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MG-129 Our experience of in silico gene panel testing for clinically heterogeneous disorders using exome sequencing
  1. Raveen K Basran,
  2. Christian R Marshall,
  3. Adam Shlien,
  4. Marianne Eliou,
  5. Jennifer Orr,
  6. Lynette Lau,
  7. Dimitri J Stavropoulos,
  8. Peter N Ray
  1. Molecular Genetics Laboratory, Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada

Abstract

Background The implementation of next generation sequencing technology (NGS) in a molecular diagnostics laboratory has resulted in a major transformation in service delivery. The ability to generate accurate sequence data from thousands of genes in a single experiment has facilitated the development of comprehensive gene panel tests for genetically heterogeneous disorders. Previous methodology of gene panel testing included Sanger sequencing, which was time-consuming, labour-intensive and costly and therefore restricted the number of genes that were included in a panel.

Methods/results At The Hospital for Sick Children (Toronto, Canada), we have developed and clinically validated in silico gene panels using whole exome sequencing (WES) for several heterogeneous disorders including hereditary spastic paraplegia (HSP), connective tissue and bone disorders (CT), hereditary hearing loss (HL), Noonan syndrome (NS) and autoimmune disorders (AI). Our laboratory’s current strategy of using WES has several advantages including: (1) standardised workflows that facilitate the development of additional gene panels; (2) expansion of current gene panel as new disease associations are discovered; and (3) building of an internal database of allele frequencies to aid in interpretation of variants. Through our validation studies we have shown high reproducibility and accuracy with >99% sensitivity for detection of single nucleotide variants (SNVs) and >95% for detection of small insertion/deletions (indels).

Conclusions NGS technologies have enabled our laboratory to expand our testing menu to include genes that comprise part of the differential diagnoses for several disorders which will lead to improved detection rates, increased genetic diagnoses and ultimately better clinical care.

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