Personalized Personalized MedicineMedicineWilliam SchwarzWilliam Schwarz

BackgroundBackground

Goal: To measure the risk an individual Goal: To measure the risk an individual has of contracting a disease based on has of contracting a disease based on their genetic makeup.their genetic makeup.

How is this done?How is this done? Using genotyping technology an individual’s Using genotyping technology an individual’s

genome can be analyzed against a general genome can be analyzed against a general population to determine differences.population to determine differences.

These differences can then be compared to These differences can then be compared to association studies of various diseases to association studies of various diseases to determine if this individual has an increased determine if this individual has an increased risk due to variation in their genetic structure.risk due to variation in their genetic structure.

Existing CompaniesExisting Companies 23 and me23 and me deCODEmedeCODEme NavigenicsNavigenics Etc..Etc.. These companies utilize SNP mapping These companies utilize SNP mapping

chips that have probes that bind to chips that have probes that bind to particular SNP versions. Fluorescent particular SNP versions. Fluorescent markers glow so that the chips can be markers glow so that the chips can be visually analyzed for SNP variations.visually analyzed for SNP variations. 23 and me analyzes 550,000 SNPs23 and me analyzes 550,000 SNPs deCODEme analyzes 1 million (using Illumina deCODEme analyzes 1 million (using Illumina

Human 1M Beadchip)Human 1M Beadchip)

DiseasesDiseases Abdominal aneurysmAbdominal aneurysm Alzheimer's diseaseAlzheimer's disease AtrialAtrial fibrillation fibrillation Brain aneurysmBrain aneurysm Breast cancerBreast cancer Celiac diseaseCeliac disease Colon cancerColon cancer Crohn'sCrohn's disease disease Deep vein thrombosisDeep vein thrombosis Diabetes, type 2Diabetes, type 2 GlaucomaGlaucoma Graves' diseaseGraves' disease Heart attackHeart attack HemochromatosisHemochromatosis Lactose intoleranceLactose intolerance Lung cancerLung cancer LupusLupus Macular degenerationMacular degeneration MelanomaMelanoma Multiple sclerosisMultiple sclerosis ObesityObesity OsteoarthritisOsteoarthritis Prostate cancerProstate cancer PsoriasisPsoriasis Restless legs syndromeRestless legs syndrome Rheumatoid arthritis Rheumatoid arthritis Sarcoidosis Sarcoidosis Stomach cancer, diffuse Stomach cancer, diffuse

From Navigenics.comFrom Navigenics.com Criteria for disease Criteria for disease

selectionselection These diseases have causal These diseases have causal

SNPs verified by multiple SNPs verified by multiple studies studies

The diseases must be The diseases must be possible to act on.possible to act on.

Other companies’ policies Other companies’ policies may vary.may vary.

AssumptionsAssumptions

From project description:From project description: Use 2 disease mutations each increasing an Use 2 disease mutations each increasing an

individuals risk by 20%individuals risk by 20% Assume a 5% frequency for the disease in the Assume a 5% frequency for the disease in the

population.population. Other assumptionsOther assumptions

Assume only these two SNP mutations affect the Assume only these two SNP mutations affect the disease risk.disease risk.

Assume MAF of 25%.Assume MAF of 25%. Risk Factors behave independently (joint Risk Factors behave independently (joint

conditional probabilities can be represented as conditional probabilities can be represented as products).products).

Using our AssumptionsUsing our Assumptions

RR(x1) = 1.20RR(x1) = 1.20 F = 0.05F = 0.05 p = 0.25p = 0.25 The risk to someone who has the SNP is The risk to someone who has the SNP is

RR*F = 0.06 or 6% of contracting the RR*F = 0.06 or 6% of contracting the diseasedisease

With MAF of 0.25, 25% of the With MAF of 0.25, 25% of the population has the allele.population has the allele.

How do these values change when How do these values change when analyzing multiple SNPs?analyzing multiple SNPs?

Measuring WorthMeasuring Worth Is this SNP worth testing?Is this SNP worth testing? General Rules for choosing a SNP to test.General Rules for choosing a SNP to test.

Prevalence of risk allelePrevalence of risk allele Low p value correlation (< 0.001 lower the Low p value correlation (< 0.001 lower the

better)better) High relative risk High relative risk Validated studies showing correlationValidated studies showing correlation

We can pick a lower bound to represent a We can pick a lower bound to represent a SNP being worth testingSNP being worth testing >5% prevalence in the population >5% prevalence in the population RR > 2.0RR > 2.0

Easy ProjectEasy Project

Compute risks for multiple disease Compute risks for multiple disease mutations assuming independence.mutations assuming independence.

Combining risk from multiple markers Combining risk from multiple markers is done as the product of the estimates is done as the product of the estimates from the individual markers.from the individual markers. RR(x1,x2) = RR(x1)RR(x2)RR(x1,x2) = RR(x1)RR(x2) (Note) This is assuming independence(Note) This is assuming independence So Pr(A|x1, x2) = Pr(A|x1)Pr(A|x2)/Pr(A) So Pr(A|x1, x2) = Pr(A|x1)Pr(A|x2)/Pr(A)

and Pr(x1, x2) = Pr(x1)Pr(x2)and Pr(x1, x2) = Pr(x1)Pr(x2)

ResultsResults Now that we know the relative Now that we know the relative

risk for a specific genotype we risk for a specific genotype we can take what an individual has can take what an individual has and analyze.and analyze.

Going back to the original Going back to the original assumptionsassumptions

RR(x1) = 1.20, RR(x2) = 1.20RR(x1) = 1.20, RR(x2) = 1.20 RR(x1,x2) = RR(x1)RR(x2)RR(x1,x2) = RR(x1)RR(x2) Overall risk = 1.20 * 1.20 = 1.44Overall risk = 1.20 * 1.20 = 1.44 1.44*F (avg. population risk) = 1.44*F (avg. population risk) =

Individuals riskIndividuals risk 1.44*0.05 = 0.072 or 7.2% 1.44*0.05 = 0.072 or 7.2%

chance of having the disease.chance of having the disease.Individual hasIndividual has RR(x1)RR(x1) RR(x2)RR(x2) Total RRTotal RR FF Total RiskTotal Risk

(-x1,-x2)(-x1,-x2) 1.01.0 1.01.0 1.01.0 0.050.05 0.050.05

(x1, -x2)(x1, -x2) 1.21.2 1.01.0 1.21.2 0.050.05 0.060.06

(-x1, x2)(-x1, x2) 1.01.0 1.21.2 1.21.2 0.050.05 0.060.06

(x1, x2)(x1, x2) 1.21.2 1.21.2 1.441.44 0.050.05 0.0720.072

Individual hasIndividual has MAF x1MAF x1 MAF x2MAF x2total total

MAFMAF

(-x1, -x2)(-x1, -x2) 0.750.75 0.750.75 0.56250.5625

(x1, -x2)(x1, -x2) 0.250.25 0.750.75 0.18750.1875

(-x1, x2)(-x1, x2) 0.750.75 0.250.25 0.18750.1875

(x1, x2)(x1, x2) 0.250.25 0.250.25 0.06250.0625

Results (cont.)Results (cont.)

Lets look at another exampleLets look at another example SNP A(x1, x2) and SNP B(y1,y2)SNP A(x1, x2) and SNP B(y1,y2) A has MAF 0.20, RR 2.0(per instance)A has MAF 0.20, RR 2.0(per instance) B has MAF 0.40, RR 1.5(per instance)B has MAF 0.40, RR 1.5(per instance)

AA BB MAFMAF RRRR BB MAFMAF RRRR BB MAFMAF RRRR

(x1, (x1, x2)x2)

(-y1,-(-y1,-y2)y2)

0.0140.01444 44

(-y1, (-y1, y2y2))

0.0190.01922 66

(y1, (y1, y2y2))

0.0060.00644 99

(-x1, (-x1, x2)x2)

(-y1,-(-y1,-y2)y2)

0.1150.11522 22

(-y1, (-y1, y2y2))

0.1530.15366 33

(y1, (y1, y2y2))

0.0510.05122 4.54.5

(-x1, -(-x1, -x2)x2)

(-y1,-(-y1,-y2)y2)

0.2300.23044 11

(-y1, (-y1, y2y2))

0.3070.30722 1.51.5

(y1, (y1, y2y2))

0.1020.10244 2.252.25

ThoughtsThoughts Having multiple mutations has a multiplicative instead of Having multiple mutations has a multiplicative instead of

additive effect.additive effect. This means that the more mutations that can be tested will This means that the more mutations that can be tested will

give a better understanding and a higher risk value.give a better understanding and a higher risk value. In our previous examples it would require 4 SNPs with RR of In our previous examples it would require 4 SNPs with RR of

1.2 to meet the overall RR of 2.0.1.2 to meet the overall RR of 2.0. However, the more SNPs we analyze the lower chance of an However, the more SNPs we analyze the lower chance of an

individual having all of them.individual having all of them. For the 2 SNPs in the example the prob of having both is 0.0625 For the 2 SNPs in the example the prob of having both is 0.0625

so we are above the threshold but if we add another SNP we so we are above the threshold but if we add another SNP we would drop to 0.015625 which is below our thresholdwould drop to 0.015625 which is below our threshold

SNPs that we definitely want to test for have high RR and SNPs that we definitely want to test for have high RR and a relatively small MAF.a relatively small MAF. These SNPs have a high impact on the total risk and are the These SNPs have a high impact on the total risk and are the

major SNPs in a group of SNPs that are associated with a major SNPs in a group of SNPs that are associated with a disease.disease.

Future WorkFuture Work

Analyze risk using different models.Analyze risk using different models. This analysis was done using the This analysis was done using the

multiplicative model. multiplicative model. Dominant modelDominant model Recessive modelRecessive model

Estimate the variance of the risk.Estimate the variance of the risk.

Individual MarkersIndividual Markers Sample Analysis (Using the multiplicative model)Sample Analysis (Using the multiplicative model) GivenGiven

Rs1799950 CEU pop SNP freq AA-0.9167 GG-0.0000 AG-Rs1799950 CEU pop SNP freq AA-0.9167 GG-0.0000 AG-0.0833 A-0.9583 G-0.04170.0833 A-0.9583 G-0.0417

Odds ratio calculated at 1.72 (Breast Cancer)Odds ratio calculated at 1.72 (Breast Cancer) G is the risk alleleG is the risk allele

AnalysisAnalysis p = Pr(G), q = Pr(A)p = Pr(G), q = Pr(A) Pr(GG) = p^2 = 0.00, Pr(AG) = 2pq = 0.08, Pr(AA) = q^2 Pr(GG) = p^2 = 0.00, Pr(AG) = 2pq = 0.08, Pr(AA) = q^2

= 0.92= 0.92 R(GG) = 1.72^2 = 2.9584, R(AG) = 1.72, R(AA) = 1.0R(GG) = 1.72^2 = 2.9584, R(AG) = 1.72, R(AA) = 1.0 R = 0*2.9584 + 0.08*1.72 + 1*0.92 = 1.0576 (baseline R = 0*2.9584 + 0.08*1.72 + 1*0.92 = 1.0576 (baseline

risk)risk) RR(GG) = 2.9584/1.0576 = 2.80, RR(AG) = 1.72/1.0576 = RR(GG) = 2.9584/1.0576 = 2.80, RR(AG) = 1.72/1.0576 =

1.63, RR(AA) = 1/1.0576 = 0.951.63, RR(AA) = 1/1.0576 = 0.95

ResourcesResources

SNPedia (http://www.snpedia.com)SNPedia (http://www.snpedia.com) SNP Nexus (http://snp-nexus.org)SNP Nexus (http://snp-nexus.org)

Using sites like these an individual Using sites like these an individual can calculate their own risks if they can calculate their own risks if they receive their genetic information.receive their genetic information.