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AMP’s guideline for sequence variants in cancer

Dec. 19, 2016—The Association for Molecular Pathology published guideline recommendations for clinical laboratory professionals and oncologists that assess the status of next-generation-sequencing–based cancer tests and establish standardized classification, annotation, interpretation, and reporting conventions for somatic sequence variants. The guideline, “Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists” (Li MM, et al. J Mol Diagn. 2017;19[1]:4–23), was developed by a working group composed of representatives from major professional associations whose members provide professional testing and treatment services to cancer patients.

The increasing use of NGS technologies has raised new challenges, especially regarding how cancer-associated sequence variants are interpreted and how molecular results are reported by different clinical laboratories. To help standardize this process, AMP convened a panel of experts to develop a new set of guidelines based on evidence from a comprehensive review of published literature, empirical data, current laboratory practice surveys, feedback from multiple public meetings, and their own professional experiences. The report proposed a four-tiered system to categorize somatic sequence variations based on their clinical significance in cancer diagnosis, prognosis, and/or therapeutics:

  • Tier 1: Variants with strong clinical significance
  • Tier 2: Variants with potential clinical significance
  • Tier 3: Variants of unknown clinical significance
  • Tier 4: Variants deemed benign or likely benign

“This joint consensus recommendation represents a significant step forward in this era of precision medicine and our fight against cancer,” Marilyn M. Li, MD, vice chief of the Division of Genomic Diagnostics and director of cancer genomic diagnostics at Children’s Hospital of Philadelphia, AMP member, and chair of the multidisciplinary working group, said in a statement. “We worked diligently to ensure the cancer genomics community was well represented and it is our hope that we will soon see the widespread adoption of these guidelines leading to improved communication between molecular pathologists, oncologists, pathologists, and most importantly, patients.”

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