Android mobile app for 23andMe data

DIYgenomics released a personal genome Android app update on January 9, 2011 adding three new elements of functionality: the ability to upload and store 23andMe data in the app, multiple views for health risk, drug response, and athletic performance (Figure 1), and a quality ranking system for each SNP.

Figure 1: DIYgenomics Android mobile app view categories.

What is this information?
Selecting any item displays a list of variants or SNPs (places of potential genetic typos), such as for Alzheimer's disease (Figure 2). The locus, gene and variant (SNP) details are shown, along with the normal type (e.g.; no mutation) for 23andMe data (if it exists) in black, an individual's 23andMe data (if loaded) with normal alleles in green and mutations (polymorphisms) in red. Stars (from 1-5) indicate the research quality of the SNP (per the journal ranking of the study, the number of cases and controls, etc.). The colored blocks show which service providers cite the SNP (per color legend), and how many studies they cite.

Figure 2: DIYgenomics health condition Alzheimer's disease.

What does this information mean?
In Health Conditions, a mutation (polymorphism) presented in red generally indicated being at higher potential risk for developing a condition. In Drug Response, a mutation could mean that the normal dose of the drug may not work as well, that there could be side effects, or that there could be a higher change of addiction (for substances). In Athletic Performance, the favorable mutation (green), suggests greater than average athletic capability.

Consumer genomic testing update

In the wake of expected industry-wide regulation of consumer genomic testing, two of the big four testing companies, Navigenics and Pathway Genomics, have pulled their direct-to-consumer offerings in the last few months. Now a doctor must order their tests.

23andMe and deCODEme still have consumer genomic tests available, covering 174 conditions for $429 and 49 conditions for $2,000, respectively (Figure 1). Sooner rather than later could be a good time to sign up for a genomic service, possibly using year-end HSA dollars.

Figure 1. Landscape of direct-to-consumer genomic testing services.

Source: DNA Testing: Living Longer Via Personal Genomics

The potential industry-wide regulation is in regard to two issues, one is whether a physician must order the tests, and two, whether companies should be able to publish their interpretations of the results.

The DIYgenomics website lists two online petitions in support of rights to one's own genetic data:

• Petition for Access to Genetic Information

• Petition for Health Data Rights

Genomics: progress in exomes and structural variance

The fast rate of progress in many areas of genomics was the most salient dynamic of the Future of Genomic Medicine III conference at Scripps in San Diego CA, March 5-6, 2010. Cancer genomics and pharmacogenomics continue to blossom as wide-ranging fields of applied genomics. Aging and genomics, and the role of genetics in studying disease and the microbiome are nascent and growing. Importantly coming to the forefront for the first time is structural analysis and exome analysis.

Structural analysis of genomes concerns copy number variation (multiple copies of genes), inserted genes, deleted genes, inverted genes and other structural changes, and is found in all classes of traits and disease. There is thought to be 12% structural variation between humans as opposed to 0.1% SNP variation between humans. SNP variation is the 'typos' at specific genetic locations where the normal nucleotide combination is 'AA' and some people have the risk alleles 'AT' or 'TT.”

Using exomes (the 1-2% of the genome that contains protein coding regions) as a cheaper alternative to whole human genome sequencing, and conducting basic SNP analysis together with more complex structural variation analysis, and possibly methylation analysis (which genes are blocked from expression), and RNA transcriptome analysis (levels of DNA expression), could bring more sophistication to DNA analysis for myriad purposes including pharmacogenomics and disease analysis.

Some interesting startup companies are starting to realize these new aspects of genomic medicine:

• Cellular Dynamics, Madison WI (human cells derived from induced pluripotent stem (iPS) cells)
• Integrated Diagnostics, Seattle WA (predictive blood assays of organ-proteins; UCLA melanoma clinical trial)
• Population Diagnostics, Melville NY (copy number variation analysis for pharmacogenomics)