Sanger Sequencing

Overview

A first-generation DNA sequencing method based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase.

Used by

  • Employed to sequence the coding exons of 601 genes in 91 glioblastoma samples, identifying key mutated genes including TP53, PTEN, NF1, EGFR, ERBB2, RB1, PIK3R1, and PIK3CA PMID:18772890.
  • Used for targeted validation of somatic mutations in 58 PanNET cases from the Johns Hopkins validation cohort; 91% of discovery-set mutations validated by Sanger PMID:21252315
  • Used to validate MEF2B mutations in 261 FL, 259 DLBCL, 17 cell lines, 35 other NHL, and 8 centroblast samples in the BCGSC NHL study PMID:21796119
  • Used for orthogonal validation of candidate somatic mutations in the JHU HNSCC WES study; confirmed 609/911 (67%) of candidate mutations PMID:21798897
  • Sanger sequencing used for validation of somatic mutations identified by WES in prostate adenocarcinoma tumors PMID:22610119
  • Sanger sequencing used to validate PREX2 and KIT mutations identified in melanoma WGS PMID:22622578
  • Used for validation sequencing of candidate mutations identified by WGS in 37 medulloblastoma tumors (PCGP cohort, mbl_pcgp) PMID:22722829
  • Sanger sequencing used to validate RAC1 P29S in an expanded melanoma cohort of 364 samples (Yale); mutation confirmed in 9.2% of sun-exposed melanomas PMID:22842228
  • Sanger sequencing used to validate somatic mutations discovered by WES/WGS in ETP-ALL tumors at St. Jude PMID:23334668
  • Sanger sequencing used to validate NOTCH1 and CASP8 mutations in a panel of 44 HNSCC cell lines, orthogonal to SOLiD/Illumina exome discovery PMID:23619168
  • Used for targeted extension sequencing of SPEN (42 additional ACC cases) and FGFR2 (25 additional ACC cases), identifying 2 additional SPEN truncating mutations in solid-histology cases and 3 activating FGFR2 mutations PMID:23778141
  • Used for PCR validation of SNVs and InDels identified by WGS in 96 pediatric pilocytic astrocytoma cases; achieved >98% SNV verification rate and >70% InDel verification rate PMID:23817572
  • Used for Sanger sequencing of all coding exons of 15 selected oncogenes/tumor suppressors in 97 high-grade bladder (BLCA) tumors PMID:23897969
  • Sanger sequencing used to validate 11,240 candidate somatic mutations; confirmed 91% of predicted substitutions and 74% of indels in 99 BLCA tumors PMID:24121792
  • Used for targeted validation sequencing of 172 MCL patients in an independent cohort to confirm WES-identified mutations PMID:24145436
  • Used to confirm 50 somatic mutations from the whole-exome discovery screen in intrahepatic cholangiocarcinoma/gallbladder carcinoma — all 50 mutations verified PMID:24185509.
  • Used to sequence CALR exon 9 in an additional 1,345 hematologic cancers, 52 controls, and 5-patient clonal colony analyses (~300 colonies) for validation of the whole-exome discovery of CALR frameshift indels in JAK2/MPL-negative MPN PMID:24325359.
  • PCR/Sanger HPV genotyping covering types 16/18/31/33/35/45 plus L1/E1 consensus primers used to exclude HPV-associated multiphenotypic sinonasal carcinoma from the sinonasal adenoid cystic carcinoma cohort (n=88); identified 11/100 HPV-positive cases for reclassification PMID:24418857
  • Validated all identified SMARCA4 mutations in 12 SCCOHT cases by Sanger sequencing of genomic DNA and cDNA (RT-PCR) PMID:24658004
  • Validated somatic mutations in ESCC cohort with a 96.2% true-positive rate across 1,847 non-silent somatic mutations PMID:24686850
  • Sanger sequencing applied to HCC cohort molecular characterisation as part of the multi-platform TCGA integrated study PMID:24798001
  • Sanger sequencing of GTF2I performed on 199 TETs with >50% cancer cells to confirm the recurrent chr7:74146970 T>A hotspot mutation PMID:24974848
  • Used for plasmid verification in functional studies of MSK-IMPACT-detected mutations (e.g., MAP2K1 Q56P) in the CRC concordance study. PMID:25164765
  • Used for orthogonal confirmation of CDKN2A deletions in Ewing sarcoma WGS discovery cohort PMID:25223734
  • Used for orthogonal indel validation in nccRCC WES study; Sanger sequencing confirmed 96% (127/132) of selected indels PMID:25401301
  • Used for confirmation sequencing of candidate somatic mutations identified by whole-exome and targeted sequencing in 103 African American MSS colorectal cancers PMID:25583493
  • Benchmarked exome mutation calling in 155 HCC tumors across 11 genes; sensitivity 88% (95% CI 82–92%), specificity 99%; systematic blind spots in GC-rich ARID1A exon 1 and large CTNNB1 exon 3 deletions. PMID:25822088
  • Validated 248 non-silent mutations across 132 genes in 84 PDA cases, confirming 92% of MuTect/VarScan calls (95% CI 87.6–94.6%). PMID:25855536
  • Used for validation of CARD11/CD79B/PRKCD/TNFAIP3 variants in PCNSL cases, complementing WES and targeted Ion Torrent sequencing. PMID:25991819
  • Sanger sequencing of TERT promoter C228T/C250T in 115 cutaneous melanoma samples confirmed mutually exclusive distribution and differential association with TERT mRNA elevation. PMID:26091043
  • Sanger sequencing used to validate somatic mutations identified by next-generation sequencing in breast cancer PMID:26168399
  • Sanger sequencing used to confirm somatic mutations detected by MSK-IMPACT panel in pancreatic cancer PMID:26278805
  • Sanger sequencing used to validate somatic mutations in colorectal cancer whole-exome and whole-genome sequencing PMID:26343386
  • Used to validate MYBL1 fusion breakpoints and to characterize MYBL1 truncations identified by whole-genome sequencing in salivary adenoid cystic carcinomas, including 3’-RACE for truncation characterization PMID:26631609.
  • Used to validate the recurrent PLCB4 p.D630Y hotspot mutation identified by WGS/WES in uveal melanoma samples; confirmed mutation in 2/28 discovery samples and 1/56 previously published UM tumors PMID:26683228.
  • Used as readout for bisulfite sequencing of the CDH1 promoter CpG island to detect hypermethylation in CDH1 wild-type plasmacytoid bladder tumors. PMID:26901067
  • Applied Sanger sequencing for targeted validation of somatic mutations PMID:28199314
  • Used Sanger sequencing for orthogonal validation of somatic variants PMID:28373299
  • Applied Sanger sequencing to validate somatic variants and germline mutations PMID:28445112
  • Sanger sequencing of 22 genes-of-interest used in the prevalence screen of 47 clear cell endometrial carcinoma (CCEC) cases from the uccc_nih_2017 cohort PMID:28485815
  • Used to PCR-validate structural variants detected by CREST in CCA WGS data (91% validation rate across ~93 somatic SVs/tumor) PMID:28667006
  • Used for validation of CRISPR base-editing outcomes (T→A and A→T conversions at rs4519489 in PC3 and DU145 cells) in the NOL10/USF1 functional study PMID:28927585
  • Used for validation of somatic variant calls from WES (1130 events across 61 genes in DLBCL cohort, 90% concordance) PMID:28985567
  • Used to confirm recombination of the artificial-telomere construct at the centromeric chr_3p break site in CRISPR-engineered AALE cell clones PMID:29622463

Notes

  • In the TCGA glioblastoma interim analysis, sequencing results were used to identify significantly mutated genes and core pathways (RTK/RAS/PI3K, p53, and RB) PMID:18772890.

Sources

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This page was processed by crosslinker on 2026-05-14. - PMID:22610119

This page was processed by crosslinker on 2026-05-14. - PMID:22622578

This page was processed by crosslinker on 2026-05-14. - PMID:22722829

This page was processed by crosslinker on 2026-05-14. - PMID:22842228

This page was processed by crosslinker on 2026-05-14. - PMID:23334668

This page was processed by crosslinker on 2026-05-14. - PMID:23619168

This page was processed by crosslinker on 2026-05-14. - PMID:23778141

This page was processed by crosslinker on 2026-05-14. - PMID:23817572

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This page was processed by crosslinker on 2026-05-14. - PMID:24121792

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:24325359

This page was processed by crosslinker on 2026-05-14. - PMID:24418857

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

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

This page was processed by crosslinker on 2026-05-14. - PMID:24798001

This page was processed by crosslinker on 2026-05-14. - PMID:24974848

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:25401301

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This page was processed by crosslinker on 2026-05-14. - PMID:25855536

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

This page was processed by crosslinker on 2026-05-14. - PMID:26091043

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:26631609

This page was processed by crosslinker on 2026-05-14. - PMID:26683228

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

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This page was processed by wiki-cli on 2026-05-14. - PMID:28485815

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:28927585

This page was processed by entity-page-writer on 2026-05-15. - PMID:28985567

This page was processed by entity-page-writer on 2026-05-15. - PMID:29622463

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