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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

Genotype calling for the Illumina platform.

Yik Ying Teo1

  • 1Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg

Methods in Molecular Biology (Clifton, N.J.)
|February 7, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces genotype calling for large-scale genetic studies using Illumina BeadArray platforms. It details the ILLUMINUS software for accurate single nucleotide polymorphism (SNP) analysis and quality control.

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Area of Science:

  • Genetics
  • Bioinformatics
  • Genomics

Background:

  • Advancements in genotyping technologies enable simultaneous assaying of over a million single nucleotide polymorphisms (SNPs).
  • Automated statistical approaches are crucial for translating probe hybridization intensities into genotype calls in large-scale genetic studies.

Purpose of the Study:

  • To introduce the process of genotype calling, focusing on Illumina BeadArray platforms.
  • To provide instructions for using the ILLUMINUS software for genotype calling in large-scale genetic studies.

Main Methods:

  • Detailed instructions for preparing input files for genotype calling.
  • Linux commands and options for executing the ILLUMINUS software.
  • Application of perturbation analysis for identifying erroneous genotype calls.

Main Results:

  • Successful implementation of automated genotype calling for high-throughput SNP analysis.
  • Identification of SNPs with potential genotype call errors using perturbation analysis.

Conclusions:

  • Genotype calling is a critical step in large-scale genetic studies, particularly with platforms like Illumina BeadArray.
  • The ILLUMINUS software and perturbation analysis enhance the accuracy and reliability of genotype data.