James Sutcliffe
Last active: 2/20/2014

Whole exome sequencing reveals minimal differences between cell line and whole blood derived DNA.

Schafer CM, Campbell NG, Cai G, Yu F, Makarov V, Yoon S, Daly MJ, Gibbs RA, Schellenberg GD, Devlin B, Sutcliffe JS, Buxbaum JD, Roeder K
Genomics. 2013 102 (4): 270-7

PMID: 23743231 · PMCID: PMC3812417 · DOI:10.1016/j.ygeno.2013.05.005

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.

Copyright © 2013 Elsevier Inc. All rights reserved.

MeSH Terms (12)

Alleles Blood Cells Cell Line Computational Biology Exome Genotype High-Throughput Nucleotide Sequencing Humans Mosaicism Mutation Reproducibility of Results Sequence Analysis, DNA

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