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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

H. Li
2011 Bioinformatics  
Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data  ...  On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping.  ...  , to Rasmus Nielsen for the observation on the occasional slow convergence of the EM algorithm and to Si Quang Le and Richard Durbin for the help on understanding the QCall model.  ... 
doi:10.1093/bioinformatics/btr509 pmid:21903627 pmcid:PMC3198575 fatcat:cjnzxoenbnf67npuuyfpehqgui

RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout

Mohamed Salem, Roger L. Vallejo, Timothy D. Leeds, Yniv Palti, Sixin Liu, Annas Sabbagh, Caird E. Rexroad, Jianbo Yao, Zhanjiang Liu
2012 PLoS ONE  
RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified  ...  The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes.  ...  Acknowledgments We thank Kyle Martin (Troutlodge, Inc), Scott LaPatra and Richard Towner (Clearsprings Food) and Ken Overturf (USDA-ARS Hagerman Station) for providing samples used in the markers polymorphism  ... 
doi:10.1371/journal.pone.0036264 pmid:22574143 pmcid:PMC3344853 fatcat:iopqatuwebhzviqz7nswpoxn6a

Dynamic Modeling of Genes Controlling Cancer Stem Cell Proliferation

Zhong Wang, Jingyuan Liu, Jianxin Wang, Yaqun Wang, Ningtao Wang, Yao Li, Runze Li, Rongling Wu
2012 Frontiers in Genetics  
cancer SC.The statistical method developed allows biologically meaningful hypotheses about the genetic control mechanisms of carcinogenesis and metastasis to be tested in a quantitative manner.  ...  Here, we address this issue by describing a conceptual strategy for identifying the genetic origins of cancer SC.  ...  Table 1 | 1 The estimation of parameters by a dynamic model for mapping cancer stem cell proliferation from a simulated mapping population of 500 individuals by assuming heritability H 2 = 0.1 AA Aa  ... 
doi:10.3389/fgene.2012.00084 pmid:22661984 pmcid:PMC3357477 fatcat:puiyahmj4rfajetzsmevnbuuzu

SNP and Mutation Data on the Web – Hidden Treasures for Uncovering

Michael R. Barnes
2002 Comparative and Functional Genomics  
These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease.  ...  Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central  ...  For the geneticist, SNP markers are a key research material for genetic association with heritable traits, but for those with a wider interest in genomics and biology, the new SNP data is also a valuable  ... 
doi:10.1002/cfg.131 pmid:18628874 pmcid:PMC2447234 fatcat:ef2g4zzkdff5fenxijehebroou

Genetic Epidemiology and Public Health: The Evolution From Theory to Technology

M. Daniele Fallin, Priya Duggal, Terri H. Beaty
2016 American Journal of Epidemiology  
Genetic epidemiology represents a hybrid of epidemiologic designs and statistical models that explicitly consider both genetic and environmental risk factors for disease.  ...  , and what remains to be done. genetic association; genetic epidemiology; genome-wide association study; linkage; sequencing; single nucleotide polymorphism Abbreviations: GWAS, genome-wide association  ...  This period could rightly be called the era of complex diseases in genetic epidemiology, because it reflects a shift in focus from gene discovery for Mendelian diseases to discovery for complex diseases  ... 
doi:10.1093/aje/kww001 pmid:26905340 fatcat:d3zrkucfafeejcf37uontmhl2q

Statistical and Computational Methods for Genetic Diseases: An Overview

Francesco Camastra, Maria Donata Di Taranto, Antonino Staiano
2015 Computational and Mathematical Methods in Medicine  
The aim of the paper is to provide an overview of statistical and computational methods paying attention to methods for the sequence analysis and complex diseases.  ...  Innovation of genetic methodologies leads to the production of large amounts of data that needs the support of statistical and computational methods to be correctly processed.  ...  Acknowledgment The authors wish to thank the anonymous reviewers for their valuable comments.  ... 
doi:10.1155/2015/954598 pmid:26106440 pmcid:PMC4464008 fatcat:movpvfpg2fehvab35atzshdwim

Status and Prospects of Association Mapping in Plants

Chengsong Zhu, Michael Gore, Edward S. Buckler, Jianming Yu
2008 The Plant Genome  
We have seen a more concerted effort in assembling various association-mapping populations and initiating experiments through either candidategene or genome-wide approaches in different plant species.  ...  There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance.  ...  If alleles have a high mutation rate and strong size constraint, SSR size homoplasy could be problematic when estimating genetic parameters in a large population (Estoup et al., 2002) .  ... 
doi:10.3835/plantgenome2008.02.0089 fatcat:aajfbapuibffnewzvtr3s4gaom

Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies

2011 The Lancet  
The first stage generated error and crossover maps as parameter estimates for imputation on a random subset of 200 samples per study over 100 iterations of the initial statistical model.  ...  between genotyped data from cases and controls in the discovery phase, which were used to adjust statistical models for covariates accounting for possible population substructure.  ... 
doi:10.1016/s0140-6736(10)62345-8 pmid:21292315 pmcid:PMC3696507 fatcat:rbrbowyeoneypobawv6rzr4duu

Fine Mapping in 94 Inbred Mouse Strains Using a High-Density Haplotype Resource

A. Kirby, H. M. Kang, C. M. Wade, C. Cotsapas, E. Kostem, B. Han, N. Furlotte, E. Y. Kang, M. Rivas, M. A. Bogue, K. A. Frazer, F. M. Johnson (+4 others)
2010 Genetics  
We demonstrated the utility of these data in high-resolution linkage mapping through power simulations and statistical power analysis and provide guidelines for developing such studies.  ...  A catalog of the genetic variation among inbred mouse strains, however, is required to enable powerful positional cloning and association techniques.  ...  This research also was supported in part by the University of California, Los Angeles, subcontract of contract N01-ES-45530 from the National Toxicology Program and National Institute of Environmental  ... 
doi:10.1534/genetics.110.115014 pmid:20439770 pmcid:PMC2907194 fatcat:mwcwepzoorbpbjdelalnumuhju

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

John A. Lees, Minna Vehkala, Niko Välimäki, Simon R. Harris, Claire Chewapreecha, Nicholas J. Croucher, Pekka Marttinen, Mark R. Davies, Andrew C. Steer, Steven Y. C. Tong, Antti Honkela, Julian Parkhill (+2 others)
2016 Nature Communications  
This plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation.  ...  Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest.  ...  relation of association studies in human genetics to prokaryotic genetics.  ... 
doi:10.1038/ncomms12797 pmid:27633831 pmcid:PMC5028413 fatcat:g6sxszdbljch3cdvy42qq6bm2e

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes [article]

John A Lees, Minna Vehkala, Niko Välimäki, Simon R Harris, Claire Chewapreecha, Nicholas J Croucher, Pekka Marttinen, Mark R Davies, Andrew C Steer, Stephen Y C Tong, Antti Honkela, Julian Parkhill (+2 others)
2016 biorxiv/medrxiv   pre-print
Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic  ...  Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest.  ...  relation of association studies in human genetics to prokaryotic genetics.  ... 
doi:10.1101/038463 fatcat:5axegzyz5bawbm4y7kfs45wwv4

ANGSD: Analysis of Next Generation Sequencing Data

Thorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus Nielsen
2014 BMC Bioinformatics  
This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly  ...  Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. Results: We present a multithreaded program suite called ANGSD.  ...  Work for this manuscript was financed through Danish National Research Foundation (DNRF94), the Villum Foundation, and grant 2R14003229-07 from the National Institutes of Health.  ... 
doi:10.1186/s12859-014-0356-4 pmid:25420514 pmcid:PMC4248462 fatcat:xujrgymmmrg2vhehih35egbc4q

Using Genotyping-By-Sequencing (GBS) for Genomic Discovery in Cultivated Oat

Yung-Fen Huang, Jesse A. Poland, Charlene P. Wight, Eric W. Jackson, Nicholas A. Tinker, Xinping Cui
2014 PLoS ONE  
We examined technical factors that influence GBS SNP calls, established a workflow that combines two bioinformatics pipelines for GBS SNP calling, and provided a nomenclature for oat GBS loci.  ...  .), seven biparental mapping populations and diverse inbred lines from breeding programs around the world were studied.  ...  Gauthier, Muriel Jatar, Sophie Ménard, and Paul Gillespie for preparing and handling DNA samples; Andrew Sharpe and Darrin Klassen for performing DNA sequencing; Stéphane Nicolas for sharing R scripts  ... 
doi:10.1371/journal.pone.0102448 pmid:25047601 pmcid:PMC4105502 fatcat:zzr4wb3xzvhubdppinorkkbpxi

Analysis of extended haplotype in Korean cattle (Hanwoo) population

Dajeong Lim, Bong Hwan Choi, Yong Min Cho, Han Ha Chai, Gul Won Jang, Cedric Gondro, Yeoung Ho Jeoung, Seung Hwan Lee
2016 BMB Reports  
To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip.  ...  We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo.  ...  ACKNOWLEDGEMENTS This work was supported by Agenda (PJ01040601 and PJ90695602) of the National Institute of Animal Science, Rural Development Administration (RDA), Republic of Korea.  ... 
doi:10.5483/bmbrep.2016.49.9.074 pmid:27470211 pmcid:PMC5227145 fatcat:hncimupjajhw7mfx4otbiiqrxe

Semiparametric Functional Mapping of Drug Response [chapter]

2008 Statistical and Computational Pharmacogenomics  
SNPs are more frequent and mutationally stable, making them suitable for association studies to map disease-causing mutations, especially useful in personalized medicine for their association with disease  ...  These statistical methods, simply called functional mapping, hold a great promise for the detection of genetic loci, or DNA sequence variants, associated with drug response on the scale of dosage and time  ... 
doi:10.1201/9781584888291-20 fatcat:ekk25fa7tjhh3okvbnmrmkhiiy
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