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.