Candidate prediction from whole genome data set
Utility of whole-genome sequence data for across-breed genomic prediction
... WGS data in ...markers from a meta-GWAS study on the accuracy of across-breed ...WGS data are selected a priori based on their potential causal effect and that the potentially non-causal markers are ...
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A Bayesian Antedependence Model for Whole Genome Prediction
... the data generation model based on thousands of generations of LD created between markers and QTL, even for simulated ...drawn from reflected Gamma distribu- tions in our simulation study as typically done ...
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Whole genome prediction for preimplantation genetic diagnosis
... found genome predictions, and thus the genome of an embryo biopsy may not fully represent the genome of the resulting ...identified from SNP array data, although this was not attempted ...
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Prediction of genetic contributions to complex traits using whole genome sequencing data
... using prediction models borrowed from animal breed- ing, GBLUP, and BayesCπ, we showed that prediction of additive genetic contributions for a complex trait using whole genome ...
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Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction
... genomic prediction is highly de- pendent on the linkage disequilibrium (LD) between the genotyped markers and actual causative variants (de Roos et ...simulated whole genome sequence data, it ...
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Using Mendelian inheritance errors as quality control criteria in whole genome sequencing data set
... substantial data cleaning. Indeed, the uncleaned sequence data for chromosome 3 includes 1,607,227 variants passing SVM and INDEL5 ...cleaned data set contained 1,215,399 ...(41,489) ...
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Optimal algorithms for haplotype assembly from whole-genome sequence data.
... the set of reads can be partitioned into two subsets that satisfy the following property: if both subsets of the reads are mapped to the two haplotypes at their corresponding intervals indicated by their starting ...
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Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole Genome Sequencing
... phenotyping data for isolates with apparently novel mutations or with nonfunction- ing resistance genes elucidate the contribution of the underlying ...resulting from the in- corporation of the novel blaZ ...
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Systematic re-evaluation of genes from candidate gene association studies in migraine using a large genome-wide association data set
... the candidate gene association studies in the literature lacked sufficient power to detect an effect that can be realistically expected for a common allele in a common disorder like ...the candidate gene ...
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Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data
... Human whole-genome sequencing with next-generation sequencing usually produces hundreds of gigabases, thus WGS mapping or assembly tools generally requires large memory such that it is intractable to use ...
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Prediction of colorectal cancer driver genes from patients’ genome data
... Identification of cancer driver genes is one of the important aspects in whole genome sequencing projects. Two prominent consortiums working on the collection of cancer genes data are Cancer ...
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Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing
... different from that of cattle (G oddard and H ayes 2009): there is a lot of LD between very closely linked SNPs, due to the relatively small prehistoric effective population size, but very little LD between the ...
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Genetic architecture of maize kernel row number and whole genome prediction
... a set of elite inbred lines, including parental lines of high vigor hybrids, inbred lines utilizing in maize breeding program, and improving lines from the germplasm enhancement of maize project ...
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Sequence-Based Deep Learning DNA Methylation Prediction and Whole-Genome Epigenetic Aging Prediction
... From these results we see that all architectures disproportionately have better specificity than sensitiv- ity. Thus, these models are quite effective at predicting sequences that are unmethylated but poor at ...
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Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica
... of whole genome sequencing (WGS) for identification and surveillance of Salmonella since April 2014 (Ashton et ...sequencing data can be used to identify resistance determinants and therefore ...
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Whole genome analyses accounting for structures in genotype data
... c, set c ∗ to be the WPPA of the current ...calculated from SNPs, for inference at QTL would be valid given the condition that SNPs in a window completely capture the signal from QTL in that window ...
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Bioinformatics analysis of whole genome resequencing data in the chicken
... the data set of indels detected using mapping distances between mate- pairs, could be the gaps and duplicated regions in the chicken genome, as such errors are not considered in the algorithm of ...
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Using imputation-based whole-genome sequencing data to improve the accuracy of genomic prediction for combined populations in pigs
... respectively, from three Yorkshire populations with different genetic backgrounds were genotyped with the PorcineSNP80 ...accuracy from 80K to WGS variants reached ...WGS data compared to the 80K SNP ...
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Detection of long repeat expansions from PCR free whole genome sequence data
... STRs from PCR- free, WGS data implemented in a software package named ...repeats from just a few units in length up to large, pathogen- ic expansions that may be significantly longer than the read ...
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Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations
... approaches from the field of machine learning that can be useful for the classification of a genomic region as either neutral or ...inferred from the available data. Such a process is called ...
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