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Grant Details

Grant Number: 5R03CA162200-02 Interpret this number
Primary Investigator: Pasaniuc, Bogdan
Organization: University Of California Los Angeles
Project Title: Metrics and Methods for Cross-Population Fine Mapping
Fiscal Year: 2013
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Abstract

DESCRIPTION (provided by applicant): Genome-wide association studies have been very successful in identifying hundreds of variants associated to complex diseases and phenotypes. In contrast, due to high levels of linkage disequilibrium at any given locus, only a handful of causal variants have been identified so far. In an attempt to bridge this gap, several fine- mapping studies involving dense genotyping or sequencing are currently being performed in multiple populations such as Europeans, Asians, African Americans or Latinos. Fine mapping studies over multiple populations can leverage different genetic variation across populations to increase the accuracy for localizing the causal variant in a joint analysis of multiple populations as compared to studies in which only one population is analyzed at a time. Surprisingly, despite the large potential of multi ethnic fine mapping studies, current multi population fine mapping studies employ standard statistical techniques within locus specific ad- hoc frameworks. In this application we will introduce novel metrics and automated frameworks for quantifying the performance of fine mapping methods as well as novel statistical methods that leverage multi ethnic genetic variation to increase the localization accuracy for fine mapping.

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Publications

Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.
Authors: Brown R. , Lee H. , Eskin A. , Kichaev G. , Lohmueller K.E. , Reversade B. , Nelson S.F. , Pasaniuc B. .
Source: European journal of human genetics : EJHG, 2016 Jan; 24(1), p. 113-9.
EPub date: 2015-04-22.
PMID: 25898925
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A spatial haplotype copying model with applications to genotype imputation.
Authors: Yang W.Y. , Hormozdiari F. , Eskin E. , Pasaniuc B. .
Source: Journal of computational biology : a journal of computational molecular cell biology, 2015 May; 22(5), p. 451-62.
EPub date: 2014-12-19.
PMID: 25526526
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Spatial localization of recent ancestors for admixed individuals.
Authors: Yang W.Y. , Platt A. , Chiang C.W. , Eskin E. , Novembre J. , Pasaniuc B. .
Source: G3 (Bethesda, Md.), 2014-11-03; 4(12), p. 2505-18.
EPub date: 2014-11-03.
PMID: 25371484
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Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.
Authors: Pasaniuc B. , Zaitlen N. , Shi H. , Bhatia G. , Gusev A. , Pickrell J. , Hirschhorn J. , Strachan D.P. , Patterson N. , Price A.L. .
Source: Bioinformatics (Oxford, England), 2014-10-15; 30(20), p. 2906-14.
EPub date: 2014-07-01.
PMID: 24990607
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Integrating functional data to prioritize causal variants in statistical fine-mapping studies.
Authors: Kichaev G. , Yang W.Y. , Lindstrom S. , Hormozdiari F. , Eskin E. , Price A.L. , Kraft P. , Pasaniuc B. .
Source: PLoS genetics, 2014 Oct; 10(10), p. e1004722.
EPub date: 2014-10-30.
PMID: 25357204
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Identifying causal variants at loci with multiple signals of association.
Authors: Hormozdiari F. , Kostem E. , Kang E.Y. , Pasaniuc B. , Eskin E. .
Source: Genetics, 2014 Oct; 198(2), p. 497-508.
EPub date: 2014-08-07.
PMID: 25104515
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Enhanced methods for local ancestry assignment in sequenced admixed individuals.
Authors: Brown R. , Pasaniuc B. .
Source: PLoS computational biology, 2014 Apr; 10(4), p. e1003555.
EPub date: 2014-04-17.
PMID: 24743331
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IBD genetics: focus on (dys) regulation in immune cells and the epithelium.
Authors: Kaser A. , Pasaniuc B. .
Source: Gastroenterology, 2014 Apr; 146(4), p. 896-9.
EPub date: 2014-02-22.
PMID: 24566108
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Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.
Authors: Yang W.Y. , Hormozdiari F. , Wang Z. , He D. , Pasaniuc B. , Eskin E. .
Source: Bioinformatics (Oxford, England), 2013-09-15; 29(18), p. 2245-52.
EPub date: 2013-07-03.
PMID: 23825370
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Enhanced localization of genetic samples through linkage-disequilibrium correction.
Authors: Baran Y. , Quintela I. , Carracedo A. , Pasaniuc B. , Halperin E. .
Source: American journal of human genetics, 2013-06-06; 92(6), p. 882-94.
EPub date: 2013-05-30.
PMID: 23726367
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Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation.
Authors: Pasaniuc B. , Sankararaman S. , Torgerson D.G. , Gignoux C. , Zaitlen N. , Eng C. , Rodriguez-Cintron W. , Chapela R. , Ford J.G. , Avila P.C. , et al. .
Source: Bioinformatics (Oxford, England), 2013-06-01; 29(11), p. 1407-15.
EPub date: 2013-04-09.
PMID: 23572411
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