ArticleNature communications2022
A rare variant analysis framework using public genotype summary counts to prioritize disease-predisposition genes.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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
16 citing papers in PubMed, 25 citations in OpenAlex.
- Germ line genetic NBN variation and predisposition to B-cell acute lymphoblastic leukemia in children.Blood · 2024Trial
- Exome sequencing points to pathogenic ATM variants in gastric cancer.European journal of human genetics : EJHG · 2026Article
- COBT: a gene-based rare variant burden test for case-only study designs using aggregated genotypes from public reference cohorts.Genome medicine · 2026Article
- A scalable framework for identifying allelic series from summary statistics.American journal of human genetics · 2025Article
- Shared burden of ultra-rare genetic variants across a spectrum of motor neuron diseases.Translational neurodegeneration · 2025Article
- HMGCR genetic variability in Parkinson's disease in a Spanish cohort: associations with lipid metabolism and early onset.Journal of neurology · 2025Article
- Understanding Parkinson disease in Spain: Genetic and clinical insights.European journal of neurology · 2025Article
- Genetic architecture of oral glucose-stimulated insulin release provides biological insights into type 2 diabetes aetiology.Nature metabolism · 2024Article
- Deciphering novel TCF4-driven mechanisms underlying a common triplet repeat expansion-mediated disease.PLoS genetics · 2024Article
- Public platform with 39,472 exome control samples enables association studies without genotype sharing.Nature genetics · 2024Article
- Genetic assessment of pathogenic germline alterations in lysosomal genes among Asian patients with pancreatic ductal adenocarcinoma.Journal of translational medicine · 2023Article
- Identification of TCF3 germline variants in pediatric B-cell acute lymphoblastic leukemia.Blood advances · 2023Article
- Germline landscape ofFrontiers in oncology · 2023Article
- Gene and pathway based burden analyses in familial lymphoid cancer cases: Rare variants in immune pathway genes.PloS one · 2023Article
- A rare variant analysis framework using public genotype summary counts to prioritize disease-predisposition genes.Nature communications · 2022Article
- Recent advances and challenges of rare variant association analysis in the biobank sequencing era.Frontiers in genetics · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Sequencing cases without matched healthy controls hinders prioritization of germline disease-predisposition genes. To circumvent this problem, genotype summary counts from public data sets can serve as controls. However, systematic inflation and false positives can arise if confounding factors are not controlled. We propose a framework, consistent summary counts based rare variant burden test (CoCoRV), to address these challenges. CoCoRV implements consistent variant quality control and filtering, ethnicity-stratified rare variant association test, accurate estimation of inflation factors, powerful FDR control, and detection of rare variant pairs in high linkage disequilibrium. When we applied CoCoRV to pediatric cancer cohorts, the top genes identified were cancer-predisposition genes. We also applied CoCoRV to identify disease-predisposition genes in adult brain tumors and amyotrophic lateral sclerosis. Given that potential confounding factors were well controlled after applying the framework, CoCoRV provides a cost-effective solution to prioritizing disease-risk genes enriched with rare pathogenic variants.
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.