ArticleG3 (Bethesda, Md.)2013
Comparison of the performance of two commercial genome-wide association study genotyping platforms in Han Chinese samples.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 23 citations in OpenAlex.
- APIS: an updated parentage assignment software managing triploids induced from diploid parents.G3 (Bethesda, Md.) · 2024Article
- Comparing feature selection and machine learning approaches for predictingFrontiers in neuroinformatics · 2023Article
- Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1.Journal of animal science · 2019Article
- FKBP5 Moderates the Association between Antenatal Maternal Depressive Symptoms and Neonatal Brain Morphology.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2018Article
- Psychiatric polygenic risk associates with cortical morphology and functional organization in aging.Translational psychiatry · 2017Article
- Effects of Antenatal Maternal Depressive Symptoms and Socio-Economic Status on Neonatal Brain Development are Modulated by Genetic Risk.Cerebral cortex (New York, N.Y. : 1991) · 2017Article
- Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome.Scientific reports · 2017Article
- Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms.Genetics, selection, evolution : GSE · 2016Article
- Modulative effects of COMT haplotype on age-related associations with brain morphology.Human brain mapping · 2016Article
- M(3)-S: a genotype calling method incorporating information from samples with known genotypes.BMC bioinformatics · 2015Article
- Coverage and efficiency in current SNP chips.European journal of human genetics : EJHG · 2014Article
- Population Genomics of Human Adaptation.Annual review of ecology, evolution, and systematics · 2013Article
Corrections and comments
- Erratum issuedCorrigendum.2013
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most genome-wide association studies to date have been performed in populations of European descent, but there is increasing interest in expanding these studies to other populations. The performance of genotyping chips in Asian populations is not well established. Therefore, we sought to test the performance of widely used fixed-marker, genome-wide association studies chips in the Han Chinese population. Non-HapMap Chinese samples (n = 396) were genotyped using the Illumina OmniExpress and Affymetrix 6.0 platforms, whereas a subset also were genotyped using the Immunochip. Genotyped markers from the Affymetrix 6.0 and Illumina OmniExpress were used for full genome imputation based on the HapMap 2 JPT+CHB (Japanese from Tokyo, Japan and Chinese from Beijing, China) reference panel. The concordance between markers genotypes for the three platforms was very high whether directly genotyped or genotyped and imputed single nucleotide polymorphisms (SNPs; >99.8% for directly genotyped and >99.5% for genotyped and imputed SNPs, respectively) were compared. The OmniExpress chip data enabled more SNPs to be imputed, particularly SNPs with minor allele frequency >5%. The OmniExpress chip achieved better coverage of HapMap SNPs than the Affymetrix 6.0 chip (73.6% vs. 65.9%, respectively, for minor allele frequency >5%). The Affymetrix 6.0 and Illumina OmniExpress chip have similar genotyping accuracy and provide similar accuracy of imputed SNPs. The OmniExpress chip however provides better coverage of Asian HapMap SNPs, although its coverage of HapMap SNPs is moderate.
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