ArticleCell genomics2023
Performance and accuracy evaluation of reference panels for genotype imputation in sub-Saharan African populations.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 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
24 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes.Nature genetics · 2024Pooled it
- Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Pooled it
- Selphi, a tool for improving genotype imputation accuracy.Scientific reports · 2026Article
- Bridging global diversity gaps in Parkinson disease research.Nature reviews. Neurology · 2026Review
- A reanalysis of a genome-wide association study on breast cancer in Asian populations using the SG10K_Health reference panel for imputation: a multi-Centre case-control analysis.Human molecular genetics · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Chimeric reference panels for genomic imputation.Genetics · 2026Article
- High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.Genomics, proteomics & bioinformatics · 2025Review
- Imputation disparities driven by recent selection and their impact on disease risk estimation in East and Southeast Asian populations.Communications biology · 2025Article
- Characterization of the complex TB pharmacogenomic landscape in Africa using bioinformatic tools.Briefings in bioinformatics · 2025Article
- A GWAS of angiotensin-converting enzyme inhibitor-induced angioedema in a South African population.The journal of allergy and clinical immunology. Global · 2025Article
- A map of blood regulatory variation in South Africans enables GWAS interpretation.Nature genetics · 2025Article
- Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population.Communications biology · 2025Article
- A Pangenomic Approach to Improve Population Genetics Analysis and Reference Bias in Underrepresented Middle Eastern and Horn of Africa Populations.Biomolecules · 2025Article
- Progress in Translating Glaucoma Genetics Into the Clinic: A Review.Clinical & experimental ophthalmology · 2025Review
- FLT1 and other candidate fetal haemoglobin modifying loci in sickle cell disease in African ancestries.Nature communications · 2025Article
- Strength of Genetic Associations with Thyrotropin Values Differs Between Populations with Similarity to African and European Reference Populations.Thyroid : official journal of the American Thyroid Association · 2025Article
- Type 1 diabetes genetic risk score variation across ancestries using whole genome sequencing and array-based approaches.Scientific reports · 2024Article
- Cohort Profile: Africa Wits-INDEPTH partnership for Genomic studies (AWI-Gen) in four sub-Saharan African countries.International journal of epidemiology · 2024Article
- Imputation accuracy across global human populations.American journal of human genetics · 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
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Based on evaluations of imputation performed on a genotype dataset consisting of about 11,000 sub-Saharan African (SSA) participants, we show Trans-Omics for Precision Medicine (TOPMed) and the African Genome Resource (AGR) to be currently the best panels for imputing SSA datasets. We report notable differences in the number of single-nucleotide polymorphisms (SNPs) that are imputed by different panels in datasets from East, West, and South Africa. Comparisons with a subset of 95 SSA high-coverage whole-genome sequences (WGSs) show that despite being about 20-fold smaller, the AGR imputed dataset has higher concordance with the WGSs. Moreover, the level of concordance between imputed and WGS datasets was strongly influenced by the extent of Khoe-San ancestry in a genome, highlighting the need for integration of not only geographically but also ancestrally diverse WGS data in reference panels for further improvement in imputation of SSA datasets. Approaches that integrate imputed data from different panels could also lead to better imputation.
Indexed as
Identifiers
What Socratic 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 Socratic graph.