Dataset Information

Phasing quality assessment in a brown layer population through family- and population-based software.

ABSTRACT: BACKGROUND:Haplotype data contains more information than genotype data and provides possibilities such as imputing low frequency variants, inferring points of recombination, detecting recurrent mutations, mapping linkage disequilibrium (LD), studying selection signatures, estimating IBD probabilities, etc. In addition, haplotype structure is used to assess genetic diversity and expected accuracy in genomic selection programs. Nevertheless, the quality and efficiency of phasing has rarely been a subject of thorough study but was assessed mainly as a by-product in imputation quality studies. Moreover, phasing studies based on data of a poultry population are non-existent. The aim of this study was to evaluate the phasing quality of FImpute and Beagle, two of the most used phasing software. RESULTS:We simulated ten replicated samples of a layer population comprising 888 individuals from a real SNP dataset of 580?k and a pedigree of 12 generations. Chromosomes analyzed were 1, 7 and 20. We measured the percentage of SNPs that were phased equally between true and phased haplotypes (Eqp), proportion of individuals completely correctly phased, number of incorrectly phased SNPs or Breakpoints (Bkp) and the length of inverted haplotype segments. Results were obtained for three different groups of individuals, with no parents or offspring genotyped in the dataset, with only one parent, and with both parents, respectively. The phasing was performed with Beagle (v3.3 and v4.1) and FImpute v2.2 (with and without pedigree). Eqp values ranged from 88 to 100%, with the best results from haplotypes phased with Beagle v4.1 and FImpute with pedigree information and at least one parent genotyped. FImpute haplotypes showed a higher number of Bkp than Beagle. As a consequence, switched haplotype segments were longer for Beagle than for FImpute. CONCLUSION:We concluded that for the dataset applied in this study Beagle v4.1 or FImpute with pedigree information and at least one parent genotyped in the data set were the best alternatives for obtaining high quality phased haplotypes.

SUBMITTER: Frioni N

PROVIDER: S-EPMC6636125 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Phasing quality assessment in a brown layer population through family- and population-based software.

Frioni N N Cavero D D Simianer H H Erbe M M

BMC genetics 20190717 1

<h4>Background</h4>Haplotype data contains more information than genotype data and provides possibilities such as imputing low frequency variants, inferring points of recombination, detecting recurrent mutations, mapping linkage disequilibrium (LD), studying selection signatures, estimating IBD probabilities, etc. In addition, haplotype structure is used to assess genetic diversity and expected accuracy in genomic selection programs. Nevertheless, the quality and efficiency of phasing has rarely ...[more]

PMID: 31311514

Similar Datasets

Project description:From a regulatory perspective, drug quality consistency evaluation must concern different processes used for the same drug. In this study, an assessment strategy based on quality by design (QbD) was developed for population pharmaceutical quality evaluation. A descriptive analysis method based on QbD concept was first established to characterize the process by critical evaluation attributes (CEAs). Then quantitative analysis method based on an improved statistical process control (SPC) method was established to investigate the process indicators (PIs) in the process population, such as mean distribution, batch-to-batch difference and abnormal quality probability. After that rules for risk assessment were established based on the SPC limitations and parameters. Both the SPC parameters of the CEAs and the risk of PIs were visualized according to the interaction test results to obtain a better understanding of the population pharmaceutical quality. Finally, an assessment strategy was built and applied to generic drug consistency assessment, process risk assessment and quality trend tracking. The strategy demonstrated in this study could help reveal quality consistency from the perspective of process control and process risk, and further show the recent development status of domestic pharmaceutical production processes. In addition, a process risk assessment and population quality trend tracking provide data-based information for approval. Not only can this information serve as a further basis for decision-making by the regulatory authority regarding early warnings, but it can also reduce some avoidable adverse reactions. With continuous addition of data, dynamic population pharmaceutical quality is meaningful for emergencies and decision-making regarding drug regulation. Graphical abstract Image 1 Highlights • Critical evaluation attributes (CEAs) is defined and to characterize the process indicators based on the QbD.• An improved SPC method was demonstrated to quantitative analyze the process indicators.• A risk assess rule based on population parameters was developed for evaluating different produce processes of the same drug.• An interaction test for CEAs was performed to find the representation of the population pharmaceutical quality.• The strategy can be applied to generic drugs consistency evaluation, process risk assessment and quality trend tracking.• The strategy can provide data-based information for approval.

Dataset Information

Phasing quality assessment in a brown layer population through family- and population-based software.

Publications

Phasing quality assessment in a brown layer population through family- and population-based software.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets