ArticleGenetic epidemiology2013
MaCH-admix: genotype imputation for admixed populations.
Article in Genetic epidemiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 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
86 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genetic variants modulate gene expression statin response in human lymphoblastoid cell lines.BMC genomics · 2020Pooled it
- A meta-analysis of gene expression quantitative trait loci in brain.Translational psychiatry · 2014Pooled it
- Trial
- Genome-wide association study identifiesPeerJ · 2026Article
- MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric.American journal of human genetics · 2024Article
- Ocular and neural genes jointly regulate the visuospatial working memory in ADHD children.Behavioral and brain functions : BBF · 2023Article
- Strategies for the Genomic Analysis of Admixed Populations.Annual review of biomedical data science · 2023Review
- Influence of gonadal steroids on cortical surface area in infancy.Cerebral cortex (New York, N.Y. : 1991) · 2022Article
- Functional abnormality in the sensorimotor system attributed to NRXN1 variants in boys with attention deficit hyperactivity disorder.Brain imaging and behavior · 2022Article
- Iam hiQ-a novel pair of accuracy indices for imputed genotypes.BMC bioinformatics · 2022Article
- Genotyping, the Usefulness of Imputation to Increase SNP Density, and Imputation Methods and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CUE: CpG impUtation ensemble for DNA methylation levels across the human methylation450 (HM450) and EPIC (HM850) BeadChip platforms.Epigenetics · 2021Article
- Common genetic variation influencing human white matter microstructure.Science (New York, N.Y.) · 2021Article
- Multilevel Twin Models: Geographical Region as a Third Level Variable.Behavior genetics · 2021Article
- Placental genomic risk scores and early neurodevelopmental outcomes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genome-Wide Association Analysis of Neonatal White Matter Microstructure.Cerebral cortex (New York, N.Y. : 1991) · 2021Article
- A Functional SNP in the Promoter ofFrontiers in cell and developmental biology · 2021Article
- Empirical comparisons of multiple Mendelian randomization approaches in the presence of assortative mating.International journal of epidemiology · 2020Article
- FAM222A encodes a protein which accumulates in plaques in Alzheimer's disease.Nature communications · 2020Article
- Heritability estimates for 361 blood metabolites across 40 genome-wide association studies.Nature communications · 2020Review
26 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
4 authors.
Funding
Abstract
Imputation in admixed populations is an important problem but challenging due to the complex linkage disequilibrium (LD) pattern. The emergence of large reference panels such as that from the 1,000 Genomes Project enables more accurate imputation in general, and in particular for admixed populations and for uncommon variants. To efficiently benefit from these large reference panels, one key issue to consider in modern genotype imputation framework is the selection of effective reference panels. In this work, we consider a number of methods for effective reference panel construction inside a hidden Markov model and specific to each target individual. These methods fall into two categories: identity-by-state (IBS) based and ancestry-weighted approach. We evaluated the performance on individuals from recently admixed populations. Our target samples include 8,421 African Americans and 3,587 Hispanic Americans from the Women' Health Initiative, which allow assessment of imputation quality for uncommon variants. Our experiments include both large and small reference panels; large, medium, and small target samples; and in genome regions of varying levels of LD. We also include BEAGLE and IMPUTE2 for comparison. Experiment results with large reference panel suggest that our novel piecewise IBS method yields consistently higher imputation quality than other methods/software. The advantage is particularly noteworthy among uncommon variants where we observe up to 5.1% information gain with the difference being highly significant (Wilcoxon signed rank test P-value < 0.0001). Our work is the first that considers various sensible approaches for imputation in admixed populations and presents a comprehensive comparison.
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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.