Copy Number Variation Analysis from SNP Genotyping Microarrays in Large Cohorts of Neurological Disorders

Pérez-Palma E.; Niestroj, Lisa-Marie; Inca-Martinez, Miguel; Villaman, Camilo; Sarihan, Elif Irem; Lal, Denn; Mata, Ignacio F.; Proukakis Christos

Keywords: genotyping, structural variation, neurological disorders, Copy number variation, GWAS, CNVs


Copy number variants (CNVs) are a major source of genetic variation in the human genome, and they are highly heterogeneous in type, size, and frequency. CNVs represent the largest portion of genomic variation between humans, and a subset of CNVs has been associated with multiple rare and common neurological disorders. Although recent sequencing-based methods deliver increased resolution and greater power in detecting CNVs, SNP genotyping microarrays still provide a scalable opportunity to analyze CNVs in large cohorts of neurological disorders. In the past 15 years, case-control genome-wide association studies and population-based biobanks have widely used SNP genotyping microarrays to understand the heritability of common variants. As a result, massive amounts of SNP microarray data are available and provide a cost-efficient opportunity to repurpose the data and study large and rare CNVs. Here we describe a workflow to detect and analyze CNVs from SNP genotyping microarrays. We describe established CNV quality control procedures, CNV downstream analyses, case-control burden analysis, and validation protocols with particular focus on nervous system disorders and non-European datasets.

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Editorial: Humana Press, New York, NY, 2022
Fecha de publicación: 2022
Idioma: English