ArticleThe Journal of molecular diagnostics : JMD2008
Performance of whole-genome amplified DNA isolated from serum and plasma on high-density single nucleotide polymorphism arrays.
Article in The Journal of molecular diagnostics : JMD, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 2 of them syntheses that pooled it.
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Who cites it
10 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2013Guideline
- Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology.Archives of pathology & laboratory medicine · 2013Guideline
- Genome-wide association study for vascular aging highlights pathways shared with cardiovascular traits in Koreans.Frontiers in cardiovascular medicine · 2022Article
- DNA extraction from fresh and frozen plasma: an alternative for real-time PCR genotyping in pharmacogenetics.Molecular biology reports · 2020Article
- Associations of common variants in the BST2 region with HIV-1 acquisition in African American and European American people who inject drugs.AIDS (London, England) · 2015Article
- Inter-chromosomal level of genome organization and longevity-related phenotypes in humans.Age (Dordrecht, Netherlands) · 2013Article
- Statistical adjustment of genotyping error in a case-control study of childhood leukaemia.BMC medical research methodology · 2012Article
- Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development.BMC genomics · 2012Article
- Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.BMC genetics · 2009Article
- High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.Genomics · 2008Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Defining genetic variation associated with complex human diseases requires standards based on high-quality DNA from well-characterized patients. With the development of robust technologies for whole-genome amplification, sample repositories such as serum banks now represent a potentially valuable source of DNA for both genomic studies and clinical diagnostics. We assessed the performance of whole-genome amplified DNA (wgaDNA) derived from stored serum/plasma on high-density single nucleotide polymorphism arrays. Neither storage time nor usage history affected either DNA extraction or whole-genome amplification yields; however, samples that were thawed and refrozen showed significantly lower call rates (73.9 +/- 7.8%) than samples that were never thawed (92.0 +/- 3.3%) (P < 0.001). Genotype call rates did not differ significantly (P = 0.13) between wgaDNA from never-thawed serum/plasma (92.9 +/- 2.6%) and genomic DNA (97.5 +/- 0.3%) isolated from whole blood. Approximately 400,000 genotypes were consistent between wgaDNA and genomic DNA, but the overall discordance rate of 4.4 +/- 3.8% reflected an average of 11,110 +/- 9502 genotyping errors per sample. No distinct patterns of chromosomal clustering were observed for single nucleotide polymorphisms showing discordant genotypes or homozygote conversion. Because the effects of genotyping errors on whole-genome studies are not well defined, we recommend caution when applying wgaDNA from serum/plasma to high-density single nucleotide polymorphism arrays in addition to the use of stringent quality control requirements for the resulting genotype data.
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