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.