Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation.

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  • Additional Information
    • Corporate Authors:
      Shariant Consortium
    • Source:
      Publisher: Cell Press Country of Publication: United States NLM ID: 0370475 Publication Model: Print Cited Medium: Internet ISSN: 1537-6605 (Electronic) Linking ISSN: 00029297 NLM ISO Abbreviation: Am J Hum Genet Subsets: MEDLINE
    • Publication Information:
      Publication: 2008- : [Cambridge, MA] : Cell Press
      Original Publication: Baltimore, American Society of Human Genetics.
    • Subject Terms:
      Databases, Genetic* ; Laboratories*; Humans ; Genetic Variation ; Australia ; Genetic Testing
    • Abstract:
      Sharing genomic variant interpretations across laboratories promotes consistency in variant assertions. A landscape analysis of Australian clinical genetic-testing laboratories in 2017 identified that, despite the national-accreditation-body recommendations encouraging laboratories to submit genotypic data to clinical databases, fewer than 300 variants had been shared to the ClinVar public database. Consultations with Australian laboratories identified resource constraints limiting routine application of manual processes, consent issues, and differences in interpretation systems as barriers to sharing. This information was used to define key needs and solutions required to enable national sharing of variant interpretations. The Shariant platform, using both the GRCh37 and GRCh38 genome builds, was developed to enable ongoing sharing of variant interpretations and associated evidence between Australian clinical genetic-testing laboratories. Where possible, two-way automated sharing was implemented so that disruption to laboratory workflows would be minimized. Terms of use were developed through consultation and currently restrict access to Australian clinical genetic-testing laboratories. Shariant was designed to store and compare structured evidence, to promote and record resolution of inter-laboratory classification discrepancies, and to streamline the submission of variant assertions to ClinVar. As of December 2021, more than 14,000 largely prospectively curated variant records from 11 participating laboratories have been shared. Discrepant classifications have been identified for 11% (28/260) of variants submitted by more than one laboratory. We have demonstrated that co-design with clinical laboratories is vital to developing and implementing a national variant-interpretation sharing effort. This approach has improved inter-laboratory concordance and enabled opportunities to standardize interpretation practices.
      Competing Interests: Declaration of interests The authors declare no competing interests.
      (Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
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    • Contributed Indexing:
      Investigator: L Akesson; R Allcock; K Ashton; DA Bell; A Brown; M Buckley; JR Burnett; L Burrows; A Byrne; E Chan; C Cliffe; R Clifton-Bligh; S Dooley; M Fanjul Fernandez; E Farnsworth; T Ha; D Henry; D Holds; K Holman; M Jackson; S Kang; C Luxford; S McManus; R Mehrtens; C Meldrum; D Mossman; SJ Pantaleo; D Phelan; E Pontikinas; A Ravine; T Roscioli; R Scott; K Simons; O Vanwageningen
    • Publication Date:
      Date Created: 20221104 Date Completed: 20221108 Latest Revision: 20230504
    • Publication Date:
      20231215
    • Accession Number:
      PMC9674965
    • Accession Number:
      10.1016/j.ajhg.2022.10.006
    • Accession Number:
      36332611