ArticleAmerican journal of human genetics2008
Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays.
Article in American journal of human genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 2 syntheses or guidelines pooled it, 45 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Common X-Chromosome Variants Are Associated with Parkinson Disease Risk.Annals of neurology · 2021Pooled it
- Chromosome X-wide common variant association study in autism spectrum disorder.American journal of human genetics · 2025Article
- Chromosome X-Wide Common Variant Association Study (XWAS) in Autism Spectrum Disorder.medRxiv : the preprint server for health sciences · 2024Article
- X-Chromosome Association Study in Latin American Cohorts Identifies New Loci in Parkinson's Disease.Movement disorders : official journal of the Movement Disorder Society · 2023Article
- Article
- Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls.BMC genomics · 2021Article
- Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes.European journal of human genetics : EJHG · 2016Article
- A method for calling copy number polymorphism using haplotypes.Frontiers in genetics · 2013Article
- Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.BMC genomics · 2012Article
- Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study.Human mutation · 2011Article
- Copy number variation across European populations.PloS one · 2011Article
- On the genome-wide analysis of copy number variants in family-based designs: methods for combining family-based and population-based information for testing dichotomous or quantitative traits, or completely ascertained samples.Genetic epidemiology · 2010Article
- cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs.Nature methods · 2010Article
- An extended IUPAC nomenclature code for polymorphic nucleic acids.Bioinformatics (Oxford, England) · 2010Article
- Multiple common variants for celiac disease influencing immune gene expression.Nature genetics · 2010Article
- Detection of disease-associated deletions in case-control studies using SNP genotypes with application to rheumatoid arthritis.Human genetics · 2009Article
- Article
- Cost-effective HLA typing with tagging SNPs predicts celiac disease risk haplotypes in the Finnish, Hungarian, and Italian populations.Immunogenetics · 2009Article
- Genotype imputation.Annual review of genomics and human genetics · 2009Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
Abstract
Copy-number variation (CNV) is a major contributor to human genetic variation. Recently, CNV associations with human disease have been reported. Many genome-wide association (GWA) studies in complex diseases have been performed with sets of biallelic single-nucleotide polymorphisms (SNPs), but the available CNV methods are still limited. We present a new method (TriTyper) that can infer genotypes in case-control data sets for deletion CNVs, or SNPs with an extra, untyped allele at a high-resolution single SNP level. By accounting for linkage disequilibrium (LD), as well as intensity data, calling accuracy is improved. Analysis of 3102 unrelated individuals with European descent, genotyped with Illumina Infinium BeadChips, resulted in the identification of 1880 SNPs with a common untyped allele, and these SNPs are in strong LD with neighboring biallelic SNPs. Simulations indicate our method has superior power to detect associations compared to biallelic SNPs that are in LD with these SNPs, yet without increasing type I errors, as shown in a GWA analysis in celiac disease. Genotypes for 1204 triallelic SNPs could be fully imputed, with only biallelic-genotype calls, permitting association analysis of these SNPs in many published data sets. We estimate that 682 of the 1655 unique loci reflect deletions; this is on average 99 deletions per individual, four times greater than those detected by other methods. Whereas the identified loci are strongly enriched for known deletions, 61% have not been reported before. Genes overlapping with these loci more often have paralogs (p = 0.006) and biologically interact with fewer genes than expected (p = 0.004).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.