CAP publishes revised version of molecular pathology checklist with dedicated section on NGS

The College of American Pathologists (CAP) published a revised version of its molecular pathology checklist with a dedicated section on next generation sequencing (NGS) as part of the new edition of the CAP Laboratory Accreditation Program checklists released July 31, 2012. The CAP is the first to publish an accreditation checklist that addresses NGS, advancing standardized practice in genomic testing.

CAP checklists are used in the accreditation process to help laboratories meet Centers for Medicare and Medicaid Services (CMS) requirements. CMS regulates all human clinical laboratory testing, other than research and clinical trials, in the United States through the Clinical Laboratory Improvement Amendments (CLIA). The CAP accredits more than 7,000 laboratories in the United States and abroad.

"Pathologists, trained to provide medical direction of NGS testing, and the CAP, experienced in laboratory quality assurance programs, are not only leading this NGS initiative, but collaborating with other medical organizations to advance the science of genomic medicine," said Karl V. Voelkerding, MD, FCAP, Professor of Pathology, University of Utah, and Medical Director for Genomics and Bioinformatics, ARUP Laboratories, Salt Lake City, Utah. Dr. Voelkerding is the CAP member lead of the CAP's NGS Working Group that created the NGS section of the molecular pathology checklist.

"The publication of this checklist demonstrates CAP's leadership in advancing standards of practice in genomic medicine," said Nazneen Aziz, PhD, Director of Molecular Medicine and CAP staff lead for the CAP's NGS Working Group. "The workgroup was judicious in developing the requirements by creating the necessary framework for clinical testing using next generation sequencing and yet not being overly prescriptive to accommodate the differences in the technology platforms and the growth of the rapidly evolving technology".

The new NGS section has 18 requirements that address the analytical wet bench process including conversion of DNA into a NGS library followed by sequencing, and the subsequent bioinformatics analyses comprised of sequence alignment and mapping, variant calling, and annotation.

The CAP's efforts to further advance clinical testing using NGS go beyond accreditation and will include development of NGS proficiency testing products in the near future. The CAP supports and continues to work with other organizations, including the American College of Medical Genetics and Genomics (ACMG), the Association for Molecular Pathology (AMP), and Health Level 7 (HL-7), to develop standards for reporting genetic variants, for their interpretation for clinical use and interoperability of results in healthcare information systems.