ArticleEuropean journal of human genetics : EJHG2014
Coverage and efficiency in current SNP chips.
Article in European journal of human genetics : EJHG, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed.
- Heterogeneity in the association between APOE ε4 carrier status and dementia risk by modifiable and non-modifiable risk factors.GeroScience · 2026Article
- Development and Applications of a 1K SNP Panel for Whiteleg Shrimp: From Pedigree Reconstruction to Genomic Selection.International journal of molecular sciences · 2026Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Evaluating Kinship Estimation Methods for Reduced-Representation SNP Data in Non-model Species.Molecular ecology resources · 2025Article
- Aggregating single nucleotide polymorphisms improves filtering for false-positive associations postimputation.G3 (Bethesda, Md.) · 2025Article
- Genetic predisposition to adiposity, and type 2 diabetes: the role of lifestyle and phenotypic adiposity.European journal of endocrinology · 2025Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.Genome biology · 2025Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.bioRxiv : the preprint server for biology · 2024Article
- A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software.Life (Basel, Switzerland) · 2022Review
- A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing.Basic & clinical pharmacology & toxicology · 2022Review
- A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations.Scientific reports · 2022Article
- Iam hiQ-a novel pair of accuracy indices for imputed genotypes.BMC bioinformatics · 2022Article
- A comparison of genotyping arrays.European journal of human genetics : EJHG · 2021Article
- Genetic testing for men with infertility: techniques and indications.Translational andrology and urology · 2021Review
- Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers.Planta · 2021Article
- Assessment of Imputation Quality: Comparison of Phasing and Imputation Algorithms in Real Data.Frontiers in genetics · 2021Article
- Genome-Wide Association Study of Sleep Disturbances in Depressive Disorders.Molecular neuropsychiatry · 2020Article
- Global, pathway and gene coverage of three Illumina arrays with respect to inflammatory and immune-related pathways.European journal of human genetics : EJHG · 2019Article
- Polygenic risk associated with post-traumatic stress disorder onset and severity.Translational psychiatry · 2019Article
- Cross-ethnicity tagging SNPs for HLA alleles associated with adverse drug reaction.The pharmacogenomics journal · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To answer the question as to which commercial high-density SNP chip covers most of the human genome given a fixed budget, we compared the performance of 12 chips of different sizes released by Affymetrix and Illumina for the European, Asian, and African populations. These include Affymetrix' relatively new population-optimized arrays, whose SNP sets are each tailored toward a specific ethnicity. Our evaluation of the chips included the use of two measures, efficiency and cost-benefit ratio, which we developed as supplements to genetic coverage. Unlike coverage, these measures factor in the price of a chip or its substitute size (number of SNPs on chip), allowing comparisons to be drawn between differently priced chips. In this fashion, we identified the Affymetrix population-optimized arrays as offering the most cost-effective coverage for the Asian and African population. For the European population, we established the Illumina Human Omni 2.5-8 as the preferred choice. Interestingly, the Affymetrix chip tailored toward an Eastern Asian subpopulation performed well for all three populations investigated. However, our coverage estimates calculated for all chips proved much lower than those advertised by the producers. All our analyses were based on the 1000 Genome Project as reference population.
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.