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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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An updated Pig Haplotype Reference Panel (PHARP 4.0) comprising 13,298 haplotypes.

Qingyu Wang1, Zhenyang Zhang1,2, Xiaowei Ye1

  • 1Key Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.

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|November 20, 2025
PubMed
Summary
This summary is machine-generated.

The new Pig Haplotype Reference Panel (PHARP) 4.0 improves genotype imputation accuracy for pig genetic research and breeding. This large, diverse panel enhances genome-wide association studies and genomic prediction cost-effectively.

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Area of Science:

  • Animal Genomics
  • Bioinformatics
  • Quantitative Genetics

Background:

  • High-throughput sequencing accelerates genetic research but WGS is costly for large studies.
  • Genotype imputation offers a cost-effective alternative for inferring genetic variants.
  • Existing pig reference panels have limitations in size and diversity.

Purpose of the Study:

  • To present the updated Pig Haplotype Reference Panel (PHARP) 4.0, the largest and most diverse pig reference panel to date.
  • To evaluate the imputation accuracy of PHARP 4.0 compared to existing panels.
  • To optimize imputation pipelines and assess their utility in genome-wide association studies (GWAS).

Main Methods:

  • Assembled PHARP 4.0 from 6449 pig genomes across 154 breeds, containing 50.3 million SNPs and 5.8 million indels.
  • Compared imputation accuracy of PHARP 4.0 against SWIM, AHC, AGIDB, and PGRP panels using low-density SNP data.
  • Optimized an RNA-seq-based imputation pipeline and evaluated the impact of reference panel size on rare variant imputation.

Main Results:

  • PHARP 4.0 demonstrated superior imputation accuracy (CR > 0.99, R² > 0.98) in European breeds and improved accuracy (CR = 0.936, R² = 0.924) in Chinese Jinhua pigs.
  • Optimized RNA-seq pipeline achieved high accuracy (CR > 0.95, R² > 0.90) in European breeds and (CR = 0.93, R² = 0.92) in Chinese Jinhua pigs.
  • Increased reference panel size improved rare variant imputation; PHARP 4.0 facilitated successful GWAS by imputing causal variants.

Conclusions:

  • PHARP 4.0 is a valuable resource for pig genetic research, offering enhanced imputation accuracy and diversity.
  • Optimized imputation methods, including RNA-seq-based approaches, improve cost-effectiveness and accuracy in pig genomics.
  • PHARP 4.0 supports large-scale genetic studies and breeding programs by enabling accurate genotype imputation.