ArticleBioinformatics (Oxford, England)2016
Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 4 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
40 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Matching heterogeneous cohorts by projected principal components reveals two novel Alzheimer's disease-associated genes in the Hispanic population.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Pooled it
- Identification of 16 novel Alzheimer's disease loci using multi-ancestry meta-analyses.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Pooled it
- Pooled it
- Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2.Molecular psychiatry · 2022Pooled it
- Intracellular protein GBF1 displays significant associations with amyloid pathology in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Eduomics: a Nextflow pipeline to simulate -omics data for education.NAR genomics and bioinformatics · 2026Article
- Genome-mining revealed biosurfactant production capacity and gene co-occurrence patterns in diverse ecosystems.Microbial cell factories · 2026Article
- Article
- The gain-of-function TREM2-T96K mutation increases risk for Alzheimer's disease by impairing microglial function.Neuron · 2026Article
- Inter-segmental coordination patterns in Parkinson's disease are particularly disturbed during preferred walking speed: a data-driven network approach.Journal of neuroengineering and rehabilitation · 2025Article
- Matching Heterogeneous Cohorts by Projected Principal Components Reveals Two Novel Alzheimer's Disease-Associated Genes in the Hispanic Population.medRxiv : the preprint server for health sciences · 2025Article
- A PKCη missense mutation enhances Golgi-localized signaling and is associated with recessively inherited familial Alzheimer's disease.Science signaling · 2025Article
- Analyzing the relationship of RNA and DNA methylation with gene expression.Genome biology · 2025Article
- Protein kinase C eta enhances Golgi-localized signaling and is associated with Alzheimer's disease using a recessive mode of inheritance.medRxiv : the preprint server for health sciences · 2025Article
- Identification of 16 novel Alzheimer's disease susceptibility loci using multi-ancestry meta-analyses of clinical Alzheimer's disease and AD-by-proxy cases from four whole genome sequencing datasets.medRxiv : the preprint server for health sciences · 2024Article
- CRISPR-based functional profiling of the Toxoplasma gondii genome during acute murine infection.Nature microbiology · 2024Article
- Article
- Embracing firefly flash pattern variability with data-driven species classification.Scientific reports · 2024Article
- Fast computation of the eigensystem of genomic similarity matrices.BMC bioinformatics · 2024Article
- A machine learning-based strategy to elucidate the identification of antibiotic resistance in bacteria.Frontiers in antibiotics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
motivationPopulation stratification is one of the major sources of confounding in genetic association studies, potentially causing false-positive and false-negative results. Here, we present a novel approach for the identification of population substructure in high-density genotyping data/next generation sequencing data. The approach exploits the co-appearances of rare genetic variants in individuals. The method can be applied to all available genetic loci and is computationally fast. Using sequencing data from the 1000 Genomes Project, the features of the approach are illustrated and compared to existing methodology (i.e. EIGENSTRAT). We examine the effects of different cutoffs for the minor allele frequency on the performance of the approach. We find that our approach works particularly well for genetic loci with very small minor allele frequencies. The results suggest that the inclusion of rare-variant data/sequencing data in our approach provides a much higher resolution picture of population substructure than it can be obtained with existing methodology. Furthermore, in simulation studies, we find scenarios where our method was able to control the type 1 error more precisely and showed higher power. AVAILABILITY AND IMPLEMENTATION: CONTACT: dmitry.prokopenko@uni-bonn.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.