{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:32Z","timestamp":1772138012513,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,6,12]],"date-time":"2021-06-12T00:00:00Z","timestamp":1623456000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"CDMRP Breast Cancer Research Program","award":["BC132057"],"award-info":[{"award-number":["BC132057"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54 CA217376"],"award-info":[{"award-number":["U54 CA217376"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U2C CA233254"],"award-info":[{"award-number":["U2C CA233254"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P01 CA91955"],"award-info":[{"award-number":["P01 CA91955"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 CA170595"],"award-info":[{"award-number":["R01 CA170595"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 CA185138"],"award-info":[{"award-number":["R01 CA185138"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 CA140657"],"award-info":[{"award-number":["R01 CA140657"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008335","name":"Arizona Biomedical Research Commission","doi-asserted-by":"publisher","award":["ADHS18-198847"],"award-info":[{"award-number":["ADHS18-198847"]}],"id":[{"id":"10.13039\/100008335","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Most tissue collections of neoplasms are composed of formalin-fixed and paraffin-embedded (FFPE) excised tumor samples used for routine diagnostics. DNA sequencing is becoming increasingly important in cancer research and clinical management; however it is difficult to accurately sequence DNA from FFPE samples. We developed and validated a new bioinformatic pipeline to use existing variant-calling strategies to robustly identify somatic single nucleotide variants (SNVs) from whole exome sequencing using small amounts of DNA extracted from archival FFPE samples of breast cancers. We optimized this strategy using 28 pairs of technical replicates. After optimization, the mean similarity between replicates increased 5-fold, reaching 88% (range 0\u2013100%), with a mean of 21.4 SNVs (range 1\u201368) per sample, representing a markedly superior performance to existing tools. We found that the SNV-identification accuracy declined when there was less than 40\u00a0ng of DNA available and that insertion\u2013deletion variant calls are less reliable than single base substitutions. As the first application of the new algorithm, we compared samples of ductal carcinoma in situ of the breast to their adjacent invasive ductal carcinoma samples. We observed an increased number of mutations (paired-samples sign test, P\u2009&amp;lt;\u20090.05), and a higher genetic divergence in the invasive samples (paired-samples sign test, P\u2009&amp;lt;\u20090.01). Our method provides a significant improvement in detecting SNVs in FFPE samples over previous approaches.<\/jats:p>","DOI":"10.1093\/bib\/bbab221","type":"journal-article","created":{"date-parts":[[2021,5,22]],"date-time":"2021-05-22T07:07:44Z","timestamp":1621667264000},"source":"Crossref","is-referenced-by-count":11,"title":["A new method to accurately identify single nucleotide variants using small FFPE breast samples"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7363-0423","authenticated-orcid":false,"given":"Angelo","family":"Fortunato","sequence":"first","affiliation":[{"name":"Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA"},{"name":"Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA"},{"name":"School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA"}]},{"given":"Diego","family":"Mallo","sequence":"additional","affiliation":[{"name":"Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA"},{"name":"Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA"},{"name":"School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA"}]},{"given":"Shawn M","family":"Rupp","sequence":"additional","affiliation":[{"name":"Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA"},{"name":"Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA"}]},{"given":"Lorraine M","family":"King","sequence":"additional","affiliation":[{"name":"Department of Surgery, Duke University, Durham, NC, USA"}]},{"given":"Timothy","family":"Hardman","sequence":"additional","affiliation":[{"name":"Department of Surgery, Duke University, Durham, NC, USA"}]},{"given":"Joseph Y","family":"Lo","sequence":"additional","affiliation":[{"name":"Department of Radiology, Duke University, Durham, NC, USA"}]},{"given":"Allison","family":"Hall","sequence":"additional","affiliation":[{"name":"Department of Pathology, Duke University, Durham, NC, USA"}]},{"given":"Jeffrey R","family":"Marks","sequence":"additional","affiliation":[{"name":"Department of Surgery, Duke University, Durham, NC, USA"}]},{"given":"E Shelley","family":"Hwang","sequence":"additional","affiliation":[{"name":"Department of Surgery, Duke University, Durham, NC, USA"}]},{"given":"Carlo C","family":"Maley","sequence":"additional","affiliation":[{"name":"Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA"},{"name":"Biodesign Center for Biocomputing, Security and Society, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281 USA"},{"name":"School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,6,11]]},"reference":[{"key":"2021110815063921200_ref1","first-page":"105","article-title":"Tumor heterogeneity: causes and consequences","volume":"1805","author":"Marusyk","year":"2010","journal-title":"Biochim Biophys Acta"},{"key":"2021110815063921200_ref2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.ccell.2014.12.001","article-title":"Biological and therapeutic impact of intratumor heterogeneity in cancer evolution","volume":"27","author":"McGranahan","year":"2015","journal-title":"Cancer Cell"},{"key":"2021110815063921200_ref3","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nm.3984","article-title":"Pan-cancer analysis of the extent and consequences of intratumor heterogeneity","volume":"22","author":"Andor","year":"2016","journal-title":"Nat Med"},{"key":"2021110815063921200_ref4","doi-asserted-by":"crossref","first-page":"10051","DOI":"10.18632\/oncotarget.7067","article-title":"Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival","volume":"7","author":"Morris","year":"2016","journal-title":"Oncotarget"},{"key":"2021110815063921200_ref5","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nature12627","article-title":"Tumour heterogeneity in the clinic","volume":"501","author":"Bedard","year":"2013","journal-title":"Nature"},{"key":"2021110815063921200_ref6","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/nrc.2017.69","article-title":"Classifying the evolutionary and ecological features of neoplasms","volume":"17","author":"Maley","year":"2017","journal-title":"Nat Rev Cancer"},{"key":"2021110815063921200_ref7","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1038\/s41598-018-37835-6","article-title":"Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations","volume":"9","author":"Dash","year":"2019","journal-title":"Sci Rep"},{"key":"2021110815063921200_ref8","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1038\/ng1768","article-title":"Genetic clonal diversity predicts progression to esophageal adenocarcinoma","volume":"38","author":"Maley","year":"2006","journal-title":"Nat Genet"},{"key":"2021110815063921200_ref9","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1158\/1940-6207.CAPR-10-0108","article-title":"A comprehensive survey of clonal diversity measures in Barrett\u2019s esophagus as biomarkers of progression to esophageal adenocarcinoma","volume":"3","author":"Merlo","year":"2010","journal-title":"Cancer Prev Res"},{"key":"2021110815063921200_ref10","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms12158","article-title":"Dynamic clonal equilibrium and predetermined cancer risk in Barrett\u2019s oesophagus","volume":"7","author":"Martinez","year":"2016","journal-title":"Nat Commun"},{"key":"2021110815063921200_ref11","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0127353","article-title":"Robustness of next generation sequencing on older formalin-fixed paraffin-embedded tissue","volume":"10","author":"Carrick","year":"2015","journal-title":"PLoS One"},{"key":"2021110815063921200_ref12","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1007\/s40291-014-0115-2","article-title":"Cytosine deamination is a major cause of baseline noise in next-generation sequencing","volume":"18","author":"Chen","year":"2014","journal-title":"Mol Diagn Ther"},{"key":"2021110815063921200_ref13","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1373\/clinchem.2014.223040","article-title":"Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization","volume":"61","author":"Do","year":"2015","journal-title":"Clin Chem"},{"key":"2021110815063921200_ref14","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/gm481","article-title":"Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies","volume":"5","author":"Sah","year":"2013","journal-title":"Genome Med"},{"key":"2021110815063921200_ref15","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1863-4","article-title":"Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data","volume":"20","author":"Liu","year":"2019","journal-title":"Genome Biol"},{"issue":"44","key":"2021110815063921200_ref16","article-title":"A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing","volume":"10","author":"Kato","year":"2018","journal-title":"Genome Med"},{"key":"2021110815063921200_ref17","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nrg3655","article-title":"The role of replicates for error mitigation in next-generation sequencing","volume":"15","author":"Robasky","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2021110815063921200_ref18","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0119230","article-title":"Reproducibility of variant calls in replicate next generation sequencing experiments","volume":"10","author":"Qi","year":"2015","journal-title":"PLoS One"},{"key":"2021110815063921200_ref19","doi-asserted-by":"crossref","DOI":"10.1186\/s12920-020-00803-z","article-title":"Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data","volume":"13","author":"Karimnezhad","year":"2020","journal-title":"BMC Med Genomics"},{"key":"2021110815063921200_ref20","article-title":"The use of technical replication for detection of low-level somatic mutations in next-generation sequencing","volume":"10","author":"Kim","year":"2019","journal-title":"Nat Commun"},{"key":"2021110815063921200_ref21","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1097\/GRF.0b013e318207ffe9","article-title":"Breast development and anatomy","volume":"54","author":"Pandya","year":"2011","journal-title":"Clin Obstet Gynecol"},{"key":"2021110815063921200_ref22","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/ncponc0908","article-title":"Origins of breast cancer subtypes and therapeutic implications","volume":"4","author":"Sims","year":"2007","journal-title":"Nat Clin Pract Oncol"},{"key":"2021110815063921200_ref23","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1038\/ng.3036","article-title":"Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications","volume":"46","author":"Rimmer","year":"2014","journal-title":"Nat Genet"},{"key":"2021110815063921200_ref24","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-35499-w","article-title":"The central exons of the human MUC2 and MUC6 mucins are highly repetitive and variable in sequence between individuals","volume":"8","author":"Svensson","year":"2018","journal-title":"Sci Rep"},{"key":"2021110815063921200_ref25","doi-asserted-by":"crossref","DOI":"10.1111\/his.14091","article-title":"The 2019 WHO classification of tumours of the breast","author":"Tan","year":"2020","journal-title":"Histopathology"},{"key":"2021110815063921200_ref26","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/j.1365-2559.1991.tb00229.x","article-title":"Pathological prognostic factors in breast cancer. I. the value of histological grade in breast cancer: experience from a large study with long-term follow-up. C. W. Elston & I. O. Ellis","volume":"19","author":"Elston","year":"1991","journal-title":"Histopathology"},{"key":"2021110815063921200_ref27","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1016\/S0046-8177(97)90193-3","article-title":"Consensus conference on the classification of ductal carcinoma in situ","volume":"28","year":"1997","journal-title":"Hum Pathol"},{"key":"2021110815063921200_ref28","first-page":"35","article-title":"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift","volume":"3","author":"Ruden","year":"2012","journal-title":"Front Genet"},{"key":"2021110815063921200_ref29","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1093\/bioinformatics\/bts277","article-title":"BEDOPS: high-performance genomic feature operations","volume":"28","author":"Neph","year":"2012","journal-title":"Bioinformatics"},{"key":"2021110815063921200_ref30","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","article-title":"The mutational constraint spectrum quantified from variation in 141,456 humans","volume":"581","author":"Karczewski","year":"2020","journal-title":"Nature"},{"key":"2021110815063921200_ref31","article-title":"Calling Somatic SNVs and Indels with Mutect2","author":"Benjamin","year":"2019","journal-title":"bioRxiv"},{"key":"2021110815063921200_ref32","author":"R Core Team","year":"2018"},{"key":"2021110815063921200_ref33","author":"Navarro","year":"2015"},{"key":"2021110815063921200_ref34","author":"Wilke","year":"2019"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/22\/6\/bbab221\/41088672\/bbab221.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/22\/6\/bbab221\/41088672\/bbab221.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,8]],"date-time":"2021-11-08T10:10:59Z","timestamp":1636366259000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbab221\/6296507"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,11]]},"references-count":34,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2021,11,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbab221","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.10.22.350983","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,11]]},"published":{"date-parts":[[2021,6,11]]},"article-number":"bbab221"}}