assay (>300 cancer genes, 500–1000x depth) used to validate in 161 prospective GCT patients the TP53/MDM2 alteration findings discovered by WES in the 19-patient discovery cohort PMID:27646943
  • Used for targeted DNA sequencing (230-gene panel, avg 348x tumour / 280x normal coverage) to characterize 62 high-grade unclassified renal cell carcinoma (uRCC) tumours at MSKCC; variant calling via MuTect and GATK Somatic Indel Detector on hg19-aligned reads. PMID:27713405
  • MSK-IMPACT panel sequencing (341 and 410-gene versions) applied to 10,945 tumors across 62 cancer types for clinical actionability PMID:28336552
  • MSK-IMPACT hybridization-capture Illumina HiSeq 2500 platform with full exon coverage of 410 cancer-related genes used to characterize 19 anaplastic oligodendroglioma tumors in the odg_msk_2017 cohort PMID:28472509
  • Prospective CLIA-certified hybrid-capture sequencing of 10,945 advanced/metastatic tumors from 10,336 patients across 62 tumor types; catalogued 78,066 non-synonymous mutations, 22,989 CNAs, and 1,875 rearrangements PMID:28481359
  • Sequenced 105 NMIBC tumors and 40 MIBC comparators with matched germline DNA; ARID1A mutation was the only gene significantly associated with BCG recurrence (HR=3.14, p=0.002) PMID:28583311
  • Hybridization-capture targeted DNA panel covering >300 cancer-related genes (SNVs, indels, somatic CNAs, structural rearrangements) applied to 504 tumors from 451 prostate cancer patients spanning locoregional to mCRPC; matched normal blood used for germline filtering; 68% sequencing success rate PMID:28825054
  • CLIA-certified hybrid-capture targeted NGS assay applied to 295 metastatic esophagogastric adenocarcinoma (EGC) patients at MSKCC; mean coverage 744X; detected mutations, copy-number alterations, and select rearrangements PMID:29122777
  • MSK-IMPACT prospectively sequenced 1,134 COADREAD tumors (panels IMPACT341, IMPACT410, IMPACT468) with 98.6% MMR-IHC/MSIsensor concordance; characterized recurrently mutated genes, APC intronic variants, and CTNNB1 exon-3 deletions in MSS and MSI-H CRC PMID:29316426
  • Central sequencing of 91 archival FFPE tumors and 15 plasma cfDNA samples from the SUMMIT neratinib basket trial using IMPACT341 (n=18) or IMPACT410 (n=88) at mean 738× coverage; concordance with local testing 95% PMID:29420467
  • MC3 capture-kit mask excluded 170 CDS-altering calls in MSK-IMPACT’s 410-gene panel that fall outside the Broad capture BED, including TERT promoter hits, CIC truncations, and CRLF2 splice alterations PMID:29596782
  • 706 advanced prostate cancers from MSK-IMPACT (msk_impact_2017) used as validation cohort for the prad_p1000 WES SMG analysis PMID:29610475

Notes

  • Targeted-panel scope limits subtype calls and mutational-signature resolution; both papers note this limitation, and the LUAD study partially mitigates it with a WES subcohort PMID:36493333 PMID:37084736.
  • For panel-specific analyses (IMPACT341/410/468/505), see the dedicated canonical-panel pages.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:36593350

This page was processed by crosslinker on 2026-05-14. - PMID:36543146

This page was processed by crosslinker on 2026-05-14. - PMID:36517593

This page was processed by crosslinker on 2026-05-14. - PMID:36355783

This page was processed by crosslinker on 2026-05-14. - PMID:36228155

This page was processed by crosslinker on 2026-05-14. - PMID:36038778

This page was processed by crosslinker on 2026-05-14. - PMID:24658004

This page was processed by crosslinker on 2026-05-14. - PMID:25092538

This page was processed by crosslinker on 2026-05-14. - PMID:25164765

This page was processed by crosslinker on 2026-05-14. - PMID:25240281

This page was processed by crosslinker on 2026-05-14. - PMID:26278805

This page was processed by crosslinker on 2026-05-14. - PMID:26878173

This page was processed by entity-page-writer on 2026-05-15. - PMID:26901067

This page was processed by entity-page-writer on 2026-05-15. - PMID:27442865

This page was processed by entity-page-writer on 2026-05-15. - PMID:27646943

This page was processed by entity-page-writer on 2026-05-15. - PMID:27713405

This page was processed by entity-page-writer on 2026-05-15. - PMID:28336552

This page was processed by wiki-cli on 2026-05-14. - PMID:28472509

This page was processed by entity-page-writer on 2026-05-15. - PMID:28481359

This page was processed by entity-page-writer on 2026-05-15. - PMID:28583311

This page was processed by entity-page-writer on 2026-05-15. - PMID:28825054

This page was processed by entity-page-writer on 2026-05-15. - PMID:29122777

This page was processed by entity-page-writer on 2026-05-15. - PMID:29316426

This page was processed by wiki-cli on 2026-05-15. - PMID:29420467

This page was processed by wiki-cli on 2026-05-15. - PMID:29596782

This page was processed by wiki-cli on 2026-05-15. - PMID:29610475

This page was processed by wiki-cli on 2026-05-15.