Strategies for processing and quality control of Illumina genotyping arrays

• Published in: Briefings in bioinformatics Vol. 19; no. 5; pp. 765 - 775
• Main Authors: Zhao, Shilin, Jing, Wang, Samuels, David C, Sheng, Quanghu, Shyr, Yu, Guo, Yan
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 28.09.2018; Oxford Publishing Limited (England)
• Subjects: Algorithms; Arrays; Cluster Analysis; Computational Biology - methods; Continental Population Groups - genetics; data collection; Female; Gene Frequency; Genome-wide association studies; genome-wide association study; Genome-Wide Association Study - methods; Genome-Wide Association Study - statistics & numerical data; Genomes; Genotype; Genotyping; Genotyping Techniques - methods; Genotyping Techniques - standards; Genotyping Techniques - statistics & numerical data; High-Throughput Nucleotide Sequencing - methods; High-Throughput Nucleotide Sequencing - standards; Humans; Male; Models, Genetic; Nucleotides; Oligonucleotide Array Sequence Analysis; Polymorphism, Single Nucleotide; Quality Control; Single-nucleotide polymorphism; Software; cluster; SNP array; quality control; genotyping array; genotyping
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbx012

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.