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Evolution of a Human-Specific Tandem Repeat Associated with ALS.

Meredith M Course1, Kathryn Gudsnuk1, Samuel N Smukowski1

  • 1Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA.

American Journal of Human Genetics
|August 5, 2020
PubMed
Summary

A human-specific tandem repeat in WDR7 shows increased copy number in amyotrophic lateral sclerosis (ALS) patients. This repeat’s expansion mechanism offers insights into neurological disease and human evolution.

Keywords:
WD repeat domain 7, WDR7amyotrophic lateral sclerosis, ALSancient genomesevolutionary geneticslong-read sequencingmodifier geneneurodegenerative diseasenoncoding RNAtandem repeat expansionvariable number tandem repeat, VNTR

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Area of Science:

  • Genetics
  • Human Evolution
  • Neurological Disorders

Background:

  • Tandem repeats are implicated in human-specific traits and neurological diseases.
  • Over 40 tandem repeat expansions are linked to neurological conditions.
  • The WDR7 gene's last intron contains a human-specific tandem repeat.

Purpose of the Study:

  • To characterize a novel human-specific 69 bp variable number tandem repeat (VNTR) in the WDR7 gene.
  • To investigate the association between VNTR copy number and sporadic amyotrophic lateral sclerosis (ALS).
  • To elucidate the expansion mechanism and evolutionary history of this VNTR.

Main Methods:

  • Long-read sequencing to analyze VNTR copy number and composition.
  • Analysis of three independent cohorts of individuals with sporadic ALS.
  • Sequence variability analysis to determine expansion patterns in 288 samples.
  • Comparative genomics including Denisovan, Neanderthal, and non-human primate genomes.

Main Results:

  • The WDR7 VNTR exhibits significant variability in copy number and nucleotide sequence.
  • Increased VNTR copy number is significantly enriched in individuals with sporadic ALS.
  • The VNTR expands via duplication events and template switching in the 3'-5' direction.
  • The VNTR is expanded in archaic hominins but largely absent in non-human primates.
  • Population-specific presence or absence of repeat segments was observed in the 1000 Genomes Project.

Conclusions:

  • The WDR7 VNTR is a dynamic genetic element associated with ALS risk.
  • Its unique expansion mechanism provides a model for studying tandem repeat disorders.
  • This VNTR offers a framework for understanding VNTR roles in human evolution and disease.