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Related Experiment Video

Updated: Jun 4, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

A multi-site study using high-resolution HLA genotyping by next generation sequencing.

C L Holcomb1, B Höglund, M W Anderson

  • 1Roche Molecular Systems Inc. (RMS), Pleasanton, CA 94588, USA.

Tissue Antigens
|February 9, 2011
PubMed
Summary

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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...

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This summary is machine-generated.

High-resolution human leukocyte antigen (HLA) typing is now achievable with next-generation sequencing. The GS FLX platform provides reliable and accurate HLA genotyping, overcoming limitations of previous methods.

Area of Science:

  • Immunogenetics
  • Molecular Biology
  • Genomics

Background:

  • Human leukocyte antigen (HLA) class I and II loci exhibit high polymorphism, complicating high-resolution typing.
  • Existing methods like Sanger sequencing often result in ambiguous typing due to incomplete coverage and phasing issues.

Purpose of the Study:

  • To evaluate the capability of the 454 Life Sciences Genome Sequencer (GS FLX) system with CONEXIO ATF software for high-resolution HLA genotyping.
  • To assess the reliability and concordance of this next-generation sequencing approach across multiple laboratory sites.

Main Methods:

  • Utilized GS FLX next-generation sequencing with standard chemistry for amplicon sequencing.
  • Employed multiplex identifier (MID) tags for high-throughput, pooled sequencing of 20 samples across eight sites.

Related Experiment Videos

Last Updated: Jun 4, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

  • Genotyped HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, and DRB3/4/5 loci.

    • Main Results:

    • Achieved an average sequence read length of 250 base pairs and 672 reads per amplicon, ensuring confidence in allele assignments.
    • Successfully assigned 95% of the 1280 genotypes considered; failures were attributed to procedural errors or novel alleles.
    • Demonstrated high concordance with known genotypes, ranging from 95.3% to 99.4% across sites, with an overall concordance of 97.2%.

    Conclusions:

    • Clonal pyrosequencing on the GS FLX platform with CONEXIO ATF software enables reliable, high-resolution HLA genotyping.
    • This next-generation sequencing method overcomes the limitations of traditional techniques for complex HLA typing.