Genomics 101

Murugu Manickam, MD discloses no significant financial interests or other relationships with commercial interests. Presentation will not include discussion of commercial products or services and will not include unapproved or off-label usage of a commercial product or device.

The following planning committee members have no significant financial interests or relationships with commercial interests to disclose, their educational unit does not have a financial interest or affiliation with an organization that may receive direct benefit from the subject of the proposed CME activity, and they will not be personally compensated for their role in the planning or execution of this proposed CME activity by an organization other than The Ohio State University: Amy Ehrlich, MA and Henry Zheng, PhD, MBA

Murugu Manickam, MDClinical Assistant ProfessorDivision of Human Genetics

Genetics and Genomics • Genetics

– Rare disease oriented– Single gene– Absolute risk– Direct results

– Examples: Breast cancer and BRCA1/2: 70-80% chance of developing breast or ovarian cancer

• Genomics– Common disease oriented– Multiple genes– Relative risk– Currently indirect

inference

– Example: Celiac disease and HLA type: at highest 6% chance of developing celiac disease

Genes

• Humans have only about 23,000 genes in 6 billion base pairs (2 copies)– FYI: Frogs and wheat have more genes

• Humans are about 99.5% similar to each other

– About 3 million base pairs on average difference

Some Differences Travel TogetherA-C-T-A-G-C-T-A-G-C-T-A-C-G-T-G-A-C-A-A-C-G-T-G-A-C-A-T-AA-C-T-A-G-C-T-A-G-C-T-A-C-G-T-G-A-C-A-A-C-G-T-G-A-C-A-T-A

A-C-T-A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-C-T-A-G-C-T-A-G-C-T-A-C-G-T-G-A-C-A-A-C-G-T-G-A-C-A-T-A

A-C-T-A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-C-T-A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-A

A-C-T-A-G-C-T-A-G-C-T-A-C-G-T-G-A-C-A-A-C-G-T-G-A-C-A-T-AA-C-T-A-G-C-T-A-G-C-T-A-C-G-T-G-A-C-A-A-C-G-T-G-A-C-A-T-A

• Take a small stretch of DNA- the differences tend to be common differences between any two people

• If you have a G at position 5, you will have a C at 13 and an A at 25; if you have a T at position 5, it is an A and G respectively

HAP-MAP Project• Too expensive to look at every single base

pair, so a short cut was developed- look at the areas that are different

• Hap-Map project looked first at four ethnically diverse populations and then compared them as to which changes traveled together

Single Nucleotide Polymorphism

• Caucasians from Utah have mostly the GCA combo- only measure the G and you know the other two spots

• Yoruba from western Africa have the TAG combo- only measure the T and you know the other two spots

• This reduced the number of places you had to look to look for differences down to about 1 million single nucleotide polymorphisms (SNPs)

A-C-T-A-G-C-T-A-G-C-T-A-C-G-T-G-A-C-A-A-C-G-T-G-A-C-A-T-AA-C-T-A-G-C-T-A-G-C-T-A-C-G-T-G-A-C-A-A-C-G-T-G-A-C-A-T-A

A-C-T-A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-C-T-A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-A

• It became cheap to compare large populations using a 1 million SNPs by technology on a chip platform– About $1000 x 10,000 samples would cost= $10 Million to tell the

common differences between cases and controlsCases of disease X

A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-T-C-T-A-G-G-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-A

A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-C-T-A

A-T-C-T-A-G-G-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-A-T-A

A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-T-C-T-A-G-G-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-A

A-T-C-T-A-G-G-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-AA-T-C-T-A-G-C-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-A

Controls without disease X

A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-AA-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-A

A-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-AA-T-C-T-A-G-C-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-A

A-T-C-T-A-G-C-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-AA-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-A

A-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-AA-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-A

A-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-A-T-AA-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-C-T-A

Genome Wide Association Studies

Cases of disease XA-T-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-A

A-T-C-T-A-G-G-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-A-T-A

A-A-C-T-A-G-C-T-A-A-G-T-G-A-C-A-A-C-G-T-G-G-C-C-T-A

Controls without disease XA-T-C-T-A-G-G-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-A

A-A-C-T-A-G-C-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-AA-T-C-T-A-G-C-T-A-A-G-T-G-A-C-G-A-C-G-T-G-G-C-C-T-A

• SNP #16- A appears to increase risk for the disease

• Maybe SNP #24 also but less frequently

Genome Wide Association Studies

– First large study to show this was for macular degeneration where a certain SNP, tripled your risk for the development of wet macular degeneration (Odds ratio of 3.5)

• The SNP was in a gene associated with inflammation so this made some biological sense

– However, no studies have achieved this same significant odds ratio- most show a modest increase between 1.2 and 2 [see primer on risk assessment]

– But it was relatively cheap (now less than $500) and easy to do

Genome Wide Association Studies

Weaknesses of GWA Studies• Associations only, not causation

– Not always in a gene

• Replication is absolute requirement – Need large populations to pick out small effects (more than

50,000 patients plus controls)

• Dependent on the data collected– Significant problem with definition of schizophrenia in older

studies

• Not applicable to non-Europeans as of now• Not consistent with evolution theory

Copy Number Variant

• When multiple people were fully sequenced, there were more differences in the number of copies of some genes than in the sequence of the gene

• Multiple copies of the gene influence regulation and may allow minor mutations to go unnoticed

Extra/Missing copies

• Charcot Marie Tooth disease (foot neuropathy with poor sensation)– When you have missing copy of the PMP22

gene

• Hereditary neuropathy with liability to pressure palsy (hereditary carpel tunnel syndrome)– When you have an extra copy of the PMP22

gene

Copy Number Variant• Many more dosage effects noted

especially with deletions leading to mental retardation and seizures disorders

• Now seeing links to autism as well

• But can be protective as was occurs with Spinal Muscular Atrophy where an “old” version of the gene has some protective effects if the primary copy has a mutation

Then and Now and TomorrowCost

Circa 2000Human Genome Project (multi-center) cost $3 billion for one person’s whole sequence (poor quality)

2010– Can do in a

commercial lab for around $15000 (low quality)

Circa 2015– Will do in an

office setting for less than $500 (high quality)

Then and Now and TomorrowTime

Circa 2000– Human

Genome Project took 9 years

2010– Can do in a

commercial lab for in about 6-10 weeks

Circa 2015– Will do in an

office setting in 15 minutes

Then and Now and TomorrowComparison to Others

Circa 2000– No

comparison on sequence available

2010– About 5000

people have been fully sequenced

Circa 2015– More than 100

million people will likely be sequenced

Sequencing

• Shortcut– Exon sequencing: only looking at the

“functional” part of the genome that codes proteins

• Very popular because it is cheaper and more focused than sequencing everything

• In several diseases the gene/genetic mutation has been found (rare diseases)

Sequencing• Whole genome sequencing

– Enormous amount of data (5TB at poor quality sequencing)

– Not enough “normal” samples to compare to currently therefore changes are hard to interpret

– But this will improve and get cheaper and faster and some day we will get a flash drive with every base pair (all 6 billion) to interpret and decipher

Relative Risk/ Absolute Risk

• Important concept to understand with genetic risk factors– Analogy by Francis Collins of the NIH of “genes as

the gun but environment is the trigger”

• Very few genetic conditions are absolutes- just because you have the genetic change you may or may not develop disease– Few exceptions such as Huntington disease (HD) or

Familial Adenomatous Polyposis (FAP)

Relative Risk/ Absolute Risk

• Relative risk- risk on comparison to someone else– E.g. smokers and non-smokers; abnormal

gene carriers and normal gene carriers

• Absolute risk- risk compared to yourself– Risk that you/patient will develop the disease

Relative Risk/ Absolute Risk

Example

• Celiac disease– There are certain HLA types that increase

your risk for celiac disease• If you do not have one of the these HLA types, you

apparently cannot develop celiac disease

– The highest risk group has a 10x increase in risk (relative risk)

• Absolute risk of developing celiac is only 6%

Relative Risk/ Absolute Risk

Prevention example

• Celiac disease– However, with a known relative risk you can

take action to prevent the development or early diagnosis of celiac disease

• Know symptoms/signs to look for• Avoid high gluten diet

Relative Risk

Risk and protection

• As more about the genome is known, genetic relative risk will become both risk and protective factors

RR <1: protective RR >1: riskR=1 no relationship

Relative Risk

Risk is a continuum

But dependent on baseline risk (1.5%)RR= 1.5

Absolute risk- 2.25%

RR= 2

Absolute risk- 3%

RR= 5

Absolute risk- 7.5%

RR= 1.5-50% increase risk-1.5 times more likely because of risk factor

RR= 5-400% increase risk-5 times more likely because of risk factor

RR= 2-100% increase risk-2 times more likely because of risk factor

Relative Risk

Risk is a continuumRR= 1.5-50% increase risk-1.5 times more likely because of risk factor

RR= 5-400% increase risk-5 times more likely because of risk factor

RR= 2-100% increase risk-2 times more likely because of risk factor

But dependent on baseline risk (7.5%)RR= 1.5

Absolute risk- 11.25%

RR= 2

Absolute risk- 15%

RR= 5

Absolute risk- 37.5%

Relative Risk

Risk is a continuumRR= 1.5-50% increase risk-1.5 times more likely because of risk factor

RR= 5-400% increase risk-5 times more likely because of risk factor

RR= 2-100% increase risk-2 times more likely because of risk factor

Plus additive/multiplicative risk and protective factors that individually might be small but collectively

have a large effect over time

Relative Risk

Risk is a continuumRR= 0.1-900% increase decreased-10 times less likely because of protective factor

RR= 0.5-100% decreased risk-1/2 times less likely because of protective factor

RR= 0.33-200% decreased risk-2/3 times less likely because of protective factor

So a SNPs changes that increase risk could be offset by behavioral changes that decrease risk.

Comparison to Other Risk Stratification

• Framingham Heart study– Using 10 year risk for

coronary heart disease• Showed age, LDL, cholesterol, HDL,

BP, diabetes, smoking status all influenced risk

– Modest relative risks– Continuum of risk and

protective effects that are additive/ multiplicative

Age RR

50-54 2

LDL >190 1.6

HDL <35 1.6

SBP <160 3

Diabetes 1.6

Smoker 1.6

• Framingham Heart study–Revolutionized cardiac

care• Cholesterol reduction • Blood pressure control• Diabetes control• Smoking cessation• Indications for cardiac

catherization

Subject to pharmaceutical and lifestyle interventionsConservatively a $100 billion industry

Comparison to Other Risk Stratification

– Recent study through the Women’s Health Initiative (WHI) has shown that genetic SNP markers do not change risk as much as the known environmental risk factors….

– But we do not know the additive/multiplicative/ protective effects that are being measured as of now

Comparison to Other Risk Stratification

Direct to Consumer Companies

• In 2008, three companies that offered SNP panels directly to the public

• In 2010, more than 30 companies that offer SNP panels to the public plus a few that offer full genome sequencing…

Direct to Consumer Companies• Various SNPs used

– Different results dependent on which company you use: higher/lower risk, less than population risk/greater than population risk

• Various interpretations• Some are medically-oriented* but some

are “fun fact”– Does your urine smell if you have asparagus

is given the same analysis as for colon cancer risk related SNPs

* Many have a disclaimer that the information gained is not for medical use

Direct to Consumer Companies

• Bypass physician orders and therefore put the “power” in the patients’ hands– Can be a boon if patients use this information

to make lifestyle changes that positively impact health

– Can be a bust if patients use this information to think they are protected from a disease or unnecessarily worry about low absolute risk

Preventative Health

• Multiple studies have showed some effect from knowing risk influencing patient behavior– But generally highly motivated patient

population– No studies with intensive interventions with

“high” risk populations (e.g. medication or surgery)

Do you feel comfortable talking to a patient if they bring in a

report like this to you…

• But very important to differentiate genomic testing from “traditional genetic” testing for highly penetrate, Mendellian disorders that have specific therapeutic interventions available whether for cancer syndromes, cardiac disorders or any number of other disorders– IF IN DOUBT, CONTACT A SPECIALIST TO

FIND OUT