title: A cancer cell-line titration series for evaluating somatic classification.
abstract: BACKGROUND
  Accurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.
  
  
  RESULTS
  Cell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.
  
  
  CONCLUSIONS
  Our cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO).
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. rob.denroche@oicr.on.ca.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Denroche
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. laura.mullen@oicr.on.ca.
authors.forename: Laura
authors.initials: L
authors.lastname: Mullen
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. lee.timms@oicr.on.ca.
authors.forename: Lee
authors.initials: L
authors.lastname: Timms
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. timothy.beck@oicr.on.ca.
authors.forename: Timothy
authors.initials: T
authors.lastname: Beck
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. christina.yung@oicr.on.ca.
authors.forename: Christina K
authors.initials: CK
authors.lastname: Yung
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. lincoln.stein@gmail.com.|Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. lincoln.stein@gmail.com.
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. john.mcpherson@oicr.on.ca.|Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. john.mcpherson@oicr.on.ca.
authors.forename: John D
authors.initials: JD
authors.lastname: McPherson
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON, Canada. andrew.brown@oicr.on.ca.
authors.forename: Andrew M K
authors.initials: AM
authors.lastname: Brown
mesh_terms: D000465:Algorithms; D021441:Carcinoma, Pancreatic Ductal / Q000235:genetics; D045744:Cell Line, Tumor; D019295:Computational Biology; D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000235:genetics*; D030561:Databases, Nucleic Acid; D059472:Exome / Q000235:genetics; D005787:Gene Frequency; D015723:Gene Library; D014644:Genetic Variation; D006801:Humans; D054643:INDEL Mutation; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D010190:Pancreatic Neoplasms / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D004273:DNA, Neoplasm