BACKGROUND AND PURPOSE: 

• For decades, routine chromosome analysis was used to analyze amniocentesis and CVS samples, however technique was limited as karyotyping could not assess smaller microdeletions  
• Microarray analysis is now recommended in the presence of fetal structural abnormalities 
• Microarrays can detect small, submicroscopic changes, but cannot identify smaller base pair mutations which may be associated with single gene disorders  
• Petrovski et al. (The Lancet, 2019) sought to determine the incremental diagnostic yield of whole-exome sequencing (WES) following uninformative results of karyotype testing and chromosomal microarray

METHODS: 

• Prospective cohort study of parents of anomalous fetuses identified on ultrasound  
  • Fetuses with known chromosomal or microdeletion were excluded   
• Among fetuses and parents (parent-fetus trios) WES was performed and ‘qualifying’ variants were classified as either Tier 1 or Tier 2 
  • Tier 1: Highly penetrant | Absent in the parents and controls 
  • Tier 2: Previously categorized as ‘likely pathogenic” or protein truncating variant where protein-truncation is a known mechanism of disease  
• Variant classification followed ACMG guidelines and also used previously published bioinformatic approaches  
• Primary outcome: Detection of disease causing variants that could explain the fetal anatomical abnormalities  
• Secondary outcomes 
  • Frequency of fetuses with a diagnostic genetic variant comparing  
    • Cultured vs direct sampling 
    • Single versus multiple anomalies

RESULTS: 

• 517 women anomalous fetuses were screened for eligibility  
  • 71 (14%) couples declined testing 
  • 87 (17%) trios were missing at least one DNA sample (from either parent or the fetus) 
  • 69 (13%) trios had a clinically relevant abnormal karyotype or chromosomal microarray finding 
  • 51 (10%) couples did not consent to WES or withdrew consent 
  • 5 (1%) samples were not of good enough quality for analysis 
• DNA samples from 234 (45%) eligible trios were included in the study  
  • Known genetic variants were identified in 24 (10%) families  
  • Mutations indicative of pathogenicity but with insufficient evidence to be considered diagnostic were identified in another 46 (20%) of the families 
    • Under ACMG guidelines, 15 would have been considered pathogenic   
• There was no difference between cultured and direct samples  
• Frequency of genetic diagnoses based on fetal anomaly were highest in the following 
  • Lymphatic or effusion (24%) 
  • Skeletal (24%) 
  • CNS (22%) 
  • Renal (16%)  
• Lowest frequency of genetic diagnoses: Cardiac anomalies (5%)

CONCLUSION: 

• WES can provide important additional genetic diagnostic information in the setting of structural anomalies following a negative karyotype and microarray

Learn More – Primary Sources: 

Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study

Related ObG Topics:

The Exome and Whole Exome Sequencing: Prenatal Testing Recommendations

Can Whole Exome Sequencing Explain Prenatal Loss With Insufficient Fetal DNA?

The Genome and Whole Genome Sequencing