A Journey into my Genome - Tentative steps into Personalized Medicine

    29/08/2015

    Genome

    I have been suffering from spontaneous bouts of diarrhea and loose stool. Bear with me, this will get more interesting. In the past I have taken pride in being able to eat what I want without gaining or losing a single ounce of weight. My medical checkups have always given me a clean slate of health and after testing my stool samples with the gastroenterologist he could find nothing wrong. But with the increased frequency of bowl movements and weight loss I knew something in my body was not right. I did a self-diagnosis by looking up the symptoms I had on the internet - a last resort when no diagnosis exists. After a few google and pubmed searches I concluded I probably have Irritable Bowel Syndrome (IBS). IBS, it turns out, is an illusive disorder with no known causes or treatments. Yet there are hundreds of speculative therapies, ranging from changing your gut bacteria with probiotics to taking anti-depressants to changing to a low FODMAP diet.

    In my quest to find the root cause of my IBS symptoms and to nail down a practical therapy I decided for the first time to sequence my own genome and microbiome. As a consumer I am faced with a panoply of choices for personal health diagnostics, some of which are more expensive and reliable than others. A few blogs ago I wrote about the burgeoning industry of direct-to-consumer pharmacogenomics companies that have sprouted up in the last few years. Some of them have gotten into serious trouble because they violated medicare contracts and lacked regulatory oversight. In spite of this I still think direct-to-consumer diagnostic testing is an excellent way for maintaining a modern healthy life style tailored to you and finding the best dose of the most adequate drug when treating a disorder. Given the high costs of medical insurance and novel prescription drugs it also allows us to get a more informed decision about the treatments we take instead of solely relying on doctors' opinions. I went with the cheaper diagnostic options and decided to use 23andMe to sequence my genome and Ubiome to sequence my microbiome. Here is my experience with using the two services:

    23andMe

    This was one of the first DNA analysis companies to emerge in the US and is considered relatively reliable. I placed an order for $99 and they sent me a test sample for my saliva. I then registered my sample online for an account to store my data and sent off my saliva sample. The lab sequences my DNA using microarray chips. After around 6 weeks they posted my DNA data onto the account. The data generated consists of pairs of single nucleotide polymorphisms (SNPs) from all of my genes. SNPs are common nucleotide changes inside all our genes that occur in over 1% of the population that serve as a kind of fingerprint. A detailed explanation of SNPs can be found here. Although 23andMe used to provide customers with both ancestry and medical results, the FDA sent a warning letter recently banning them from continuing to publish medical disease data. Now they just process your ancestry and family heritage data.

    23andMe Home Page:

    In order to acquire medical data I signed up separately for Promethease, paying $5 to upload my data straight from my 23andMe account. Promethease gives me a detailed view of which diseases or traits I am more at risk for and which ones I am less likely to have according to my SNPs. The results can be viewed in a search index based on the gene, disease, frequency of SNP occurrence with that disease and other parameters depending on what you look for. If a disease is more likely to be associated with that particular SNP, the box will be shaded pink, along with the explanation. If a positive trait or resistance to a disease is associated with that particular SNP, it will be shaded green. You can also search for potential side-effects of various common drugs on the market when you take them with your genotype. Much of the data can be edited by anyone and is dependent on SNPedia - a wiki that allows people to share information about variations in DNA, citing peer-reviewed scientific literature. Thus the results for each gene shows you the number of references that cite the association of the gene or SNP with the disease.

    An example of a Promethease page displaying an individual's genes, SNPs and information associated with those particular SNPs. Green boxes represent possible good news, red boxes for possible bad news:

    Ubiome

    This diagnostics company sends you swabs to sample microbes in your gut, mouth, skin, nose and genitalia. Since there are billions of microorganisms in the human body, the combination of which outnumber our own cells, they are essential for every process in our lives, including digesting food, regulating mood and preventing diseases. I paid $127 for a bacteria test on two parts of the body - a gut test by swabbing my toilet tissue after going to the bathroom and a mouth test by swabbing the insides of my cheeks. I registered my samples online for an account to store my data, sent off the samples and waited around 4 weeks for them to upload the results. From my samples the lab sequences bacterial DNA, analyze the most common types of bacteria and compile them into graphs comparing my results to that of other populations. I can see how my bacteria differ from the average bacterial content of vegetarians, omnivores, alcoholics, men, women and other groups. I also set up a system of recurring orders to re-test my microbiome every month as I change my diet or life style. The ability to re-test your bacteria provides a way to “life-hack” your way into a better diet or health outcome. An example can be found here.

    Ubiome Home page:

    Ubiome

    An example of an individual's Ubiome analysis showing the percentage of each type of most commonly occurring bacteria at that site:

    As sexy and cool as it might seem to have your entire genome and microbiome sequenced with hip start-up companies, it pays to remember that none of these diagnostic tests are 100% accurate and the interpretation of this data can be sketchy given the lack of scientific literature from medical research and from controlled clinical trials. Both these self-diagnostics companies have blogs and social media sites. Both allow individual users to provide feedback about their experience using the services and to report any correlations they notice about their personalized data with their actual health. Each of these sites have additional initiatives, often in collaboration with the National Institutes of Health, which encourage customers to voluntarily submit their samples for clinical research data.

    My Results

    The results of these tests are now back and the amount of data they gave me seems, at first, overwhelming. Bearing all this in mind, here are some results about my propensity for Irritable Bowel Syndrome:

    The promeathease search generated information about my propensity for Irritable Bowel Disease (IBD). IBD includes Crohn’s Disease and Ulcerative Colitis, which are commonly associated with, but much more severe than IBS. Many of the symptoms of IBS, such as diarrhea and constipation often lead to intestinal disorders of IBD, but not always. Most genetic studies associated with IBD and IBS have revealed issues with inflammatory mediators that attack the intestinal lining, preventing proper food digestion. Often these inflammatory mediators are activated due to an immune response against the body's own intestinal epithelia due to stress, cortisol or over stimulation of the enteric nervous system. According to Promeathease my SNPs for the genes rs1861494, rs11209026, rs1373692, rs11747270, rs8050910, rs6426833, rs224136 put me in a higher risk of developing IBD. However, my SNP for gene rs1992660 places me in a lower risk for Crohn’s disease, which places me at a lower risk for IBS.

    My first results from Ubiome are very rudimentary. Their analysis only showed the presence of two types of bacteria in my gut: Fermicutes and Bacteroidetes. Out of the billions of possibilities, there is no mention of any other bacteria species. According to their explanation, Bacteroidetes and Fermicutes are the most common types of gut bacteria in people with Western diets. People with more Fermicutes and less Bacteroidetes are likely to digest dietary fat better. Interestingly, from my mouth sample the analysis generated 6 types of bacteria. These included Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, Actinobacteria and Tenericutes. Proteobacteria is most commonly found in people with IBS so its presence in my mouth gives me some explanation as to my symptoms. Actinobacteria is supposed to be a "Good Bacteria" commonly found in probiotic supplements and also more commonly found in women. An increase in this bacteria could help reduce IBS.

    Overall there is still no magic bullet to treat IBS. I have to watch my food intake and perhaps switch to fermented foods with more probiotic "Good Bacteria" and adhere to foods that are less acidic. Despite the use of these self-diagnostic tools to generate huge amounts of genomic data I am unable to find an underlying cause or treatment for IBS. What these tests have shown me is that there are ways to change my life style in future according to my genetic and microbial makeup and as more clinical research becomes published, I can be more certain about ways to improve my health.

    23andMe has revealed a treasure trove of data about a host of other diseases I could be susceptible to as well as many disorders I am more resistant to. I want to write about some of these traits in the days to come. In the mean time, if you are interested in improving your nutrition and have sequenced your genome, there is a fantastic video by Rhonda Patrick explaining which SNPs you should look for in yourself and which foods you should eat to live longer.