ArticleCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology2008
Performance of amplified DNA in an Illumina GoldenGate BeadArray assay.
Article in Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The Minnesota Center for Twin and Family Research genome-wide association study.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2012Trial
- Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality.Molecular genetics and metabolism reports · 2017Article
- Maternal and infant genetic variants, maternal periconceptional use of selective serotonin reuptake inhibitors, and risk of congenital heart defects in offspring: population based study.BMJ (Clinical research ed.) · 2017Article
- Genome-wide scans of genetic variants for psychophysiological endophenotypes: a methodological overview.Psychophysiology · 2014Review
- Gene-based SNP discovery and genetic mapping in pea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Genetic ancestry is associated with colorectal adenomas and adenocarcinomas in Latino populations.European journal of human genetics : EJHG · 2014Article
- Conotruncal heart defects and common variants in maternal and fetal genes in folate, homocysteine, and transsulfuration pathways.Birth defects research. Part A, Clinical and molecular teratology · 2014Article
- Associations between maternal genotypes and metabolites implicated in congenital heart defects.Molecular genetics and metabolism · 2012Article
- A mechanistic basis for amplification differences between samples and between genome regions.BMC genomics · 2012Article
- Regular Multivitamin Supplement Use, Single Nucleotide Polymorphisms in ATIC, SHMT2, and SLC46A1, and Risk of Ovarian Carcinoma.Frontiers in genetics · 2012Article
- Xenobiotic-Metabolizing gene polymorphisms and ovarian cancer risk.Molecular carcinogenesis · 2011Article
- MTHFR polymorphisms in relation to ovarian cancer risk.Gynecologic oncology · 2010Article
- Evaluation of candidate stromal epithelial cross-talk genes identifies association between risk of serous ovarian cancer and TERT, a cancer susceptibility "hot-spot".PLoS genetics · 2010Article
- In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?PloS one · 2010Article
- Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation.BMC research notes · 2010Article
- Variation at 8q24 and 9p24 and risk of epithelial ovarian cancer.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2010Article
- Article
- Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.BMC genetics · 2009Article
- Cell cycle genes and ovarian cancer susceptibility: a tagSNP analysis.British journal of cancer · 2009Article
- Polymorphisms in TCEAL7 and risk of epithelial ovarian cancer.Gynecologic oncology · 2009Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Whole genome amplification (WGA) offers a means to enrich DNA quantities for epidemiologic studies. We used an ovarian cancer study of 1,536 single nucleotide polymorphisms (SNPs) and 2,368 samples to assess performance of multiple displacement amplification (MDA) WGA using an Illumina GoldenGate BeadArray. Initial screening revealed successful genotyping for 93.4% of WGA samples and 99.3% of genomic samples, and 93.2% of SNPs for WGA samples and 96.3% of SNPs for genomic samples. SNP failure was predicted by Illumina-provided designability rank, %GC (P < or = 0.002), and for WGA only, distance to telomere and Illumina-provided SNP score (P < or = 0.002). Distance to telomere and %GC were highly correlated; adjustment for %GC removed the association between distance to telomere and SNP failure. Although universally high, per-SNP call rates were related to designability rank, SNP score, %GC, minor allele frequency, distance to telomere (P < or = 0.01), and, for WGA only, Illumina-provided validation class (P < 0.001). We found excellent concordance generally (>99.0%) among 124 WGA:genomic replicates, 15 WGA replicates, 88 replicate aliquots of the same WGA preparation, and 25 genomic replicates. Where there was discordance, it was across WGA:genomic replicates but limited to only a few samples among other replicates suggesting the introduction of error. Designability rank and SNP score correlated with WGA:genomic concordance (P < 0.001). In summary, use of MDA WGA DNA is feasible; however, caution is warranted regarding SNP selection and analysis. We recommend that biological SNP characteristics, notably distance to telomere and GC content (<50% GC recommended), as well as Illumina-provided metrics be considered in the creation of GoldenGate assays using MDA WGA DNA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.