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
Open accessAbstract
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 × 10-6 and p = 0.034, respectively), indicating that such co-existence of CNV and SNV alleles might generally influence data interpretation and potential outcomes of a GWAS. We also verified and assessed the influence of colocalizing CNVs to the detection sensitivity of disease-associated SNP variant alleles in another adolescent idiopathic scoliosis (AIS) genome-wide association study. We proposed that detecting co-existent CNVs when evaluating the association signals between SNPs and disease traits could improve genetic model analyses and better integrate GWAS with robust Mendelian principles.
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C10orf11 (LRMDA) has been associated with craniofacial traits such as adolescent idiopathic scoliosis, heel bone mineral density, and chin shape.
“This gene has been associated with craniofacial traits such as adolescent idiopathic scoliosis [40], heel bone mineral density [41], and chin shape [21].”
From Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci (2023) · cites this paper as [40]
The citation [40] is attached only to the adolescent idiopathic scoliosis association, not the heel-density or chin-shape claims. The Introduction and Results discuss TBX6 in congenital scoliosis, and the paper also examines an adolescent idiopathic scoliosis cohort, but searches for C10orf11 and LRMDA found no passage linking either name to that condition. No page numbers were available in our copy. (LLM, conf=0.75)
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Self-citationAssociation betweenADAMTS-4gene polymorphism and lumbar disc degeneration in Chinese Han population
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Self-citationThe clustering of functionally related genes contributes to CNV-mediated diseasePreprint
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Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation
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Flagged first, then by citations
Research works printed but not linked: 1
- NCBI:dbGaP Genotyping NIGMS Chromosomal Aberration and Inherited Disorder Samples. (Study Accession ID:phs000269.v1.p1) https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000269.v1.p1
Cited by
Sorted by citations
Li, Y., Xiong, Z., Zhang, M., Hysi, P. G., Qian, Y., Adhikari, K., Weng, J., Wu, S., Du, S., Gonzalez-Jose, R., et al. (2023) · PLOS Genetics · doi:10.1371/journal.pgen.1010786 · Cited by 9 · see citing works
- Authors
- Study, D. (. D. I. S. A. C., Liu, J., Zhou, Y., Liu, S., Song, X., Yang, X.-Z., Fan, Y., Chen, W., Akdemir, Z. C., Yan, Z., Zuo, Y., Du, R., Liu, Z., Yuan, B., Zhao, S., Liu, G., Chen, Y., Zhao, Y., Lin, M., Zhu, Q., Niu, Y., Liu, P., Ikegawa, S., Song, Y.-Q., Posey, J. E., Qiu, G., Zhang, F., Wu, Z., Lupski, J. R., & Wu, N.
- Affiliations
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Baylor College of Medicine (US)
- RIKEN (JP)
- Corresponding author
- Wu, Nan
- ORCID
- Venue
- Human Genetics
- Published
- 2018-07
- Volume
- 137
- Issue
- 6-7
- Pages
- 553-567
- ISSN
- 0018-7348 (ISSN-L)
- 0340-6717
- 1432-1203
- PMC
- PMC6200315
- OpenAlex
- W2884987722
- Cited by
- 77
- References
- 92
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 10 · 2023: 20 · 2022: 12 · 2021: 6 · 2020: 8 · 2019: 11 · 2018: 1
- FWCI
- 3.99
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Human Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Natural Science Foundation of China (81501852, 81472046, 81772299, 81472045, 81772301)
- Beijing Natural Science Foundation (7172175)
- Beijing Nova Program (Z161100004916123)
- Beijing Nova Program Interdisciplinary Collaborative Project (xxjc201717)
- 2016 Milstein Medical Asian American Partnership Foundation Fellowship Award in Translational Medicine
- The Central Level Public Interest Program for Scientific Research Institute (2016ZX310177)
- PUMC Youth Fund & the Fundamental Research Funds for the Central Universities (3332016006)
- CAMS Initiative Fund for Medical Sciences (2016-I2M-3-003, 2016-I2M-2-006, 2017-I2M-2-001)
- the Distinguished Youth Foundation of Peking Union Medical College Hospital (JQ201506)
- the 2016 PUMCH Science Fund for Junior Faculty (PUMCH-2016-1.1)
- National Institute of Neurological Disorders and Stroke (NINDS R01NS058529, R35NS105078)
- National Human Genome Research Institute (NHGRI/NHLBI UM1 HG006542, NHGRI K08 HG008986)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- copy number variation, single nucleotide polymorphisms, Tbx6, congenital scoliosis, adolescent idiopathic scoliosis, null alleles, colocalization, Mendelian inheritance
- MeSH terms
- Congenital Abnormalities, Adolescent, Female, Genotype, Haplotypes, Humans, Phenotype, Scoliosis, Genome, Human, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genomics, Genome-Wide Association Study, DNA Copy Number Variations
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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