ArticleHGG advances2022
Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.
Article in HGG advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data.BMC bioinformatics · 2025Article
- Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland populations.Scientific reports · 2025Article
- The Estonian Biobank's journey from biobanking to personalized medicine.Nature communications · 2025Review
- Genome-wide association testing beyond SNPs.Nature reviews. Genetics · 2025Review
- Genome-Wide Scan for Copy Number Variations in Chinese Merino Sheep Based on Ovine High-Density 600K SNP Arrays.Animals : an open access journal from MDPI · 2024Article
- Genetic determinants of plasma protein levels in the Estonian population.Scientific reports · 2024Article
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Authors and funding
19 authors.
Funding
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Abstract
Copy-number variations (CNV) are believed to play an important role in a wide range of complex traits, but discovering such associations remains challenging. While whole-genome sequencing (WGS) is the gold-standard approach for CNV detection, there are several orders of magnitude more samples with available genotyping microarray data. Such array data can be exploited for CNV detection using dedicated software (e.g., PennCNV); however, these calls suffer from elevated false-positive and -negative rates. In this study, we developed a CNV quality score that weights PennCNV calls (pCNVs) based on their likelihood of being true positive. First, we established a measure of pCNV reliability by leveraging evidence from multiple omics data (WGS, transcriptomics, and methylomics) obtained from the same samples. Next, we built a predictor of omics-confirmed pCNVs, termed omics-informed quality score (OQS), using only PennCNV software output parameters. Promisingly, OQS assigned to pCNVs detected in close family members was up to 35% higher than the OQS of pCNVs not carried by other relatives (p < 3.0 × 10
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