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Principles of Pharmacogenetics: Types of Genetic Variants01:27

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The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Rare variants in ischemic stroke: an exome pilot study.

John W Cole1, O Colin Stine, Xinyue Liu

  • 1Veterans Administration Medical Center, Baltimore, Maryland, United States of America. jcole@som.umaryland.edu

Plos One
|April 27, 2012
PubMed
Summary

This pilot study explored rare genetic variants in ischemic stroke (IS) cases. While exome sequencing identified novel variations, definitive proof of rare coding variants predisposing to IS requires further research and optimized analytical methods.

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Area of Science:

  • Genetics
  • Neurology
  • Genomics

Background:

  • Ischemic stroke (IS) has a complex genetic architecture.
  • Rare variants with high penetrance may offer greater insights into IS pathogenesis than common variants.
  • The human exome, comprising protein-coding regions, is a key area for identifying functional genetic variation.

Purpose of the Study:

  • To conduct a pilot study identifying variations across the human exome in ischemic stroke cases.
  • To evaluate the feasibility and challenges of exome sequencing research for ischemic stroke.
  • To identify potential rare coding variants associated with ischemic stroke risk.

Main Methods:

  • Exome sequencing was performed on 10 ischemic stroke cases (8 African-Americans, 2 Caucasians) selected for genetic contribution to stroke risk.
  • Paired-end sequencing libraries were constructed, capturing and sequencing all predicted human exons.
  • Exome data was screened against dbSNP to identify novel single nucleotide polymorphisms (SNPs).

Main Results:

  • Sequencing generated substantial data (average 25.5 million read pairs, 3.8 Gbp per sample).
  • An average of 2839 novel SNPs were found in African-Americans and 1105 in Caucasians.
  • 48 genes showed rare variants across all stroke cases; the CSN3 gene exhibited notable rare variation and a coding polymorphism.

Conclusions:

  • Rare coding variants may contribute to ischemic stroke risk, but this requires definitive proof.
  • This study highlights the complexities of exome sequencing research in ischemic stroke.
  • Exome data acquisition is feasible, but optimal analytical methods are still under development.