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Search Results: 1 - 10 of 1518 matches for " Bogdan Pasaniuc "
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Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
Robert Brown ,Bogdan Pasaniuc
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003555
Abstract: Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g., Latino Americans) plays a major role in medical and population genetic inferences, ranging from finding disease-risk loci, to inferring recombination rates, to mapping missing contigs in the human genome. Although many methods for local ancestry inference have been proposed, most are designed for use with genotyping arrays and fail to make use of the full spectrum of data available from sequencing. In addition, current haplotype-based approaches are very computationally demanding, requiring large computational time for moderately large sample sizes. Here we present new methods for local ancestry inference that leverage continent-specific variants (CSVs) to attain increased performance over existing approaches in sequenced admixed genomes. A key feature of our approach is that it incorporates the admixed genomes themselves jointly with public datasets, such as 1000 Genomes, to improve the accuracy of CSV calling. We use simulations to show that our approach attains accuracy similar to widely used computationally intensive haplotype-based approaches with large decreases in runtime. Most importantly, we show that our method recovers comparable local ancestries, as the 1000 Genomes consensus local ancestry calls in the real admixed individuals from the 1000 Genomes Project. We extend our approach to account for low-coverage sequencing and show that accurate local ancestry inference can be attained at low sequencing coverage. Finally, we generalize CSVs to sub-continental population-specific variants (sCSVs) and show that in some cases it is possible to determine the sub-continental ancestry for short chromosomal segments on the basis of sCSVs.
GEDI: Scalable Algorithms for Genotype Error Detection and Imputation
Justin Kennedy,Ion I. Mandoiu,Bogdan Pasaniuc
Computer Science , 2009,
Abstract: Genome-wide association studies generate very large datasets that require scalable analysis algorithms. In this report we describe the GEDI software package, which implements efficient algorithms for performing several common tasks in the analysis of population genotype data, including genotype error detection and correction, imputation of both randomly missing and untyped genotypes, and genotype phasing. Experimental results show that GEDI achieves high accuracy with a runtime scaling linearly with the number of markers and samples. The open source C++ code of GEDI, released under the GNU General Public License, is available for download at http://dna.engr.uconn.edu/software/GEDI/
Genotyping common and rare variation using overlapping pool sequencing
He Dan,Zaitlen Noah,Pasaniuc Bogdan,Eskin Eleazar
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-s6-s2
Abstract: Background Recent advances in sequencing technologies set the stage for large, population based studies, in which the ANA or RNA of thousands of individuals will be sequenced. Currently, however, such studies are still infeasible using a straightforward sequencing approach; as a result, recently a few multiplexing schemes have been suggested, in which a small number of ANA pools are sequenced, and the results are then deconvoluted using compressed sensing or similar approaches. These methods, however, are limited to the detection of rare variants. Results In this paper we provide a new algorithm for the deconvolution of DNA pools multiplexing schemes. The presented algorithm utilizes a likelihood model and linear programming. The approach allows for the addition of external data, particularly imputation data, resulting in a flexible environment that is suitable for different applications. Conclusions Particularly, we demonstrate that both low and high allele frequency SNPs can be accurately genotyped when the DNA pooling scheme is performed in conjunction with microarray genotyping and imputation. Additionally, we demonstrate the use of our framework for the detection of cancer fusion genes from RNA sequences.
Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits
Noah Zaitlen ,Peter Kraft,Nick Patterson,Bogdan Pasaniuc,Gaurav Bhatia,Samuela Pollack,Alkes L. Price
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003520
Abstract: Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.
Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies
Gleb Kichaev,Wen-Yun Yang,Sara Lindstrom,Farhad Hormozdiari,Eleazar Eskin,Alkes L. Price,Peter Kraft,Bogdan Pasaniuc
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004722
Abstract: Standard statistical approaches for prioritization of variants for functional testing in fine-mapping studies either use marginal association statistics or estimate posterior probabilities for variants to be causal under simplifying assumptions. Here, we present a probabilistic framework that integrates association strength with functional genomic annotation data to improve accuracy in selecting plausible causal variants for functional validation. A key feature of our approach is that it empirically estimates the contribution of each functional annotation to the trait of interest directly from summary association statistics while allowing for multiple causal variants at any risk locus. We devise efficient algorithms that estimate the parameters of our model across all risk loci to further increase performance. Using simulations starting from the 1000 Genomes data, we find that our framework consistently outperforms the current state-of-the-art fine-mapping methods, reducing the number of variants that need to be selected to capture 90% of the causal variants from an average of 13.3 to 10.4 SNPs per locus (as compared to the next-best performing strategy). Furthermore, we introduce a cost-to-benefit optimization framework for determining the number of variants to be followed up in functional assays and assess its performance using real and simulation data. We validate our findings using a large scale meta-analysis of four blood lipids traits and find that the relative probability for causality is increased for variants in exons and transcription start sites and decreased in repressed genomic regions at the risk loci of these traits. Using these highly predictive, trait-specific functional annotations, we estimate causality probabilities across all traits and variants, reducing the size of the 90% confidence set from an average of 17.5 to 13.5 variants per locus in this data.
Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
Bogdan Pasaniuc,Noah Zaitlen,Huwenbo Shi,Gaurav Bhatia,Alexander Gusev,Joseph Pickrell,Joel Hirschhorn,David P Strachan,Nick Patterson,Alkes L. Price
Quantitative Biology , 2013, DOI: 10.1093/bioinformatics/btu416
Abstract: Imputation using external reference panels is a widely used approach for increasing power in GWAS and meta-analysis. Existing HMM-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (>5%) and low-frequency (1-5%) variants (increasing to 87% (60%) when summary LD information is available from target samples) versus 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and is computationally very fast. As an empirical demonstration, we apply our method to 7 case-control phenotypes from the WTCCC data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95% (105%) of the effective sample size (as quantified by the ratio of $\chi^2$ association statistics) compared to HMM-based imputation from individual-level genotypes at the 227 (176) published SNPs in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of 4 lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic vs. non-genic loci for these traits, as compared to an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses.
Quantifying Missing Heritability at Known GWAS Loci
Alexander Gusev ,Gaurav Bhatia,Noah Zaitlen,Bjarni J. Vilhjalmsson,Dorothée Diogo,Eli A. Stahl,Peter K. Gregersen,Jane Worthington,Lars Klareskog,Soumya Raychaudhuri,Robert M. Plenge,Bogdan Pasaniuc,Alkes L. Price
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003993
Abstract: Recent work has shown that much of the missing heritability of complex traits can be resolved by estimates of heritability explained by all genotyped SNPs. However, it is currently unknown how much heritability is missing due to poor tagging or additional causal variants at known GWAS loci. Here, we use variance components to quantify the heritability explained by all SNPs at known GWAS loci in nine diseases from WTCCC1 and WTCCC2. After accounting for expectation, we observed all SNPs at known GWAS loci to explain more heritability than GWAS-associated SNPs on average (). For some diseases, this increase was individually significant: for Multiple Sclerosis (MS) () and for Crohn's Disease (CD) (); all analyses of autoimmune diseases excluded the well-studied MHC region. Additionally, we found that GWAS loci from other related traits also explained significant heritability. The union of all autoimmune disease loci explained more MS heritability than known MS SNPs () and more CD heritability than known CD SNPs (), with an analogous increase for all autoimmune diseases analyzed. We also observed significant increases in an analysis of Rheumatoid Arthritis (RA) samples typed on ImmunoChip, with more heritability from all SNPs at GWAS loci () and more heritability from all autoimmune disease loci () compared to known RA SNPs (including those identified in this cohort). Our methods adjust for LD between SNPs, which can bias standard estimates of heritability from SNPs even if all causal variants are typed. By comparing adjusted estimates, we hypothesize that the genome-wide distribution of causal variants is enriched for low-frequency alleles, but that causal variants at known GWAS loci are skewed towards common alleles. These findings have important ramifications for fine-mapping study design and our understanding of complex disease architecture.
Robust Stability and Stability Radius for Variational Control Systems
Bogdan Sasu
Abstract and Applied Analysis , 2008, DOI: 10.1155/2008/381791
Abstract: We consider an integral variational control system on a Banach space and we study the connections between its uniform exponential stability and the ((?
On Exponential Dichotomy of Variational Difference Equations
Bogdan Sasu
Discrete Dynamics in Nature and Society , 2009, DOI: 10.1155/2009/324273
Abstract: We give very general characterizations for uniform exponential dichotomy of variational difference equations. We propose a new method in the study of exponential dichotomy based on the convergence of some associated series of nonlinear trajectories. The obtained results are applied to difference equations and also to linear skew-product flows.
On Dichotomous Behavior of Variational Difference Equations and Applications
Bogdan Sasu
Discrete Dynamics in Nature and Society , 2009, DOI: 10.1155/2009/140369
Abstract: We give new and very general characterizations for uniform exponential dichotomy of variational difference equations in terms of the admissibility of pairs of sequence spaces over ? with respect to an associated control system. We establish in the variational case the connections between the admissibility of certain pairs of sequence spaces over ? and the admissibility of the corresponding pairs of sequence spaces over ?. We apply our results to the study of the existence of exponential dichotomy of linear skew-product flows.
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