23andMe as genomic social network research tool

Good article on how lower pricing has increased accessibility to 23andMe. Let’s see how long direct-to-consumer testing is available. You own your own results and that alone may be very valuable in the future. Without personal health history genetic data alone isn’t really meaningful. That’s where The DNA Diet comes in.

Our Microbial Self – does it determine our weight?

Scientists in Denmark note a difference in bacterial colonies and number of bacterial genes between lean and overweight or obese individuals. Is this a cause or result? Old Danish question – do storks bring babies or do babies simply arrive 9 months after most people go on vacation?
Interesting facts about the microbes that live inside us
100 trillion microbial cells in the human gut – 10 times more than body cells. Most of us have about 160 different species with two families dominating, Bacteroidetes and Firmicutes. The amount and ratio of these types in the gut appear to be associated with the weight of the person. Add fiber to your diet, increase fruit and vegetables, include probiotic rich foods like yogurt or sauerkraut for a healthy weight.

Just when it seemed easy in genomics…

Just as we thought we had the human genome identified and sorted – even though each individual whole genome sequence (WGS) has about half a million unique characteristics there is a whole new arena to discover.  The number of microbes that live on and in us now are thought to have profound effects on our internal metabolism.  Estimates vary but J Craig Venter, someone worth listening to, estimates that there are 200 trillion microbes providing 10 million extra genes.  Animals raised in germ free environments have significantly different metabolisms.  Sandrine Claus in a new study notes that mice raised in this way who were then exposed to bedding of mice with normal microbiota (their digestive systems had the usual amount of probiotics or additional genetic contribution from microorganisms) showed rapid increases in weight and changes in liver metabolism.   Food for thought.

23andMe receives more funding

Google has invested 7 Million total (2.6 Million more today) in 23andMe believing in its capacity to deliver in the future. With the number of participants and data collected this may well be true however on the day 23andMe announced they had partnered with another company to provide genetic counseling I am confident that my expertise will be recognized for its value. We all eat but once you learn your perceived risk for a disease that’s all to learn. I integrate this data to provide action plans, tailored recipes and make this knowledge helpful and proactive.

Validation of Genomic Data becomes Crucial

One reason why the genomic revolution is not yet as advanced as many had hoped is the huge amount of variability between individual genomes and challenges surrounding data validation.

At a recent meeting of Human Genome Organization (HGM) in Montpelier, France a number of presentations noted the widespread variation among human genomes that are challenging the current high throughput technologies.

Validation protocols for the 100 sample genomes required to win the Archon Genomics X Prize will require highly sophisticated bioinformatics software to capture this inter-individual variability. Simply conceiving of such variability mentally is already enough to give one a headache!

Unrealistic expectations lead to disappointment for genomics

Nicholas Wade, science writer for New York Times describes his disappointment in genomics for personalized medicine but this misses the point in my opinion. Genomic discoveries like any diagnostic tool are part of a larger picture of health. It is in integrating this knowledge along with family medical history and personal life experience that true medical advances will be realized. Over reliance on any screening tool is bound to lead to disappointment especially when people come at the field with such high expectations. Identifying individuals using DNA is a very different project than identifying their risk factors for chronic disease beyond what we already know to be true – smoking, being overweight and sedentary, etc. Mitochondrial DNA and how it influences gene expression is another dimension of genomics yet to be understood or integrated into nuclear DNA genomic discovery. If mitochondria are relics of symbiotic bacteria then this would probably be highly relevant to our current health status. I think we have to be patient and continue to use sensible public health applications while slowly integrating what is valuable from genomic scientific discoveries. Just my personal view – I’d be interested in what others think.


Single Molecule Sequencing (SMS)

Helicos Biosciences Corp. is advancing single molecule sequencing http://www.helicosbio.com/Technology/TrueSingleMoleculeSequencing/tabid/64/Default.aspx

Stanford professor Stephen Quake has made his entire genome available for research purposes using SMS. One more step towards cheap and available GWAS for all. Lee Hood and George Church are members of Scientific Advisory Board.

UCLA sequences genome of brain tumor cancer cell line

Stan Nelson a genetics researcher and director of UCLA’s Jonsson Comprehensive Cancer Center, senior author of PLOS article identifying a glioblastoma multiforme (GBM). This is the first time a GBM cell line has had its whole genome sequenced. They used U87MG, a well studied line derived from a grade IV gliomaBy comparing SNPs in the cell line genome with those found in dbSNP and two previously published genomes — the Watson genome and first Asian genome — they found that the prevalence of SNPs in the U87MG genome was comparable to that in normal genomes. “Most of the variation is still dominated by the inherited polymorphisms,” Nelson explained. Even so, the team detected mutations affecting 512 protein-coding genes, including PTEN, a gene previously implicated in brain cancer. Many of these involve small insertions and deletions. As the brain is encased in a rigid skull structure, speed and accuracy of treatment decisions is crucial and this research will significantly add to the personalization of future treatments of those with this aggressive brain tumor.

Identifying Natural Selection at work in the Genome

A new technique of identifying distinctive signals in the genome that track natural selection is described by Harvard researchers and the Broad Institute. It is called Composite of Multiple Signals and allows a more specific identification of genetic changes teasing out needles from the haystack even further.