Thursday, March 23, 2017

CAP, AMP Release New Clinical Gene Panel Validation Guidelines; Also noted: New proposals for evidence levels in genome libraries

On March 23, 2017, CAP and AMP released a new, 25-page guideline to validation of next generation sequence panels.   The article, Jennings et al, has its journal home page here, PDF link here, and in the cloud, here.

For coverage at Genomeweb, here.

This is the fourth recent guidance for fundamental standards in next generation sequencing and data archiving.

See also Ritter et al. for guidelines on new standards for annotating and curating somatic tumor variants in libraries like ClinVar (here) and Li et al. on new standards for clinical reporting that is specific to somatic variants (here).  Li et al. note that most prior work has focused on clinical reporting of germline variants.   Finally, in May 2017, Strande et al. published guidelines for the firmness of validity or the evidence level of reported associations; this has relevance for both germline and tumor information archives; see Strande et al. here.
Though not related to somatic mutations, see also Richard et al., 2015, ACMG/AMP standards for reporting [germline] sequence variants (here), and a May 2017 paper by Invitae staff on SHERLOC, an interpretation system for germline variants (Nykamp et al.here) which is asserted to refine some ambiguities in AMP guidelines.

Abstract of Jennings et al. clipped after the break.

Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels

A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists




Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels

A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists

Jennings LJ et al. 


Article Outline