Children's Hospital Colorado
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Improving Outcomes of Fetal Whole-exome Sequencing With a Multidisciplinary Approach

8/21/2023

A researcher uses a syringe and test tube

Key takeaways

  • The multidisciplinary approach for fetal whole-exome sequencing improved care.

  • The study offers an overview of the Fetal Precision Medicine Board workflow and the impact of the pilot.

  • The approach produced a 41% yield, compared to 31% in other studies.

  • The board clarified uncertain results in half of the cases in this study.


Background: a multidisciplinary approach to whole-exome sequencing in prenatal settings

Whole-exome sequencing is becoming a more common tool in prenatal genetic testing and screening for suspected genetic syndromes when other testing strategies have been exhausted.

Fetal whole-exome sequencing has established yields of 31 percent when performed for fetal anomalies, but barriers have kept whole-exome sequencing from being widely integrated into prenatal clinical practice.

Challenges included:

  • Cost of testing
  • Lengthy turnaround time
  • Poor fetal phenotype‐genotype correlation of known pediatric disorders
  • Concern for variants of uncertain significance and impact on pregnancy decision-making
  • Lack of prenatal provider expertise for results interpretation/discussion

Children’s Hospital Colorado was one of the first institutions to pilot a multidisciplinary Fetal Precision Medicine Board to address these obstacles:

  • Reviews, select cases for whole-exome sequencing versus other testing pathways
  • Assists in variant reinterpretation

This published case report from researchers Michael Zaretsky, MD, Bettina Cuneo, MD, Manesha Putra, MD, Hannah Elfman, Shawn McCandless, MD, Kestutis Micke, Austin Larson, MD, and Regina Reynolds, MD, representing the University of Colorado School of Medicine and the Colorado Fetal Care Center, Neonatal Intensive Care Unit and Genetics and Inherited Metabolic Diseases Program at Children’s Hospital Colorado, offer a detailed overview of the board structure and workflow highlighting its impacts on patient care and testing efficiency. This approach was initiated in February 2021.

Methods: creating the Fetal Precision Medicine Board, workflow for prenatal whole-exome sequencing

Members

  • Multiple providers from Children’s Colorado
  • Diverse range of expertise
  • Regular attendees
    • Genetics fellows
    • Laboratory, genomics fellows
    • Molecular geneticists
    • Developmental biology researchers
    • Translational researchers
    • Other care team members

Meeting format

A Standing weekly virtual meeting is led by the primary genetic counselor.

Agenda includes:

  • Cases for whole-exome sequencing consideration
  • Published study reviews, discussion of potential impacts
  • Discussion on methods for biobanking samples for research

Case selection

Patients are referred to Colorado Fetal Care Center if maternal‐fetal medicine physicians or fetal cardiologists detect anomalies on ultrasounds or fetal echocardiograms.  

  • Fetal MRI, ultrasound, echocardiogram scheduled
  • Multidisciplinary team reviews imaging study results
  • Fetal genetic counselor meets with patient

The genetic counselor identifies cases for whole-exome sequencing consideration.

  • ~1 to 2 cases of multiple fetal anomalies without clear genetic diagnosis presented each week
  • Cases not reviewed:
    • Clearer precited diagnosis
    • Congenital anomalies not considered genetic
    • Anomalies with well-described singular genetic association

The board reviews existing genetic information and fetal findings from imaging.

  • Discuss potential genetic syndromes
  • Determine if targeted panel is more appropriate or move forward with prenatal whole-exome sequencing

Testing process

Fetal sample collection

  • Chorionic Villus Sampling or amniocentesis at fetal care clinic or referring provider’s office
  • Cell cultures from cryopreserved samples or leftover extracted DNA from cytogenetic testing
  • If fetal sample not available or sufficient, second diagnostic procedure offered as last case scenario

Children’s Colorado prioritizes preserving fetal specimens in case of potential whole-exome sequencing

  • Relies on strong communication with testing laboratories
  • Not all institutions have capacity for complex sample coordination

Parental sample collection

  • Collected in anticipation of whole-exome sequencing
  • Undergo DNA extraction
  • Board prefers whole-exome sequencing performed as trio, including both parental samples
    • Duo may be performed with one parent sample or only fetal sample if necessary

Whole-exome sequencing

  • Performed by commercial laboratory after completion, confirmation of normal microarray results
  • Board may approve performing with cytogenetic testing if:
    • Risk for a single gene disorder is higher than copy number variant
    • Patient using genetic testing information in pregnancy decision-making, approaching gestational age limits
    • Patient ≥30 weeks gestational age, results could impact pregnancy, delivery and/or postnatal care
  • To expedite testing, reporting and results discussion, board defers family opt-in for reanalysis until after delivery for:
  • Secondary findings
  • Variants associated with pediatric or adult‐onset genetic syndromes
  • Carrier screening results

Results discussion and management

Due to the urgency of diagnosis, results are called into the patient upon receipt from laboratory prior to board review.

  • Board review of all variants
  • Assessment from numerous angles
  • Reclassified if indicated
  • Multiple reviews if any disagreement
  • If consensus is not reached, board defers to postnatal evaluation
    • Postnatal management driven by fetal findings
    • Follows standard treatment for identified fetal anomalies
  • Review even if no diagnosis achieved
  • Review of results with patient
  • Updated results or confirmation reviewed with patient via phone
  • Possible additional discussion during genetic counseling or follow-up maternal fetal medicine appointments
  • Management
    • Recommendations collected, shared with neonatologist to ensure NICU team is aware

Long-term follow up

All patients offered long-term follow-up appointment, despite outcome, 3 to 6 months after delivery at maternal fetal genetics clinic.

  • In-person or telemedicine
  • Results review, questions
  • Discussion of future options for pregnancy, fertility management
  • Offered whole-exome sequencing reanalysis
    • Secondary findings
    • Adult on-set disorders
    • Carrier screening

Whole-exome sequencing funding/payment

The board seeks to establish appropriate use of financial resources:

  • Children’s Colorado funds whole-exome sequencing if insurance denies request
    • Prior authorization always attempted
    • Patient financial responsibility subject to co-pay, deductible, etc.
  • Alternative genetic testing pathways always discussed before recommending whole-exome sequencing
  • Reanalysis costs subject to laboratory policy
    • Often no charge
    • Carrier status billed to insurance

Future directions

  • Adjustments to clinical pathways, workflow made as part of ongoing assessment of recent publications
  • Board is building partnerships with research colleagues, including:
    • Patient samples biobanking
    • Samples for translational researchers
    • Post-delivery, retrospective analysis of patients who decline diagnostic testing to determine if whole-exome sequencing would have aided postnatal management
    • Cost benefit analysis

Results: Implementation data

Role of the board in variant interpretation

45 patients completed whole-exome sequencing during study period

  • 19 cases completely negative, no reported variants of interest
  • 26 cases single or multiple variants reported
  • 32 total variants

Of the 17 pathogenic or likely variants, board concluded:

  • 12 were diagnostic
  • 4 were unrelated to fetal findings
  • 1 uncertain significance

Of the 32 total variants reported:

  • 15 variants of uncertain significance
    • 8 were reclassified to pathogenic/likely pathogenic
    • 1 remained uncertain with unclear significance
    • 5 remained uncertain but considered unrelated
    • 1 reclassified as benign

After variant reinterpretation:

  • 20 likely pathogenic/pathogenic, diagnostic of genetic syndrome
  • 2 uncertain related to fetal findings
  • 10 unrelated or benign

Case example: approach to implementing whole-exome sequencing into maternal-fetal care

Results from fetal anatomy ultrasound (21 weeks, 1 day):

A referral to maternal fetal medicine for follow-up confirmed:

Consult

A referral to Colorado Fetal Care Center resulted in additional evaluation and diagnostic testing.

  • Amniocentesis (23 weeks, 3 days) performed and sent for analysis
    • Results from cytogenetic testing ultimately normal
  • Fetus measured at 5th percentile
    • Elevated umbilical artery Dopplers
    • Marginal umbilical cord insertion
  • Unilateral Cleft lip/palate, tetralogy of Fallot confirmed
  • Parental samples collected
  • Whole-exome sequencing recommended after cytogenic testing

Whole-exome sequencing results and management plan

Board meeting

The board reviewed the case and approved whole-exome sequencing. A single, de novo, pathogenic variant in the CDC42 gene, associated with autosomal dominant Takenouchi‐Kosaki syndrome and characterized by anomalies in many different organ systems, was found.

Results

The board affirmed the variant explained prior fetal findings and made several postnasal management recommendations, including:

  • Brain MRI
  • Eye exam
  • Complete blood count
  • Bony X‐rays
  • Renal ultrasound (pre-discharge)

Delivery

The infant was delivered at 37 weeks’ gestation, transitioned normally in the delivery room, and admitted to the NICU for an extensive genetic diagnosis workup.

  • Physical exam findings:
    • 945kg birth weight
    • Right cleft lip and palate
    • Deep sacral dimple with visible base
  • Echo findings:
  • Brain MRI findings:
    • Polymicrogyria
    • Cerebellar vermian hypoplasia
    • Normal-sized optic nerves with abnormal optic nerve sheath
  • Additional exam findings:
  • No optic nerve hypoplasia
  • Normal renal and spine ultrasounds
  • No hematologic abnormalities
  • Moderate to severe hearing loss
  • No aspiration on swallow study
  • Clinical observations:
    • Early presence of hypoglycemia controlled by intravenous fluids until transition to full oral feedings
    • Gastrostomy tube placed to address feeding challenges, allow for discharge to home at 1 month old

Follow up: postnatal management

Long-term recommendations from genetic consultation included:

  • Annual vision and hearing screening
  • Regular neurology follow-up
  • Skeletal development, growth monitoring
  • Routine cleft lip and palate care
  • Developmental therapies

Observations from case example

The prenatal diagnosis informed a comprehensive neonatal evaluation not likely performed otherwise, as well as an earlier transition to the gastrotomy tube.

Discussion and conclusion: multidisciplinary approach helps overcome barriers, improve outcomes

The board has reduced the number of variants of uncertain significance results from 46 percent of all laboratory-reported variants to 6 percent of all reported variants in the study cohort.

Study authors demonstrated how this multidisciplinary approach can help overcome barriers to prenatal whole-exome sequencing:

  • Enables communication with prenatal, postnatal care teams
  • Offers accurate interpretation, recommendations for identified fetal variants, aiding:
    • Pregnancy management
    • Family decision-making
    • Clinical care of neonates
  • Model can be replicated at every level to improve care, effectively integrate new genomic technologies in prenatal care