Pathology Checklist a First for Next Generation Sequencing Laboratory Standards

A gold standard molecular pathology checklist has been revised to include a dedicated section on next generation sequencing (NGS), the first published laboratory accreditation checklist that addresses NGS, advancing standardized practice in genomic testing.

The College of American Pathologists (CAP; Northfield, IL, USA), the largest association of board-certified pathologists and a global leader in laboratory quality assurance, has now published the new edition of the CAP Laboratory Accreditation Program checklists, released July 31, 2012. CAP checklists are used to guide accreditation of more than 7,000 laboratories in the US 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 at the University of Utah, and Medical Director for Genomics and Bioinformatics at ARUP Laboratories (Salt Lake City, UT, USA). Dr. Voelkerding led the CAP working group that created the NGS section of the molecular pathology checklist. 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 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 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 NGS and yet not being overly prescriptive to accommodate the differences in the technology platforms and the growth of the rapidly evolving technology”.

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.

Related Links:
College of American Pathologists
ARUP Laboratories