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

  • ️Thu Jan 01 2009

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

Joshua T Herbeck et al. PLoS One. 2009.

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Genotypic fidelity of LCL.

Genotypic fidelity is shown as mean pairwise distances among 19 paired comparisons of LCL and PBMC genotypes, for increasingly stringent SNP filtering by population call rate. A) Genotypic fidelity between LCL and PBMC source DNA from the same individual, estimated using the Affymetrix GeneChip Human Mapping 500 k Array set. B) SNP numbers remaining after filtering, shown for the combined 500 k array. C) Genotypic fidelity between LCL and PBMC source DNA from the same individual shown for the Nsp 250 k array. D) Genotypic fidelity between LCL and PBMC for the Sty 250 k array.

Figure 2
Figure 2. Power curve for comparisons of mismatch rates between LCL and PBMC pairs and duplicate pairs.

Relationship between effect size, in units of (pooled) standard deviation, and statistical power, for a Mann-Whitney U test (one-sided, unequal sample sizes) with group samples sizes of 19 and 4. There is power of 0.62 to detect a difference in means of one standard deviation between LCL and PBMC pairs and duplicate pairs, equal to ∼90 SNPs out of >300,000 compared.

Figure 3
Figure 3. Effect of genotype array call rate on LCL versus PBMC genotypic fidelity.

Relationship between genotypic fidelity of LCL and PBMC pairs (mismatch rate, estimated using pairwise distance) and the array call rate. For each LCL versus PBMC genotypic pair, we compared the LCL versus PBMC mismatch rate to the lesser of the two array call rates. Mismatch rates are estimated at different levels of SNP filtering by population call rate: no filtering, 90%, 95%, and 99% percent population call rate.

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