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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Updated: Feb 17, 2026

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
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Noncoding copy-number variations are associated with congenital limb malformation.

Ricarda Flöttmann1,2, Bjørt K Kragesteen1,2, Sinje Geuer1

  • 1Max Planck Institute for Molecular Genetics, Berlin, Germany.

Genetics in Medicine : Official Journal of the American College of Medical Genetics
|December 14, 2017
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Summary

Copy-number variants (CNVs) significantly contribute to congenital limb malformations, with most affecting noncoding regulatory DNA rather than dosage-sensitive genes. This highlights the critical role of regulatory elements in developmental disorders.

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Area of Science:

  • Genetics
  • Developmental Biology
  • Genomic Medicine

Background:

  • Copy-number variants (CNVs) are crucial in genetic disorders, but interpreting noncoding CNVs remains a challenge.
  • Understanding the genetic basis of congenital limb malformations is vital for diagnosis and treatment.

Purpose of the Study:

  • To determine the proportion of disease-associated CNVs affecting noncoding cis-regulatory sequences versus dosage-sensitive genes in congenital limb malformations.
  • To identify novel candidate CNVs responsible for isolated limb malformations.

Main Methods:

  • High-resolution copy-number analysis in 340 unrelated individuals with isolated limb malformation.
  • CRISPR-based genome editing in mice to re-engineer and study novel candidate CNVs.
  • Analysis of CNV segregation with phenotypes in affected families.

Main Results:

  • 10% of individuals studied had CNVs segregating with limb malformations.
  • 31 known and 4 novel candidate CNVs were identified.
  • 57% of disease-associated CNVs affected noncoding cis-regulatory regions, while 43% involved dosage-sensitive genes.
  • Transgenic mice models showed altered gene expression, confirming regulatory effects of novel CNVs.

Conclusions:

  • CNVs impacting noncoding regulatory elements are a significant cause of congenital limb malformations.
  • Noncoding CNVs play a more substantial role than previously recognized in these developmental disorders.