Dataset Information

Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference.

ABSTRACT: We developed a general framework for family-based imputation using single-nucleotide polymorphism data and sequence data distributed by Genetic Analysis Workshop 18. By using PedIBD, we first inferred haplotypes and inheritance patterns of each family from SNP data. Then new variants in unsequenced family members can be obtained from sequenced relatives through their shared haplotypes. We then compared the results of our method against the imputation results provided by Genetic Analysis Workshop organizers. The results showed that our strategy uncovered more variants for more unsequenced relatives. We also showed that recombination breakpoints inferred by PedIBD have much higher resolution than those inferred from previous studies.

SUBMITTER: Song S

PROVIDER: S-EPMC4143700 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference.

Song Sunah S Shields Robert R Li Xin X Li Jing J

BMC proceedings 20140617 Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo

We developed a general framework for family-based imputation using single-nucleotide polymorphism data and sequence data distributed by Genetic Analysis Workshop 18. By using PedIBD, we first inferred haplotypes and inheritance patterns of each family from SNP data. Then new variants in unsequenced family members can be obtained from sequenced relatives through their shared haplotypes. We then compared the results of our method against the imputation results provided by Genetic Analysis Workshop ...[more]

PMID: 25519372

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Project description:BackgroundGenomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation by breeders. Low density panels imputed to higher densities offer a cheaper alternative during the first stages of genomic resources development. Our study is the first to explore the imputation in a tree species: black poplar. About 1000 pure-breed Populus nigra trees from a breeding population were selected and genotyped with a 12K custom Infinium Bead-Chip. Forty-three of those individuals corresponding to nodal trees in the pedigree were fully sequenced (reference), while the remaining majority (target) was imputed from 8K to 1.4 million SNPs using FImpute. Each SNP and individual was evaluated for imputation errors by leave-one-out cross validation in the training sample of 43 sequenced trees. Some summary statistics such as Hardy-Weinberg Equilibrium exact test p-value, quality of sequencing, depth of sequencing per site and per individual, minor allele frequency, marker density ratio or SNP information redundancy were calculated. Principal component and Boruta analyses were used on all these parameters to rank the factors affecting the quality of imputation. Additionally, we characterize the impact of the relatedness between reference population and target population.ResultsDuring the imputation process, we used 7540 SNPs from the chip to impute 1,438,827 SNPs from sequences. At the individual level, imputation accuracy was high with a proportion of SNPs correctly imputed between 0.84 and 0.99. The variation in accuracies was mostly due to differences in relatedness between individuals. At a SNP level, the imputation quality depended on genotyped SNP density and on the original minor allele frequency. The imputation did not appear to result in an increase of linkage disequilibrium. The genotype densification not only brought a better distribution of markers all along the genome, but also we did not detect any substantial bias in annotation categories.ConclusionsThis study shows that it is possible to impute low-density marker panels to whole genome sequence with good accuracy under certain conditions that could be common to many breeding populations.

Dataset Information

Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference.

Publications

Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference.

Similar Datasets

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