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Genome-wide Association Studies-GWAS01:11

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Published on: June 21, 2018

hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework.

Ryan Abo1, Stacey Knight, Jathine Wong

  • 1Department of Biomedical Informatics, University of Utah, UT, USA. ryan.abo@hsc.utah.edu

Bioinformatics (Oxford, England)
|July 26, 2008
PubMed
Summary
This summary is machine-generated.

HapConstructor software identifies optimal single nucleotide polymorphism (SNP) sets for genetic association studies. This tool aids researchers in pinpointing susceptibility variants by efficiently analyzing multi-locus SNP data.

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Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Candidate gene association studies often utilize multiple tagging single nucleotide polymorphisms (tSNPs).
  • Determining optimal SNP sets and tests for haplotype analysis can be challenging.
  • Identifying susceptibility variants requires robust analytical methods.

Purpose of the Study:

  • To develop a program, hapConstructor, for automatically building multi-locus SNP sets for case-control association studies.
  • To enhance the power and efficiency of haplotype-based genetic association analyses.
  • To provide a tool for exploring multi-locus associations in candidate genes and regions.

Main Methods:

  • hapConstructor program utilizes a Monte Carlo framework.
  • Automatically constructs multi-locus SNP sets based on significance.
  • Incorporates missing data imputation using full dataset for consistency.
  • Extends to significance testing and false discovery rates, accounting for the construction process.

Main Results:

  • hapConstructor successfully builds SNP sets for association testing.
  • The program facilitates exploration of multi-locus associations.
  • Missing data imputation is performed effectively within the framework.

Conclusions:

  • Haplotypes provide crucial information for identifying susceptibility variants.
  • hapConstructor is a valuable tool for optimizing SNP selection in association studies.
  • The software aids in uncovering complex genetic associations by analyzing multi-locus SNP data.