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Related Concept Videos

Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...

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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

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing.

A Eliot Shearer1, Adam P DeLuca, Michael S Hildebrand

  • 1Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, IA 52242, USA.

Proceedings of the National Academy of Sciences of the United States of America
|November 17, 2010
PubMed
Summary
This summary is machine-generated.

Massively parallel sequencing effectively diagnoses nonsyndromic hearing loss (NSHL). This genetic testing approach is sensitive, specific, and reproducible, overcoming challenges posed by NSHL

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Area of Science:

  • Genetics
  • Genomic Medicine
  • Molecular Biology

Background:

  • Nonsyndromic hearing loss (NSHL) presents extreme genetic heterogeneity, complicating diagnosis.
  • Current genetic diagnostic methods for NSHL are expensive and time-consuming.
  • Novel sequencing technologies are needed to improve NSHL genetic diagnosis.

Purpose of the Study:

  • To evaluate the feasibility of target-enrichment and massively parallel sequencing for NSHL genetic diagnosis.
  • To compare solid-phase (NimbleGen) and solution-based (SureSelect) sequence capture methods.
  • To assess the sensitivity and specificity of next-generation sequencing for identifying NSHL pathogenic variants.

Main Methods:

  • Target enrichment using NimbleGen or SureSelect followed by 454 or Illumina sequencing.
  • Read mapping with GSMAPPER, BFAST, and BOWTIE.
  • Variant calling and annotation using a custom pipeline (ASAP) with in silico prediction tools (SIFT, BLOSUM, Polyphen2, Align-GVGD).
  • Validation of 605 single nucleotide polymorphisms (SNPs) by Sanger sequencing.

Main Results:

  • Causative mutations were identified in positive controls but not in the negative control.
  • Pathogenic mutations were identified in five out of six patients with idiopathic hearing loss.
  • The methods demonstrated high sensitivity, specificity, and reproducibility.

Conclusions:

  • Massively parallel sequencing technologies are suitable for genetic diagnosis of hearing loss.
  • Target-enrichment sequencing significantly improves the efficiency of NSHL genetic testing.
  • These advanced genomic approaches can overcome the genetic heterogeneity challenges in NSHL.