College of American Pathologists

  Shorts on Standards


CAP Today




September 2010

The CAP has 30 official liaisons to various organizations who attend scientific meetings or designate others to do so. They report to the Standards Committee, which reports to the Council on Scientific Affairs. We began recently to publish on a periodic basis bits of what the CAP’s outbound liaisons hear and see in their liaison roles.

Clinical genetics meeting update

Gaurav Sharma, MD
Jeffrey A. Kant, MD, PhD

The Annual Meeting of the American College of Medical Genetics brings together medical professionals whose focus is genetically influ-enced health problems with researchers active in the discovery and treatment of genetic disorders. The most recent meeting (Albuquerque, March 24–28) was held in conjunction with the Annual Meeting of the Society for Inherited Metabolic Diseases.

Several presentations described the use of high-resolution microarrays that detect copy number variants (CNVs) to identify contiguous gene and microdeletion syndromes as well as other disorders. Both commercial and academic laboratories are now moving toward oligonucleotide arrays that detect single nucleotide polymorphisms and regions of homozygosity in addition to CNVs. A new and important theme of this year’s meeting was the application of next-generation sequencing of clinical samples. This is a prelude to full genome sequencing, for $1,000 or less, probably by the end of this decade. Also discussed was the use of informatics tools to assist in the appropriate ordering of genetic tests and in communicating results to clinicians.

The genetics field continues to grapple with how to assess the clinical significance of broad genetic variation in individual patients. There is reimbursement resistance from payers, who are demanding data demonstrating clinical validity and utility. A consortium of laboratories called the International Standard Cytogenomic Array Consortium has been assembled to construct a database of all abnormalities identified (including raw data files), with phenotypic, demographic and other information if available. A document in preparation will cover when such arrays are appropriate for constitutional disorders. The Human Variome Project is also assembling genotypic and phenotypic information in a central repository, in collaboration with groups interested in specific diseases (for example, gastrointestinal carcinoma). These efforts demonstrate the continued expansion of work around genetic variation, and its extension from germline to somatic disorders, especially cancer.

This year’s meeting showcased present and emerging laboratory genetics methods, the need for advances in converting large amounts of raw “data” into clinically useful “information,” and the importance of interdisciplinary groups in advancing the field of genomics. A new term, “genomicist,” was coined to describe a health care professional who could put all this together. Although it is unlikely this level of expertise will be required of practicing pathologists, there will be many opportunities for pathologists to answer clinicians’ questions about laboratory applications in genomics. This is especially true because the supply of clinical geneticists and genetic counselors is likely to remain limited. Look to the CAP to continue providing helpful resources to keep the membership current in this area.

Dr. Sharma is a member of the CAP Standards Committee and an informatics fellow in the Department of Pathology, University of Pittsburgh Medical Center. Dr. Kant, also of the Department of Pathology at the University of Pittsburgh Medical Center, serves as the CAP’s outbound liaison to the American College of Medical Genetics.