ArticleBriefings in bioinformatics2018
Strategies for processing and quality control of Illumina genotyping arrays.
Article in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
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- Genetic Diversity Evaluation of Shanghai Local Pig Breeds Using Liquid-Phase Chip Technology.Animals : an open access journal from MDPI · 2026Article
- Multi-omics Data Integration.Advances in experimental medicine and biology · 2026Review
- CNV-Finder: streamlining copy number variation discovery.Bioinformatics advances · 2026Article
- Polygenic risk scores in routine genetic diagnostics: what lies ahead?Journal of community genetics · 2025Article
- Polygenic score from MODY genes is associated with type 1 diabetes and disease characteristics.Acta diabetologica · 2025Article
- Transcriptional impacts of substance use disorder and HIV on human ventral midbrain neurons and microglia.Nature communications · 2025Article
- Impact of polymorphisms on gene expression and splicing in response to exercise and diet-induced weight loss in human skeletal muscle tissues.Cell genomics · 2025Article
- Genetic Diversity and Population Structure of Five Pig Breeds from Chongqing, China.Animals : an open access journal from MDPI · 2025Article
- CNV-Finder: Streamlining Copy Number Variation Discovery.bioRxiv : the preprint server for biology · 2025Article
- GWAS links APOE to neuropsychiatric symptoms in mild cognitive impairment and dementia.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
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- Genetic and phenotypic heterogeneity of type 2 diabetes across Russian ancestry groups.Frontiers in endocrinology · 2025Article
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- Polygenic associations with clinical and neuropathological trait heterogeneity across TDP-43 proteinopathies.PloS one · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Illumina genotyping arrays have powered thousands of large-scale genome-wide association studies over the past decade. Yet, because of the tremendous volume and complicated genetic assumptions of Illumina genotyping data, processing and quality control (QC) of these data remain a challenge. Thorough QC ensures the accurate identification of single-nucleotide polymorphisms and is required for the correct interpretation of genetic association results. By processing genotyping data on > 100 000 subjects from >10 major Illumina genotyping arrays, we have accumulated extensive experience in handling some of the most peculiar scenarios related to the processing and QC of Illumina genotyping data. Here, we describe strategies for processing Illumina genotyping data from the raw data to an analysis ready format, and we elaborate on the necessary QC procedures required at each processing step. High-quality Illumina genotyping data sets can be obtained by following our detailed QC strategies.
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