I’m From the Future

I recently had my first visit to a doctor since getting my results from 23andMe. I have only been in New Mexico for six months, and hadn’t yet selected a primary care physician from the list provided by my employer, the University of New Mexico. The health insurance plan has a website with all of the available primary care physicians. There are a lot of them. As a geneticist, I am familiar with the concept of a screen, used to identify interesting genetic variants in an experimental organism. Here was my screen: I needed an internist rather than someone specializing in family medicine or general practice. Although I knew that genetics, let alone genomics, is given very little coverage in medical school, I still wanted someone who had graduated relatively recently from a good medical school with a strong record of externally funded research.

While going through lists of physicians, I had in mind much of the reading that I have done in the area of personal genomics over the last several months, and some of the presentations from the GET 2012 conference in April. Several participants in the Personal Genome Project have brought in very detailed genetic information to their doctors, and recounted their experience. I think that it is fair to say that there is a consensus that most physicians are not prepared to deal well with patients with genomic data. They are not specifically trained to deal with data of this kind. There has also been a fairly high-level reaction from physicians against personal genomics. One of the warning shots came in 2008, when An Unwelcome Side Effect of Direct-to-Consumer Personal Genome Testing by Amy McGuire and Wylie Burke appeared in Journal of the American Medical Association (1).

McGuire and Burke remind us that physicians are accustomed to talking to patients about health information from the Internet and other media. My father, who was a physician, talked about the “Reader’s Digest” effect in medical practice. In the 1960s and 1970s, every month there was a cluster of patients asking to be checked for some specific malady, typically one that had just been covered by a popular article in Reader’s Digest. Of course, this was before the proliferation of cable TV channels and the limitless supply of medical advice, some of it terrible, to be found on the Internet. McGuire and Burke point out that physicians have limited time with patients and are poorly compensated for preventative care. I understand that and sympathize, but if we are ever going to make any progress on containing the costs of health care, patients and physicians are going to have to become partners in preventative care. If the system is not set up to facilitate that, we will have to change the system.

McGuire and Burke write “The clinical value, if any, of most direct-to-consumer personal genome tests remains unproven.” They take particular aim at the long list of risk estimates for specific diseases that is provided by direct-to-consumer genetic testing firms like 23andMe. Here is what the top of my “Elevated Disease Risk” page looks like at 23andMe:

I am only showing the results that place me at increased risk. There is a list of conditions for which I have a reduced risk, and a list for which I have an typical risk (shown later). When you look at my elevated risk list, you would have to conclude that I am a really lucky guy with a great genome. Clicking the links takes you to more detailed information. I discover that my top risk, for Venous Thromboembolism, results from my blood type (I’m AB+). Venous Thromboembolism has a heritability of 55%, which means that 45% of your risk is due to non-genetic factors. There is some advice on prevention. Don’t smoke (always good advice; I have never smoked). Keep your weight in check (good advice for many reasons). Get up and move, because sitting still for long periods of time places you at risk for Deep Vein Thrombosis (“economy class syndrome”). I wish I could get my employer to spring for First Class when I fly, but they won’t.

The other elevated risks are marginally elevated risks for rare conditions. I can see the point that McGuire and Burke are making here. There is no way that I am bringing this list in to a physician. There is nothing here that is medically actionable. I already know that the best general preventative health information that you can currently give to anyone would fit on an index card: Don’t Smoke, Maintain an Ideal Weight, Eat a Balanced Diet, Get Regular Exercise, Reduce Stress.

McGuire and Burke raise the problem of the burden on the health care system of increased testing due to requests by patients. Tests may produce ambiguous, incidental, or false-positive results. This might cause another round of more expensive, invasive, and dangerous tests in the pursuit of nothing. I understand this argument. It is therefore my responsibility as a patient (albeit an overeducated one) to avoid this downward cycle by asking only about genomic findings that are clinically relevant and medically actionable. I am in an excellent position to do that.

The current consensus is that the average person, at this time, will get one medically significant result from having their genome analyzed. Some people get zero (that’s actually good news), some people get two. I got one: increased risk of hemochromatosis. There is a wonderful discussion area on 23andMe where people write about their findings and report new information from the medical literature. I quickly found some highly informative discussion threads on hemochromatosis. I found many people with my genotype (HFE – H63D/C282Y). They described their experiences with their physicians, and gave advice on which blood tests to get done: serum ferritin, serum iron, total iron binding capacity, transferrin saturation. They told me to go see a doctor, and asked me to let them know how things turned out.

My screening of the physician list turned up some promising candidates. I decided to start with Dr. Patricia Morrow, who graduated from medical school in 1986 from the University of Texas at San Antonio. She was accepting new patients, but those appointments were on days that conflicted with my teaching schedule, so we had to set a date after classes were over, a month from when I first called. But that was fine with me, no emergency.

In the month leading up to my appointment, I had a look at my other results (Decreased Risk and Typical Risk) from 23andMe, shown in part below:

Wow, forget my elevated risk for Ulcerative Colitis at 1.1%. Look at my risk for Obesity (63.4%) or Type 2 Diabetes (18.7%). I click through on the Diabetes link and find out that Type 2 Diabetes has a heritability of only 26%. That’s actually good news; 74% of the risk is up to me. This is where it gets familiar. Maintain an Ideal Weight. Eat a Balanced Diet. What about my 50.2% risk of Coronary Heart Disease? This one is a little foggy, with the heritability estimated at 39-56%. What can I do to avoid this? Maintain an Ideal Weight. Eat a Balanced Diet. Don’t Smoke. Exercise Regularly.

So I decided to make my visit to the doctor as productive as possible. I printed out the summary page on Hemochromatosis. I had already modified my diet. I cut down my consumption of red meat, with its high availability of heme iron, to perhaps once or twice a week, a pretty big change for me. I knew the blood tests that I wanted, but because my last physical was in 2009, I decided that I needed the usual reports on triglycerides, HDL, and LDL. The high incidence of Type 2 Diabetes bothered me, so I decided to get a fasting glucose level as well.

Finally, the big day came. I skipped breakfast and lunch to be ready for a fasting glucose level test at 2:00 pm. Because my wife and I are down to one car since we moved to New Mexico, and it was a nice day, I walked the three miles to the doctor’s office.

Dr. Morrow’s office is in a wonderful old building not far from Old Town in Albuquerque. I checked in, filled out the insurance and medical history forms, and presented the summary page on hemochromatosis for my file. A nurse checked by blood pressure (118/80, not bad at all) and asked a few questions before Dr. Morrow came in.

She knew that I was a new patient and that I was there to get a primary care physician to allow me to navigate the health care system here if need be. She also knew that I had come to be evaluated for hemochromatosis. She opened my folder, took out the report from 23andMe, and asked, “What is this?”

“It’s a report from a personal genomics company. I had my genome analyzed, and I found that I’m at risk for hemochromatosis. I’d like to get some specific blood tests,” I said. “I’m from the future,” I continued, “In ten years, most of your patients will be coming in here with reports like this.”

Dr. Morrow took it really well, and we had a great conversation. At one point I told her that she should get CME credits for talking to me, but she knew which activities got her points and which didn’t. She got my medical history, which is unremarkable, and we talked about a few specifics. My family history is uncommonly free of major heritable illnesses. There is no family history of hemochromatosis. I have moderate ocular hypertension, monitored by my eye doctor but never progressing to the point at which it required medication (my mother and my brother have been treated for this). I have Seasonal Affective Disorder, managed by diet and light therapy in our parrot room. Managed is an inadequate word for this, of course. Mitigated would be better. Medical language attempts to be polite, which is why we call it Seasonal Affective Disorder, rather than Having Your Mind Dragged Off to Hell by Demons During the Winter.

“So,” she asked, “What are you going to die of, then?”

“Not boredom,” I immediately replied. We got back onto hemochromatosis. Dr. Morrow pointed out that I didn’t have any symptoms, and asked me what my chances were of developing them. I told her that most people with my genotype never develop any symptoms, but I was likely to have high levels of iron. She asked whether we knew what caused iron to deposit in tissues, and of course I said no. Studies in mice show that there are several genes, some of whose identity is unknown, that affect the level of serum iron in mice lacking a functional HFE gene (2, 3, 4). In humans, there is a wide range in iron levels in people with the same HFE genotype, and there is genetic variation in genes that may modify the development of hemochromatosis. In both humans and mice, it seems likely that there are unknown genes that affect the level of iron accumulation in tissues. I said that I thought that the medical literature at the present time was mostly written backwards: most of the studies are of people with symptoms of hemochromatosis, who are then genotyped. As far as I know, we don’t have any prospective studies that follow a group of people with a genotype like mine to see how many develop symptoms.

We got down to figuring out which blood tests to order. At this point, Dr. Morrow was ticking boxes off on a form: ferritin, serum iron, total iron binding capacity, transferrin saturation. Glucose and lipids. That should do it.

“I need a code,” she said.

All I could think of was the genetic code. Sixty-four triplets of A, T, C, or G. Good for encoding twenty amino acids with some degeneracy, plus start and stop signals. I decided not to say anything about the genetic code, as we had already had a fairly extensive conversation about genetics. So I just asked what sort of code she needed.

“A reason that we are ordering these tests,” she said. “I know. Fatigue.”

“Yes,” I said, “I’m very tired, and I hurt all over.” Actually, I was fine. The walk to her office had lifted my spirits.

She mentioned that one of the consequences of genome analysis might be unnecessary testing. I told her that I was confident that the testing was necessary, and that in the long run we were going to save the health care system a lot of money by engaging in preventative care. If my iron levels were dangerously high, I would be bled on a regular basis to get back to normal levels and prevent the progression of the disease.

We were still talking when the nurse came back in to remind her that she had a patient waiting. We had talked for over half an hour.

About a week later, my results were in. My serum ferritin was 351, at the high end of the normal range of 30 – 400 for males. I have corresponded with people who have my HFE genotype with ferritin levels of 1000; they were bled regularly until they reached 500. I knew right away that I did not have to start a program of leeching. My other iron-related numbers were a bit above normal, but not dangerously so: serum iron, 184 (normal 65-176); total iron-binding capacity 297 (normal 240-450); transferrin saturation 62% (normal 20-50%); hematocrit 51.4 (usually up to 45). Dr. Morris told me that we were not going to have to start a course of phlebotomy. If she was surprised that a genetic test had predicted my blood chemistry in the absence of a family history, she didn’t show it on the phone.

Everything else was fine, as it always has been. My fasting glucose was 94, so I am not pre-diabetic. My triglycerides were 68, HDL was 74, LDL was 121. The last is a bit high, but I haven’t been working out in a gym since I relocated. I am going to have to get back to that.

My experience with Dr. Morris was terrific. She was really interested in learning about how personal genomics was going to impact the practice of medicine. I think that she is glad to have a patient who is going to be an educated partner in preventative care.

So, it’s working out well for me, even though we need to change the system. There is no box to check to tell the insurance company that I need a test as part of a program of preventative care based on the results of having my genome analyzed. We are a long way from the system of personalized medicine that I have been hearing about in seminars for the last ten years.

As I was writing this, I went back into the literature to see if we know anything about genes that interact with HFE. Hemochromatosis is a disease that has incomplete penetrance, which is a fancy way of saying that not everyone who is HFE – H63D/C282Y like me develops symptoms. Do we know anything yet about genetic variation that modifies the risk of developing hemochromatosis given a particular genotype at HFE?

There are some promising studies in mice. The TMPRSS6 gene encodes a transmembrane serine protease that, in both humans and mice, has the opposite effect of the HFE gene on serum levels of hepcidin, a peptide hormone that inhibits dietary iron uptake. HFE/HFE mice resemble HFE – C282Y/C282Y humans in that they have high serum levels of iron and accumulate iron in the liver. When HFE/HFE mice are heterozygous for a loss-of-function mutation in TMPRSS6, they have reduced iron overload. HFE/HFE mice that are homozygous for a loss-of-function mutation in TMPRSS6 actually have an iron deficiency (5). This also suggests a therapy: “Furthermore, these results suggest that natural genetic variation in the human ortholog TMPRSS6 might modify the clinical penetrance of HFE-associated hereditary hemochromatosis, raising the possibility that pharmacologic inhibition of TMPRSS6 could attenuate iron loading in this disorder.”

It is known that there is genetic variation in human populations for TMPRSS6 (6). People who are homozygous for a loss-of-function allele of TMPRSS6 have an inherited disease called Iron-Refractory Iron Deficient Anemia (IRIDA). In this condition, patients have anemia with no evidence of reduced dietary iron. They fail to respond to oral iron therapy. They respond somewhat to intramuscular iron injection (not a pleasant prospect). This condition is the opposite of hemochromatosis. People with IRIDA may have adequate levels of iron in their diet, but they don’t take it up, and their blood levels of iron are far below normal.

The studies in mice show us that these two genes with opposite effects interact. Let us simplify the situation by considering only normal (HFE+ and TMPRSS6+) and loss-of-function alleles (HFE and TMPRSS6). Here is a summary table to show the interaction.

HFE TMPRSS6 Phenotype
+/+ +/+ Normal
+/+ -/- IRIDA (anemia)
-/- +/+ Hemochromatosis
-/- +/- Hemochromatosis, but more normal
+/- -/- IRIDA (anemia), but more normal?

 

It is also possible to imagine that heterozygosity for the common alleles of HFE (HFE+/HFE) might somewhat protect a person homozygous for a loss-of-function allele (TMPRSS6/TMPRSS6) from the symptoms of IRIDA.

So, is there any evidence that I am heterozygous for a protective allele of TMPRSS6? While my 23andMe results show my genotype with respect to SNPs in TMPRSS6, none of these SNPs is associated with loss-of-function alleles. The variant alleles of the HFE gene that I carry, HFE – H63D and HFE – C282Y, are identified in the 23andMe test by specific oligonucleotides that detect these variants, which are common in human populations. The discovery of variation in the TMPRSS6 gene is relatively recent (6), and the 23andMe test does not include results that will predict my genotype at TMPRSS6.

In February, I became part of a pilot program at 23andMe to have my exome sequenced. Most of the human genome does not encode proteins. The small portion of the human genome that does encode proteins is called the “exome.” The exome is only about 2% of the genome. In exome sequencing, genomic DNA is melted to single strands and hybridized to a vast array of oligonucleotides designed with knowledge of the sequence of the human genome. Strands of DNA from the genome being analyzed hybridize to the collection of oligonucleotides that selects for coding sequences, and are then sequenced. The rest of the genome is not. Exome sequencing is the poor man’s way of having the most highly informative parts of the genome sequenced while we wait for the cost of whole-genome sequencing to drop further.

I am still waiting for my exome sequence from 23andMe. They promised a four-month wait, which would give me my results in the middle of June, not long from now. I may very well be heterozygous for a loss-of-function allele of TMPRSS6, or have some other kind of genetic variation that protects me from hemochromatosis despite my HFE – H63D/C282Y genotype.

There is independent evidence to suggest that I carry a protective allele of TMPRSS6 or some other modifier gene. My mother has been borderline anemic all of her life. She tells me that she was given oral iron therapy as a child, and even intramuscular iron injections to treat her anemia. Her current physician has been campaigning to get her to add more red meat and other iron sources to her diet. This does not appear to be having any effect. It may be that my mother has IRIDA, modified by her genotype at HFE. Although she has not had her genome analyzed, she must be at least heterozygous for one of the two HFE alleles that I carry, HFE – H63D or HFE – C282Y, because I had to inherit one of my two alleles from her.

We’ll see when I get my exome results. I will post the findings when I get them.


References

1. Amy L. McGuire and Wylie Burke (2008). An Unwelcome Side Effect of Direct-to-Consumer Personal Genome Testing. Raiding the Medical Commons. JAMA. 300(22):2669-2671.

2. Joanne E. Levy, Lynne K. Montross and Nancy C. Andrews (2000). Genes that modify the hemochromatosis phenotype in mice. J Clin Invest. 105(9):1209–1216.

3. Mounia Bensaid, Séverine Fruchon, Christine Mazères, Seiamak Bahram, Marie-paule Roth, Hélène Coppin (2003). Multigenic control of hepatic iron loading in a murine model of hemochromatosis. Gastroenterology 126: 1400-1408.

4. Gaël Nicolas, Nancy C. Andrews, Axel Kahn, and Sophie Vaulont (2004). Hepcidin, a candidate modifier of the hemochromatosis phenotype in mice. Blood 103: 2841-2843.

5. Karin E. Finberg, Rebecca L. Whittlesey, and Nancy C. Andrews (2011). Tmprss6 is a genetic modifier of the Hfe-hemochromatosis phenotype in mice. Blood 117: 4590-4599.

6. Karin E Finberg, Matthew M Heeney, Dean R Campagna, Yeim Aydnok, Howard A Pearson, Kip R Hartman, Mary M Mayo, Stewart M Samuel, John J Strouse, Kyriacos Markianos, Nancy C Andrews & Mark D Fleming (2008). Mutations in TMPRSS6 cause iron-refractory iron deficiency anemia (IRIDA). Nature Genetics 40:569 – 571.

Hard Times for My Ancestors Have Marked My Genome

In this post, I present one small part of the tale of how the tribulations of my ancestors have left their mark upon my genome. I’m not sure who is reading this blog. I don’t know the average level of understanding of genetics among my readers. I have recently participated in the online discussions at 23andMe, where it is clear that many subscribers are struggling with the basics. This post will therefore contain a bit more background information than the average genomics blog. Some of the more technical information and citations are included in the footnotes.

Inherited genetic variation makes us different from each other. We all have the same genes, but every gene comes in different “flavors,” called alleles. Different alleles of a gene differ in their DNA sequence. Under some circumstances, alleles that eliminate the function of a gene can confer a selective advantage, meaning that people carrying that allele are likely to have more offspring. Changes in the frequency of a particular allele in a population (the “allele frequency”) over time can alert researchers to interesting problems in biology and medicine.

Most of the single nucleotide polymorphisms (SNPs) that are typed by 23andMe are “neutral.” They are sequence variants in parts of the genome that do not encode proteins. It doesn’t matter which base is present at that position, so natural selection does not change the frequency of a particular variant of this type directly. A small fraction of the SNPs typed by 23andMe are diagnostic for a variant allele of a gene that changes the sequence of the protein encoded by that gene. These variants have been discovered through research on people affected by an inherited disorder. A probe specific for the disease allele has been incorporated into the tests done by 23andMe. In my last post, I discussed three such variant alleles that I carry.

The variant allele that I carry for the PEX1 gene, PEX1-G843D, has an allele frequency of 0.001-0.002 (1). This means that if we look at all of the PEX1 alleles in a population, 0.1-0.2% of the alleles are the PEX1-G843D variant. The PEX1-G843D allele is a bad thing. While carriers like myself are unaffected, homozygotes (PEX1-G843D/PEX1-G843D) usually die before they reach one year of age. Why doesn’t natural selection “get rid of” this nasty allele?

The frequency of PEX1-G843D is at most 0.002. Assume for simplicity that there are no other variant alleles of PEX1, so the frequency of the wild-type (normal) allele is 0.998. If people mate at random without regard to their PEX1 genotype, we can calculate the frequency of the three possible genotypes as PEX1/PEX1 = 99.6%, PEX1/PEX1-G843D = 0.4%, and PEX1-G843D/PEX1-G843D = 0.0004% or 4/1,000,000 (2). PEX1-G843D is subject to negative selection, but this no longer changes the allele frequency of PEX1-G843D very much. There are about 1000 times as many heterozygotes (PEX1/PEX1-G843D) as there are homozygotes (PEX1-G843D/PEX1-G843D), so the allele frequency can’t be driven much lower by selection alone.

What about hemochromatosis? I am a “compound heterozygote” for two different variant alleles of HFE: HFE-H63D and HFE-C282Y. HFE-H63D has an allele frequency of 0.108 (10.8%) in a large diverse population sample from the Exome Sequencing Project and an allele frequency of 0.179 (17.9%) in a sample confined to Europeans (3). It is hardly surprising that I carry one HFE-H63D allele given my European ancestry. HFE-C282Y has an allele frequency of 0.047 in the sample from the Exome Sequencing Project and an allele frequency of 0.042 in a sample confined to Europeans (4). The protein encoded by the HFE-H63D allele has greatly reduced function, while the protein encoded by the HFE-C282Y allele is almost completely nonfunctional.

We know from studies of patients with hemochromatosis that the vast majority are HFE-C282Y/HFE-C282Y. A small fraction of hemochromatosis patients are HFE-C282Y/HFE-H63D like me. The rest have other variant alleles of HFE, or variant alleles of one of four other genes that predispose to hemochromatosis (5). The high frequency of variant HFE alelles raises an interesting question. Why might being a carrier for an inherited disorder be a good thing?

There are plenty of examples of disease genes that confer an advantage on carriers. Among people of European descent, the second most common inherited disorder (after hemochromatosis) is cystic fibrosis, resulting from defects in the CFTR gene. It is the most frequent inherited disorder leading to childhood deaths. The cumulative allele frequency for all variant alleles (there are many) is around 0.03 – 0.05 in people of European descent (6). Taking the low number (0.03) gives us the following genotype frequencies: CFTR/CFTR = 94%, CFTR/CFTR-variant = 5.8%, and CFTR-variant/CFTR-variant = 0.09% or 9/10,000 (7).

Almost 1/1000 children born to parents of European descent are afflicted with cystic fibrosis, in contrast to 4/1,000,000 for PEX1 variants (Zellweger Syndrome). About one person out of twenty of European descent is a carrier of a variant allele of CFTR, while only one person in 250 is a carrier of PEX1-G843D. People who are heterozygous for a variant allele of CFTR are healthy, but have additional genetic advantages: they are resistant to cholera and typhoid fever. Although these diseases are present outside of Europe, carriers of cystic fibrosis have salty sweat, and the loss of salt in hot climates may outweigh the advantages of disease resistance.

There are other examples of disease resistance conferred to carriers of genetic disorders. Three well-known inherited diseases confer resistance to malaria: sickle-cell anemia (HBB), thallasemia (HBB), and Favism or G6PD deficiency (G6PD). In a sample of 114 chromosomes from sub-Saharan Africa, the frequency of the sickle-cell allele of HBB was 11.4%, but it is not found in European populations. In some African populations, the allele frequency of a common variant of G6PD conferring malaria resistance is 20%. Other loss-of-function alleles of G6PD are common in Mediterranean or South Asian populations (8, 9).

Why might loss of function of the HFE gene, which leads to hemochromatosis, have a selective advantage? There are two interesting ideas about this. The first idea is that reduced function of HFE was a useful adaptation to the neolithic diet (10). When our ancestors switched from being hunter-gatherers to the practice of agriculture, the amount of red meat (a great source of iron) in people’s diets fell. The switch to a grain-based diet meant that careful biological regulation of the amount of iron taken in from the diet was no longer optimal. People with a defect in the signaling mechanism controlling iron uptake (of which the HFE gene product is a part) would experience iron overload, but might have an advantage during times of iron starvation, because it takes longer to deplete their body’s supply of iron.

While this allowed the allele frequency for variant alleles of HFE to rise, it might not fully account for the high frequency of HFE-H63D among people of European descent. There is a really great story here, first proposed by Sharon Moalem in a scientific paper (11) and popularized in his book Survival of the Sickest (12). Dr. Moalem has proposed that variant alleles of HFE rose to their current high frequencies because they confer resistance to bubonic plague, also known as the Black Death.

The Black Death is a bacterial infection caused by Yersinia pestis. People are infected with the bacterium when they are bitten by infected fleas, which are carried throughout the population by rats. When the plague bacterium enters the bloodstream, it is attacked by white blood cells called macrophages, which travel to the lymph nodes to carry out the destruction of the invaders. For most bacterial infections, this is usually a good strategy. However, the plague bacterium is often able to survive as a passenger in the macrophage, permitting the bacterium to attack the lymph nodes, causing one of the ghastly symptoms of bubonic plague: lymph nodes that swell to the size of an egg, sometimes bursting through the skin.

The plague bacterium needs nutrients to thrive, and one nutrient in particular is usually in short supply: iron. While people with reduced HFE function generally experience iron overload, this does not affect all cells in the body equally. Macrophages from people carrying variant alleles of HFE are deficient in iron. The iron-poor environment in the macrophage among HFE-deficient people allows the macrophage to gain the upper hand against the bacterium. The Black Death of the 14th century killed 30-50% of the population in a number of European countries. If variant HFE alleles conferred an advantage against this devastation, the allele frequency could have risen sharply among the survivors. While the Black Death is no longer part of the landscape in Europe, there is not much selection against variant HFE alleles. People with hemochromatosis do not usually display symptoms until they are past the age where most people have already had children. Because hemochromatosis does not interfere with reproduction, there is no selection against it.

In my case, it is possible that there was selection for incresed body stores of iron (and hence reduced HFE function) in my immediate ancestry. Both of my parents survived starvation during World War II. My mother, who is Dutch, lived in Holland through the entire war, and endured the Hongerwinter (“hunger winter”) of 1944. My father, who was Hungarian, spent the last 18 months of the war in a Soviet POW camp under harsh conditions. Both of my parents survived conditions in which there was widespread death from malnutrition, or from causes in which malnutrition was a factor.

I don’t wish to make light of my parent’s experience, or of the experience of my more remote ancestors who lived through the Black Death. Yet we have the genetic hand that we were dealt, and it is up to each of us to play it well. I intend to be evaluated for iron overload by a physician, and have already changed my diet, sharply reducing my intake of red meat. Humor is also an important aspect of health. In that spirit, I made this slide for one of my recent talks.

In my next post, I will go more deeply into my ancestry, as revealed by genetic testing.


Footnotes

1. The allele frequency of the PEX1-G843D allele is taken from the OMIM entry for PEX1

2. The frequency of the three PEX1 genotypes is calculated given an allele frequency of 0.002 for PEX1-G843D and 0.998 for the normal PEX1 allele as follows:
PEX1/PEX1 = 0.998 * 0.998 = 0.996 or 99.6%
PEX1/PEX1-G843D = 2 * 0.998 * 0.002 = 0.003992 = 0.4%
PEX1-G843D/PEX1-G843D = 0.002 * 0.002 = 0.000004 or 4/1,000,000

3. The allele frequency for HFE-H63D is taken from the dbSNP entry for rs1799945.

4. The allele frequency for HFE-C282Y is taken from the dbSNP entry for rs1800562.

5. Please see the OMIM entry for HFE and hemochromatosis  and for four other genes causing hemochromatosis (HJV, HAMP, TFR2, and SLC40A1).

6. Please see the OMIM entry for CFTR.

7. The frequency of the three CFTR genotypes is calculated given an allele frequency of 0.03 for all CFTR-variant alleles and 0.97 for the normal CFTR allele as follows:
CFTR/CFTR = 0.97 * 0.97 = 0.9409
CFTR/CFTR-variant = 2 * 0.97 * 0.03 = 0.0582
CFTR-variant/CFTR-variant = 0.03 * 0.03 = 0.0009 or 9/10,000

8. Please see the OMIM entry for HBB for more information about sickle-cell anemia and thalassemia. 

9. Please see the OMIM entry for G6PD for more information about favism.

10. Christopher Naugler (2008) Hemochromatosis: A Neolithic adaptation to cereal grain diets. Medical Hypotheses 70: 691-692.

11. S. Moalem, M.E. Percy, T.P.A. Kruck, and R.R. Gelbart (2002) Epidemic pathogenic selection: an explanation for hereditary hemochromatosis? Medical Hypotheses 59: 325-329.

12. Sharon Moalem with Jonathan Price (2008) Survival of the Sickest, Harper Perennial.

Getting My Genome Done

I am a geneticist with a varied career that has included research and teaching at a variety of academic institutions. In 2000, I shut down my research lab and took a job in bioinformatics, just as the human and mouse genome sequences were being completed. In November of 2011, I moved to a new position at the University of New Mexico, funded in part by the National Human Genome Research Institute. My new position involves teaching and public outreach. Recent progress in human genomics has been spectacular, and it is a great story to tell. I thought that knowledge about my own genome would motivate my learning about human genetics and would also personalize my presentations, so I decided to “get my genome done.”

There are several ways of getting a look at your own genome. Of the direct-to-consumer companies, I liked 23andMe. At the 2011 SACNAS National Conference in October, I heard a talk by Dr. Joanna Mountain, Senior Director of Research at 23andMe. Dr. Mountain talked us through 23andMe’s website as seen by a user. The 23andMe website offers information on inherited health conditions and ancestry based on a person’s genome. I liked their user interface. They present results in language accessible to people without an extensive background in science. Users are only a few clicks away from full technical data, including complete raw data that can be uploaded to third-party sites for further analysis.

I signed up for 23andMe using their website, and soon received a kit in the mail for sample collection. They recover DNA from saliva using a very clever method. Following the illustrated instructions, I spit into a plastic tube equipped with a funnel. When my saliva reached the fill line, I flipped a cap into place that dumped a solution into the saliva sample. I capped the tube and inverted it a few times. As I did this, I saw the familiar sight of DNA coming out of solution in an ethanol precipitation. I have isolated plenty of DNA in my days as a researcher, but this was the first time that it was my own. I packed the tube in the postpaid return mailer, dropped it off at the Post Office, and waited.

After a few weeks, I got an email from 23andMe that my results were ready. I had purchased their only offering at the time, a survey of my genotype using the Illumina OmniExpress Plus Genotyping BeadChip. This technology allows genotyping of a human DNA sample at about one million genomic sites. The sites that are genotyped are Single Nucleotide Polymorphisms (SNPs) that have been identified as sites of variation in survey sequencing of human populations. The 23andMe chip includes some SNPs that are the sites of mutation in well-studied genetic disorders. For example, the chip tests for 31 different sequence variants of the CFTR gene associated with Cystic Fibrosis.

Although I am healthy and free from any known genetic disease, I looked at my Carrier Status. The screenshot below shows part of the 23andMe report.

There are 44 genetic disorders listed on this page. The disorders are listed in alphabetical order. If you have a variant allele for any of them, it sorts to the top of the page. I had two: Zellweger Syndrome Spectrum, and variants associated with hemochromatosis, a disorder in which excess iron is taken in from the diet.

The Zellweger Syndrome Spectrum gene tested for is PEX1, a gene required for the normal formation of peroxisomes. Peroxisomes are membrane-bound vesicles inside of cells that are required for the catabolism of fatty acids and other compounds. Fortunately for me, I am a carrier, which means that I am heterozygous. I have one working copy of PEX1 and one bad copy. There are no health consequences for carriers. People homozygous for the allele of PEX1 that I carry generally die before they are one year old. This is why this gene is listed on the Carrier Status page; no one homozygous for the mutant PEX1 allele G843D has a computer, a credit card, and a 23andMe account.

My Hemochromatosis report is more complex. I have two different variant alleles of the HFE gene, one of which slightly predisposes to hemochromatosis, while the other causes a considerable increase in risk of the disease. Here is a screenshot of the page that appears when you click on the Hemochromatosis link.

There is a link to a technical report. The technical report is very detailed. Part of it is shown below.

The good news is that my risk for developing hemochromatosis is quite low. Nevertheless, I decided to modify my diet and to ask for some specialized tests the next time I visit a doctor. I will discuss this in greater detail in another post.

There are also discussion forums at 23andMe. I participated in these for a couple of weeks before launching this blog. Not everyone has training in genetics, even among 23andMe subscribers, so I will take this opportunity to explain the language used in the technical report.

Most genes encode proteins. A protein (polypeptide) is a chain of amino acids; there are twenty primary amino acids that make up the set that can be encoded by the 64 three-base codons of the genetic code. There are single letter codes for each of the twenty primary amino acids. The HFE gene encodes a protein 348 amino acids long. The H63D allele changes the 63rd amino acid from histidine (H) to aspartic acid (D). The C282Y allele changes the 282nd amino acid from cysteine (C) to tyrosine (Y).

The C282Y allele results in a significant loss of function of the HFE protein. The cysteine residue at that position is highly conserved, meaning that when you look at the HFE gene in other organisms, there is usually a cysteine at that position. This is a highly significant risk allele. From the OMIM entry:

“In patients with hemochromatosis, Feder et al. (1996) identified an 845G-A transition in the HFE gene (which they referred to as HLA-H or ‘cDNA 24’), resulting in a cys282-to-tyr (C282Y) substitution. This missense mutation occurs in a highly conserved residue involved in the intramolecular disulfide bridging of MHC class I proteins, and could therefore disrupt the structure and function of this protein. Using an allele-specific oligonucleotide-ligation assay on their group of 178 patients, they detected the C282Y mutation in 85% of all HFE chromosomes. In contrast, only 10 of the 310 control chromosomes (3.2%) carried the mutation, a carrier frequency of 10/155 = 6.4%. One hundred forty-eight of 178 HH patients were homozygous for this mutation, 9 were heterozygous, and 21 carried only the normal allele. These numbers were extremely discrepant from Hardy-Weinberg equilibrium. The findings corroborated heterogeneity among the hemochromatosis patients, with 83% of cases related to C282Y homozygosity.”

In other words, looking at this from the perspective of a physician, most people who receive a clinical diagnosis of hemochromatosis are homozygous for the C282Y allele of HFE.

In contrast, also from the OMIM entry, the H63D allele of HFE confers a minor risk of hemochromatosis. Here is one part of the OMIM entry:

“Jouanolle et al. (1996) commented on the significance of the C282Y mutation on the basis of a group of 65 unrelated affected individuals who had been under study in France for more than 10 years and identified by stringent criteria. Homozygosity for the C282Y mutation was found in 59 of 65 patients (90.8%); 3 of the patients were compound heterozygotes for the C282Y mutation and the H63D mutation (613609.0002); 1 was homozygous for the H63D mutation; and 2 were heterozygous for H63D. These results corresponded to an allelic frequency of 93.1% for the C282Y and 5.4% for the H63D mutations, respectively. Of note, the C282Y mutation was never observed in the family-based controls, whereas it was present in 5.8% of the general Breton population. This corresponds to a theoretical frequency of about 1 per 1,000 for the disease, which is slightly lower than generally estimated. In contrast, the H63D allelic frequency was nearly the same in both control groups (15% and 16.5% in the family-based and general population controls, respectively). While the experience of Jouanolle et al. (1996) appeared to indicate a close relationship of C282Y to hemochromatosis, the implication of the H63D variant was not clear.”

So, while the H63D allele of HFE appears to alter the function of HFE, it is almost as frequent among patients lacking a diagnosis of hemochromatosis as among those who are diagnosed with hemochromatosis. People have two alleles, so “having” the H63D allele in this case usually means also having a normal allele. I should also point out that there are other genes, different from HFE, that predispose to hemochromoatosis.

The Zellweger Syndrome Spectrum (PEX1) allele that I carry occurs at a frequency of around 0.2%. For hemochromatosis, among the 4,552 chromosomes sampled from the publicly-funded Exome Sequencing Project, the HFE-H63D allele occurs at a frequency of about 10.8%, while the HFE-C282Y allele occurs at a frequency of about 0.2%. Why is there such a wide range in the frequency of disease-causing alleles? I will cover that in my next post.