Genetic Testing for the Clinician James Strait M

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

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

National Institute on Aging National Institutes of Health Baltimore Longitudinal Study of Aging Sardi. NIA 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 A 2 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 1. Effectiveness of Plavix depends on activation to an active metabolite by the cytochrome P 450 (CYP) system, principally CYP 2 C 19 2. Tests are available to identify a patient's CYP 2 C 19 genotype and can be used as an aid in determining therapeutic strategy.

1. What is CYP 2 C 19 and what are we measuring? • CYP 2 C 19 = gene • We typically measure a SNP (single nucleotide polymorphism) within the gene

What is a SNP? Single-Nucleotide Polymorphism CYP 2 C 19 Example: 85% of population has major allele G rs 4244285 15% has minor allele A Poor Metabolizers From Wikipedia Commons, David Hall (Granger)

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

Spectrum of Clinical Genetic Testing 1. Rare Mutation Testing – Test for rare mutations in single genes associated with rare diseases; sequence gene for mutation Clinics Today 2. Common Polymorphism Testing (SNP) – Test for SNPs/markers in genes with small individual effects associated with common diseases 3. Sequencing Entire Genome/Exome Future Clinical

SNPs in Candidate Genes Patient in Cath Lab, use 25 ul 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/ 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