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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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.
GWAS does not require the identification of the target gene involved in...
Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...

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Infinium Assay for Large-scale SNP Genotyping Applications
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A reference panel of 64,976 haplotypes for genotype imputation.

Shane McCarthy1, Sayantan Das2,3, Warren Kretzschmar4

  • 1Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.

Nature Genetics
|August 23, 2016
PubMed
Summary

This study presents a large human haplotype reference panel for accurate genotype imputation and increased SNP testing in genetic association studies. This resource aids in discovering and refining causal genetic loci efficiently.

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Area of Science:

  • Genetics
  • Genomics
  • Bioinformatics

Background:

  • Genetic association studies require large reference panels for accurate imputation.
  • Existing panels may have limitations in SNP coverage and imputation accuracy for low-frequency variants.

Purpose of the Study:

  • To create a comprehensive human haplotype reference panel using whole-genome sequence data.
  • To improve genotype imputation accuracy, especially for low-frequency variants.
  • To enhance the discovery and refinement of causal loci in genetic studies.

Main Methods:

  • Construction of a reference panel with 64,976 human haplotypes and 39,235,157 single nucleotide polymorphisms (SNPs).
  • Utilized whole-genome sequence data from 20 studies, primarily of European ancestry.
  • Developed remote server resources for consistent and efficient imputation and phasing.

Main Results:

  • The reference panel enables accurate genotype imputation down to 0.1% minor allele frequency.
  • Significant increase in the number of SNPs testable in association studies.
  • Facilitates the discovery and refinement of causal genetic loci.

Conclusions:

  • The developed reference panel is a valuable resource for genetic research.
  • It enhances the power and precision of genetic association studies.
  • Remote server access ensures efficient and widespread use by researchers.