339 Citations
Parente2: a fast and accurate method for detecting identity by descent
- Computer ScienceGenome research
- 2015
Parente2 is a novel method for detecting IBD segments based on an embedded log-likelihood ratio and uses a model that accounts for linkage disequilibrium by explicitly modeling haplotype frequencies, and provides substantially higher accuracy compared to previous state-of-the-art methods while maintaining high computational efficiency.
Fast pairwise IBD association testing in genome-wide association studies
- Computer ScienceBioinform.
- 2014
A new pairwise method 'Fast-Pairwise', which uses importance sampling to improve efficiency and enable approximation of extremely small P-values, is introduced and successfully fine-maps a known human leukocyte antigen gene that is known to cause the disease.
Identity by descent estimation with dense genome‐wide genotype data
- Computer ScienceGenetic epidemiology
- 2011
IBDLD overcomes the challenges of exact multipoint estimation of IBD in pedigrees of potentially large size and eliminates the difficulty of accommodating the background linkage disequilibrium (LD) that is present in high‐density genotype data.
Using identity by descent estimation with dense genotype data to detect positive selection
- BiologyEuropean Journal of Human Genetics
- 2013
This work uses IBD to find signals of selection in the Maasai from Kinyawa, Kenya, and uses the advantage of statistical tools that can probabilistically estimate IBD sharing without having to thin genotype data because of linkage disequilibrium (LD), and that allow for both inbreeding and more than one allele to be shared IBD.
An Effective Filter for IBD Detection in Large Data Sets
- BiologyPloS one
- 2014
To enable the study of large cohorts, SpeeDB is introduced, a method that facilitates fast IBD detection in large unphased genotype data sets and applies an efficient opposite-homozygous filter, which excludes chromosomal segments from the database that are highly unlikely to be IBD with the corresponding segment from the target individual.
A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data
- BiologyEuropean Journal of Human Genetics
- 2017
A new IBD segment detection program, FISHR (Find IBD Shared Haplotypes Rapidly), is developed in an attempt to accurately detect IBD segments and to better estimate their endpoints using an algorithm that is fast enough to be deployed on very large whole-genome SNP data sets.
Recent identity by descent in human genetic data - methods and applications
- Computer Science
- 2014
The utility of the inferred IBD regions depends on accuracy of detection, time to most recent common ancestors and mutation rates since, and whether regions of identity by descent can be used for genomic predictions.
Detecting Rare Variant Associations by Identity-by-Descent Mapping in Case-Control Studies
- MathematicsGenetics
- 2012
The results suggest that IBD mapping may have higher power than association analysis of SNP data when multiple rare causal variants are clustered within a gene, however, for outbred populations, very large sample sizes may be required for genome-wide significance unless the causal variants have strong effects.
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data
- Computer ScienceGenetics
- 2013
Refined IBD allows for IBD reporting on a haplotype level, which facilitates determination of multi-individual IBD and allows for haplotype-based downstream analyses and is implemented in Beagle version 4.
A fast and simple method for detecting identity by descent segments in large-scale data
- Computer SciencebioRxiv
- 2019
Harp-IBD is shown to be the only method that can rapidly and accurately detect short 2-4 cM IBD segments in the full UK Biobank data and is the only way to detect identical-by-descent haplotype segments for large-scale genotype data.
References
SHOWING 1-10 OF 30 REFERENCES
High-resolution detection of identity by descent in unrelated individuals.
- Computer ScienceAmerican journal of human genetics
- 2010
Whole population, genome-wide mapping of hidden relatedness.
- BiologyGenome research
- 2009
This work uses GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals, to comprehensively survey hidden relatedness both in the HapMap as well as in a densely typed island population of 3000 individuals.
Relatedness mapping and tracts of relatedness for genome‐wide data in the presence of linkage disequilibrium
- BiologyGenetic epidemiology
- 2009
A new method for identifying IBD tracts among individuals from genome‐wide single nucleotide polymorphisms data using a continuous time Markov model that accurately accounts for linkage disequilibrium using pairwise haplotype probabilities.
A SNP Streak Model for the Identification of Genetic Regions Identical-by-descent
- BiologyStatistical applications in genetics and molecular biology
- 2008
A simple method for using dense SNP maps to identify regions of the genome likely to be inherited IBD by family members, based on identifying obligate recombination events and examining the pattern of distribution of such events along the genetic map is described.
Detection of sharing by descent, long-range phasing and haplotype imputation
- BiologyNature Genetics
- 2008
This work shows how to phase more than 1,000 SNPs simultaneously for a large fraction of the 35,528 Icelanders genotyped by Illumina chips, which is particularly powerful in studies of the inheritance of recurrent mutations and fine-scale recombinations in large sample sets.
PLINK: a tool set for whole-genome association and population-based linkage analyses.
- BiologyAmerican journal of human genetics
- 2007
This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
- BiologyNature Genetics
- 2006
A unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers is developed and provides a powerful complement to currently available methods for association mapping.
Novel case-control test in a founder population identifies P-selectin as an atopy-susceptibility locus.
- BiologyAmerican journal of human genetics
- 2003
This work proposes a method for case-control association studies of binary traits that is suitable for any set of related individuals, provided that their genealogy is known, and bases inference on a quasi-likelihood score (QLS) function and constructs a QLS test for allelic association.
Merlin—rapid analysis of dense genetic maps using sparse gene flow trees
- BiologyNature Genetics
- 2002
The multipoint engine for rapid likelihood inference (Merlin) is a computer program that uses sparse inheritance trees for pedigree analysis; it performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.
Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.
- BiologyAmerican journal of human genetics
- 2009