title: Whole exome sequencing reveals minimal differences between cell line and whole blood derived DNA.
abstract: Two common sources of DNA for whole exome sequencing (WES) are whole blood (WB) and immortalized lymphoblastoid cell line (LCL). However, it is possible that LCLs have a substantially higher rate of mutation than WB, causing concern for their use in sequencing studies. We compared results from paired WB and LCL DNA samples for 16 subjects, using LCLs of low passage number (<5). Using a standard analysis pipeline we detected a large number of discordant genotype calls (approximately 50 per subject) that we segregated into categories of "confidence" based on read-level quality metrics. From these categories and validation by Sanger sequencing, we estimate that the vast majority of the candidate differences were false positives and that our categories were effective in predicting valid sequence differences, including LCLs with putative mosaicism for the non-reference allele (3-4 per exome). These results validate the use of DNA from LCLs of low passage number for exome sequencing.
authors.affiliation: Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
authors.forename: Chad M
authors.initials: CM
authors.lastname: Schafer
authors.forename: Nicholas G
authors.initials: NG
authors.lastname: Campbell
authors.forename: Guiqing
authors.initials: G
authors.lastname: Cai
authors.forename: Fei
authors.initials: F
authors.lastname: Yu
authors.forename: Vladimir
authors.initials: V
authors.lastname: Makarov
authors.forename: Seungtai
authors.initials: S
authors.lastname: Yoon
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Daly
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.forename: Gerard D
authors.initials: GD
authors.lastname: Schellenberg
authors.forename: Bernie
authors.initials: B
authors.lastname: Devlin
authors.forename: James S
authors.initials: JS
authors.lastname: Sutcliffe
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Buxbaum
authors.forename: Kathryn
authors.initials: K
authors.lastname: Roeder
mesh_terms: D000483:Alleles; D001773:Blood Cells / Q000502:physiology*; D002460:Cell Line; D019295:Computational Biology; D059472:Exome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009030:Mosaicism; D009154:Mutation; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
keywords: Graphical diagnostics; Lymphoblastoid cell line; Mosaicism; Sequence variant call; Somatic mutation; Strand bias