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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
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Genome-wide array-based copy number profiling in human placentas from unexplained stillbirths.

R Alan Harris1, Francesca Ferrari, Shay Ben-Shachar

  • 1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

Prenatal Diagnosis
|July 7, 2011
PubMed
Summary

Genomic array analysis of placental and fetal samples identified novel copy number variations (CNVs) in unexplained stillbirths. This whole-genome placental profiling may reveal small genomic imbalances contributing to stillbirth cases.

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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Area of Science:

  • Genetics
  • Reproductive Medicine
  • Genomic Medicine

Background:

  • Genomic structural variations, including copy number variations (CNVs), are common in humans and can have phenotypic consequences.
  • Large-scale karyotypic abnormalities are found in 6-12% of stillbirths (SB), but this figure may be underestimated due to limitations of conventional cytogenetics.
  • High-resolution copy number variant analysis using genomic array-based profiling offers a potential method to overcome these limitations.

Purpose of the Study:

  • To investigate the utility of high-resolution genomic array-based profiling for identifying copy number variations (CNVs) in unexplained stillbirths (SB).
  • To assess the potential of whole-genome placental profiling to detect small genomic imbalances contributing to stillbirth.

Main Methods:

  • Prospective collection of stillbirth (SB) cases > 22 weeks gestation, classified as 'unexplained' after rigorous multidisciplinary audit and extensive testing.
  • Genome-wide analysis using high-resolution Illumina single nucleotide polymorphism (SNP) arrays (Human CNV370-Duo) on placental and fetal samples.
  • Confirmation of potential CNVs using independent methods including quantitative PCR, Illumina1M, or Agilent105K comparative genomic hybridization arrays.

Main Results:

  • In a cohort of 54 stillbirths, 29 met strict unexplained criteria.
  • Twenty-four putative novel copy number variations (CNVs) were identified in the unexplained stillbirth cases.
  • Eighteen of 24 identified CNVs (75%) were detected in placental samples, with 8 confirmed in fetal samples; none were found in maternal blood.

Conclusions:

  • Whole-genome placental profiling demonstrates potential for identifying small genomic imbalances.
  • This approach may contribute to understanding the genetic basis of a subset of unexplained stillbirths.
  • Genomic array analysis can reveal novel CNVs in stillbirth cases previously classified as unexplained.