title: The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology.
abstract: BACKGROUND
  Whole-exome sequencing (WES) has recently emerged as an appealing approach to systematically study coding variants. However, the requirement for a large amount of high-quality DNA poses a barrier that may limit its application in large cancer epidemiologic studies. We evaluated the performance of WES with low input amount and saliva DNA as an alternative source material.
  
  
  METHODS
  Five breast cancer patients were randomly selected from the Pathways Study. From each patient, four samples, including 3 μg, 1 μg, and 0.2 μg blood DNA and 1 μg saliva DNA, were aliquoted for library preparation using the Agilent SureSelect Kit and sequencing using Illumina HiSeq2500. Quality metrics of sequencing and variant calling, as well as concordance of variant calls from the whole exome and 21 known breast cancer genes, were assessed by input amount and DNA source.
  
  
  RESULTS
  There was little difference by input amount or DNA source on the quality of sequencing and variant calling. The concordance rate was about 98% for single-nucleotide variant calls and 83% to 86% for short insertion/deletion calls. For the 21 known breast cancer genes, WES based on low input amount and saliva DNA identified the same set variants in samples from a same patient.
  
  
  CONCLUSIONS
  Low DNA input amount, as well as saliva DNA, can be used to generate WES data of satisfactory quality.
  
  
  CONCLUSIONS
  Our findings support the expansion of WES applications in cancer epidemiologic studies where only low DNA amount or saliva samples are available.
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York. qianqian.zhu@roswellpark.org song.yao@roswellpark.org.
authors.forename: Qianqian
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Lori
authors.initials: L
authors.lastname: Shepherd
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Lei
authors.initials: L
authors.lastname: Wei
authors.affiliation: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Carl D
authors.initials: CD
authors.lastname: Morrison
authors.affiliation: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Conroy
authors.affiliation: Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Sean T
authors.initials: ST
authors.lastname: Glenn
authors.affiliation: Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Warren
authors.initials: W
authors.lastname: Davis
authors.affiliation: Division of Research, Kaiser Permanente Northern California, Oakland, California.
authors.forename: Marilyn L
authors.initials: ML
authors.lastname: Kwan
authors.affiliation: Division of Research, Kaiser Permanente Northern California, Oakland, California.
authors.forename: Isaac J
authors.initials: IJ
authors.lastname: Ergas
authors.affiliation: Division of Research, Kaiser Permanente Northern California, Oakland, California.
authors.forename: Janise M
authors.initials: JM
authors.lastname: Roh
authors.affiliation: Division of Research, Kaiser Permanente Northern California, Oakland, California.
authors.forename: Lawrence H
authors.initials: LH
authors.lastname: Kushi
authors.affiliation: Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Christine B
authors.initials: CB
authors.lastname: Ambrosone
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York.
authors.forename: Song
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York. qianqian.zhu@roswellpark.org song.yao@roswellpark.org.
authors.forename: Song
authors.initials: S
authors.lastname: Yao
mesh_terms: D004247:DNA / Q000235:genetics*; D059472:Exome / Q000235:genetics*; D023281:Genomics; D006801:Humans; D009369:Neoplasms / Q000453:epidemiology*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA