Somatic Reference Samples

Cancer Genomic Somatic Reference Samples

Project Goal: Develop reference samples that can be made available to the public to improve the accuracy, reliability and transparency of NGS-based oncology tests.

Project Impact:

  • Aid in efficient NGS test development and validation
  • Streamline and possibly obviate steps in the regulatory process for diagnostic companies
  • Provide transparency
  • Compress development timelines for targeted therapeutics developers

Public Comment Period Now Open Until December 6, 2018

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Draft Variants List for Review (excel) (pdf)

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Click here to download a pdf version of instructions

Cancer Genomic Somatic Reference Samples – Draft Prioritized Variant List Process for Providing Input

Public Comment Period: November 8, 2018 – December 6, 2018

The Medical Device Innovation Consortium’s Clinical Diagnostics Cancer Genomic Somatic Reference Samples working group seeks your comments on the draft list of prioritized variants.

The goal of the initiative is to develop reference samples that can be made available to the public to improve the accuracy, reliability and transparency of Next-Generation-Sequencing (NGS) based oncology tests. In addition, the samples will improve the efficiency and cost-effectiveness of accurate NGS-based test development and validation by establishing and organizing a collaborative effort to develop the needed reference samples.

Availability of reference samples will aid in efficient NGS test development and validation which will, in turn, streamline and possibly obviate steps in the regulatory process for diagnostic companies, provide transparency, and compress development timelines for targeted therapeutics developers.

The team was asked to create a prioritized list of variants that would be covered in an ideal set of reference materials. To ensure that this list identifies the most useful targets to benefit the most patients today, they drew the targets from the work of objective third parties without vested commercial interests in any particular target.  Sources should, therefore:

  • Represent current standard medical practice
  • Originate from a public sector or independent non-profit organizations
  • Represent the collective opinion of a broad swathe of clinicians and/or laboratory scientists.

The sources used included: OncoKB (oncokb.org), Clinical Interpretation of Variants in Cancer (CIViC) Knowledge base (civicdb.org), and Cancer Genome Interpreter (cancergenomeintrepreter.org)

We prioritized variants with Levels 1 and 2 clinical evidence as defined in CDRH’s tiering system for NGS. Level 1 representing those variants that are associated with approved companion diagnostics and Level 2 representing mutation with evidence of clinical significance, such as by inclusion in guidelines. Level 3 Variants will be presented later.  We also prioritized variants relevant to solid tumors.  Hemonc variants are out of the current scope.

We ask for you to review the list and answer the following questions:

  1. Are there any variants missing? Rationale why?
  2. Is there a variant on the list that should not be on the list? Rationale why?
  3. Are any of the variants miscategorized? Rationale why?

You can access the draft Levels 1 & 2 Variant list at http://mdic.org/clinicaldx/somatic-reference-samples/

REVIEW the list – please use ‘Variant UID’ when providing comments about an existing variant.

SHARE your comments – December 6, 2018 deadline

Email your comments to SRS-Variants@mdic.org

We will present the finalized list January 23, 2019, at the MDIC SRS Variant Workshop to be held at the FDA.

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Additional Resources:

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Project Proposal pdf download

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