Upload
mikaia
View
54
Download
0
Tags:
Embed Size (px)
DESCRIPTION
Clinical Applications of Whole Genome/Whole Exome Sequencing. Robert L. Nussbaum, MD, FACMG Division of Genomic Medicine, UCSF AMA – November 11, 2012. Conflict of Interest Disclosures. Chair of Genomic Medicine Advisory Board of Complete Genomics, Inc. Mythical Scenario. - PowerPoint PPT Presentation
Citation preview
Clinical Applications of Whole Genome/Whole Exome Sequencing
Robert L. Nussbaum, MD, FACMGDivision of Genomic Medicine, UCSF
AMA – November 11, 2012
Chair of Genomic Medicine Advisory Board of Complete Genomics, Inc.
Conflict of Interest Disclosures
Mythical ScenarioA newborn blood spot undergoes whole genome sequencing. It is analyzed for• Personal risk for a Mendelian disorder (BRCA1)• Pharmacogenetic variants that predict efficacy, side-effects,
adverse reactions (CYP2C19 and clopidogrel)• Risk for carrying mutations that future children at risk (Ta-Sachs
carrier)• Tissue-type and Blood type (HLA, ABO)• Variants (rare and common) that increase risk for common
disorders (CFH and macular degeneration)
All the results are recorded in an EMR, communicated to his health care providers, and used to guide health care over the lifespan
Outline• Whole Genome and Whole Exome Sequencing• Factors Impeding Implementation of
WGS/WES sequencing– Limits of the Technology– Limits of Knowledge– Limits of Genetic Determinism
Evaluating A Genetic Test Patient Sample
Right result from the right patient
Test has predictive value for patient care
Results have value for the patient and doctor
There is value to society in generalizing the testing
Analytical Validity
Clinical Validity
Clinical Utility(“Actionability”)
Social Utility
Whole Genome Sequencing (WGS)CLIA ’88 Test Performance Metrics
Reportable Range: Portion of the genome from which sequence information can be reliably derived from WGS = ~96.5%
Reference Range: • Homopolymers, di- and tri-nucleotide repeats, microsatellites • Deletions and duplications ~ 100-500 bp• Single nucleotide variants sitting at the end of homopolymersAre outside the typical Reference Range of WGS
Whole Exome Sequencing (WES) by Exon Capture
Elute
Sequence
~3-5% of Exons, Promoters, Untranslated Regions, and the Bulk
of Intron Sequences are not Included in Exome Sequencing
StartStop
What Do You Miss With Whole Exome Sequencing?
5’-UTR 3’-UTR
Why Do WES Rather Than WGS?
• Because you only sequence ~2% of the genome, what you do sequence is covered to tremendous depth
• You are sequencing the part of the genome we are better at interpreting
• Current cost of WES is ~$750-$1000 versus $4,000-$10,000 for WGS
HOWEVER………
How Good are WES and WGS at Identifying Variants?
Because of False Positives, neither approach provides stand-alone “clinical grade” sequencing at the present time and Variants need to be confirmed by conventional sequencing
Increases the cost tremendously
WES for research = $750
WES for Clinical Use = $8,000 -10,000
Variants in Whole Genome Sequence
“The” Human Genome
• There is no such thing – there are only Human Genomes
• There is a “Reference Genome” in databases but it is incomplete
• Variants are defined as differences from the Reference
• The more we learn, the more we realize that there are alternative Reference Genomes
Evaluating A Genetic TestPatient Sample
Right result from the right patient
Test has predictive value for patient care
Results have value for the patient and doctor above
and beyond current practice
There is value to society in generalizing the testing
Analytical Validity
Clinical Validity
Clinical Utility(“Actionability”)
Social Utility
Clinical Validity
• Positive Predictive ValueGiven a + test, how frequently does the patient have, or how frequently will he develop the disease? (“Penetrance”)
• Negative Predictive ValueGiven a – test, how frequently is the patient unaffected and will remain so?
The Reason for the Test Matters
“Screening” a healthy executive for variants in her DNA that might be of interest
Versus
“Scanning” a child with a serious disorder for variants in her DNA that might explain
the disease and suggest therapy
Genome-Wide Association Studies in Eight Common Diseases
SNPS in a Region on Chr 9 are associated with CAD at P < 10-15
Palomaki et al.
Odds of Developing CAD Depending on 9p21 Genotype
65 year old maleNo CAD risk factors
40 year old femaleNo CAD risk factors
9p21Genotype 2 Risk 0 Risk Unknown Alleles Alleles
11% 13.2% 9.2%
2% 2.4% 1.7%
Risk for Coronary Artery Disease Events over the Next 10 Years
Palomaki et al.
PPV for 9p21 Genotype for CAD
Combine 13 SNP Loci To Generate Genetic Risk Score for CAD
Sipatti et al. A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses , The Lancet Volume 376, Issue 9750, Pages 1393-1400 (October 2010)
Frac
tion
of th
e P
opul
atio
n
Established Common Breast-Cancer Susceptibility Alleles.
Pharoah PD et al. N Engl J Med 2008;358:2796-2803.
Pharoah P et al., N Engl J Med 2008; 358:2796-803.
56 of 10M UK women carry 14 low risk alleles
(0.00056%)
7 of 10M UK women carry 14 high risk alleles
(0.00007%)
Distribution of Genetic Risk in the Population: Seven Breast Cancer Risk Alleles
(Avg. risk allele freq. = ~0.35)20,000 of 10M carry BRCA1/2 mutations
Assuming a multiplicative model for interaction between these alleles
Evaluating A Genetic TestPatient Sample
Right result from the right patient
Test has predictive value for patient care
Results have value for the patient and doctor above and beyond current practice
There is value to society in generalizing the testing
Analytical Validity
Clinical Validity
Clinical Utility(“Actionability”)
Social Utility
Clinical Utility of Genetic Testing
• Explain why a disease occurs• Institute preventive measures • Anticipate and prevent complications• Affect choice of therapy• Avoid adverse reactions• Determine risk in other family members
or in future offspring
Clinical Pharmacogenetics Implementation ConsortiumGene-Drug Pairs
Clinical Validity ✔
Clinical Utility ?
CYP2C19 genotype was not associated with modification of the effect of clopidogrel on CVD end points or bleeding…Overall there was no significant association of genotype with cardiovascular events
Individuals with 1 or more CYP2C19 alleles associated with lower enzyme activity had • lower levels of active clopidogrel metabolites • less platelet inhibition• lower risk of bleeding
Actionability: In the Eye of the Beholder
What is “Actionable Information”?How does it differ from Clinical Utility?
• Information with high Clinical Validity• Information that allows a medical decision to
be made or therapeutic action to be taken (or not).
• Founded on evidence (A real problem in genetics where diseases are rare)
• Information that informs an individual and helps him/her make health decisions
Berg J. et al. Genetics IN Medicine • Volume 13, Number 6, June 2011
“Actionability” Rating
Conclusions
1. Genetic Testing is often not straightforward and requires substantial interpretation
2. We do not know how to interpret a lot of genetic information
3. Genetic Testing is not static and what a result means can change over time.
WES/WGS only magnify the problems enormously
Barriers to the adoption of pharmacogenetic tests in clinical practice
• Fragmentation of health-care systems that preclude linking a “lifetime” genetic test result with future medical care (exception: the VA)
• Limited use of electronic medical records vital to linking test results with medication prescribing/dispensing
• Health-care systems that do not reward the prevention of disease (or adverse drug effects),
Barriers to the adoption of pharmacogenetic tests in clinical practice
• Lack of sufficient awareness about genomics on the part of many clinicians,
• Little of such testing is done preemptively and therefore the results are not available when the prescribing decision is made.
Some of these barriers will persist for many years to come.