ArticleHuman genetics2018
The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease.
Article in Human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Genes linked to schistosome resistance identified in a genome-wide association study of African snail vectors.Nature communications · 2025Article
- Genome-wide association testing beyond SNPs.Nature reviews. Genetics · 2025Review
- The genetics of hyper IgE syndromes.Frontiers in immunology · 2025Review
- A Systematic Review of SNPs Screening for Platinum-Related Pharmacodynamics and Pharmacokinetics Genes in Non-Small Cell Lung Cancer for Precision Medicine.The application of clinical genetics · 2025Review
- Exploring the Intersection of Schizophrenia, Machine Learning, and Genomics: Scoping Review.JMIR bioinformatics and biotechnology · 2024Article
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- Genome-wide analysis to uncover how Pocillopora acuta survives the challenging intertidal environment.Scientific reports · 2024Article
- Integrated DNA methylation analysis reveals a potential role for PTPRN2 in Marfan syndrome scoliosis.JOR spine · 2024Article
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- Maternal pre-pregnancy BMI, offspring epigenome-wide DNA methylation, and childhood obesity: findings from the Boston Birth Cohort.BMC medicine · 2023Article
- Functional characterization of human genomic variation linked to polygenic diseases.Trends in genetics : TIG · 2023Review
- Pharmaco-Omics in Psoriasis: Paving the Way towards Personalized Medicine.International journal of molecular sciences · 2023Review
- Deep Learning-Based Feature Extraction with MRI Data in Neuroimaging Genetics for Alzheimer's Disease.Genes · 2023Article
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30 authors.
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Abstract
With the recent advance in genome-wide association studies (GWAS), disease-associated single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) have been extensively reported. Accordingly, the issue of incorrect identification of recombination events that can induce the distortion of multi-allelic or hemizygous variants has received more attention. However, the potential distorted calculation bias or significance of a detected association in a GWAS due to the coexistence of CNVs and SNPs in the same genomic region may remain under-recognized. Here we performed the association study within a congenital scoliosis (CS) cohort whose genetic etiology was recently elucidated as a compound inheritance model, including mostly one rare variant deletion CNV null allele and one common variant non-coding hypomorphic haplotype of the TBX6 gene. We demonstrated that the existence of a deletion in TBX6 led to an overestimation of the contribution of the SNPs on the hypomorphic allele. Furthermore, we generalized a model to explain the calculation bias, or distorted significance calculation for an association study, that can be 'induced' by CNVs at a locus. Meanwhile, overlapping between the disease-associated SNPs from published GWAS and common CNVs (overlap 10%) and pathogenic/likely pathogenic CNVs (overlap 99.69%) was significantly higher than the random distribution (p < 1 × 10
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