Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.
paper
Cited
Public
- Authors
- Harismendy, Olivier; Schwab, Richard B; Bao, Lei; Olson, Jeff; Rozenzhak, Sophie; Kotsopoulos, Steve K; Pond, Stephanie; Crain, Brian; Chee, Mark S; Messer, Karen; Link, Darren R; Frazer, Kelly A
- Year
- 2011
- Journal
- Genome biology
- PMID
- 22185227
- DOI
- 10.1186/gb-2011-12-12-r124
- PMCID
- PMC3334619
Ultra-deep targeted sequencing (UDT-Seq) can identify subclonal somatic mutations in tumor samples. Early assays' limited breadth and depth restrict their clinical utility. Here, we target 71 kb of mutational hotspots in 42 cancer genes. We present novel methods enhancing both laboratory workflow and mutation detection. We evaluate UDT-Seq true sensitivity and specificity (> 94% and > 99%, respectively) for low prevalence mutations in a mixing experiment and demonstrate its utility using six tumor samples. With an improved performance when run on the Illumina Miseq, the UDT-Seq assay is well suited for clinical applications to guide therapy and study clonal selection in heterogeneous samples.
Performance evaluation. (a) The positive predictive value (PPV) and sensitivity of UDT-Seq for each of the five calibration datasets. The error bars represent the standard deviation of the values obtained from different calibration schemes (Table S5 in Additional file 2). (b) Average sensitivity estimation for the calibration SNPs at different prevalence's. The error bars represent the standard deviation over all calibration-tested sample combinations. (c) PPV at increasing prevalence intervals. (d) Expected prevalence of the calibration SNPs (x-axis) are highly correlated (r = 0.97) with the observed prevalence (y-axis) across all calibration samples. The width of the boxes is proportional to the root mean square of the number of SNPs in each category. The whiskers extend to the closest data point within 1.5-fold of the inter-quartile distance. On average, the mutations expected at 1%, 5%, 20% and 74% where observed at 1.5% (± 0.9), 5.4% (± 2.8), 20.3% (± 7.9) and 72.1% (± 10.6), respectively. The minor differences are likely due to measurement errors during the preparation of the calibration samples. (e) Average PPV and sensitivity calculated using samples CAL-C and CAL-D trained with CAL-B after random sampling the reads to lower coverage. The error bars represent the standard deviation of the results obtained from the two samples. (f) The prevalence of the calibration SNPs identified in CAL-B with and without whole genome amplification (WGA) (log scale x- and y-axis, respectively) is plotted against the prevalence estimated from the WGA sample replicates (red and blue). The minimum specified prevalence of the assay (1%) is indicated by dotted lines.
Mutational profiles of the colon primary and xenograft tumor samples. Histogram showing the prevalence of the 11 colon primary (dark blue) and 11 xenograft (light blue) mutations. In the primary tumor, ten of the mutations were identified using the UDT-Seq method and one (STK11-R304W) by visual inspection of the reads after it was observed in the xenograft. All mutations validated by a sequence-based assay (SNaPshot or Sanger) are indicated by a green dot. Mutations not examined by independent assay are indicated by a grey dot.
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| Citation | PMID | DOI | Status |
|---|---|---|---|
| AndresonRPuurandTRemmMSNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.Nucleic Acids Res200634W65165510.1093/nar/gkl12516845091PMC1538889 | — | — | — |
| Bar-EliMAhujaHGonzalez-CadavidNFotiAClineMJAnalysis of N-RAS exon-1 mutations in myelodysplastic syndromes by polymerase chain reaction and direct sequencing.Blood1989732812832642713 | — | — | — |
| BentleyDRBalasubramanianSSwerdlowHPSmithGPMiltonJBrownCGHallKPEversDJBarnesCLBignellHRBoutellJMBryantJCarterRJKeira CheethamRCoxAJEllisDJFlatbushMRGormleyNAHumphraySJIrvingLJKarbelashviliMSKirkSMLiHLiuXMaisingerKSMurrayLJObradovicBOstTParkinsonMLPrattMRAccurate whole human genome sequencing using reversible terminator chemistry.Nature2008456535910.1038/nature0751718987734PMC2581791 | — | — | — |
| BoulalasIZaravinosAKaryotisIDelakasDSpandidosDAActivation of RAS family genes in urothelial carcinoma.J Urol20091812312231910.1016/j.juro.2009.01.01119303097 | — | — | — |
| ChouTYChiuCHLiLHHsiaoCYTzenCYChangKTChenYMPerngRPTsaiSFTsaiCMMutation in the tyrosine kinase domain of epidermal growth factor receptor is a predictive and prognostic factor for gefitinib treatment in patients with non-small cell lung cancer.Clin Cancer Res2005113750375710.1158/1078-0432.CCR-04-198115897572 | — | — | — |
| CollinsSJHowardMAndrewsDFAguraERadichJRare occurrence of N-ras point mutations in Philadelphia chromosome positive chronic myeloid leukemia.Blood198973102810322645946 | — | — | — |
| DematteoRPBallmanKVAntonescuCRMakiRGPistersPWDemetriGDBlacksteinMEBlankeCDvon MehrenMBrennanMFPatelSMcCarterMDPolikoffJATanBROwzarKAdjuvant imatinib mesylate after resection of localised, primary gastrointestinal stromal tumour: a randomised, double-blind, placebo-controlled trial.Lancet20093731097110410.1016/S0140-6736(09)60500-619303137PMC2915459 | — | — | — |
| DingLEllisMJLiSLarsonDEChenKWallisJWHarrisCCMcLellanMDFultonRSFultonLLAbbottRMHoogJDoolingDJKoboldtDCSchmidtHKalickiJZhangQChenLLinLWendlMCMcMichaelJFMagriniVJCookLMcGrathSDVickeryTLAppelbaumEDeschryverKDaviesSGuintoliTCrowderRGenome remodelling in a basal-like breast cancer metastasis and xenograft.Nature2010464999100510.1038/nature0898920393555PMC2872544 | — | — | — |
| DruleyTEVallaniaFLWegnerDJVarleyKEKnowlesOLBondsJARobisonSWDonigerSWHamvasAColeFSFayJCMitraRDQuantification of rare allelic variants from pooled genomic DNA.Nat Methods2009626326510.1038/nmeth.130719252504PMC2776647 | — | — | — |
| ForbesSABhamraGBamfordSDawsonEKokCClementsJMenziesATeagueJWFutrealPAStrattonMRThe Catalogue of Somatic Mutations in Cancer (COSMIC).Curr Protoc Hum Genet20081010111842842110.1002/0471142905.hg1011s57PMC2705836 | — | — | — |
| Integrated genomic analyses of ovarian carcinoma.Nature4746096152172036510.1038/nature10166PMC3163504 | — | — | — |
| JonesSWangTLShih IeMMaoTLNakayamaKRodenRGlasRSlamonDDiazLAJrVogelsteinBKinzlerKWVelculescuVEPapadopoulosNFrequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma.Science201033022823110.1126/science.119633320826764PMC3076894 | — | — | — |
| LaskenRSEgholmMWhole genome amplification: abundant supplies of DNA from precious samples or clinical specimens.Trends Biotechnol20032153153510.1016/j.tibtech.2003.09.01014624861 | — | — | — |
| LearyRJKindeIDiehlFSchmidtKClouserCDuncanCAntipovaALeeCMcKernanKDe La VegaFMKinzlerKWVogelsteinBDiazLAJrVelculescuVEDevelopment of personalized tumor biomarkers using massively parallel sequencing.Sci Transl Med2010220ra1410.1126/scitranslmed.300070220371490PMC2858564 | — | — | — |
| LievreABachetJBLe CorreDBoigeVLandiBEmileJFCoteJFTomasicGPennaCDucreuxMRougierPPenault-LlorcaFLaurent-PuigPKRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer.Cancer Res2006663992399510.1158/0008-5472.CAN-06-019116618717 | — | — | — |
| LiHDurbinRFast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics2009251754176010.1093/bioinformatics/btp32419451168PMC2705234 | — | — | — |
| LiHHandsakerBWysokerAFennellTRuanJHomerNMarthGAbecasisGDurbinRThe Sequence Alignment/Map format and SAMtools.Bioinformatics2009252078207910.1093/bioinformatics/btp35219505943PMC2723002 | — | — | — |
| LiMDiehlFDressmanDVogelsteinBKinzlerKWBEAMing up for detection and quantification of rare sequence variants.Nat Methods20063959710.1038/nmeth85016432518 | — | — | — |
| MacConaillLECampbellCDKehoeSMBassAJHattonCNiuLDavisMYaoKHannaMMondalCLuongoLEmeryCMBakerACPhilipsJGoffDJFiorentinoMRubinMAPolyakKChanJWangYFletcherJASantagataSCorsoGRovielloFShivdasaniRKieranMWLigonKLStilesCDHahnWCMeyersonMLProfiling critical cancer gene mutations in clinical tumor samples.PLoS One20094e7887e788710.1371/journal.pone.000788719924296PMC2774511 | — | — | — |
| MarguliesMEgholmMAltmanWEAttiyaSBaderJSBembenLABerkaJBravermanMSChenYJChenZDewellSBDuLFierroJMGomesXVGodwinBCHeWHelgesenSHoCHIrzykGPJandoSCAlenquerMLJarvieTPJirageKBKimJBKnightJRLanzaJRLeamonJHLefkowitzSMLeiMLiJGenome sequencing in microfabricated high-density picolitre reactors.Nature20054373763801605622010.1038/nature03959PMC1464427 | — | — | — |
| MatthewsBWComparison of the predicted and observed secondary structure of T4 phage lysozyme.Biochim Biophys Acta1975405442451118096710.1016/0005-2795(75)90109-9 | — | — | — |
| NCBI Short Read Archive.http://www.ncbi.nlm.nih.gov/sra | — | — | — |
| NgSBTurnerEHRobertsonPDFlygareSDBighamAWLeeCShafferTWongMBhattacharjeeAEichlerEEBamshadMNickersonDAShendureJTargeted capture and massively parallel sequencing of 12 human exomes.Nature200946127227610.1038/nature0825019684571PMC2844771 | — | — | — |
| OligoAnalyzer.http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/ | — | — | — |
| OutAAvan MinderhoutIJGoemanJJAriyurekYOssowskiSSchneebergerKWeigelDvan GalenMTaschnerPETopsCMBreuningMHvan OmmenGJden DunnenJTDevileePHesFJDeep sequencing to reveal new variants in pooled DNA samples.Hum Mutat2009301703171210.1002/humu.2112219842214 | — | — | — |
| RestaNSimoneCMareniCMonteraMGentileMSuscaFGristinaRPozziSBertarioLBufoPCarlomagnoNIngrossoMRossiniFPTenconiRGuantiGSTK11 mutations in Peutz-Jeghers syndrome and sporadic colon cancer.Cancer Res199858479948019809980 | — | — | — |
| SuZDias-SantagataDDukeMHutchinsonKLinY-LBorgerDRChungCHMassionPPVnencak-JonesCLIafrateAJPaoWA platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer.J Mol Diagn201113748410.1016/j.jmoldx.2010.11.01021227397PMC3070558 | — | — | — |
| TewheyRWarnerJBNakanoMLibbyBMedkovaMDavidPHKotsopoulosSKSamuelsMLHutchisonJBLarsonJWTopolEJWeinerMPHarismendyOOlsonJLinkDRFrazerKAMicrodroplet-based PCR enrichment for large-scale targeted sequencing.Nat Biotechnol2009271025103110.1038/nbt.158319881494PMC2779736 | — | — | — |
| ThomasRKNickersonESimonsJFJannePATengsTYuzaYGarrawayLALaFramboiseTLeeJCShahKO'NeillKSasakiHLindemanNWongKKBorrasAMGutmannEJDragnevKHDeBiasiRChenTHGlattKAGreulichHDesanyBLubeskiCKBrockmanWAlvarezPHutchisonSKLeamonJHRonanMTTurenchalkGSEgholmMSensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing.Nat Med20061285285510.1038/nm143716799556 | — | — | — |
| VarelaITarpeyPRaineKHuangDOngCKStephensPDaviesHJonesDLinMLTeagueJBignellGButlerAChoJDalglieshGLGalappaththigeDGreenmanCHardyCJiaMLatimerCLauKWMarshallJMcLarenSMenziesAMudieLStebbingsLLargaespadaDAWesselsLFRichardSKahnoskiRJAnemaJExome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.Nature201146953954210.1038/nature0963921248752PMC3030920 | — | — | — |
| VogelsteinBKinzlerKWDigital PCR.Proc Natl Acad Sci USA1999969236924110.1073/pnas.96.16.923610430926PMC17763 | — | — | — |
| WangKLiMHakonarsonHANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.Nucleic Acids Res201038e16410.1093/nar/gkq60320601685PMC2938201 | — | — | — |
In this knowledge base
| Title | Year | PMID |
|---|---|---|
| Statistical modeling for sensitive detection of low-frequency single nucleotide variants. | 2016 | 27556804 |
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking. | Sergi A et al. | — | 2024 | → |
| Histologic and Genotypic Characterization of Lung Cancer in the Inuit Population of the Eastern Canadian Arctic. | Goss GD et al. | — | 2022 | → |
| Lipoprotein(a) beyond the kringle IV repeat polymorphism: The complexity of genetic variation in the LPA gene. | Coassin S et al. | — | 2022 | → |
| Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory. | Craven KE et al. | — | 2022 | → |
| Combined landscape of single-nucleotide variants and copy number alterations in clonal hematopoiesis. | Saiki R et al. | — | 2021 | → |
| Multiregion Sequence Analysis to Predict Intratumor Heterogeneity and Clonal Evolution. | Ahn S et al. | — | 2021 | → |
| Novel Genetic Variations in Acute Myeloid Leukemia in Pakistani Population. | Shahid S et al. | — | 2020 | → |
| A comprehensive map of single-base polymorphisms in the hypervariable <i>LPA</i> kringle IV type 2 copy number variation region. | Coassin S et al. | — | 2019 | → |
| CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing. | Jiang Y et al. | — | 2018 | → |
| IDH1/2 Mutations Predict Shorter Survival in Chondrosarcoma. | Lugowska I et al. | — | 2018 | → |
| Low frequency of Fabry disease in patients with common heart disease. | Schiffmann R et al. | — | 2018 | → |
| Urinary Exosomal and cell-free DNA Detects Somatic Mutation and Copy Number Alteration in Urothelial Carcinoma of Bladder. | Lee DH et al. | — | 2018 | → |
| Applications of molecular testing in surgical pathology of the head and neck. | Hunt JL | — | 2017 | → |
| Detection of false positive mutations in BRCA gene by next generation sequencing. | Suryavanshi M et al. | — | 2017 | → |
| Droplet-Based Digital PCR: Application in Cancer Research. | Perkins G et al. | — | 2017 | → |
| Drug-sensitive FGFR3 mutations in lung adenocarcinoma. | Chandrani P et al. | — | 2017 | → |
| Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. | Artyomenko A et al. | — | 2017 | → |
| MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. | Shugay M et al. | — | 2017 | → |
| Microfluidics for genome-wide studies involving next generation sequencing. | Ma S et al. | — | 2017 | → |
| RareVar: A Framework for Detecting Low-Frequency Single-Nucleotide Variants. | Hao Y et al. | — | 2017 | → |
| Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq. | Wang K et al. | — | 2017 | → |
| Circulating tumor DNA for triple-negative breast cancer diagnosis and treatment decisions. | Saliou A et al. | — | 2016 | → |
| Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants | Artyomenko A et al. | — | 2016 | — |
| Statistical modeling for sensitive detection of low-frequency single nucleotide variants. | Hao Y et al. | — | 2016 | → |
| Ultra-precise detection of mutations by droplet-based amplification of circularized DNA. | Wang K et al. | — | 2016 | → |
| Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis. | Wang K et al. | — | 2016 | → |
| AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries. | Hsu AL et al. | — | 2015 | → |
| An advanced preclinical mouse model for acute myeloid leukemia using patients' cells of various genetic subgroups and in vivo bioluminescence imaging. | Vick B et al. | — | 2015 | → |
| Gene expression-based prognostic and predictive tools in breast cancer. | Munkácsy G et al. | — | 2015 | → |
| MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. | Suyama Y et al. | — | 2015 | → |
| MSIplus for Integrated Colorectal Cancer Molecular Testing by Next-Generation Sequencing. | Hempelmann JA et al. | — | 2015 | → |
| Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization. | Do H et al. | — | 2015 | → |
| Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. | Patel A et al. | — | 2014 | → |
| A unique case of refractory primary mediastinal B-cell lymphoma with JAK3 mutation and the role for targeted therapy. | Hanna DM et al. | — | 2014 | → |
| Detection of minimal residual disease in NPM1-mutated acute myeloid leukemia by next-generation sequencing. | Salipante SJ et al. | — | 2014 | → |
| Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel. | Choudhary A et al. | — | 2014 | → |
| False positives in multiplex PCR-based next-generation sequencing have unique signatures. | McCall CM et al. | — | 2014 | → |
| Genomic technologies and the new era of genomic medicine. | Ankala A et al. | — | 2014 | → |
| Microsatellite instability detection by next generation sequencing. | Salipante SJ et al. | — | 2014 | → |
| Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment. | Yu Z et al. | — | 2014 | → |
| Next-generation sequencing-based multigene mutational screening for acute myeloid leukemia using MiSeq: applicability for diagnostics and disease monitoring. | Luthra R et al. | — | 2014 | → |
| Novel droplet platforms for the detection of disease biomarkers. | Zec H et al. | — | 2014 | → |
| Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. | Spencer DH et al. | — | 2014 | → |
| PyClone: statistical inference of clonal population structure in cancer. | Roth A et al. | — | 2014 | → |
| Simultaneous genomic identification and profiling of a single cell using semiconductor-based next generation sequencing. | Watanabe M et al. | — | 2014 | → |
| t(14;18) Translocation: A predictive blood biomarker for follicular lymphoma. | Roulland S et al. | — | 2014 | → |
| Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. | Pritchard CC et al. | — | 2014 | → |
| Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations. | Sweeney RT et al. | — | 2013 | → |
| Evaluation of ultra-deep targeted sequencing for personalized breast cancer care. | Harismendy O et al. | — | 2013 | → |
| Heterogeneity of colorectal cancer (CRC) in reference to KRAS proto-oncogene utilizing WAVE technology. | Perez K et al. | — | 2013 | → |
| High-throughput sequencing of the melanoma genome. | Kunz M et al. | — | 2013 | → |
| Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing. | Yost SE et al. | — | 2013 | → |
| Mutation detection by clonal sequencing of PCR amplicons and grouped read typing is applicable to clinical diagnostics. | Chambers PA et al. | — | 2013 | → |
| Next generation analysis of breast cancer genomes for precision medicine. | Previati M et al. | — | 2013 | → |
| Next-generation sequencing - feasibility and practicality in haematology. | Kohlmann A et al. | — | 2013 | → |
| Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates. | Do H et al. | — | 2013 | → |
| Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. | Hiatt JB et al. | — | 2013 | → |
| Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours. | Wong SQ et al. | — | 2013 | → |
| Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. | Hadd AG et al. | — | 2013 | → |
| The implications of clonal genome evolution for cancer medicine. | Aparicio S et al. | — | 2013 | → |
| Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers. | Li X et al. | — | 2013 | → |
| Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. | Kreso A et al. | — | 2013 | → |
| Concordance and discordance in tumor genomic profiling. | Garraway LA | — | 2012 | → |
| Detecting biomarkers with microdroplet technology. | Taly V et al. | — | 2012 | → |
| [Genome sequencing for personalized cancer treatment]. | Skotheim RI et al. | — | 2012 | → |
| Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer. | Yeo ZX et al. | — | 2012 | → |
| LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. | Wilm A et al. | — | 2012 | → |
| Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. | Forshew T et al. | — | 2012 | → |