Grand Rounds

Can Whole-Exome Sequencing Help Diagnose Otherwise Unexplained Fetal Structural Anomalies?

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

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

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%)

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

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