ArticleGenes & genomics2019
SNP genotype calling and quality control for multi-batch-based studies.
Article in Genes & genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 2 of them syntheses that pooled it.
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Who cites it
14 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Genome-Wide Association Study on Longitudinal Change in Fasting Plasma Glucose in Korean Population.Diabetes & metabolism journal · 2023Pooled it
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- Effects of polygenic risk score and sodium and potassium intake on hypertension in Asians: A nationwide prospective cohort study.Hypertension research : official journal of the Japanese Society of Hypertension · 2024Article
- Genetic determinants of obesity in Korean populations: exploring genome-wide associations and polygenic risk scores.Briefings in bioinformatics · 2024Article
- Structural variant landscapes reveal convergent signatures of evolution in sheep and goats.Genome biology · 2024Article
- Epigenetic link between Agent Orange exposure and type 2 diabetes in Korean veterans.Frontiers in endocrinology · 2024Article
- Heritability of cognitive abilities and regional brain structures in middle-aged to elderly East Asians.Cerebral cortex (New York, N.Y. : 1991) · 2023Article
- Identification of genetic variants associated with diabetic kidney disease in multiple Korean cohorts via a genome-wide association study mega-analysis.BMC medicine · 2023Article
- A genome-wide association study implicates the pleiotropic effect of NMUR2 on asthma and COPD.Scientific reports · 2022Article
- rs2671655 single nucleotide polymorphism modulates the risk for gastric cancer in Helicobacter pylori-infected individuals: a genome-wide association study in the Korean population.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2022Article
- Unveiling genetic variants for age-related sarcopenia by conducting a genome-wide association study on Korean cohorts.Scientific reports · 2022Article
- Unveiling Genetic Variants Underlying Vitamin D Deficiency in Multiple Korean Cohorts by a Genome-Wide Association Study.Endocrinology and metabolism (Seoul, Korea) · 2021Article
- Genome-Wide Association Study of Korean Asthmatics: A Comparison With UK Asthmatics.Allergy, asthma & immunology research · 2021Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundIn genetic analyses, the term 'batch effect' refers to systematic differences caused by batch heterogeneity. Controlling this unintended effect is the most important step in quality control (QC) processes that precede analyses. Currently, batch effects are not appropriately controlled by statistics, and newer approaches are required.
methodsIn this report, we propose a new method to detect the heterogeneity of probe intensities among different batches and a procedure for calling genotypes and QC in the presence of a batch effect. First, we conducted a multivariate analysis of variance (MANOVA) to test the differences in probe intensities among batches. If heterogeneity is detected, subjects should be clustered using a K-medoid algorithm using the averages of the probe intensity measurements for each batch and the genotypes of subjects in different clusters should be called separately.
resultsThe proposed method was used to assess genotyping data of 3619 subjects consisting of 1074 patients with Alzheimer's disease, 296 with mild cognitive impairment (MCI), and 1153 controls. The proposed method improves the accuracy of called genotypes without the need to filter a lot of subjects and SNPs, and therefore is a reasonable approach for controlling batch effects.
conclusionsWe proposed a new strategy that detects batch effects with probe intensity measurement and calls genotypes in the presence of batch effects. The application of the proposed method to real data shows that it produces a balanced approach. Furthermore, the proposed method can be extended to various scenarios with a simple modification.
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