2023 ACMG Annual Clinical Genetics Meeting Digital Edition: Poster Gallery-Clinical RNA Sequencing to Clarify Variants of Uncertain Significance and Identify Missing Variants

Pdf Summary

Clinical genetic testing often results in the identification of variants of uncertain significance (VUS) or fails to detect disease-causing variants in suspected genes. Therefore, there is a need for clinical testing to clarify uncertain or nondiagnostic results. This study aimed to determine the best utilization of clinical RNA sequencing in the pediatric population and how RNA sequencing results would impact variant and clinical interpretation.<br /><br />The results of sequenced samples found that clinical RNA sequencing can clarify VUSs identified by prior genetic testing, but the number of easily testable genes is limited due to tissue-specific expression. The study also found the highest yield in evaluating variants suspected to alter splicing, but the decay of aberrant transcripts may affect reporting. Variance in reporting criteria by clinical laboratories is likely to affect results, and reporting standards may be needed. Identifying individuals who would benefit from RNA sequencing can be challenging.<br /><br />Only 2 out of 9 results were reported as positive, but 5 out of 9 were considered clinically positive, indicating unique challenges when counseling on the utility of RNA sequencing. Therefore, consultation with a genetic counselor or medical geneticist is recommended prior to ordering RNA sequencing and for result interpretation.<br /><br />The study included cases with VUSs or no candidate variants identified by prior testing. Inclusion criteria for sequenced samples included VUS clarification, deep intronic variants predicted to affect splicing, missing second variants in recessive conditions, suspicion of X-linked disorders with negative prior testing, and high suspicion for a specific genetic biochemical disease. The workflow involved sequencing, case submission, sample collection, and family consent.<br /><br />The study presented indeterminate and positive results. The indeterminate result involved a deep intronic variant in the ZEB2 gene in a patient with a high suspicion of Mowat-Wilson syndrome. The positive result involved a CTC1 splice variant in a patient with poikiloderma and Coats plus disease.<br /><br />In conclusion, clinical RNA sequencing can help clarify VUSs from prior genetic testing, but challenges exist in determining the utility and interpretation of results. Further research and consultation with genetic professionals are necessary for effective implementation of RNA sequencing in the clinical setting.

Asset Subtitle

Presenting Author - Jennifer Cech, PhD MS CGC; Co-Author - Danny E. Miller, MD, PhD; Co-Author - Cate R. Paschal, PhD, FACMG; Co-Author - Bri Dingmann, MS, CGC; Co-Author - Anna I. Scott, PhD, FACMG; Co-Author - Jenny Thies, MS, CGC; Co-Author - Maria R. Mills, MS; Co-Author - Lawrence Merritt, II, MD; Co-Author - Ghayda M. Mirzaa, MD; Co-Author - James T. Bennett, MD, PhD; Co-Author - Ian A. Glass, MBChB, MD, FACMG; Co-Author - Darci L. Sternen, MS, CGC; Co-Author - Heather C. Mefford, MD PhD;

Meta Tag

Bioinformatics

Companion Diagnostics

Genomic Methodologies

NextGen Sequencing

Sequencing

Variant Detection

Co-Author Danny E. Miller, MD, PhD

Co-Author Cate R. Paschal, PhD, FACMG

Co-Author Bri Dingmann, MS, CGC

Co-Author Anna I. Scott, PhD, FACMG

Co-Author Jenny Thies, MS, CGC

Co-Author Maria R. Mills, MS

Co-Author Lawrence Merritt, II, MD

Co-Author Ghayda M. Mirzaa, MD

Co-Author James T. Bennett, MD, PhD

Co-Author Ian A. Glass, MBChB, MD, FACMG

Co-Author Darci L. Sternen, MS, CGC

Co-Author Heather C. Mefford, MD PhD

Presenting Author Jennifer Cech, PhD MS CGC

Keywords

clinical genetic testing

variants of uncertain significance

disease-causing variants

clinical testing

clinical RNA sequencing

pediatric population

variant interpretation

splicing variants

reporting standards

genetic counselor