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Lessons learnt from prenatal exome sequencing.

Natalie J Chandler1, Elizabeth Scotchman1, Rhiannon Mellis1,2

  • 1North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.

Prenatal Diagnosis
|May 4, 2022
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Summary
This summary is machine-generated.

Prenatal exome sequencing (ES) for fetal anomalies improves diagnosis. Challenges in interpretation and reporting were identified, highlighting the need for clear communication and ongoing literature review for accurate genetic diagnoses.

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Area of Science:

  • Genetics
  • Prenatal Diagnosis
  • Bioinformatics

Background:

  • Prenatal exome sequencing (ES) is increasingly used for diagnosing monogenic disorders in fetuses with structural anomalies.
  • A national trio ES service in England utilizes a 1205-gene panel to minimize incidental findings and focus variant analysis.
  • This review examines early experiences with ES service delivery, focusing on interpretation and reporting challenges.

Purpose of the Study:

  • To review early laboratory experiences with prenatal exome sequencing (ES) service delivery.
  • To identify challenges in variant interpretation and reporting within a national ES program.
  • To inform future development and optimization of prenatal diagnostic services.

Main Methods:

  • Retrospective review of laboratory records for completed prenatal exome sequencing cases.
  • Analysis of cases identified as challenging, including those with interpretation difficulties, missed diagnoses due to inheritance filtering, and lack of prenatal diagnosis.
  • Inclusion of cases with copy number variants not detectable by standard microarray analysis.

Main Results:

  • Out of 116 completed cases, 24 presented challenges, including 13 with analysis/reporting difficulties.
  • Trio inheritance filtering would have missed diagnoses in nine cases.
  • Two cases lacked a prenatal diagnosis due to pipeline sensitivity or the causative gene not being on the panel; two copy number variant cases were missed by microarray.

Conclusions:

  • Accurate variant interpretation necessitates close collaboration between referring clinicians and laboratory staff.
  • Inheritance filtering can miss approximately 5% of diagnoses, and panel analysis does not eliminate incidental findings.
  • Continuous review of scientific literature is crucial for classifying variants and improving diagnostic accuracy.