Genetic Testing for the Clinician James Strait M.D., Ph.D. Head, Human Cardiovascular Studies Lab of Cardiovascular Sciences National Institute on Aging National Institutes of Health

I have no real or apparent conflicts of interest to report. James Strait, MD, PhD I have no real or apparent conflicts of interest to report.

National Institute on Aging National Institutes of Health Baltimore Longitudinal Study of Aging SardiNIA Study

DNA

The modern era of Genetic Medicine Rare vs. Common Diseases Cystic Fibrosis Hypertension CFTR Gene Adenosine Deaminase Alpha Adducin Gamma Adducin Adrenomedullin Adenosine A2 Receptor Beta Adrenergic Receptor MANY, MANY MORE (116) Rare Diseases (e.g. Cystic Fibrosis) are due to changes in single genes Common diseases (e.g. Hypertension) result from changes in multiple genes that have small effects in isolation but can lead to disease when interacting with one another and the environment

So, what Is the Minimum that a clinician needs to know About Genetic Testing?

Deciphering the FDA Clopidogrel Black Box Warning Effectiveness of Plavix depends on activation to an active metabolite by the cytochrome P450 (CYP) system, principally CYP2C19. Tests are available to identify a patient's CYP2C19 genotype and can be used as an aid in determining therapeutic strategy.

1. What is CYP2C19 and what are we measuring? CYP2C19 = gene We typically measure a SNP (single nucleotide polymorphism) within the gene

What is a SNP? Single-Nucleotide Polymorphism CYP2C19 Example: 85% of population has major allele G rs4244285 Poor Metabolizers 15% has minor allele A From Wikipedia Commons, David Hall (Granger)

Marker SNPs & Causal SNPs Haplotype Blocks Blocks of DNA tend to stay together throughout recombination Linkage A nucleotide on same block of DNA can be used as a marker Linkage analysis; Wellcome Trust Website 20/3/03. Richard Twyman Ardie et al. Nature Reviews, 3, 299-309 (April 2002)

Spectrum of Clinical Genetic Testing Rare Mutation Testing Test for rare mutations in single genes associated with rare diseases; sequence gene for mutation Common Polymorphism Testing (SNP) Test for SNPs/markers in genes with small individual effects associated with common diseases Sequencing Entire Genome/Exome Clinics Today Future Clinical

SNPs in Candidate Genes Patient in Cath Lab, use 25ul blood, get point of care test results in 60 minutes <$50

Genome Wide Association Studies (GWAS) $200 Measure 2 million SNPs across genome Can now look at copy number variation, etc Christensen and Murray, NEJM, 2007

Advances in Genome Sequencing Sanger Method $3,000,000,000/ genome Step-Over” Repeated Segments of DNA Sequence short fragments in parallel fashion Reassemble short sequenced fragments Use Physical Location to id unique reads Next Generation Sequencing $5,000/genome

Exome Sequencing $1500 Exons are the genomic DNA parts translated into protein 180,000 exons: about 1% of the human genome = 30 (Mb) Constitute about 85% of the disease-causing mutations From: Wikipedia Commons, Sarah Kusala Exome Sequencing

Whole Genome Sequencing $5000 (intentionally left small)

Epigenome

Thank you

Additional slides

Types of Genetic Changes Coding vs. Non Coding Causal variant vs. marker Types of genetic changes Polymorphisms Mutations structural variants tissue-specific epigenetic DNA methylation, histone modifications, and chromatin state

How SNPs are measured Schematic showing blood to tube to cells to DNA to sequence to machine

Currently useful tests

Definitions: Mutation vs. Polymorphism Mutation: <1% of time Often has functional effects Polymorphism: >1% of time Define SNP