Targeted DNA sequencing

Overview

Targeted DNA sequencing uses hybrid-capture or amplicon panels to deeply sequence a predefined set of loci, enabling sensitive detection of low-allele-fraction and sub-clonal variants. In the corpus it is used as an orthogonal validation and deep-coverage method alongside WGS/WES PMID:25730765.

Used by

  • PMID:25730765 — Andersson et al., applied targeted DNA sequencing in infant MLL-rearranged ALL as part of a multi-platform strategy combining WGS, WES, and RNA-seq.
  • PMID:37730754 — a custom 36-gene RMS targeted panel used for SNV/fusion detection from 62 plasma samples (10 patients) in the ctDNA arm of the rhabdomyosarcoma progression/relapse study; a separate Dragon targeted DNA panel also used at Institut Curie in 15 patients PMID:37730754.
  • PMID:38488813 — T200.1 targeted sequencing panel (263 genes, 400X) used alongside WGS (30X) and RNA-seq for integrative molecular characterization of 44 prostate cancer PDX models PMID:38488813.
  • PMID:18948947 — Sequenced all coding exons and splice sites of 623 candidate cancer genes (247 Mb) in 188 primary LUAD tumours with matched normals, identifying 1,013 non-synonymous somatic mutations and 26 significantly mutated genes PMID:18948947.
  • Applied in UC-GENOME study: Agilent SureSelect XT targeting 591 genes on Illumina NextSeq sequenced 191 of 218 metastatic urothelial carcinoma patients; treatment options identified in 69.3% but only 5.0% received targeted therapy PMID:36333289
  • Used in a two-panel design (50-gene and 95-gene clinical panels) to profile 235 MDS bone marrow samples, linking somatic mutations (STAG2, ASXL1) to morphologic dysplasia features PMID:21909114
  • Applied to 172 MCL patients in an independent validation cohort to confirm WES-identified mutations including NOTCH1/2, NSD2, BIRC3, and ATM PMID:24145436
  • Custom Ion AmpliSeq panel targeting 17 driver genes (AKT1, ARID1A, BAP1, CDKN2A, CTNNB1, IDH1/2, KRAS, NRAS, PBRM1, PIK3C2A/G, PIK3CA, PTEN, SMAD4, TGFBR2, TP53) run on Ion Torrent PGM (318 chip) at mean 1,276× depth for a prevalence screen of 40 additional IHCH/GBC tumors PMID:24185509.
  • Frequency Cohort of 119 additional matched ESCC germline/tumor pairs plus 10 ESCC cell lines sequenced by targeted deep sequencing (mean coverage 111×) covering all coding exons of discovery-cohort mutated genes plus 277 cancer-relevant genes PMID:24686850
  • Targeted DNA-seq via MSK-IMPACT capture panel applied to 109 bladder carcinomas (blca_mskcc_solit_2014); orthogonal sequencing of all coding exons of STAG2, KDM6A, ARID1A, and KMT2D confirmed 99.3% of mutation calls; mean coverage 579x PMID:25092538
  • MSK-IMPACT 230-gene targeted sequencing used to profile 69 matched CRC primary/metastasis trios, supporting clinical use of either primary or metastatic tissue for mutation profiling. PMID:25164765
  • Used in Ewing sarcoma follow-up cohort (199 patients) for targeted capture sequencing of STAG2 and TP53 to validate discovery WGS findings PMID:25223734
  • MSK-IMPACT targeted hybrid-capture sequencing used in MPNST validation cohort (37 tumors, 7 neurofibromas) to confirm PRC2 alteration frequency PMID:25240281
  • NuGEN Ovation Cancer Panel (344-gene SPET capture) used for targeted sequencing of 19 pRCCs as orthogonal validation of WES findings PMID:25401301
  • Deep targeted amplicon sequencing of 3,187 somatic SNVs and 132 SVs across 56 additional breast cancer PDX passages to track clonal dynamics across serial transplant generations PMID:25470049
  • Ion Torrent PGM targeted sequencing of 103 recurrently mutated Wnt/ERBB/HR pathway genes in a 216-case gastric adenocarcinoma validation cohort; 86/103 (83%) recurrent genes were re-identified PMID:25583476
  • Used for validation sequencing of 74 AA CRC samples against 78 candidate genes (custom Agilent SureSelectXT bait library); confirmed 20 significantly mutated genes in African American colorectal cancer, including EPHA6 and FLCN as AA-specific drivers PMID:25583493
  • Ion Torrent PGM targeted sequencing of MYD88 coding regions (~2,005× average depth) used to characterize the near-ubiquitous L265P hotspot in PCNSL; combined with WES to achieve 14/19-case mutation coverage. PMID:25991819
  • Targeted DNA sequencing used to profile somatic mutations in breast cancer samples PMID:26168399
  • Targeted DNA sequencing via MSK-IMPACT panel applied to pancreatic ductal adenocarcinoma PMID:26278805
  • Targeted DNA sequencing used alongside WES and WGS in colorectal cancer genomic profiling PMID:26343386
  • Hybrid-capture targeted sequencing across the TERT/CLPTM1L locus used alongside FISH to validate TERT 5p15.33 rearrangements in 161-sample neuroblastoma cohort; orthogonal confirmation by both methods required to call a rearrangement PMID:26466568
  • A 300-gene exon-capture panel was applied to 19 additional plasmacytoid-variant bladder tumors as a validation cohort, identifying CDH1 truncating mutations in 14/19 (74%) cases. PMID:26901067
  • Targeted 111-gene DNA sequencing panel applied to 1540 AML patients in three AMLSG trials to identify 5234 driver mutations across 76 genes and define 11 genomic subgroups PMID:27276561
  • Targeted NGS studies in young-onset lung cancer (YLC) employed targeted DNA sequencing alongside WES and WGS to profile germline susceptibility variants and somatic drivers PMID:27346245
  • The Columbia Comprehensive Cancer Panel (CCCP) targeted-sequencing backup (467 cancer-associated genes on a 5.59 Mb Custom Agilent SureSelectXT library, optimized for FFPE material) was applied to 13 of 120 pediatric oncology samples in the PIPseq program achieving >500-fold average coverage PMID:28007021.
  • Targeted exon-capture sequencing using MSK-IMPACT 341- or 410-gene panels on 105 NMIBC pretreatment index tumors with matched germline DNA; the largest NGS effort focused on NMIBC at time of publication PMID:28583311
  • SureSelect XT2 capture panel targeting 404 cancer-related genes applied to 188 CCA cases (HiSeq 4000, 99.6% coding coverage) as one of three DNA-sequencing tiers in the ICGC cholangiocarcinoma study PMID:28667006
  • MSK-IMPACT targeted NGS (341/410/468-gene panels) applied prospectively to 295 metastatic EGC patients; demonstrated that targeted capture at 744X mean depth enables reliable detection of mutations, CNAs, MSI status, and ERBB2 amplification levels relevant to treatment selection PMID:29122777

Notes

  • Used to validate and extend findings from whole-genome and whole-exome sequencing in infant MLL-R ALL PMID:25730765.
  • Enables detection of sub-clonal kinase/PI3K/RAS pathway mutations that may be missed at lower depth PMID:25730765.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:36333289

This page was processed by crosslinker on 2026-05-14. - PMID:21909114

This page was processed by crosslinker on 2026-05-14. - PMID:24145436

This page was processed by crosslinker on 2026-05-14. - PMID:24185509

This page was processed by crosslinker on 2026-05-14. - PMID:24686850

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:25223734

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

This page was processed by crosslinker on 2026-05-14. - PMID:25401301

This page was processed by crosslinker on 2026-05-14. - PMID:25470049

This page was processed by crosslinker on 2026-05-14. - PMID:25583476

This page was processed by crosslinker on 2026-05-14. - PMID:25583493

This page was processed by crosslinker on 2026-05-14. - PMID:25991819

This page was processed by crosslinker on 2026-05-14. - PMID:26168399

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

This page was processed by crosslinker on 2026-05-14. - PMID:26343386

This page was processed by crosslinker on 2026-05-14. - PMID:26466568

This page was processed by crosslinker on 2026-05-14. - PMID:26901067

This page was processed by entity-page-writer on 2026-05-15. - PMID:27276561

This page was processed by wiki-cli on 2026-05-14. - PMID:27346245

This page was processed by entity-page-writer on 2026-05-15. - PMID:28007021

This page was processed by wiki-cli on 2026-05-14. - PMID:28583311

This page was processed by entity-page-writer on 2026-05-15. - PMID:28667006

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.