Evidence map›Paper›PMID 35879321›Full record

ArticleScientific reports2022

PHARP: a pig haplotype reference panel for genotype imputation.

Zhen Wang, Zhenyang Zhang, Zitao Chen, Jiabao Sun, Caiyun Cao, Fen Wu, Zhong Xu, Wei Zhao, Hao Sun, Longyu Guo and 3 more

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In one paragraph

Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
29citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

29 citing papers in PubMed, 2 syntheses or guidelines pooled it.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Zhen WangCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Zhenyang ZhangCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Zitao ChenCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Jiabao SunCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Caiyun CaoCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Fen WuCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Zhong XuHubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China.
Wei ZhaoDepartment of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Hao SunDepartment of Animal Science, School of Animal Science, Jilin University, Changchun, 130062, China.
Longyu GuoDepartment of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Zhe ZhangCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. zhe_zhang@zju.edu.cn.
Qishan WangCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. wangqishan@zju.edu.cn.
Yuchun PanCollege of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. panyc@zju.edu.cn.

Funding

Investigation of metabolites related to manganese exposureF31ES027304 · NIEHS · UNIVERSITY OF WASHINGTON · PI BAKER, MARISSA GAYL · 2016 to 2017
$61k
NIEHS NIH HHS 27304C2054
6 · The paper itself

Abstract

Pigs not only function as a major meat source worldwide but also are commonly used as an animal model for studying human complex traits. A large haplotype reference panel has been used to facilitate efficient phasing and imputation of relatively sparse genome-wide microarray chips and low-coverage sequencing data. Using the imputed genotypes in the downstream analysis, such as GWASs, TWASs, eQTL mapping and genomic prediction (GS), is beneficial for obtaining novel findings. However, currently, there is still a lack of publicly available and high-quality pig reference panels with large sample sizes and high diversity, which greatly limits the application of genotype imputation in pigs. In response, we built the pig Haplotype Reference Panel (PHARP) database. PHARP provides a reference panel of 2012 pig haplotypes at 34 million SNPs constructed using whole-genome sequence data from more than 49 studies of 71 pig breeds. It also provides Web-based analytical tools that allow researchers to carry out phasing and imputation consistently and efficiently. PHARP is freely accessible at http://alphaindex.zju.edu.cn/PHARP/index.php . We demonstrate its applicability for pig commercial 50 K SNP arrays, by accurately imputing 2.6 billion genotypes at a concordance rate value of 0.971 in 81 Large White pigs (~ 17 × sequencing coverage). We also applied our reference panel to impute the low-density SNP chip into the high-density data for three GWASs and found novel significantly associated SNPs that might be casual variants.

Indexed as

BreedingGenome-Wide Association StudyAnimalsGenomeGenotypeHaplotypesHumansPolymorphism, Single NucleotideSwine

Identifiers

PMID35879321
PMCPMC9314402

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.