ArticleGenome research2004
Haplotype and missing data inference in nuclear families.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT00005268 (Family Blood Pressure Program - GenNet Network), which is not on this map. Cited by 18 papers.
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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.
Family Blood Pressure Program - GenNet Network
Who cites it
18 citing papers in PubMed.
- DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering.Briefings in bioinformatics · 2024Article
- XHap: haplotype assembly using long-distance read correlations learned by transformers.Bioinformatics advances · 2023Article
- ACKR1 Alleles at 5.6 kb in a Well-Characterized Renewable US Food and Drug Administration (FDA) Reference Panel for Standardization of Blood Group Genotyping.The Journal of molecular diagnostics : JMD · 2020Article
- Population genomics reveals the origin and asexual evolution of human infective trypanosomes.eLife · 2016Article
- A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data.EURASIP journal on bioinformatics & systems biology · 2014Article
- An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.Genome research · 2013Article
- Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure.Genome biology · 2013Article
- Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data.BMC genetics · 2012Article
- A haplotype inference algorithm for trios based on deterministic sampling.BMC genetics · 2010Article
- Rapid haplotype inference for nuclear families.Genome biology · 2010Article
- Haplotyping methods for pedigrees.Human heredity · 2009Review
- Methods to impute missing genotypes for population data.Human genetics · 2007Article
- Dense SNP association study for bipolar I disorder on chromosome 18p11 suggests two loci with excess paternal transmission.Molecular psychiatry · 2007Article
- A model-based approach to selection of tag SNPs.BMC bioinformatics · 2006Article
- A comparison of phasing algorithms for trios and unrelated individuals.American journal of human genetics · 2006Article
- Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data.Human genetics · 2006Article
- A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.Human genomics · 2005Review
- Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.American journal of human genetics · 2005Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Determining linkage phase from population samples with statistical methods is accurate only within regions of high linkage disequilibrium (LD). Yet, affected individuals in a genetic mapping study, including those involving cases and controls, may share sequences identical-by-descent stretching on the order of 10s to 100s of kilobases, quite possibly over regions of low LD in the population. At the same time, inferring phase from nuclear families may be hampered by missing family members, missing genotypes, and the noninformativity of certain genotype patterns. In this study, we reformulate our previous haplotype reconstruction algorithm, and its associated computer program, to phase parents with information derived from population samples as well as from their offspring. In applications of our algorithm to 100-kb stretches, simulated in accordance to a Wright-Fisher model with typical levels of LD in humans, we find that phase reconstruction for 160 trios with 10% missing data is highly accurate (>90%) over the entire length. Furthermore, our algorithm can estimate allelic status for missing data at high accuracy (>95%). Finally, the input capacity of the program is vast, easily handling thousands of segregating sites in > or = 1000 chromosomes.
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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.