ArticleGigaScience2015
Second-generation PLINK: rising to the challenge of larger and richer datasets.
Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7,613 papers, 6 of them syntheses that pooled it.
What it found
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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
7,613 citing papers in PubMed, 6 syntheses or guidelines pooled it.
- Genome-Wide Association Studies of Hospitalized Influenza Identify Four Risk Loci and Reveal Shared and Unique Genetic Factors Compared With COVID-19.Influenza and other respiratory viruses · 2026Pooled it
- Large-scale GWAS meta-analysis of serum antibody levels in healthy individuals reveals distinct genetic architectures.Genes and immunity · 2026Pooled it
- Contribution of copy number variants to schizophrenia in East Asian populations.Nature genetics · 2026Pooled it
- Interrogating DNA methylation associated with Lewy body pathology in a cross brain-region and multi-cohort study.Nature communications · 2026Pooled it
- Genome-wide association studies of infant and toddler temperament in European and multi-ancestry populations.Nature human behaviour · 2026Pooled it
- GWAS meta-analysis provides new insights into uveal melanoma risk.British journal of cancer · 2026Pooled it
- Multi-omic modelling of body mass index response to a dietary weight loss intervention.Gut microbes · 2026Article
- Feasibility and pitfalls of combining small subpopulations for genome-wide association analysis of maize (Zea mays L.) kernel traits.The plant genome · 2026Article
- Development and deployment of a public mid-density genotyping panel for crimson clover (Trifolium incarnatum L.) based on whole-genome re-sequencing of diverse germplasm.The plant genome · 2026Article
- Identifying differential interactions of potentially traumatic experiences with genetic risk for posttraumatic stress disorder.European journal of psychotraumatology · 2026Article
- Linking suspects to an illegally felled incense tree (Forensic science international. Synergy · 2026Article
- Population Differentiation and Polygenic Selection in the Finnish Ayrshire Cows Selected on Genomic Information.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Disentangling direct and indirect genetic pathways to neurodevelopmental risk: brain structure and behavior in a population-based parent-offspring trio study.Journal of child psychology and psychiatry, and allied disciplines · 2026Article
- Evaluating the Predictive Value of Estimated Breeding Values of Piétrain Sires for Uniformity and Survival in Their Crossbred Progeny.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Polygenic Risk Scores Show Distinct Genetic Architectures of IBD-Associated Comorbidities.Digestive diseases and sciences · 2026Article
- Plasma proteomics of sleep traits reveals systemic immune-metabolic pathways and genetically prioritized proteins.Molecular psychiatry · 2026Article
- Association between human genomes and mycobacterial genomes contributes to severity and transmissibility of pulmonary tuberculosis.iScience · 2026Article
- Genome-wide analysis of common structural variants in Alzheimer's disease identifies a risk-associated regulatory CCG repeat in FAM193B.Nature neuroscience · 2026Article
- Geographic barrier contributed to the diversity of maternal and paternal lineages in New Guinea Island.Human genetics · 2026Article
- Landscape transcriptomics reveals ecological constraints on fish under anthropogenic coastal change.Nature communications · 2026Article
7,553 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
6 authors.
Funding
Abstract
backgroundPLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format.
findingsTo address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, [Formula: see text]-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0).
conclusionsThe second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.
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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.