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Evaluation of Vicinity-based Hidden Markov Models for Genotype Imputation [article]

Su Wang, Miran Kim, Xiaoqian Jiang, Arif Ozgun Harmanci
2021 bioRxiv   pre-print
Here we assess the accuracy of local-HMMs, where each untyped variant is imputed using the typed variants in a small window around itself (as small as 1 centimorgan).  ...  Imputation methods compare the genotypes of the typed variants with the large population-specific reference panels and estimate the genotypes of untyped variants by making use of the linkage disequilibrium  ...  that must be considered and evaluated for increasing the imputation accuracy while providing privacy and confidentiality to the genetic data.  ... 
doi:10.1101/2021.09.28.462261 fatcat:ihbdogmgunfyvixuhdgamhb5ju

FAPI: Fast and accurate P-value Imputation for genome-wide association study

Johnny SH Kwan, Miao-Xin Li, Jia-En Deng, Pak C Sham
2015 European Journal of Human Genetics  
Thus imputing these summary statistics of different variant sets into a common reference panel for meta-analyses is impossible using traditional genotype imputation methods.  ...  Meta-analysis of publicly available GWAS summary statistics can allow more disease-associated loci to be discovered, but these data are usually provided for various variant sets.  ...  Then we compute the distribution of the normal test statistic of an untyped common variant conditional on the P-values at neighboring typed variants and the observed LD structure using a multivariate normal  ... 
doi:10.1038/ejhg.2015.190 pmid:26306642 pmcid:PMC4930094 fatcat:4vwmbtcsebeszm32n3lkbehkmq

TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population

Tulio C Lins, Breno S Abreu, Rinaldo W Pereira
2009 Journal of Biomedical Science  
Variability coverage and the prediction accuracy for tagSNPs in the selected genomic regions of HapMap phase II were computed using a prediction accuracy algorithm.  ...  The application of a subset of single nucleotide polymorphisms, the tagSNPs, can be useful in capturing untyped SNPs information in a genomic region.  ...  Dario Grattapaglia for the ABI3100 sharing and providing the Brazilian samples and Rodrigo G Vieira for extensive work of genotyping and estimating the individual ancestry of the Brazilian samples.  ... 
doi:10.1186/1423-0127-16-73 pmid:19682379 pmcid:PMC2737315 fatcat:drfvoeu22zezvgkq26jvwozb5i

Intra- and interpopulation genotype reconstruction from tagging SNPs

P. Paschou, M. W. Mahoney, A. Javed, J. R. Kidd, A. J. Pakstis, S. Gu, K. K. Kidd, P. Drineas
2006 Genome Research  
Furthermore, we test these methods in the setting of a real association study using a publicly available family data set.  ...  We also evaluate these algorithms on a second data set consisting of genotypes available from the HapMap database (1336 SNPs for four populations) over the same genomic regions.  ...  In addition, some of the cell lines were obtained from the National Laboratory for the Genetics of Israeli Populations at Tel Aviv University, Israel, and the African American samples were obtained from  ... 
doi:10.1101/gr.5741407 pmid:17151345 pmcid:PMC1716273 fatcat:df4wn7zqybelncqjdskg3jf2da

Celer: an Efficient Program for Genotype Elimination

Nicoletta De Francesco, Giuseppe Lettieri, Luca Martini
2010 Electronic Proceedings in Theoretical Computer Science  
We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures.  ...  This paper presents an efficient program for checking Mendelian consistency in a pedigree.  ...  Genotypes are organized in data structures called pedigrees, that besides genetic data, record which individuals mate and their offspring.  ... 
doi:10.4204/eptcs.33.4 fatcat:dw66wwwmjzaurkd5356jepnyri

Analyses and Comparison of Accuracy of Different Genotype Imputation Methods

Yu-Fang Pei, Jian Li, Lei Zhang, Christopher J. Papasian, Hong-Wen Deng, Peter Heutink
2008 PLoS ONE  
Our results showed that a stronger LD and a lower MAF for an untyped marker produced better ARs for all the five methods.  ...  The power of genetic association analyses is often compromised by missing genotypic data which contributes to lack of significant findings, e.g., in in silico replication studies.  ...  Analyzed the data: YFP LZ. Contributed reagents/ materials/analysis tools: JL. Wrote the paper: YFP. Helped revise the paper: HWD JL LZ CP.  ... 
doi:10.1371/journal.pone.0003551 pmid:18958166 pmcid:PMC2569208 fatcat:ex2ie3gumneg5albuad3rsa4xa

DNA identification by pedigree likelihood ratio accommodating population substructure and mutations

Jianye Ge, Bruce Budowle, Ranajit Chakraborty
2010 Investigative Genetics  
Because biologically related family members are not genetically independent, more information and thus greater power can be attained by simultaneous use of all pedigree members in most cases, although  ...  In this study, an improvement was made on the method for missing-person identification for autosomal and lineage-based markers, by considering jointly the DNA profile data of all available family reference  ...  Acknowledgements This study was supported by the US Public Health Service research grant GM 41399 from the US National Institutes of Health.  ... 
doi:10.1186/2041-2223-1-8 pmid:21092343 pmcid:PMC2990736 fatcat:gk7ovhsi2fh6hbznafsd6txj5m

Common statistical issues in genome-wide association studies: a review on power, data quality control, genotype calling and population structure

Yik Y Teo
2008 Current Opinion in Lipidology  
Sim for their helpful comments in improving the article. References and recommended reading  ...  evidence of phenotypic association and use the remaining markers as the superset for identifying SNPs to use for identifying population structure.  ...  The appropriate approach here will be to pool the data using metaanalysis procedures (i.e. with a Cochran-Mantel -Haenszel test), which will correctly yield a nonsignificant result. checklist for GWAS  ... 
doi:10.1097/mol.0b013e3282f5dd77 pmid:18388693 fatcat:q6igmwf3djbnpdmnbptae3bmly

Practical consideration of genotype imputation: Sample size, window size, reference choice, and untyped rate

Guimin Gao, Nita A. Limdi, Nianjun Liu, Boshao Zhang, Kui Zhang, Degui Zhi
2011 Statistics and its Interface  
In this study, we evaluated the influence of untyped rate, sizes of the study sample and the reference sample, window size, and reference choice (for admixed population), as the factors affecting the quality  ...  Imputation offers a promising way to infer the missing and/or untyped genotypes in genetic studies. In practice, however, many factors may affect the quality of imputation.  ...  Guo-Bo Chen for his suggestions for the tables and figures.  ... 
doi:10.4310/sii.2011.v4.n3.a8 pmid:22308193 pmcid:PMC3269888 fatcat:fh3nkfqodffg7eepysnx37a5km

Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs

Mark J. Minichiello, Richard Durbin
2006 American Journal of Human Genetics  
Compared with simpler tests, our method gives increased accuracy in positioning untyped causative loci and can also be used to estimate the frequencies of untyped causative alleles.  ...  First, we infer plausible ARGs, using a heuristic algorithm, which can handle unphased and missing data and is fast enough to be applied to large-scale studies.  ...  Web Resources The URLs for data presented herein are as follows:  ... 
doi:10.1086/508901 pmid:17033967 pmcid:PMC1698562 fatcat:hvfxfdu3dfavxneslq4seedm6u

Impact of the 1000 Genomes Project on the next wave of pharmacogenomic discovery

Wei Zhang, M Eileen Dolan
2010 Pharmacogenomics (London)  
markers for clinical evaluation.  ...  The 1000 Genomes Project aims to provide detailed genetic variation data on over 1000 genomes from worldwide populations using the next-generation sequencing technologies.  ...  Thus, for example, untyped or unknown rarer SNPs with large effects cannot be identified using the currently available data on these samples.  ... 
doi:10.2217/pgs.09.173 pmid:20136363 pmcid:PMC2833269 fatcat:jlh4y2y6njaovnzaiddlqyarvq

The Impact of Using Related Individuals for Haplotype Reconstruction in Population Studies

M. T. Schouten
2005 Genetics  
Recent studies have highlighted the dangers of using haplotypes reconstructed directly from population data for a fine-scale mapping analysis.  ...  This study is concerned with the following question: How much family data (if any) should be used to facilitate haplotype reconstruction in a population study?  ...  Michael Schouten also thanks Michalis Titsias for his technical insight and Alan Stubbs and Vivian Fu for their comments on the manuscript.  ... 
doi:10.1534/genetics.105.042762 pmid:15944347 pmcid:PMC1456835 fatcat:pfzzhjorhzdstawyfil6mrhtcq

ATRIUM: Testing Untyped SNPs in Case-Control Association Studies with Related Individuals

Zuoheng Wang, Mary Sara McPeek
2009 American Journal of Human Genetics  
Incorporation of such external information can allow one to perform tests of association between untyped variants and phenotype, thereby making more efficient use of the available genotype data.  ...  We address this challenge with ATRIUM, a method for case-control association testing with untyped SNPs, based on genome screen data in samples in which some individuals are related.  ...  The Framingham SHARe data used for the analyses described in this manuscript were obtained through dbGaP (phs000007.v6.p3).  ... 
doi:10.1016/j.ajhg.2009.10.006 pmid:19913122 pmcid:PMC2775837 fatcat:nuiik5gkvbda7kpbwqwvmaqshu

Multipoint Genetic Mapping with Uniparental Disomy Data

Hongyu Zhao, Jinming Li, Wendy P. Robinson
2000 American Journal of Human Genetics  
In particular, for a general crossoverprocess model that assumes only that there exists in each interval at most one crossover, we describe how to use the expectation-maximization algorithm to examine  ...  However, genetic information in such data has not been fully utilized because of the limitations of the existing statistical methods for UPD data.  ...  Acknowledgments We thank two reviewers for their detailed and constructive comments.  ... 
doi:10.1086/303072 pmid:10958760 pmcid:PMC1287890 fatcat:alxwir2jzfetfn7334gladhjpy
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