{"paper_id":"40e5b71f-e0e6-4b37-9b5a-a1cba5c95e6b","body_text":"Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for Yoo-Jin Jiny Ha\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for Kristin Ardlie\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for Robert S. Fulton\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for Soren Germer\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for Richard Gibbs\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for Gabor T. Marth\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for James T. Bennett\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\n- Find this author on Google Scholar\n- Find this author on PubMed\n- Search for this author on this site\n- ORCID record for Peter J. Park\n- For correspondence: yoojinha{at}hanyang.ac.kr kardlie{at}broadinstitute.org rfulton22{at}wustl.edu sgermer{at}nygenome.org agibbs{at}bcm.edu gmarth{at}genetics.utah.edu James.Bennett{at}seattlechildrens.org peter_park{at}hms.harvard.edu\nAbstract\nMosaic mutations in normal tissues occur at low variant allele fractions (VAFs), complicating detection. To benchmark strategies, the SMaHT Network created a cell-line mixture (1:49) and produced ultra-deep whole-genome sequencing using short and long reads (five centers, 180–500× each). We assembled a reference of 44,008 mosaic SNVs and 2,059 Indels, cross-validation between platforms to expose limits of short-read analysis. We also partitioned the genome by mappability to examine the impact of genomic context, added a negative reference set, and accounted for culture-derived mutations. When seven institutions applied eleven algorithms to mixture data, call sets were largely discordant across tools and replicates, partly reflecting stochastic presence of low-VAF mutations in biological replicants. For >2% VAF SNVs, sensitivity and precision approached ∼80% at ≥300×, with little gain from additional sequencing. This work provides a comprehensive framework for reliable detection of low-VAF mutations in non-cancer tissues and a valuable resource for the community.\nCompeting Interest Statement\nPeter Park a member of the Scientific Advisory Board for Bioskryb Genomics. James Bennett is a consultant for Mosaica Medicines. Andrew Stergachis is a co-inventor on a patent relating to the Fiber-seq and DAF-seq methods.\nFunder Information Declared\nSubject Area\n- Biochemistry (17691)\n- Bioengineering (13892)\n- Bioinformatics (41937)\n- Biophysics (21452)\n- Cancer Biology (18588)\n- Cell Biology (25504)\n- Clinical Trials (138)\n- Developmental Biology (13378)\n- Ecology (19899)\n- Epidemiology (2067)\n- Evolutionary Biology (24320)\n- Genetics (15609)\n- Genomics (22506)\n- Immunology (17736)\n- Microbiology (40394)\n- Molecular Biology (17181)\n- Neuroscience (88605)\n- Paleontology (666)\n- Pathology (2832)\n- Pharmacology and Toxicology (4824)\n- Physiology (7641)\n- Plant Biology (15156)\n- Synthetic Biology (4294)\n- Systems Biology (9825)\n- Zoology (2271)","source_license":"CC-BY-4.0","license_restricted":false}