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Literature DB >> 25147361

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.

Paula Tataru¹, Jasmine A Nirody¹, Yun S Song².

Abstract

UNLABELLED: We present a tool, diCal-IBD, for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. Our method builds on a recent demographic inference method based on the coalescent with recombination, and is able to incorporate demographic information as a prior. Simulation study shows that diCal-IBD has significantly higher recall and precision than that of existing single-nucleotide polymorphism-based IBD detection methods, while retaining reasonable accuracy for IBD tracts as small as 0.1 cM. AVAILABILITY: http://sourceforge.net/projects/dical-ibd.

Entities: Disease

Mesh：

Year: 2014 PMID： 25147361 PMCID： PMC4296155 DOI： 10.1093/bioinformatics/btu563

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

13 in total

1. Generating samples under a Wright-Fisher neutral model of genetic variation.

Authors: Richard R Hudson
Journal: Bioinformatics Date: 2002-02 Impact factor: 6.937

2. Natural selection and the distribution of identity-by-descent in the human genome.

Authors: Anders Albrechtsen; Ida Moltke; Rasmus Nielsen
Journal: Genetics Date: 2010-06-30 Impact factor: 4.562

3. Whole population, genome-wide mapping of hidden relatedness.

Authors: Alexander Gusev; Jennifer K Lowe; Markus Stoffel; Mark J Daly; David Altshuler; Jan L Breslow; Jeffrey M Friedman; Itsik Pe'er
Journal: Genome Res Date: 2008-10-29 Impact factor: 9.043

4. Detecting identity by descent and estimating genotype error rates in sequence data.

Authors: Brian L Browning; Sharon R Browning
Journal: Am J Hum Genet Date: 2013-10-24 Impact factor: 11.025

5. Length distributions of identity by descent reveal fine-scale demographic history.

Authors: Pier Francesco Palamara; Todd Lencz; Ariel Darvasi; Itsik Pe'er
Journal: Am J Hum Genet Date: 2012-10-25 Impact factor: 11.025

6. Evolution and functional impact of rare coding variation from deep sequencing of human exomes.

Authors: Jacob A Tennessen; Abigail W Bigham; Timothy D O'Connor; Wenqing Fu; Eimear E Kenny; Simon Gravel; Sean McGee; Ron Do; Xiaoming Liu; Goo Jun; Hyun Min Kang; Daniel Jordan; Suzanne M Leal; Stacey Gabriel; Mark J Rieder; Goncalo Abecasis; David Altshuler; Deborah A Nickerson; Eric Boerwinkle; Shamil Sunyaev; Carlos D Bustamante; Michael J Bamshad; Joshua M Akey
Journal: Science Date: 2012-05-17 Impact factor: 47.728

7. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

Authors: Radoje Drmanac; Andrew B Sparks; Matthew J Callow; Aaron L Halpern; Norman L Burns; Bahram G Kermani; Paolo Carnevali; Igor Nazarenko; Geoffrey B Nilsen; George Yeung; Fredrik Dahl; Andres Fernandez; Bryan Staker; Krishna P Pant; Jonathan Baccash; Adam P Borcherding; Anushka Brownley; Ryan Cedeno; Linsu Chen; Dan Chernikoff; Alex Cheung; Razvan Chirita; Benjamin Curson; Jessica C Ebert; Coleen R Hacker; Robert Hartlage; Brian Hauser; Steve Huang; Yuan Jiang; Vitali Karpinchyk; Mark Koenig; Calvin Kong; Tom Landers; Catherine Le; Jia Liu; Celeste E McBride; Matt Morenzoni; Robert E Morey; Karl Mutch; Helena Perazich; Kimberly Perry; Brock A Peters; Joe Peterson; Charit L Pethiyagoda; Kaliprasad Pothuraju; Claudia Richter; Abraham M Rosenbaum; Shaunak Roy; Jay Shafto; Uladzislau Sharanhovich; Karen W Shannon; Conrad G Sheppy; Michel Sun; Joseph V Thakuria; Anne Tran; Dylan Vu; Alexander Wait Zaranek; Xiaodi Wu; Snezana Drmanac; Arnold R Oliphant; William C Banyai; Bruce Martin; Dennis G Ballinger; George M Church; Clifford A Reid
Journal: Science Date: 2009-11-05 Impact factor: 47.728

5. Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations.

Authors: Juba Nait Saada; Georgios Kalantzis; Derek Shyr; Fergus Cooper; Martin Robinson; Alexander Gusev; Pier Francesco Palamara
Journal: Nat Commun Date: 2020-11-30 Impact factor: 14.919

5 in total

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.

1. Generating samples under a Wright-Fisher neutral model of genetic variation.

2. Natural selection and the distribution of identity-by-descent in the human genome.

3. Whole population, genome-wide mapping of hidden relatedness.

4. Detecting identity by descent and estimating genotype error rates in sequence data.

5. Length distributions of identity by descent reveal fine-scale demographic history.

6. Evolution and functional impact of rare coding variation from deep sequencing of human exomes.

7. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

8. Inference of human population history from individual whole-genome sequences.

9. Detecting rare variant associations by identity-by-descent mapping in case-control studies.

10. Improving the accuracy and efficiency of identity-by-descent detection in population data.

1. Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.

2. Inference of complex population histories using whole-genome sequences from multiple populations.

Review 3. Inference of population history using coalescent HMMs: review and outlook.

4. Robust and scalable inference of population history from hundreds of unphased whole genomes.

5. Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations.