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Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Haploview: Visualization and analysis of SNP genotype data.

Jeffrey C Barrett

Cold Spring Harbor Protocols

|February 12, 2010

Summary

Haploview is a user-friendly software package that simplifies complex genetic association studies. It aids in analyzing large datasets, selecting tag single-nucleotide polymorphisms (SNPs), and evaluating genotype data quality for improved research efficiency.

Area of Science:

Genetics and Genomics
Bioinformatics and Computational Biology
Statistical Genetics

Background:

Association studies require extensive data analysis, often spanning months.
Large-scale genetic variation data (e.g., International HapMap Project) and single-nucleotide polymorphism (SNP) genotyping data present analysis challenges.
Efficient curation and analysis of large genetic datasets are crucial for advancing association studies.

Purpose of the Study:

To introduce Haploview, a software package designed to streamline genetic association study workflows.
To demonstrate the utility of Haploview across various stages of an association study, from design to execution.
To provide a practical guide for researchers utilizing Haploview for data analysis and interpretation.

Main Methods:

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Infinium Assay for Large-scale SNP Genotyping Applications

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

Utilized Haploview software for data analysis tasks.
Demonstrated Haploview's application in analyzing International HapMap Project data.
Illustrated the use of Haploview for selecting tag-SNPs and evaluating genotype data quality.

Main Results:

Haploview effectively bundles common analysis tasks into an accessible package.
The software facilitates the analysis of HapMap data and the selection of tag-SNPs.
Haploview aids in assessing disease genotype data quality, testing for associations, and evaluating regions for follow-up.

Conclusions:

Haploview is a valuable tool for researchers conducting genetic association studies.
The software enhances efficiency and ease of use in analyzing large-scale genetic datasets.
Haploview supports critical phases of association studies, including data quality control, association testing, and follow-up analysis.