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Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: Implications for genome-wide association studies

Herbeck, JT and Gottlieb, GS and Wong, K and Detels, R and Phair, JP and Rinaldo, CR and Jacobson, LP and Margolick, JB and Mullins, JI (2009) Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: Implications for genome-wide association studies. PLoS ONE, 4 (9).

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Abstract

Background: As availability of primary cells can be limited for genetic studies of human disease, lymphoblastoid cell lines (LCL) are common sources of genomic DNA. LCL are created in a transformation process that entails in vitro infection of human B-lymphocytes with the Epstein-Barr Virus (EBV). Methodology/Principal Findings: To test for genotypic errors potentially induced by the Epstein-Barr Virus transformation process, we compared single nucleotide polymorphism (SNP) genotype calls in peripheral blood mononuclear cells (PBMC) and LCL from the same individuals. The average mismatch rate across 19 comparisons was 0.12% for SNPs with a population call rate of at least 95%, and 0.03% at SNPs with a call rate of at least 99%. Mismatch rates were not correlated across genotype subarrays run on all sample pairs. Conclusions/Significance: Genotypic discrepancies found in PBMC and LCL pairs were not significantly different than control pairs, and were not correlated across subarrays. These results suggest that mismatch rates are minimal with stringent quality control, and that most genotypic discrepancies are due to technical artifacts rather than the EBV transformation process. Thus, LCL likely constitute a reliable DNA source for host genotype analysis. © 2009 Herbeck et al.

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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Herbeck, JT
Gottlieb, GS
Wong, K
Detels, R
Phair, JP
Rinaldo, CRRINALDO@pitt.eduRINALDO
Jacobson, LP
Margolick, JB
Mullins, JI
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorAwadalla, PhilipUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 4 September 2009
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 4
Number: 9
DOI or Unique Handle: 10.1371/journal.pone.0006915
Refereed: Yes
MeSH Headings: Adult; B-Lymphocytes--metabolism; B-Lymphocytes--virology; Cell Line, Transformed; Cell Line, Tumor; Cell Transformation, Viral--genetics; Genome-Wide Association Study; Genotype; HIV Infections--complications; Herpesvirus 4, Human--genetics; Humans; Male; Oligonucleotide Array Sequence Analysis; Phenotype; Polymorphism, Single Nucleotide; Prospective Studies
Other ID: NLM PMC2731852
PubMed Central ID: PMC2731852
PubMed ID: 19730697
Date Deposited: 03 Aug 2012 16:16
Last Modified: 25 Jan 2019 23:55
URI: http://d-scholarship.pitt.edu/id/eprint/13268

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