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McCarthy NS, Allan SM, Chandler D, et al. Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines. Genom Data. 2016;9:18-21doi: 10.1016/j.gdata.2016.05.006.
McCarthy, N. S., Allan, S. M., Chandler, D., Jablensky, A., & Morar, B. (2016). Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines. Genomics data, 918-21. https://doi.org/10.1016/j.gdata.2016.05.006
McCarthy, Nina S, et al. "Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines." Genomics data vol. 9 (2016): 18-21. doi: https://doi.org/10.1016/j.gdata.2016.05.006
McCarthy NS, Allan SM, Chandler D, Jablensky A, Morar B. Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines. Genom Data. 2016 May 12;9:18-21. doi: 10.1016/j.gdata.2016.05.006. eCollection 2016 Sep. PMID: 27330997; PMCID: PMC4909818.
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Genom Data. 2016 May 12;9:18-21. doi: 10.1016/j.gdata.2016.05.006. eCollection 2016 Sep.

Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines.

Genomics data

Nina S McCarthy, Spencer M Allan, David Chandler, Assen Jablensky, Bharti Morar

Affiliations

  1. Centre for the Genetic Origins of Health and Disease, The University of Western Australia, Perth, Australia; Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia; Cooperative Research Centre for Mental Health, Carlton South, Victoria, Australia.
  2. Centre for the Genetic Origins of Health and Disease, The University of Western Australia, Perth, Australia.
  3. Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia.
  4. Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia; Cooperative Research Centre for Mental Health, Carlton South, Victoria, Australia.
  5. Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia; Cooperative Research Centre for Mental Health, Carlton South, Victoria, Australia; Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, Australia.

PMID: 27330997 PMCID: PMC4909818 DOI: 10.1016/j.gdata.2016.05.006

Abstract

We compared genotype data from the HumanExomeCore Array in peripheral blood mononuclear cells and low passage lymphoblastoid cell lines from the same 24 individuals to test for genotypic errors caused by the Epstein-Barr Virus transformation process. Genotype concordance across the 24 comparisons was 99.57% for unfiltered genotype data, and 99.63% following standard genotype quality control filters. Mendelian error rates and levels of heterozygosity were not significantly different between lymphoblastoid cell lines and their parent peripheral blood mononuclear cells. These results show that at low passage numbers, genotype discrepancies are minimal even before stringent quality control, and extend current evidence qualifying the use of low-passage lymphoblastoid cell lines as a reliable DNA source for genotype analysis.

Keywords: Genotyping; Lymphoblastoid cell line; Single nucleotide polymorphism

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