Missing: Patient phenotype and identity Another confl ict is that only about 0.05% of the databases contain phe- notypes, apparently for HIPAA and political correctness considerations. Omissions may also include identifi cation of the disease understudy in the data set. Slow data sharing is a related problem.
Databases usually claim that the patient data are “de-identified,” but several lectures pointed out that phenotype or ethnic group is an im- portant variable. Databases have other difficulties. Dr. Karen Eilbeck of the University of Utah (Salt Lake City) discussed problems with variant files and data. Files are not typed consistently (e.g., chromosome 1, chr1, or 1). Semantic inconsistences are common, e.g., the same word might have several meanings, or many words are used synonymously. Research databases are not compatible with health provider IT. Different assembly versions of the genome often correct errors in position, so one should be clear about which database version is used. These and other potential and often invisible inconsistencies make it difficult for diagnostic labs to exchange or compare interlaboratory results.
Clinical genomics will be a much more complicated and information-rich topic than most envision today.
Credits
This report focused on the current state-of-conflict in adoption of clinical genomics. The conference cast a wider net, including exogenous RNA, differential expression and classification of cis and trans eQTLs (ex- pression quantitative trait loci), standard reference materials, newborn screening, entrepreneurship, etc.
These topics added color to the main program, and showed that clinical genomics will be a much more complicated and information-rich topic than most envision today. The staff of Cambridge Healthtech Institute (CHI), in particular, Mary Ann Brown, deserve special credit for orga- nizing a strong, multifaceted technical program and for managing the creature comforts that are essential for a great meeting.
References 1. Hagenkord, J. “The changing definition of utility in the era of genetic abundance”; Lecture, Clinical Genome Conference, June 10–12, 2014, San Francisco, CA.
2. O’Daniel, J. “Making meaning from genome sequencing”; Lecture, Clinical Genome Conference, June 10–12, 2014, San Francisco, CA.
Robert L. Stevenson, Ph.D., is Editor, American Laboratory/Labcompare; e-mail:
rlsteven@yahoo.com.
AMERICAN LABORATORY • 33 • SEPTEMBER 2014
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