ArticleNature genetics2008
Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.
Article in Nature genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05277116 (The Electronic Medical Records and GEnomics), which is not on this map. Cited by 497 papers, 7 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.
The Electronic Medical Records and GEnomics (eMERGE) Network Genomic Risk Assessment
Who cites it
497 citing papers in PubMed, 7 syntheses or guidelines pooled it, 809 citations in OpenAlex.
- Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses.Nature medicine · 2023Pooled it
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Polygenic Risk for Major Depression Interacts with Parental Criticism in Predicting Adolescent Depressive Symptom Development.Journal of youth and adolescence · 2021Pooled it
- Genome-wide Burden of Rare Short Deletions Is Enriched in Major Depressive Disorder in Four Cohorts.Biological psychiatry · 2019Pooled it
- Multi-ethnic genome-wide association study for atrial fibrillation.Nature genetics · 2018Pooled it
- Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs.Scientific reports · 2016Pooled it
- Association of mitochondrial DNA levels with frailty and all-cause mortality.Journal of molecular medicine (Berlin, Germany) · 2015Pooled it
- Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese.Scientific reports · 2017Trial
- Trial
- Methylation at CPT1A locus is associated with lipoprotein subfraction profiles.Journal of lipid research · 2014Trial
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Immune gene diversity and STING1 variants in shaping cancer immunity across different genetic ancestry populations.Cell reports · 2026Article
- Genome wide landscaping of copy number variations for horse inter-breed variability.Animal biotechnology · 2025Article
- Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells.Molecular biology and evolution · 2025Article
- PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis.Briefings in bioinformatics · 2025Article
- Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.Cell genomics · 2025Article
- iModEst: disentangling -omic impacts on gene expression variation across genes and tissues.NAR genomics and bioinformatics · 2025Article
- Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential.Nature communications · 2025Article
- Genetic regulation ofmedRxiv : the preprint server for health sciences · 2024Article
- Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations.Genome biology · 2024Article
437 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 4 institutions in 1 country.
Funding
Abstract
Accurate and complete measurement of single nucleotide (SNP) and copy number (CNV) variants, both common and rare, will be required to understand the role of genetic variation in disease. We present Birdsuite, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus (for example, including genotypes such as A-null, AAB and BBB in addition to AA, AB and BB calls). Such genotypes more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies. The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype.
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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.