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Grand Rounds

Can we Sequence an Entire Fetal Genome from an Amniocentesis Sample?

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BACKGROUND AND PURPOSE: 

  • There are potentially thousands of genes where loss of function could impact health 
  • There have been limited studies using high coverage whole genome sequencing (WGS) on fetal cells and cell free DNA obtained through amniocentesis  
  • Mao et al. (Clinical Chemistry, 2018) aimed to acquire whole-genome sequence of a fetus from either cellular or cell-free DNA (cfDNA) of an amniotic sample 

METHODS: 

  • There were 31 amniocentesis samples  
  • DNA was obtained from two sources 
    • cfDNA (DNA freely circulating in the amniotic fluid) outside of cells 
    • Whole cells in the amniotic fluid  
  • DNA was sequenced to approximately 50x genome coverage 

RESULTS: 

  • Up to 97% of the fetal genome could be confidently called from freely circulating DNA in the amniotic fluid or the cell pellet after spinning down the amniotic fluid  
    • WGS could be added to leftover amniotic fluid specimens without disturbing current standard of care  
  • Two fetal genomes were found to harbor potentially detrimental variants in two genes 
    • Chromodomain helicase DNA binding protein 8 (CHD8) 
    • LDL receptor-related protein 1 (LRP1) 
  • CHD8 and LRP1 are associated with higher risk for autism spectrum disorder and keratosis pilaris atrophicans, respectively 
  • Drug sensitivities and carrier information of fetuses was also collected 

CONCLUSION: 

  • Whole genome sequences of 31 fetuses demonstrated that the cfDNA or DNA from the cell pellet can be analyzed with little difference in quality 
  • This authors suggest that accurate and complex fetal analyses could soon become available 

Note: ACOG and other professional associations consider WGS appropriate in research settings only (see ‘Related ObG Topics’ below)

Learn More – Primary Sources: 

Advanced Whole-Genome Sequencing and Analysis of Fetal Genomes from Amniotic Fluid 

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Related ObG Topics:

ISPD, SMFM and PQF Release a Joint Position Statement on Fetal Genome-Wide Sequencing
The Genome and Whole Genome Sequencing
The Exome and Exome Sequencing: Prenatal Testing Recommendations

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