Genotype imputation and reference panel: a systematic evaluation on haplotype size and diversity
Sign Up to like & getrecommendations! Published in 2020 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbz108
Abstract: Here, 622 imputations were conducted with 394 customized reference panels for Han Chinese and European populations. Besides validating the fact that imputation accuracy could always benefit from the increased panel size when the reference panel… read more here.
Keywords: reference panel; imputation; reference; size ... See more keywords
36 A large multi-breed reference panel and maximizes genotype imputation accuracy in cattle
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Animal Science"
DOI: 10.1093/jas/skz122.033
Abstract: The use of array-based SNP genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data in the last decade. While low-density assays work exceptionally well in the context… read more here.
Keywords: reference panel; imputation accuracy; imputation;
Gene expression networks in the Drosophila Genetic Reference Panel.
Sign Up to like & getrecommendations! Published in 2020 at "Genome research"
DOI: 10.1101/gr.257592.119
Abstract: A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping… read more here.
Keywords: reference panel; drosophila genetic; gene expression; genetic reference ... See more keywords
Establishment of a reference panel of Helicobacter pylori strains for antimicrobial susceptibility testing
Sign Up to like & getrecommendations! Published in 2022 at "Helicobacter"
DOI: 10.1111/hel.12874
Abstract: Eradication treatment for Helicobacter pylori gastritis is covered by national health insurance since 2013 in Japan. However, eradication failure due to the increase of antimicrobial resistance has become a serious problem. The present study aims… read more here.
Keywords: pylori strains; reference panel; helicobacter; strains antimicrobial ... See more keywords
A genotype imputation method for de-identified haplotype reference information by using recurrent neural network
Sign Up to like & getrecommendations! Published in 2020 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1008207
Abstract: Genotype imputation estimates the genotypes of unobserved variants using the genotype data of other observed variants based on a collection of haplotypes for thousands of individuals, which is known as a haplotype reference panel. In… read more here.
Keywords: reference panel; information; imputation; genotype imputation ... See more keywords
Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2022.872486
Abstract: Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA… read more here.
Keywords: imputation; reference panel; sus; imputation ancient ... See more keywords
Opening the Black Box of Imputation Software to Study the Impact of Reference Panel Composition on Performance
Sign Up to like & getrecommendations! Published in 2023 at "Genes"
DOI: 10.3390/genes14020410
Abstract: Genotype imputation is widely used to enrich genetic datasets. The operation relies on panels of known reference haplotypes, typically with whole-genome sequencing data. How to choose a reference panel has been widely studied and it… read more here.
Keywords: reference; reference panel; panel; diversity ... See more keywords