WHAT IS IT?

• The exome refers to the expressed regions of the genome, or the exons, which code for proteins
  • The exome constitutes about 2%-3% of the genome
  • There are about 180,000 exons in the over 20,000 genes in the human genome

DNA sequence analysis of all of the expressed genes in the genome is referred to as Whole Exome Sequencing (WES) or now more commonly referred to as Exome Sequencing (ES) in the professional literature

• ES  generally allows for simultaneous analysis of all exons in one test
  • ES  will analyze close to 95% of the exons
• ES is usually considered for individuals with rare diseases or syndrome for whom testing of specific potentially disease causing genes have not identified any disease causing gene mutations
• ES will not detect all types of genetic changes in the exome, so there are limitations
• Costs tend to be lower than genome sequencing (GS)

WHEN TO CONSIDER PRENATAL SEQUENCING:

ISPD/ SMFM / PQF (see ‘Related ObG Topics’ below)

Routine use of Prenatal Sequencing

• The routine use of prenatal sequencing is not recommended, including cases where fetal DNA has already been obtained via amniocentesis, CVS or cordocentesis
  • Clinical validation data are currently insufficient and prospective studies are required to determine clinical utility and risks vs harms

Appropriate Circumstances to Consider Prenatal Sequencing in a Non-Research Setting

• Fetal anomalies or a single major anomaly suggestive of a genetic disorder
  • Microarray is negative
  • No microarray results is available but the fetus exhibits anomalies strongly suggesting of a single gene disorder
• Previous undiagnosed fetus (or child) from either parent, with single or multiple anomalies suspicious for a genetic syndrome that has now recurred in the current pregnancy
  • Karyotype and microarray in the current pregnancy have not yielded a diagnosis
  • Make every effort to obtain a sample from the current pregnancy or previously affected offspring
  • If samples are unavailable from previously affected offspring or the current pregnancy, consider offering parents sequencing to determine if they may be carriers for an autosomal recessive disorder
• History of recurrent stillbirths with negative karyotype and/or microarray, where the fetus is exhibiting a similar pattern of anomalies

ACMG

Consider ES for the Following

• Fetus with ultrasound anomalies and no results from CMA and karyotype
  • In the case of concern related to a specific phenotype or disorder, start with more targeted molecular testing  (single-gene test or gene panel)
• Do not use ES for other indications such as soft markers for Down syndrome or recurrent pregnancy loss

ISPD UPDATE

ES is beneficial in the following clinical situations 

• Fetus with a major single anomaly or multiple organ system anomalies
• Maternal or Paternal history of a prior undiagnosed fetus or child affected with a major single or multiple anomalies

KEY POINTS:

• ES analysis will generally require a blood sample
  • Requirements will vary by laboratory
• Results from ES will not always yield definitive, actionable results that confirm a diagnosis
  • Findings may indicate a Variant of Uncertain Significance (VUS) that may be tracked over time to determine if the variant is ultimately benign or pathogenic
  • ES testing may often be most informative when an individual’s family members are also tested or willing to be tested to clarify result interpretation
• Genetic counseling is recommended pre and post ES analysis
• Thorough informed consent process is imperative given the potential for results that may or may not be definitive

Additional Points When Considering use in Prenatal Period (ACMG)

• ES result yield is higher with
  • Accurate, comprehensive clinical information | Successful interpretation of variants dependent on accuracy of phenotype
  • Trios: Samples from mother, father and fetus that can be used for molecular analysis
• Labs should report back
  • Variants that are likely and known pathogenic
  • Consider reporting VUS “in genes that fit the fetal phenotype, especially in autosomal recessive conditions if the VUS is found in trans with a pathogenic or likely pathogenic variant”

Incidental Findings (genetic findings not related to the fetal phenotype and not on ACMG secondary findings list)

• Report highly penetrant pathogenic variants that are known to cause moderate to severe childhood onset disorders
• Do not report if there is no known fetal or childhood phenotype, even if the variant involves a severe disorder
• Do not report fetal carrier status for
  • Autosomal recessive (male and female fetuses)
  • X-linked disorders (female fetuses)

Secondary Findings (on ACMG list of known pathogenic variants that should be reported as lifesaving interventions may be available) 

• It is important that the issue of secondary findings be addressed in the consent, including if positive results should be reported for fetus only, or parents too
• ‘Opt out’ option should be available

Misattributed Parentage

• Not specific to ES, but especially with trio samples, it may come to light that a parent is not the biologic parent (e.g, mistaken paternity)
  • Critical that this possibility be included in pretest counseling and laboratories should have policies in place to deal with this issue

Reanalysis

• It may be reasonable to reanalyze results after 12 months (or sooner at the discretion of the lab) if there is no definitive answer  because
  • Children may manifest new signs and symptoms that further refine the phenotype
  • New genetic discoveries are being uploaded daily to databases and may contribute to a final molecular diagnosis

Learn More – Primary Sources:

The Promise of Whole-Exome Sequencing in Medical Genetics

ACMG: Points to Consider for Informed Consent for Genome/Exome Sequencing

10 Things Exome Sequencing Can’t Do-but Why It’s Still Powerful

ACOG Committee Opinion 682: Microarrays and Next-Generation Sequencing Technology: The Use of Advanced Genetic Diagnostic Tools in Obstetrics and Gynecology

The use of fetal exome sequencing in prenatal diagnosis: a points to consider document of the American College of Medical Genetics and Genomics (ACMG)

ACMG Recommendations for Reporting of Incidental Findings in Clinical Exome and Genome Sequencing

ISPD: Updated Position Statement on the use of genome‐wide sequencing for prenatal diagnosis

Locate a Genetic Counselor or Genetics services:

Genetic Services Locator-ACMG

Genetic Services Locator-NSGC

Genetic Services Locator-CAGC

Related ObG Topics:

ISPD, SMFM and PQF Release a Joint Position Statement on Fetal Genome-Wide Sequencing

The Chromosome – Structure and Number

The Genome and Whole Genome Sequencing

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