ArticleGenetic epidemiology2007
Understanding the accuracy of statistical haplotype inference with sequence data of known phase.
Article in Genetic epidemiology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed, 73 citations in OpenAlex.
- Identifying Single-Origin Rare Variants in Population Genomic Data.Molecular biology and evolution · 2025Article
- The hazards of genotype imputation when mapping disease susceptibility variants.Genome biology · 2024Article
- Article
- Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.Genome research · 2022Article
- Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model.Systematic biology · 2022Article
- Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power.Nature genetics · 2021Article
- A general statistic to test an optimally weighted combination of common and/or rare variants.Genetic epidemiology · 2019Article
- An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations.PLoS genetics · 2019Article
- GenHap: a novel computational method based on genetic algorithms for haplotype assembly.BMC bioinformatics · 2019Article
- Test Gene-Environment Interactions for Multiple Traits in Sequencing Association Studies.Human heredity · 2019Article
- Testing an optimally weighted combination of common and/or rare variants with multiple traits.PloS one · 2018Article
- Detecting association of rare and common variants based on cross-validation prediction error.Genetic epidemiology · 2017Article
- Joint Analysis of Multiple Traits in Rare Variant Association Studies.Annals of human genetics · 2016Article
- References for Haplotype Imputation in the Big Data Era.Molecular biology (Los Angeles, Calif.) · 2015Article
- Novel genomic signals of recent selection in an Ethiopian population.European journal of human genetics : EJHG · 2015Article
- Test of rare variant association based on affected sib-pairs.European journal of human genetics : EJHG · 2015Article
- A rare variant association test based on combinations of single-variant tests.Genetic epidemiology · 2014Article
- Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes.Genetics, selection, evolution : GSE · 2014Article
- GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans.PLoS computational biology · 2014Article
- Detecting association of rare variants by testing an optimally weighted combination of variants for quantitative traits in general families.Annals of human genetics · 2013Article
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 at 4 institutions in 1 country.
Funding
Abstract
Statistical methods for haplotype inference from multi-site genotypes of unrelated individuals have important application in association studies and population genetics. Understanding the factors that affect the accuracy of this inference is important, but their assessment has been restricted by the limited availability of biological data with known phase. We created hybrid cell lines monosomic for human chromosome 19 and produced single-chromosome complete sequences of a 48 kb genomic region in 39 individuals of African American (AA) and European American (EA) origin. We employ these phase-known genotypes and coalescent simulations to assess the accuracy of statistical haplotype reconstruction by several algorithms. Accuracy of phase inference was considerably low in our biological data even for regions as short as 25-50 kb, suggesting that caution is needed when analyzing reconstructed haplotypes. Moreover, the reliability of estimated confidence in phase inference is not high enough to allow for a reliable incorporation of site-specific uncertainty information in subsequent analyses. We show that, in samples of certain mixed ancestry (AA and EA populations), the most accurate haplotypes are probably obtained when increasing sample size by considering the largest, pooled sample, despite the hypothetical problems associated with pooling across those heterogeneous samples. Strategies to improve confidence in reconstructed haplotypes, and realistic alternatives to the analysis of inferred haplotypes, are discussed.
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.