ArticleAmerican journal of human genetics2002
Haplotype inference in random population samples.
Article in American journal of human genetics, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 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
62 citing papers in PubMed, 183 citations in OpenAlex.
- SPEARS: Standard Performance Evaluation of Ancestral haplotype Reconstruction through Simulation.Bioinformatics (Oxford, England) · 2021Article
- A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures.Genes · 2021Article
- Improving Imputation Quality in BEAGLE for Crop and Livestock Data.G3 (Bethesda, Md.) · 2020Article
- CSHAP: efficient haplotype frequency estimation based on sparse representation.Bioinformatics (Oxford, England) · 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
- High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium.Molecular ecology resources · 2016Article
- Article
- Article
- Whole genome SNP genotype piecemeal imputation.BMC bioinformatics · 2015Article
- FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model.Bioinformatics (Oxford, England) · 2014Article
- A general approach for haplotype phasing across the full spectrum of relatedness.PLoS genetics · 2014Article
- Complex multilocus effects of catechol-O-methyltransferase haplotypes predict pain and pain interference 6 weeks after motor vehicle collision.Neuromolecular medicine · 2014Observational
- A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data.EURASIP journal on bioinformatics & systems biology · 2014Article
- Whole-genome haplotyping approaches and genomic medicine.Genome medicine · 2014Article
- Article
- Review
- Haplotype-based profiling of subtle allelic imbalance with SNP arrays.Genome research · 2013Article
- Complete genome phasing of family quartet by combination of genetic, physical and population-based phasing analysis.PloS one · 2013Article
- Phasing of many thousands of genotyped samples.American journal of human genetics · 2012Article
- Fast accurate missing SNP genotype local imputation.BMC research notes · 2012Article
2 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 at 1 institution in 1 country.
Funding
Abstract
Contemporary genotyping and sequencing methods do not provide information on linkage phase in diploid organisms. The application of statistical methods to infer and reconstruct linkage phase in samples of diploid sequences is a potentially time- and labor-saving method. The Stephens-Smith-Donnelly (SSD) algorithm is one such method, which incorporates concepts from population genetics theory in a Markov chain-Monte Carlo technique. We applied a modified SSD method, as well as the expectation-maximization and partition-ligation algorithms, to sequence data from eight loci spanning >1 Mb on the human X chromosome. We demonstrate that the accuracy of the modified SSD method is better than that of the other algorithms and is superior in terms of the number of sites that may be processed. Also, we find phase reconstructions by the modified SSD method to be highly accurate over regions with high linkage disequilibrium (LD). If only polymorphisms with a minor allele frequency >0.2 are analyzed and scored according to the fraction of neighbor relations correctly called, reconstructions are 95.2% accurate over entire 100-kb stretches and are 98.6% accurate within blocks of high LD.
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.