Showing posts with label personal genomics. Show all posts
Showing posts with label personal genomics. Show all posts

Sunday, December 27, 2009

Got Gout?

After returning to work from the Thanksgiving holiday, I was asked by Marc and Janet if my 23andme report contained anything about Gout. Janet said Gout was a topic of conversation while visiting with her family. Sure enough, I found Gout listed in my elevated-risk section of the Research Report. (Remember, the information in the research report section “has not yet gained enough scientific consensus to be included in [23andme’s] clinical report.”


Click to enlarge image

Two stars means the confidence level in the research is currently low. The website instructs me that “the condition (Gout) is caused by the accumulation of crystallized uric acid in the internal organs and joints – particularly in the big toe – which causes painful arthritic inflammation.”

23andMe looks at 3 SNPs in the SLC2A9 gene to determine my risk for developing Gout. If you have a certain mutation in these three SNPs, your odds increase by 1.3, 1.3, and 1.4 times (for each SNP). I have one mutation out of the three possible, so I only have “slightly higher odds”.


Click to enlarge image

The most interesting bit of knowledge I learned is the dietary factors that increase risk for Gout – high fat, alcohol and protein consumption are common for those who develop the disease. One fellow 23andMe customer shared that he was eating meat and drinking beer everyday for a year for his Adkins diet. He didn’t say if he lost weight, but did say his Gout was painful - and his diet has since changed. Another person commented that a study found a supplement of 500mg of vitamin C per day over 2 months reduced uric acid levels in the blood of 184 men.



The Gout. James Gillray, 1799. From the Philadelphia Museum of Art.

See You Next Year

Taking a two-week vacation for the holidays took a toll on the timeliness of this post. So let me wish everybody a belated Seasons Greetings, and an extra wish for that Happy New Year.





Perspective from a Certified Genetic Counselor




Gout and the Holidays

It is difficult to find time to write a blog submission in this season of merriment. Saturday evening is the church wine and cheese party; Sunday evening is the book club potluck; Monday is team breakfast, followed by small group lunch potluck, followed by a departmental dinner that evening. This is just the next three days! With the holiday season comes all the wonderful food. So you might think that we decided to talk about risk association and gout because of the known relationship between wonderful food and gout. It is a reasonable assumption. However, the truth is that while I was home over Thanksgiving I learned that more than one of my family members is reported to have had gout—including my mother! I made the mistake of musing aloud with Marc, “I wonder if the 23andme report addresses risk for gout?” upon which Marc, ever resourceful and ready to delegate [dump!], replied, “Yours, December 14th”.


Gout is famous for its appearance in royal families throughout many centuries. It is more recently that the general diet for people living in Western societies has “improved” to the point that gout is more common. Gout is a great example of the complexity of common adult onset disease. It is quite significantly impacted by familial factors. But genetic factors are NOT the whole picture. It is influenced by gender and age (more men develop gout than women and older age increases appearance especially in women post-menopause), obesity and metabolic syndrome increase the chance that gout may develop, and those with hypertension and cardiovascular disease more often are diagnosed with gout. Finally, specific dietary choices and life events may lead to gout symptoms. The challenge has been to identify the specific contributors that lead to gout in the hope that effective medications can be given to prevent the painful episodes and joint damage that result from uric acid deposition.


Elegantly Balanced

The work to elucidate the mechanisms, metabolism and mystery of gout has led to new understanding of pathways and inter-relatedness of human (mammal) systems biology. We are so very complex and elegantly balanced, physiologically speaking! The development of gout is, for the most part, dependent on the levels of uric acid floating around in the blood stream. People with gout either produce too much uric acid, or more commonly, their bodies have a problem in removing it. Uric acid is one of the inescapable products of the breakdown of food and processing of cells. The kidneys are responsible for the majority of the management of uric acid. This is a version of gout for dummies—please use your healthcare provider for a real discussion of gout!

Grant’s 23andme report indicates that he is at elevated risk for gout. The report lists identified markers in the SLC2A9 urate transporter which is formally known as the solute carrier family 2 member 9 and its function is to move uric acid and glucose/fructose. Common variants in SLC2A9 are associated with increased levels of uric acid and gout. Of the three markers assessed in his report, he had two which conveyed typical risk and one (rs737267 “GG”) which conveyed 1.3 times the odds of gout. Grant’s result is given two stars (out of 4?) in research confidence. This may be because so many other SNPs appear to affect uric acid levels. In a recent meta-analysis published in Public Library of Science Genetics, researchers evaluated 28,141 participants of European descent and identified 954 SNPs in 9 locations that had genome-wide significance with impact on serum uric acid levels. Certain SNPs lead to more pronounced effect in uric acid levels in women, while other SNPs elevate uric acid more strongly in men. The writers go on to suggest that it is the interplay between the SNPs, other proteins in the cellular environment and the uric acid levels in the blood that will contribute to whether one develops gout.


Gout and the Family

What about me and gout in my family? First of all, I do have two first degree relatives known to have gout. I recall that a brother had one experience with a really painful big toe that was labeled gout. I knew that my maternal uncle had to give up milking up cows because of arthritis in his knees—reported as osteoarthritis due to repeatedly kneeling to hook-up milking machines (pretty plausible). I knew that my grandfather had arthritis so bad that he sometimes had to crawl to the barn (no milking machines). I knew that my mother had a serious flare of non-rheumatoid arthritis in her feet, so bad that she could not keep the sheet resting on her toes. But I did not know that it was labeled gout and I haven’t even mentioned the family history of kidney stones. The brother above has had kidney stones that tested positive for uric acid. Now comes the “do I have…”, the episodes of curiously sharp pain in my big toe joint??? Was it just the choice of shoes????

Monday, November 23, 2009

Pass the Turkey, Pie, Football, … and Family Health History

Because Thanksgiving Day is also Family Health History Day, we’ve decided to suspend showing results from my 23andMe report for this post and review Family Health History activities Intermountain Healthcare’s Clinical Genetics Institute is leading. We consider clinically-used family history to be the cheapest and most effective genetic test today.

Prologue

Former Secretary of HHS Mike Leavitt tells a story of when he was governor of the State of Utah. A research program to find the genetic cause for disease needed to recruit large families for the study. Gov. Leavitt met a grandfather who said "I think there's something to this genetics thing. I'm 71 years old, and when I turned 70, I was diagnosed as having macular degeneration. When my father was 70 years old, he got macular degeneration. In fact when his father turned 70 years old, he got macular degeneration."

He said, "If there's something I can do and my family can do to keep my grandson or my great grandson from having that moment when he turns 70 years old, I want to do it, and I'm in."

We hear many stories just like this. The older generation wants to know how they can help the younger generation prevent the healthcare problems that run in their family.

This grandfather’s family, in conjunction with other families, led to the discovery of the association of changes in the Complement factor H (or CFH) gene with this form of macular degeneration. Not only was the gene identified, but it led to the understanding that some forms of macular degeneration are inflammatory diseases, and anti-inflammatory treatments are now available to slow or halt progression of the disease.

My 23andMe report includes age-related macular degeneration as one of the 11 diseases in the clinical reports category. It tells me that when I’m 70 years old, my absolute risk will be 1.4%, compared with 2.4% in the general population.

Traveling to Grandmothers House - Where Are We Today?

Obviously, we want to tell patients to do a family health history and we want them to share it with their family members - and with their healthcare providers. But where are we today with this process? Are you tired of filling out the same family history form every time you visit a new doctor? Are doctors using the information effectively? Do they have the right electronic tools that can guide them to understand your risk, or for further evaluation, order the appropriate genetic test? Sadly, the answers to these questions are most likely not very positive.

The Feast Begins - Family History in the Electronic Health Record

Within Intermountain Healthcare, there are multiple forms (both computer and paper-based) collecting family health history information from many entry points into the healthcare system. The vast majority of family history is captured by the doctor in the medical computer – but in a text-based clinical note – which means the computer can’t understand it and do anything with it.

Except for those used by genetic counselors, most family history collection tools used today do not allow for the building of pedigrees, nor do they ask for other critical information, like the age of onset of a relative’s disease. Our current tools do not gather the data required to create a disease risk assessment for the patient. The Clinical Genetics Institute at Intermountain is beginning to rewrite these family history programs in the EHR.

The Main Course - What We Want to Create

As a group focusing on family health history, we’ve had a lot of time to ponder what we want to see in future electronic tools - tools that capture and analyze family health history information to advance clinical care. We would like to start with a general tool that collects information about the common diseases your primary care physician would be interested in. The program would then expand into more targeted areas to ask questions that a specialty physician would want to know about a specific disease or condition for which the patient is seeking treatment.

A key goal for this project is to provide useful risk assessment reports for both the patient and the doctor. First, the report should contain information for the patient to act on - information that will encourage behavior change, or to seek out appropriate screening tests, or possibly further genetic testing, and hopefully, sharing the results with other family members.

Secondly, the report should provide information for the doctor to review and validate for accuracy since the information will be stored in the EHR. When the data is stored in a structured and coded format, the computer can offer the doctor clinical decision support messages - which becomes powerful when clinical and genetic/genomic data are included in the decision algorithms. Having family health history records can guide the physician in ordering the most appropriate genetic test when testing is indicated.


© Intermountain Healthcare 2009. All rights reserved.

Pouring On the Gravy - New Tools for Patients

Microsoft HealthVault announced a grant program called the Be Well Fund in 2008. The Genetics Institute became one of 15 award recipients and began a project creating a web-based, patient-entered family health history program. When completed, the program will be hosted on Intermountain’s patient portal called ‘MyHealth’. The application will store the data in Intermountain’s clinical data repository, thereby making it available to healthcare providers via the electronic health record. If the user is interested in having a HealthVault account, they upload their data to that account by simply clicking a button. We hope to have this program go live in the Spring of 2010. In the spirit of the grant, we will attempt to make the code available via open source for others to implement.

A screen shot from our family history program under development

© Intermountain Healthcare 2009. All rights reserved.

Intermountain's MyHealth patient portal already includes a family health history page that offers two PDFs for download on family history questions. The first booklet guides the patient on how to collect family history information, and how to ask family members for their history and that of deceased relatives. The second booklet teaches more about genetics and how it may affect familial disease. These booklets are availabe for anyone to use from the Genetic Alliance, and are fully customizable for use with any group or organization.

Remember Your Table Manners - We Have Standards

The international healthcare data standards group HL7 has developed the Pedigree (Family History) model as a data transmission standard to exchange family history data between systems and applications. Besides becoming an HL7 standard, the model has become an American National Standard Institute (ANSI) standard, and is in the process of being approved by the International Standards Organization (ISO). Our patient-based family history tool, along with the tools mentioned in the following paragraph, is built around this standard. However, major healthcare software vendors have yet to implement the standard in their products, even though federal standards efforts like the Healthcare Information Technology Standards Panel (HITSP) and the Center for Certification of Healthcare Information Technology (CCHIT) will require them in the near future.

A diagram of the HL7 Pedigree (family history) model - click to enlarge

© Health Level Seven 2009. All rights reserved

Here Comes the Dessert - Other Great Family History Tools Freely Available

The Office of the Surgeon General in the United States encourages people to use its web-based family health history tool while families are gathered over the Thanksgiving holiday. But did you know that the Surgeon General’s My Family Health Portrait code is also openly available? And to practice what we preach, all of the US federal healthcare computer systems, which includes the Dept. of Defense for active military, the Veterans Administration for retired military, and Indian Health Service, will be basing their family history programs on the Surgeon General’s tool, especially adhering to all of the standards upon which it was built.

One of the most advanced clinical tools centered around family history is Hughes riskApps. This program identifies and manages women at high risk for hereditary breast/ovarian cancer, although they plan to expand it in the future to handle other cancers as well. The key components of the software are that it allows for patient-entered family history and other health data via a hand-held tablet. The information goes directly to the healthcare provider where several risk models are run to help determine the cancer risk of the patient. You can download the software for free from their website.

Saving the Leftovers - Warehousing Family History Data for Research

Having great family health history data collection tools is just the beginning in reaching our goals in this area. Using the data to explore clinical research questions will open up other opportunities, which will lead to genetic/genomic - or dare I say – personalized medicine discoveries.

A diagram of a family history datamart - click to enlarge

© Intermountain Healthcare 2009. All rights reserved.

Time to be Thankful

When your belly is full, your family is around you, and everybody is healthy, it is certainly time to be grateful. I would wish that everybody could enjoy those blessings. To add to my abundant portion, I must also mention what a wonderful opportunity it is to work in healthcare IT, and more specifically, to work in the emerging and exciting field of clinical genomics and personalized medicine. My list of things to be thankful for is much longer, but to not stop you from getting that second slice of pumpkin pie, let me just say to everyone a Happy Thanksgiving, and may your plate be filled with a healthy family history.


This picture was taken in 2008 for my parents 50th wedding anniversary. Grandma would not be pleased if I didn't point out that, since the photo was taken, two granddaughters and one more great-grandson have been born.

Thursday, November 5, 2009

My Family History of Heart Disease … I Think

With November proclaimed to be Family History Awareness month, I thought I would write about a medical condition that runs in my family. But to what extent my relatives had this disease, or what it means for my risk, I’m not sure. If a doctor were to ask me if I have a family history of heart disease, my first response would be no. I’m not aware of any 1st, 2nd, or even 3rd degree relatives who have had heart attacks. But wait… My father did have that double bypass 12 years ago… It’s funny how I don’t think about it much. Maybe I should.

Dad didn’t seem to be the type that was at risk. A non-smoker, non-drinker, slender, and active, he started to feel chest pain at age 63 whenever he did something physical. The pain increased gradually over time, and Dad put off seeking medical attention until it became serious. A procedure in the cardiovascular catheter lab revealed a dangerous blockage the coronary arteries. He was immediately rushed into surgery.

It was determined that his blockage was caused by cholesterol (ding, that bell is ringing for me). His double bypass included a stent. What is interesting though is that he mostly remembers the psychotic reaction he had after the surgery (which happens to patients 10-20% of the time) because they used a heart/lung machine.

One More Time

Nine years later he started having chest pain again, but thought it was indigestion. (What do former hospital CEOs know about medicine anyway). Sometime later he was in the hospital for a MRI that was looking for a neurological problem. In the middle of that procedure, his chest pain returned and was very severe. Knowing his history, the clinical people determined he was having a heart attack – in the hospital, thank God. His blockage had returned and a new stent was installed.

Any Other History?

So I began asking my mother questions about any other family history of heart disease. Both of my grandfathers died (their hearts stopped) immediately following surgery that was not heart-related. They were 78 years old. Mom says her father may have had a heart arrhythmia. I know mom does. She had a procedure called a cardiac ablation, which seems to be a successful treatment. I haven’t experienced any arrhythmias yet, but wonder if any of this affects my risk. Besides my father, nothing is really clear about a family history of heart disease. And what should I discuss about this with my seven siblings?

23andMe Heart Disease Reports Fall Under a Different Category

Information on the 86 health and traits included in the 23andMe Research Reports section reside there because they do not establish a large enough increase in risk to be included in the Clinical Reports section. For a disease to be included in Clinical Reports, the riskiest combination of genotypes must increase a person's odds of developing the condition by a factor of three or greater and elevate absolute lifetime risk to at least 5%. The Research Reports section also includes studies that still need to be confirmed by the scientific community, and includes topics where there may be contradictory evidence. The results of these studies may not be conclusive.

Heart Attack in the Research Report Section

The heritability of death from a heart attack is estimated to be 38% for women and 57% for men. The Odds Calculator tells me my risk is 2.4 out of 100 for my age, but that risk increases more than 5 times in the next 25 years.


Click image to enlarge

It’s In the SNPs

Numerous SNPs associated with one's chances of a heart attack have been found in the chromosomal region 9p21.The reported SNP is not in a known gene, but it could affect a gene in a neighboring stretch of DNA. I think this is the first time I’ve heard that a possible pathogenic SNP is not part of a gene.


Click image to enlarge

What About High Blood Pressure

Let’s look at four other heart-related 23andMe reports. Left untreated, severe hypertension can lead to heart failure, stroke, vision loss or kidney problems. Environmental risk factors such as age, weight, inactivity, diet and stress can contribute to hypertension, but genetics also contributes.


Click image to enlarge

I learn from 23andMe that from several studies, with the total number of subjects of 5,500 individuals of European ancestry, each T at the SNP rs3754777 increased subjects' systolic blood pressure about 2 mm Hg and diastolic blood pressure about 1 mm Hg. This doesn’t seem to make that much of a difference. I have never been hypertensive, so I think I’m OK here.

If I Was Prescribed Beta Blockers

Beta-blockers are given to people who have had a recent heart attack, or who have high blood pressure.


Click image to enlarge

After development of the beta-blocker bucindolol was halted, the authors of one study found that people with the CC genotype who were given bucindolol had a 38% reduction in mortality compared to placebo. This might be an example of using pharmacogenomics to find if certain drugs can be effective for people of a particular genotype. I may need to remember this in the future.

Or Prescribed a Statin

Statin drugs are prescribed to reduce cholesterol levels in people who have a high risk of cardiovascular disease.


Click image to enlarge

Myopathy (experiences muscle pain and/or weakness) is a very rare side effect (one person in 10,000) of statins, even among those with genotypes that increase their odds of experiencing it. Having two C copies of the SNP increases a person's odds of myopathy by about 17 times, but the overall risk is still very small. If I’m ever prescribed a Statin, I won’t have to worry about this one-in-10,000 risk increasing. But My Problem Is Cholesterol From talking with the source of all family medical knowledge – Mom – I’m fairly convinced high cholesterol will be my problem.HDL, or high-density lipoprotein, is the “good” cholesterol that is considered protective against heart disease, and is another 23andMe ‘Research’ report.


Click image to enlarge

My HDL is good at 50 (normal range 40-63). But my total cholesterol has been between 267 and 295 (normal range 158-199). There is no report from 23andMe on LDL or bad cholesterol and my genotype. I would like to see this.

Doing My Own ‘Research’

When I searched for a study on LDL levels and genetics, I found a paper titled “The novel genetic variant predisposing to coronary artery disease in the region of the PSRC1 and CELSR2 genes on chromosome 1 associates with serum cholesterol”.

The study genotyped 2,037 adult individuals and measured their total cholesterol, high-density lipoprotein (HDL) cholesterol and glucose, blood pressure, body mass index and waist-hip ratio, for the lead SNPs in the seven CAD-associated loci. SNP rs599839, representing the locus in the vicinity of the PSRC1 and CELSR2 genes on chromosome 1p13.3, showed a strong association with total cholesterol. The association of the A allele with higher total cholesterol was confirmed in an independent cohort of 847 healthy adults, and related to an effect on low-density lipoprotein (LDL) cholesterol.


Click image to enlarge

When I entered SNP rs599839 into the Browse Raw Data feature of my 23andMe report, I found that I have the A allele. The study concluded that the findings support further investigation of the role of these genes in cholesterol metabolism and coronary risk. So at this point, I don’t have any analysis for my genetic risk for high total cholesterol.

He’s Still Throwing Utah Snow

Dad is still active at age 75. His favorite thing to do (besides reading my blog) is running his snow-blower multiple times a week during the winter. It's my favorite thing for him to do also. It means his ticker is still strong.

Maybe I should ask Dad to take the 23andMe test so we could compare our 9p21 SNPs and further validate my familial risk. But the longer he hangs in there is good for me - and good for me again.





Perspective from a medical geneticist



True confessions of the heart

As I read Grant’s post, my first thought was that I should ask one of my cardiology colleagues to write the response. His approach to this issue is a clear indication of what a motivated consumer can do to generate information about risk as well as defining ways to impact this risk. The stark reality is that cardiovascular disease of all types is the leading killer of Americans—responsible for 1 out of every 2.8 deaths in 2005.

As opposed to many of the other conditions we’ve talked about, there are lots of preventive measures that can reduce one’s risk of coronary artery disease and hypertension including exercise, smoking cessation, weight loss, dietary changes and many classes of medication. I faithfully take a baby aspirin every night for this very reason.

Rather than provide a “geneticist’s perspective” on Grant’s post, I’ve decided to confess my risk and behaviors following Grant’s template as I see them from my perspective as a patient who hasn’t been genotyped.

Family History

Three of my four grandparents lived into their mid-90s. My paternal grandfather died before I was born of what I think was a hemorrhagic stroke. My recollection is my father told me he had severe hypertension and smoked—two major risk factors. Of the three that lived to a ripe old age, none had any interventions or procedures for coronary disease.

In fact, my maternal grandfather died suddenly one day at age 96 (I presume of a cardiac arrest) after literally never being sick a day in his life. His only medication was a daily baby aspirin (which he began taking after his grandson, the medical student, suggested it might be a good idea). My mother is alive and extraordinarily active at age 83. She has no heart issues or hypertension. My father died in his 60s of mesothelioma due to asbestos exposure when he was an engineer; chalk one up for environment over genetics. He never experienced any cardiac issues although he had elevated cholesterol.

Examination of the extended family identifies a paternal uncle who had bypass surgery in his late 60s and another with coronary artery disease in his 70s, although he died of a blood disease. Another paternal uncle had a stroke, but - like his father - smoked and had hypertension. My maternal aunt and uncle have had no cardiac issues in their 80s (and my uncle being a lifelong smoker). I find this information to be very reassuring—perhaps too much so.

Risk of Heart Attack

While I’ve not been genotyped, according to my internist my risk for heart attack is average. This risk is based on risk assessments such as the Framingham study and the ATPIII guidelines. In my own mind, I consider myself to be at below average risk given my family history. The family history information collected by the clinical risk stratification tools noted above is rudimentary compared to my 3 generation pedigree!! I rest comfortably in my cloud of delusion and denial!

Grant mentions the 9p21 SNP that 23andMe genotypes. This is clearly the best characterized risk predicting SNP for cardiovascular disease, although there may be as many as 10 others that independently reclassify risk for coronary artery disease (according to deCODEme’s Chief Scientific Advisor Jeffrey Gulcher.) These are not currently part of the 23andMe risk stratification.

What is interesting and counterintuitive to me is that these genomic markers confer risk that seems to be completely independent of family history and clinical markers such as cholesterol. What is not known is whether modification of lifestyle or use of medications will attenuate the risk conferred by these genomic markers. So, no genotyping for me, at least for the present.

High Blood Pressure

I am proud to say that I am a hypertension carrier. That is to say my presence seems to induce hypertension in others while mine remains blissfully normal (with the exception of a systolic elevation immediately prior to my recent colonoscopy but that’s a story for another day). This is in spite of a zealous aversion to regular exercise and a penchant for salt consumption that drives Janet crazy (she has hypertension that is well controlled by medications despite much better health habits). So, no issues here (nor as best as I can determine for any of my 1st or 2nd degree relatives).

This does bring up an interesting point relative to 23andMe—if I have my blood pressure checked regularly, does my rs3754777 genotype status really matter? Would I do anything differently based on my genotype status? I think not. I would like to think that if my blood pressure was elevated it would lead to modifications in my life, at least to the extent of taking a medication.

Cholesterol

Lest you think that my heart will never give out, I will confess that cholesterol is an issue for me (and for my father, daughter and my mother to a lesser degree). My total cholesterol is elevated (last value was 235) with a borderline HDL of 40 and an elevated LDL of 179. I do drink a glass of red wine every evening, but this does not appear to elevate my HDL significantly L. I think I’ll continue this anyway.

I actually took a statin medication for a couple of years with a spectacular impact on my numbers (total cholesterol of 141, HDL 37 and LDL of 88). I experienced no problems with the drug including no muscle symptoms and normal liver function studies. A couple of years ago I lost a significant amount of weight and my internist and I decided to see how this impacted my numbers. It had a beneficial effect with a total cholesterol of 206 and LDL of 152—not perfect, but probably adequate to stay off statins. Of course my weight has crept up since the low point leading to worsening of my numbers. So, should I try to lose weight again (almost certainly yes) or should I go back on a statin given my excellent clinical response and tolerance? (Again, probably yes).

The reality is that I should probably do both given the increasing evidence of benefit of statins for a number of circumstances. I am deleted for the medication aversion gene located on the Y chromosome, so compliance has never been an issue. I would not pursue genotyping given that I’ve tolerated the drugs in the past.

Given the importance of statins in the treatment armamentarium, I would argue that given the rarity of severe reactions to statins, genotyping could lead to harm if an individual chose not to take a statin based on an increased risk of a reaction given that most individuals with the ‘at risk’ genotype would still tolerate the medication just fine. My mother, in contrast, developed muscle aches with every statin she tried so despite her mild cholesterol abnormalities, she has elected not to take these drugs and I wholeheartedly agree. Besides, living to 83 without any heart problems is probably telling us more about her risk than any test, genetic or otherwise.

I did want to comment on a functionality of 23andMe that we’ve not explored before. Grant did extensive research about factors that influence cholesterol levels and identified information about genetic factors. He was able to enter these into the raw data browser and retrieve his genomic status. This clearly demonstrates how a sophisticated and highly motivated consumer can go beyond what is presented by the testing service. As to how it will alter Grant’s health behavior, well that’s up to him isn’t it?

My Health Behavior

We all have our beliefs about health and wellness. I somewhat facetiously make two statements about exercise and eating well: 1) Regular exercise does lead to longer life, but you only extend life by how much time you have spent exercising. Stated another way, if you exercise you will live longer but you will have spent all your extra time exercising!! 2) I also believe that eating a healthy diet doesn’t help you live longer, however it will seem a lot longer. Verily my epitaph will read, “He died in search of the perfect bacon cheeseburger.” I also believe that mental well-being and stress reduction are strongly protective despite a dearth of evidence. Therefore, my music making, art business and golf take up the time that I could otherwise devote to exercise. However, I think that if I substituted exercise for these activities I would be substantially less happy.

So, I admit I’m not the best role model for healthy behaviors as we currently understand them. I would like to believe that if there was compelling information, genotypic or not, that I would use this to modify my health behaviors. Realistically, I think it may take a more significant event, i.e. a heart attack, for me to be more serious about these issues. Not the most intelligent approach given the high percentage of men that don’t survive their first MI.

There is another reality which is that no one gets out alive!! All of us will die of something (the Life Extension Institute’s beliefs to the contrary) so would dropping dead of a heart attack be so bad compared to a lingering chronic disease like cancer or my personal worst nightmare-dementia? Not in my mind, but then the choice isn’t all mine is it?

Monday, October 19, 2009

Do You Know Alpha-1 Antitrypsin Deficiency?

Let me confess this upfront. Until I met John Walsh at the 2008 Genetic Alliance conference, I was not familiar with the genetic disorder called Alpha-1 Antitrypsin Deficiency (AATD). John is one of the founders and President of AlphaNet. Since then I have learned that AATD, a genetic mutation, reduces the levels of a protective protein in the bloodstream. AAT deficiency can lead to chronic obstructive pulmonary disease (COPD), specifically emphysema, and liver disease.

John had attended a presentation I gave on improving the use of family health history and genetic/genomic data in the electronic health record. Later I was both surprised and honored when he invited me to become a member the AlphaNet board of directors. So when I saw that Alpha-1 Antitrypsin Deficiency was added in April of this year to my 23andMe Carrier Status report, I thought the timing was providential.


Click image to enlarge

As I have new opportunities to met people with Alpha-1, they would always ask if I have been tested to see if have the mutation. I hadn’t until the 23andMe result appeared. The test most people take is a simple finger-stick test for blood. But you can also get tested by genotyping, which is how I learned of my AAT deficiency carrier status.

23andMe told me that an estimated one out of every 5,000 - 7,000 North Americans has AAT deficiency. Interestingly, in Scandinavia the numbers are higher. One in every 1,500 to 3,000 people there is affected. These numbers go higher when you take into account the people who have AAT deficiency, but have not been diagnosed.


Click on image to enlarge

The main versions of the gene that encodes AATD are PI*M (the normal version), PI*S, and PI*Z. A person inherits a copy of the gene from each parent, producing six possible combinations: MM, MS, MZ, SS, SZ, and ZZ. Something I learned from 23andme - In addition to the PI*M, PI*S, and PI*Z versions of the gene for AAT, there are more than 20 known rare mutations that can lead to AAT deficiency.

The PI*Z form of the gene is the most severe mutation; the ZZ genotype accounts for 95% of AAT deficiency. People with the SZ genotype are at an increased risk for COPD, particularly if they smoke. The MZ genotype causes only mild reduction in AAT protein levels, but may lead to decreased lung function in smokers.

Difficult Diagnosis

The AlphaNet website tells us that Alpha-1 patients experience difficulty and delay in getting properly diagnosed. Clinical research studies have shown that once a patient develops symptoms, it takes an average of seven years and visits to five different doctors before the diagnosis of Alpha-1 is correctly made. I have met Alpha’s that confirm this. Many non-smoking Alpha’s are of accused of smoking by their doctor. About 3% of all people diagnosed with COPD may have undetected Alpha-1.

For treatment of lung disease caused by AAT deficiency, intravenous alpha-1-antitrypsin augmentation therapy, annual flu vaccination and a pneumococcal vaccine every 5 years are recommended. Relief of breathlessness may be obtained with long-acting bronchodilators and inhaled corticosteroids. Both end-stage lung and liver disease can be treated by organ transplantation. In AATD patients with cirrhosis of the liver, the prognosis is generally grave.

The AlphaNet Community

I began working with AlphaNet a year ago. I learned that one of the many things AlphaNet does is provide disease care coordinators for more than 7,000 people with Alpha-1. Their website further explains that “AlphaNet Coordinators are spread across the United States and subscribers to AlphaNet are assigned to a specific AlphaNet Coordinator based upon geographical location. Each AlphaNet subscriber is contacted at least monthly by his or her AlphaNet Coordinator. The AlphaNet Coordinator provides support, education and assistance with augmentation therapy infusion issues and supplies.” Since 1997, AlphaNet has donated $25 million to the Alpha-1 Foundation, which performs research to cure AAT deficiency.

More information I learn from 23andMe includes -

· Not everyone with AAT deficiency will have symptoms, leading some researchers to suggest that additional genetic factors other than mutations in the gene that encodes AAT may be involved.
· Between 15% and 19% of adults with AAT deficiency develops cirrhosis of the liver after age 50.
· The donor liver following liver transplantation will make normal AAT protein and actually cure the deficiency in the rest of the body.


Click on image to enlarge

Family History

A paper on Alpha-1 antitrypsin deficiency was published this summer in the New England Journal of Medicine. One of the authors, Dr. Robert A. Sandhaus, is also a board member and Medical Director of AlphaNet. The article states that “AAT deficiency is recognized in less than 10% of persons in whom a diagnosis would be expected on the basis of screening studies in the general population. The diagnosis of AAT deficiency is generally made after the identification of COPD or liver disease or after the deficiency has been diagnosed in a family member”.

The authors recommend that a family testing discussion be held in the initial evaluation of the newly diagnosed patient. A diagnosis of Alpha-1 could impact family including brothers, sisters, children, grandchildren, and possibly extended family members.

To assist in finding those who are still undiagnosed, Intermountain Healthcare’s Clinical Genetics Institute is designing a study using an internet-based, patient-entered family health history program. Both the software program and the research study are under development, but we hope to find that computerized family health history tools can be effective screening methods to identify and treat those families that might be at risk for an inherited, familial disease for which they are not aware. The earlier the detection, the less damage the disease will have done.





Perspective from a medical geneticist



Traditional vs. Predisposition Genetic Testing

The two results from testing discussed this month, BRCA and alpha-1 antitrypsin (AAT), represent much more traditional types of genetic testing than the predisposition testing we’ve written about in most of the posts. In contrast to the BRCA testing which was limited to only three mutations (or the Cystic Fibrosis gene CFTR where only one mutation is tested), the AAT test results report all of the recommended clinically important mutations in this gene. Grant does an excellent job of describing the disease and its implications.

From my perspective, the challenge that hasn’t been adequately met in practice is testing of individuals who are symptomatic. As Grant points out, we are not doing a very good job of identifying the disease in symptomatic individuals. In 2008, Hogarth and Rachelefsky published a review in the journal Chest that looked at testing and screening for AAT deficiency. (reference below) They highlight 4 interventions that could be used if the disease was identified early. These include: smoking prevention/cessation; minimizing the hazards of occupational respiratory pollutants; the opportunities to receive augmentation therapy; and the potential for family planning and guided genetic counseling/testing. Thus we have a situation where we can definitively characterize the results of the mutation testing; we can identify individuals at risk; we can initiate preventive measures in those at risk and start treatment in symptomatic patients. This in some ways represents an ideal genetic test.

Genetic Testing for Symptomatic Patients

While there have been some suggestions that population screening (at least in Caucasians) for AAT mutations would be beneficial, the consensus has been that this approach would be too expensive. In addition, there are many individuals who carry disease causing mutations who never develop symptoms. That said, we’re doing a very poor job testing individuals who are symptomatic, despite professional guidelines supported by strong evidence that recommend testing all individuals with emphysema, COPD, or asthma with airflow obstruction not completely reversible with the use of bronchodilators; all individuals with unexplained liver disease; asymptomatic subjects with persistent obstruction found on pulmonary function test findings and with identifiable risk factors; and adults with necrotizing panniculitis.

Informed Consumers

So it certainly appears that there would be a role for informed consumers to be able to access testing given that health care professionals are not doing an adequate job. Interestingly this has been studied in AAT, including testing of minors. (see references below). These tests seem to be well accepted. Nearly 80% of current smokers indicated that they were highly likely to stop smoking if they were ZZ. Most individuals (but not all) said they would share the results of testing with their physician, however a small number would not want the result placed in their medical record because of concerns about privacy.

The U.S. Center for AIR is performing testing under a research protocol to learn more about the risks and benefits of direct-to-consumer testing for AAT deficiency. This type of research is extremely important to better understand the role of consumer directed genetic testing. Kudos to the groups that are sponsoring this important research. Testing is also available outside of a research protocol through the AAT Deficiency Testing Center. In contrast to 23andMe that provides results, but no other support, AAT testing is sponsored by AAT organizations that can provide support for newly diagnosed patients.

It should be noted that one can also measure the level of alpha 1 antitrypsin activity in the blood stream, obviating the need for a genetic test. So, if you’re interested in being tested for AAT deficiency, probably better to use one of these services than 23andMe. However, if you have been identified as carrying a mutation through the 23andMe testing, contact one of the advocacy organizations for more information. It could save your life!

References:

Hogarth DK, Rachelefsky G. Screening and familial testing of patients for alpha 1-antitrypsin deficiency. Chest. 2008 Apr;133(4):981-8

Strange, C, Moseley, MA, Jones, Y, et al Genetic testing of minors for α1-antitrypsin deficiency. Arch Pediatr Adolesc Med 2006;160,531-534

Gitter AC, Jones Y, Schwartz L, et al. Confidential home α1-antitrypsin testing: specialty center support for rare diseases. Presented at: the American Thoracic Society Annual Meeting; May 18–23, 2007; San Francisco, CA; poster A988

Strange, C, Dickson, R, Carter, C, et al Genetic testing for alpha1-antitrypsin deficiency. Genet Med 2004;6,204-210

Monday, October 5, 2009

Can Men Understand BRCA?

I was surprised when 23andMe added selected BRCA cancer mutations to the Carrier Status list in February of 2009, especially since everybody knows that Myriad Genetics holds a controversial patent to the BRCA1 and BRCA2 genes. Because Myriad is a Salt Lake City-based company, we watch them closely. And more importantly, I have a personal story with Myriad BRCA testing and a family member - which I will share at the end of this post.

The UPDB

Myriad originated in 1991 as a gene discovery company. Their researchers were able to access and link important genealogical and medical databases, which resulted in discovering the BRCA genes. The new database was named The Utah Population Database (UPDB). It originally contained information on 200,000 Mormon family groups and most of the1.6 million descendants of the initial 10,000 Utah settlers. This database was linked to the Utah Cancer Registry (which contains more than 100,000 entries), in which generated 40,000 cross-linked entries. Since then, the database has expanded with updated genealogical and public health records, and Intermountain Healthcare has linked its clinical data with the UPDB to offer an even more powerful research tool.

Anything Here for Me?

My 23andMe report cautions me to remember that the BRCA mutations covered by the report are only three of hundreds in the BRCA1 and BRCA2 genes that can cause cancer. The absence of these mutations does however not rule out the possibility that I may carry another cancer-causing variation in one of the other genes.


Click on image to enlarge


Population Risk

It seems like a small number when one reads that only 5 to 10 percent of breast cancers occur in women with a genetic predisposition for the disease. The incidence in men only accounts for 1% of all breast cancer. In addition, I learn that these mutations greatly increase not only the risk for breast cancer in women, but also the risk for ovarian cancer in women as well as prostate cancer among men. Additionally, 23andMe provides data for only three specific cancer-associated mutations that are found mainly in people with Ashkenazi Jewish ancestry.

Since I am not a woman, nor an Ashkenazi Jew (100% European according to my 23andme ancestry painting), is any of this information important to me? I think so. Because I am not a carrier, the children I may have will be at reduced risk of breast cancer. But my interest at this moment is not for me, but rather for affected family members, for whom I care deeply.

October is Breast Cancer Awareness Month

The National Breast Cancer Awareness Month (NBCAM) program is dedicated to promoting the importance of early screening and detection of breast cancer through a nationwide campaign held during the month of October. They are celebrating their 25th anniversary. Whenever I hear about a NBCAM activity, I think about what my sister-in-law (SIL) went through. She is a breast cancer survivor.

A Personal Story

Her story starts with her maternal Grandma, who was diagnosed with breast cancer at age 45. After several surgeries failed to “hack it out”, Grandma died at 49.

My SIL’s mother was first diagnosed with breast cancer at age 29. She had surgery to remove her breasts, followed by chemotherapy, but that didn’t stop the cancer from spreading to her spine, and finally her lungs. Even after complaining about respiratory difficulties, the lung cancer was not discovered until the autopsy. Mom also fought for 4 years before dying. My sister-in-law was seven years old.

Thinking It Was Inevitable

While growing up, my SIL always thought that at some point she would die of breast cancer herself. In 2001 when she was 25 years old, she heard about the Myriad BRCA test and wanted to take it. The test came back negative for any of the BRCA mutations, so she started to think she had dodged a bullet. She did have genetic counseling, which would have told her some risk still existed. She saw an oncologist, but did not have a mammogram since she was nursing a newborn at the time.

Three years after the negative Myriad test, my SIL was pregnant once again, and for the first time ever, found a lump in her breast. She had an ultrasound and was told that the lump was benign and would disappear after the pregnancy. Two weeks later she visited her Obstetrician and told the doctor she thought the lump was getting bigger. A needle biopsy by a breast surgeon revealed she had cancer.

A Prayer Is Answered

A small miracle followed. She began chemotherapy while pregnant with her fourth child. Her daughter was born as beautiful and healthy as her other children. After the birth she had a radical bi-lateral mastectomy, reconstruction, and radiation therapy.

I asked her if she felt modern medicine had let her down. She said no, because – she explained - she had always felt that it was her responsibility to follow through with the accurate diagnosis and treatment of her healthcare. However, she did feel that she should have asked an aunt to take the BRCA test to help interpret her results. Today, she is still interested in learning about new genetic testing for breast cancer that might help her three young daughters.

As their Uncle, these three beautiful little angels give me sweet hugs and a lot of love. As I thought about their future and possible inherited risk, I found myself feeling sad thinking about what they might face in the future. I can’t imagine how I would feel if I were their mother or father.



Perspective from a Certified Genetic Counselor




BRCA Mutations and Inherited Risk for Breast Cancer









Women who talk with me about inherited risk for breast cancer often ask about “the breast cancer gene”. I think it comes as a surprise to many of these women (and their husbands) that everyone, men and women, have BRCA genes. In fact, every person has two copies each of BRCA1 and BRCA2. One of each came via the egg cell from their mother, and one came in the sperm cell donated by their father that resulted in their personal conception; talk about personalized health! So although Grant does not carry one of the three common Ashkenazi (or Eastern European) Jewish BRCA mutations, he does carry BRCA genes in which hundreds of mutations are possible. Cheery thought!

Grant shared the story of his sister-in-law and her family’s experience with relentless breast cancer. Breast cancer at ages 45, 29, and 28 are the hallmark of hereditary breast cancer caused by a BRCA mutation. How could it be that Grant’s sister-in-law tested negative for BRCA mutations and then she was diagnosed with breast cancer? Her story helps to illustrate the promise and the pitfalls of genetic and genomic testing, and it is a good example of how genetic test results may be only part of the story of risk. I appreciate her willingness to have her brother-in-law share her story. (I hope he told her he was sharing the story!)

Mutation: A gene mutation is a permanent change in the DNA sequence that makes up a gene. Mutations range in size from a single DNA building block (DNA base) to a large segment of a chromosome.

The genomic test result that Grant received as part of 23andMe represents the mutations tested for during initial testing usually offered to individuals with Eastern European Jewish ancestry who have a family history of breast or ovarian cancer. I am not sure what led the designers of the 23andMe to select and report on BRCA mutations despite the fact that another company owns the patent for those genes. I suspect it may be because other labs have been licensed to conduct screening for the three mutations in certain specific populations.

Promise and Pitfall

I have the sense that Grant was not surprised to learn he is not a carrier of a BRCA mutation. I have not heard him mention or write about cancer in his biologic family. That is little consolation for the fact that his sister-in-law has developed breast cancer and his nieces (grandnieces, etc.) could develop breast cancer. The promise with genetic testing is the possibility that knowing if you are at risk, it may offer the opportunity to prevent cancer. The pitfall is the false hope that testing that is negative (no mutation detected) has ruled out risk for the disease.

As Grant’ s sister-in-law mentioned in her reflection, she wished that her aunt had been tested for BRCA mutations to help to interpret her results. If her aunt (her mother’s sister) had breast cancer and tested negative, then her negative result would have been meaningless. It would have indicated the fact that the cause of early breast cancer in the family had not yet been linked to a BRCA mutation. In the study of families with inherited breast and ovarian cancer, we know that BRCA is not the only reason for cancer in every family. There must be other hereditary factors besides BRCA that cause breast cancer. Researchers have not been able to identify another familial breast and ovarian cancer gene with the same dramatic impact of BRCA1 and BRCA2, but others or combinations of others must exist.

The Story Is Not Over

In the same way that 23andMe updates risk assessments as new SNPS are linked to diseases and reported back to Grant, new ways to evaluate BRCA genes have been added to the analysis in high risk families. The story of Grant’s sister-in-law and her genetic testing is not over. In 2001 - and again in 2007 - Myriad Genetics updated their analysis of BRCA genes to include evaluation for large gene rearrangements.

While rearrangements are also called mutations, the original testing for mutations involved sequence analysis of the genes and did not reveal that chunks of DNA could be missing (deleted) or copied more than once (duplicated). Several families, in whom a BRCA mutation was not originally detected, have since been found to have a duplication, or - more likely - a deletion. Grant’s sister-in-law could visit with a genetic counselor about this new testing option. The original result would inform the genetic counselor of the testing completed at the time of the test in 2001. There would not be a need to repeat the sequence test that was performed, but new analysis to look for a large rearrangement of BRCA1 or BRCA2 may provide the genetic key that would allow identification of at risk family members.

The promise of genetic testing is realized in the identification of those at increased risk. Individuals and their family members may use this information to attend carefully to the possibility of the development of cancer at younger than expected ages. It may also allow for early intervention in those at risk when preventive interventions are available.

Good resources for breast cancer information:

American Cancer Society: http://www.cancer.org/
Susan G. Komen: http://www.komen.org/
Facing Our Risk of Cancer Empowered: http://www.facingourrisk.org/
National Cancer Institute: http://www.cancer.gov/

Monday, September 21, 2009

The Risk Type I Have For Diabetes



From the list of 10 diseases that 23andMe reports on, three were listed in the Elevated Risk category. We have already posted on Crohn’s disease and Prostate cancer. The remaining one is Type I Diabetes. I am lucky that I do not suffer from any of these conditions, but I value the opportunity this experience has given me to learn about them, what my risks might be, what can I do about it, and what should I discuss with my doctor if symptoms arise.


Click Image to Enlarge

Last Updated

From the graphic above, did you notice that my information on Type I Diabetes has recently changed? The date under Last Updated is July 30, 2009. The report tells me that the update is because “the risks associated with SNPs rs1990760, rs1893217, rs2476601, rs3184504 and rs725613 were updated with newer values. As a result, some customers may find that their results in the Odds Calculator differ slightly from previous values.”

When I looked back, my original lifetime scores for Type I Diabetes were Absolute Risk 1.9% (now 1.7%), and Relative Risk 1.91 (now 1.67). I must be living right.

Comparing Type I with Type II

As I learned with the other diseases, my risk changes dramatically when I use the Odds Calculator and enter my age range. Although still higher than the average, my risk of developing Type I Diabetes is only 18 out of 10,000. The calculator told me that my biggest risk would have been when I was 10-14 years old.


Click Image to Enlarge

When I look at my result for Type II Diabetes, I find it under the Typical Risk category. But the odds for me developing Type II are 130 out of 10,000, or more than 7 times that of Type I. Yet Type I is in the Elevated category. My first thought was why would my risks be so different between Type I and Type II?

I understand that these risk categories are comparing me to the general population (Relative Risk). But if I ranked the 10 diseases by Absolute Risk, they would fall into different categories I would create, like the Greatest Threat category (which would include Prostate cancer 24%, Type II Diabetes 19%, Venous Thromboembolism 12%), followed by the Moderate Concern category (Psoriasis 9.9%, Age-related macular degeneration 4.3%, Rheumatoid arthritis 2.3%), and finally the Least of My Worries category (Type I Diabetes 1.7%, Crohn’s disease 1.6%, Parkinson’s disease 1.6%, and Celiac disease 0.04%). Of course this ranking could change based on any family history I discover.

More Heritability than the Other Diseases

Although the suspected environmental factors for Type I Diabetes are interesting (living in a cold climate, not being breast fed as an infant), out of the ten 23andMe reported diseases, Type I has the highest incidence with 72-88% attributable to genetics.


Click Image To Enlarge

In second place is Celiac diseases with 57-87%. Psoriasis with 66-80% came in third. At the bottom is Parkinson’s disease with only 0-1% - which I don’t understand how that could be so low. Type II Diabetes was second to last with 26%, again quite a bit different from Type I.

8 Markers for Type I

I find myself looking more closely at the markers reported on for each disease. Crohn’s had 12. Prostate had 5. Type I Diabetes is in the middle of those two with 8. Type II is close with 9. The other reported diseases have only one or two reported markers. Why the broad range in the number of markers? This is another bit of evidence that trying to figure this out is complicated.


Click Image To Enlarge

The SNP reported here in the HLA region had the strongest association with Type 1 Diabetes in one of the largest studies done so far (see the reference below). 23andMe then made an interesting alteration with this note –

The 2007 Wellcome Trust paper reported a strong association between type 1 diabetes and the SNP rs9272346. Our quality control process flagged data for rs9272346 as unreliable, so we instead included the SNP rs3129934, which is also highly associated with type 1 diabetes. Both are in the HLA region, although the exact linkage patterns between tagging SNPs and traditionally determined HLA haplotypes is still being worked out.


Click Image To Enlarge

No Family History

I can’t think of any 1st, 2nd, or even a 3rd degree relative that has diabetes of any kind. This is good because apparently there is not much one can do try to prevent the onset of Type 1 Diabetes. Here is something I learned from the MD’s Perspective section- a Q&A with Dr. Roshanak Monzavi, M.D., Assistant Professor, Center for Diabetes, Endocrinology and Metabolism, at Children's Hospital of Los Angeles -

23andMe: Historically, how have doctors used genetics or family history when assessing a person's risk of developing Type 1 Diabetes (T1DM)?

Dr. Monzavi: Unfortunately, there is currently no proven preventive measure that can be used to decrease the risk of development of T1DM in people with family history of T1DM. However, physicians are studying some interventions that may prevent T1DM or postpone its time of presentation through clinical trials such as TrialNet. Family members of people with T1DM are evaluated for certain genetic and/or immunologic markers, which put them at high risk for T1DM, and if at high risk, they may enroll in such a study to assess the efficacy of an intervention in preventing T1DM.

I discovered that a TrialNet study tests whether a daily oral insulin capsule can prevent or delay the disease in at-risk relatives of people with Type 1 Diabetes. TrialNet is also performing a pilot study testing whether docosahexaenoic acid (DHA), and omega-3 fatty acid found in some foods can prevent or delay the autoimmunity leading to type 1 diabetes. Let’s hope they succeed.



Perspective from a medical geneticist



Communicating Risk

One of the real struggles we have in genetics is trying to explain probabilities and risks to our patients. Part of this relates to our brains operating more as pattern recognition engines than analytic computers. The second and more important issue is that there really isn’t a ‘right’ answer to the risk perception question, unless one considers the individual’s perspective. We see this in the prenatal clinical setting all the time.

For some couples a slight increase in risk for a certain birth defect (say a 5% risk of having another child with a congenital heart defect) is perceived as so high as to necessitate a battery of testing options, or in some cases choosing not to have more children. In contrast, other couples at a 50% risk for an anomaly will have very few concerns about subsequent pregnancies. Thus we must expand beyond absolute and relative risks to what might be characterized as personal perception of risk.

Aligned With Absolute Risk

In his post, Grant developed his own risk categories: Greatest Threat; Moderate Concern; and Least of My Worries. He then categorizes his diseases by absolute risk such that the highest absolute risks are in Greatest Threat (with an apparent absolute risk cutoff of 10%) and the lowest are in the Least of My Worries (with an apparent cutoff of 2%). As with previous posts, Grant has clearly aligned himself with Absolute Risk. He acknowledges that discovery of relevant family history could change the ranking (it appears daily association with geneticists has successfully brainwashed him). But how would it change the assignment? Would Grant still rank this according to an adjusted absolute risk or would family history of disease have a privileged status in ranking risk?

What If the Disease Is Preventable

Another potential factor to consider would be the availability of measures to prevent disease. Would this change Grant’s ranking of the diseases? We really can’t tell with the 10 reported diseases because only one of them (type II diabetes) has preventive interventions that seem to work—at least if one extrapolates from studies of hyperglycemic patients without diabetes. For Grant, this is a moot point, as he is at an appropriate weight, eats healthily and exercises. Frankly, based on lifestyle I’m at much higher risk than Grant, although I am also blessed with a completely negative family history of either type I or type II diabetes.

So why does this matter? One of the answers has to do with what could be characterized as the utility of the information. In the MD Perspective for both type I and type II diabetes on the 23andme website both physicians acknowledge that there is currently no way to use the genomic predisposition to prevent diabetes. From the medical perspective the testing has no utility, in that the results of the test do not lead to alterations in care that improve the patient’s health outcome. This type of information is frequently used by insurers or health systems to decide whether or not a given test should be covered or even offered to patients.

Personal Utility

There is another concept that is beginning to emerge in discussion of genomic testing which is the idea of personal utility. What will this test result mean to me as a person? What will I do if the result is positive or negative? If there is no insurance coverage what am I willing to pay out of my own pocket because I believe this will help me? This principle clearly operates in medicine all the time. The supplement and nutriceutical industry not only survives but thrives as a multi-billion dollar industry almost solely on the basis of personal utility, given that there is limited evidence of increased health benefit (and despite several instances of overt harm. Fen-Phen anyone?)

Folate Flashback

I took a daily Folate supplement for a couple of years because I knew: 1) I didn’t eat as many green vegetables as I should; 2) Folate decreases serum homocysteine levels; 3) elevated homocysteine is associated with an increased risk of cardiovascular disease; 4) Even if it doesn’t help, it surely won’t hurt (and it’s easier than eating vegetables!!); 5) It’s cheap. As Folate was systematically studied, it was found that for reasons that still are unexplained, men who had higher Folate intake had more cardiovascular events. Into the trash with my Folate pills!!

Bottom line was my decision to spend discretionary income on Folate was based on a belief that Folate supplements would reduce an outcome of concern for me (a heart attack) at an acceptable ‘cost’ (price, lifestyle, added bother to remember to take the pill, etc.). For me, the ‘cost’ of actually losing weight, eating more healthily, exercising regularly, which does have demonstrated utility, is too high. My perception of the personal utility of these health behaviors is too low to justify spending time and effort to achieve them, despite abundance evidence to the contrary.

The Patient Perception Point

So what’s the point? (Aha, you assume I have one). From my perspective the issue is that we frequently ignore the disconnect between evidence of utility and a patient’s perception of utility. This leads to recommendations based on sound evidence falling on apparently deaf ears. If we make no attempt to understand what the patient is interested in and why they are interested in it, we may miss opportunities to improve health in ways we don’t anticipate. I now know that Grant is most worried about Prostate Cancer, Type II diabetes and Venous Thromboembolism. Let’s assume that Grant’s health behaviors aren’t as good as they should be. If he were overweight, would his concern about Type II diabetes based on his 23andme results present a teachable moment about what he could do to control his risk?

No way to know for sure, but it’s more likely than if his major worry was Crohns disease. I might say, Gee, Grant, you’re really concerned about diabetes and blood clots. Did you know that being overweight really increases your risk for both of those problems? In fact, losing weight has been proven to dramatically reduce your risk of developing diabetes. Is this something you’re ready take on, because if you are, I have a dietician that can help you assess your diet, and I have a list of weight loss programs that will help you to not only lose the weight, but will help you to keep it off.

The bottom line for me is listen to the patient, read between the lines, get to the patient’s concern and help them to develop a plan to address the concern. If it takes a 23andme test to get to the concern for that patient, I can live with that—and maybe they can too!

And now for something completely different

This is a complete non-sequitur, but as I was playing in Grant’s 23andme site (he lets me log in for the purposes of the blog and I only look at the topic under discussion) I found a tab called timeline. Clicking on this gives a timeline of major discoveries for the disease of interest. In the case of diabetes this goes back to 1550 BC to a citation in the Papyrus Ebers by an Egyptian physician Hesy-Ra describing sweet urine and a variety of dietary cures and ends in 2007 with the Wellcome Trust case control genome-wide association study for type I diabetes. I’m showing my geekitude (geekosity?, geekness?), but I thought it was cool.

Monday, September 7, 2009

I Want A New Drug - One That Matches My Genotype

For the readers who are just beginning to follow this blog, please know that the posts of my experience with the 23andMe service are sequential. A list of past blog posts can be found below our pictures on the right. Reading the first post entitled What Is This All About is recommended to follow this journey in context.


Exploring 23andMe's Pharmacogenomic Information

The FDA website tells us that “genomic biomarkers can play an important role in identifying responders and non-responders, avoiding toxicity and adjusting the dosage of drugs to optimize their efficacy and safety.” Simply put, pharmacogenomics is the study of how genes affect a person’s reaction to drugs, and why different people have different side effects.

The newly appointed director of the National Institutes of Health, Dr. Francis Collins, said that "pharmacogenomics, which from my perspective has been one of the most promising areas of personalized medicine, has also turned out to be extremely complicated, not that we shouldn't have known that." He also said that a blood-thinning drug called Warfarin “has become a poster child for the future of pharmacogenomics."

Looking at the 23andMe Drug Response Section

Warfarin is one of only two drugs (the other being Plavix) that appear under 23andMe’s Drug Response clinical reports section. Another section is called the Research Report. It contains my genetic information on 85 other diseases and traits based on early research that has not qualified yet for the Clinical section. This section lists the only other drug reported on by 23andMe - Statin response. (We’ll look at this section in later posts).


Click on image to enlarge

The report tells me that I have an increased risk for Warfarin sensitivity, which means that if I were ever prescribed Warfarin, my dose should conceivably be slightly less than what is considered typical. The report goes on to tell me that the CYP2C9 and VKORC1 genes are implicated in Warfarin metabolism (which I already know from my work at the Clinical Genetics Institute), and that variants in these genes are consistently associated with Warfarin bleeding complications. A patient’s age, size, other medications, and even diet, are also factored in along with the genotype to compute the most effective dose.


Click on image to enlarge

What I Learned about Warfarin

As I read further into the 23andMe report, I learn that two million people take Warfarin. I wasn’t aware that the number is that high. Blood thinners (or anticoagulants) like Warfarin are given to people at high risk for the formation of blood clots due to conditions such as deep vein thrombosis, irregular heartbeat, and heart valve disease or replacement. The drug is also given to prevent recurrence of pulmonary embolism, heart attack and stroke. Patients taking this drug have regular blood tests to evaluate their blood's clotting ability. The doctor uses the results of these tests to adjust the dose up or down accordingly. One difference I noticed between the Drug Response section of my report and the other sections is that there is no MD’s Perspective tab like here like there are for the diseases and carrier status sections.


Click on image to enlarge

Pharmacogenomic information is contained in about ten percent of labels for drugs approved by the FDA. A significant increase of labels containing such information has been observed over the last decade. To see a list of drugs currently linked to genetics, see the Table of Valid Genomic Biomarkers in the Context of Approved Drug Labels.

A Few Questions

Every genotype variation is either typical sensitivity, or some level of increased sensitivity, which means a decreased dose. Why is it that no genotype requires an INCREASED dose. If it can take weeks of dosing adjustment, what can be the problems or risks a patient might experience during that time? Why would a patient’s age affect a dose?

Don’t Worry Doc – I’m Star One, Star One

The report shows my specific genotype (CYP2C9 *1/*1) that is included in any Warfarin dosing algorithm, of which several are being studied. Under the Resources tab, 23andMe has a link to warfarindosing.org. One 23andMe customer who takes Warfarin entered his genotype and other information into this calculator and found it to be very accurate in predicting his optimal dose.


Click on image to enlarge

The past few years have seen a multitude of pharmacogenomic studies with Warfarin dosing. Intermountain Heathcare is participating in a large multi-center, randomized clinical trial with the NIH that will enroll 1,200 participants. Besides the clinical aspects, one other question being asked in some studies is cost effectiveness. Some results show that Warfarin-related genotyping is unlikely to be cost effective for typical patients with atrial fibrillation, but may be cost effective in patients at high risk for hemorrhage.

Final Thoughts

Will we have more of this pharmacogenomic info based on or genotype to be informed consumers of medications? Can this work for diet supplements? Will I see any effect from that muscle building shake? And conversely, what fat burning pill will work best for me?
Where’s the pharmacogenomic test for brain function and memory enhancement pills? Or Rogaine effectiveness? Or anti-aging therapies?



Perspective from a medical geneticist



Warfarin Pharmacogenomics

So why did Grant specifically mention Rogaine responsiveness in his last paragraph? It wouldn’t have anything to do with our pictures would it? Look, just because you’re paranoid doesn’t mean they’re not out to get you.

Seriously, before I get to the meat of the discussion let me address one question that Grant raised, “Why is it that no genotype requires an INCREASED dose.” In fact there are patients who are resistant to Warfarin and require very high daily doses. A specific alteration in VKORC1, the same gene that Grant carries a change, has been demonstrated to confer extreme resistance to the effects of Warfarin such that patients require 4-5 times the normal dose to achieve a clinical effect. This is a rare enough occurrence that routine testing for this change has not been proposed, although it is suggested that testing be considered if a patient has severe resistance. There are also non-genetic causes of Warfarin resistance (inability to absorb the drug, medications that interfere with Warfarin action).

Putting the WARF in Warfarin

Warfarin is one of my favorite drugs because it contains a shout out to my alma mater. The ‘WARF’ in Warfarin stands for Wisconsin Alumni Research Foundation, the organization responsible for commercialization of discoveries at the University of Wisconsin-Madison. GO BADGERS! (we now return you to our regularly scheduled blog). I’ve also had a lot of experience with evaluation of the genetic tests for Warfarin dosing, including co-chairing the workgroup of the American College of Medical Genetics (ACMG) that generated an evidence review and guideline for pharmacogenomic testing for Warfarin.

Tricky Drug to Manage

As Grant notes, Warfarin is a very important drug to prevent life-threatening clots in patients with a variety of predispositions. While effective, it is a very tricky drug to manage—too little drug and the patient may clot; too much and they might experience bleeding that can be life-threatening. A number of factors have been identified that affect Warfarin including age, weight, kidney and liver function, other medications and diet. Accounting for all of these factors explains only about 40% of the dose variation from patient to patient. More recently the changes in the genes CYP2C9 and VKORC1 have been shown to explain as much as another 30-40% of the dosing variation. Thus is would seem logical that testing for these genomic variants would be very important to managing this dangerous medication. Certainly the FDA seems to think so.

Introducing ACCE

In the words of college football analyst Lee Corso, “Not so fast my friend”. Let’s examine the question more closely. Glenn Palomaki and Jim Haddow developed an evaluation paradigm for genetic tests called ACCE, where ‘A’ stands for analytic validity, ‘C’ stands for clinical validity, ‘C’ stands for clinical utility and ‘E’ stands for Ethical, Legal and Social issues. For this discussion, we’ll not address ‘E’. Analytic validity addresses the question, does the test measure what it is supposed to measure and is the measurement accurate? There are a number of ways to test for the polymorphisms in the two genes of interest, and the evidence shows that they work extremely well confirming analytic validity. So far so good. The next issue is Clinical Validity which asks, is the test result associated with the ‘disorder’ of interest. In this case, the disorder of interest is Warfarin dose. There is abundant evidence that strongly supports the association of genetic variants in these two genes with ability to predict the stable Warfarin dose.

Here’s where it gets a bit murky. Based on the robust demonstration of Clinical Validity, many began to actively promote testing in the clinical setting. The argument could be summarized as follows: Given that Warfarin is a dangerous drug if dosed improperly and given that genetic testing has been shown to improve dose prediction, it logically follows that genetic testing to inform Warfarin dose will improve patient safety. On the face of it this seems extremely reasonable however there are numerous examples in medicine that refute the idea that reasonable ideas always improve patient care. What are we missing?

Clinical Utility

This brings us to Clinical Utility which simply stated asks, does the result of the test have an impact on patient outcomes of interest? An outcome is a neutral term that encompasses both positive/desirable and negative/undesirable outcomes. In the case of Warfarin, the positive outcome of interest is achieving an appropriate level of anticoagulation for a given patient. The negative outcomes can be associated with not providing enough anticoagulation (undertreatment) leading to clotting, or providing too much anticoagulation (overtreatment) leading to bleeding. From the patient perspective neither is desirable, that is it’s just as bad to die from a clot as from a bleed.

Because these severe adverse outcomes are relatively infrequent, it is difficult to study these outcomes directly. Researchers fall back on secondary measures (e.g. time to stable dose, time in therapeutic range) that have some evidence that links them to the clinical outcomes of interest. In the case of Warfarin, there are almost no data that address the issue of clinical utility. The evidence review used by the ACMG workgroup to generate its policy statement identified numerous gaps in evidence such that the workgroup’s conclusion (subsequently endorsed by the ACMG leadership) was that there was insufficient evidence to recommend for or against testing. (Click here for the evidence report and policy statement).

The Problem of Bleeding

Another problem is that virtually all the papers addressing this issue focused on the problem of bleeding. As noted above, this is one of two potential negative outcomes and they are two sides of the same coin. To absurdly illustrate this, let’s assume that we want to eliminate all bleeding events caused by Warfarin? The obvious decision would be to not use Warfarin at all. Sure patients would experience clots, but at least they wouldn’t die of bleeds!! Returning to reasonableness requires the acknowledgement that reducing bleeds could increase the risk of clots. The evidence needs to define the relative balance between these two adverse outcomes in order to decide if a strategy has net benefit or net harm. (This problem is not unique to Warfarin. It is disturbing to me that studies consistently focus only on prevention of adverse events even when there is evidence that this could also reduce effectiveness. Subject for another rant…I mean blog).

Intermountain Healthcare Study

To attempt to answer the utility question a prospective randomized clinical trial was conducted at our institution (Intermountain Healthcare) by Dr. Jeff Anderson and his team (reference below). The results of this small trial did not show a net benefit except in certain rare genotypes and interestingly enough in patients with no polymorphisms (so called wild type). It turns out we consistently underdose wild type individuals slightly increasing their risk of clotting. The magnitude of this effect is small, but given that the wild type genotype is the most common, the collective effect may be much larger than anticipated—potentially offsetting the reduction in bleeding events.

My group in conjunction with researchers from the University of Washington used this study to examine the cost-effectiveness of testing, the results of which will appear in the journal Pharmacoeconomics in the near future (authors Meckley, Williams, Gudgeon, Anderson and Veenstra). It is interesting to note that none of the references that raise questions about the evidence for testing, or the Anderson study are listed in the 23andME reference list. Why is this? Are they deliberately trying to hide this information? (Excuse me while I adjust my tin foil hat—the black helicopters are back).

The Economic Issue

What’s the big deal? If it’s possible that we might be doing good why not test, given that the test cost is fairly cheap (estimated at ~$200 clinically). You may have heard something about the health care crisis we have—it’s been in all the papers (Oh right, we don’t read papers any more. Forget I mentioned it). Let’s do a little math. If we accept that 2 million people are on Warfarin and we assume that they all got the test at $200, then we’ve just cost somebody 400 million dollars! If we get no improvement in medical outcomes (or worse we get poorer outcomes), we’ve injected significant cost into the system with no return in improved health. We can no longer afford to behave like this.

Thankfully, others have recognized this issue and there are several large scale prospective studies that are examining genetic testing for Warfarin dosing (include a follow-up study by Dr. Anderson at our institution). Hopefully this means we will know whether or not we should do testing by the time Grant really needs to go on Warfarin!

References

McClain MR, Palomaki GE, Piper M, Haddow JE. A rapid-ACCE review of CYP2C9 and VKORC1 alleles testing to inform warfarin dosing in adults at elevated risk for thrombotic events to avoid serious bleeding. Genet Med. 2008 Feb;10(2):89-98.

Flockhart DA, O'Kane D, Williams MS, Watson MS, Flockhart DA, Gage B, Gandolfi R, King R, Lyon E, Nussbaum R, O'Kane D, Schulman K, Veenstra D, Williams MS, Watson MS; ACMG Working Group on Pharmacogenetic Testing of CYP2C9, VKORC1 Alleles for Warfarin Use. Pharmacogenetic testing of CYP2C9 and VKORC1 alleles for warfarin. Genet Med. 2008 Feb;10(2):139-50.

Anderson JL, Horne BD, Stevens SM, Grove AS, Barton S, Nicholas ZP, et al. Randomized trial of genotype-guided versus standard warfarin dosing in patients initiating oral anticoagulation. Circulation. 2007 Nov 27;116(22):2563-70.

Meckley LM, Gudgeon JM, Anderson JL, Williams MS, Veenstra DL. A Policy Model to Evaluate the Benefits, Risks, and Costs of Warfarin Pharmacogenomic Testing. Pharmacoeconomics in press.