Jan 24, 2008

Another Player Joined the Personal Genomics Craze

Announced January 24, 2008, SeqWright, a Houston, TX company, joined the recent craze of personal genomics by offering a DNA test to consumers at $998.

Another player joins the "23etAl" craze!

My friend at BioTeam -- Michael Cariaso, who is also the author of the well known SNPedia, coined a word "23atAl". I like Michael's creation!

"23atAl" describes the companies of 23andme, Navigenics, deCODEme, Knome and alike, who are trying to provide consumers with genotying service.
The information provided by SeqWright is cursory. My instinct tells me that they are using Affymetrix SNP arrays. If so, it will be a direct competitor to Navigenics.

A distinctive feature of the SeqWright offering is the copy number variation analysis. So far as I know, it is the first one providing this information to consumers, although we use it regularly in research as a by-product of running SNP arrays.

A quick update: Blogger Daniel MacArthur (his Genetic Future blog here) also created an interesting word play, "me two": 23andMe and deCODEme.

Jan 21, 2008

The Google Approach to Large Genomics Data Sets

Getting terabytes of genomics data? Yes, easily! -- via Next Generation Sequencing (NGS), microarray, mass spectrometry, consumer genotyping ... you name it.

The bioinformatics community has been working on this problem for years. A few milestones: 1) Recognized the importance of meta-data (data about data, i.e., the running conditions to acquire the scientific data). 2) Utilized XML and Ontology to communicate.

However, it is still a great challenge. So, what did Google come up with?

In summary, here is the Google paradigm to large scientific data:
  • Premises
a) The growth of scientific data (size) outpaces the growth of Internet bandwith.
b) The consumption of the data (in terms of user-comprehensible results) is largely asymmetric in terms of size, comparing to the raw data.

  • Solution:
a) UPLOAD: Ship the data to the computational engine via FedEx or UPS.
b) ANALYZE: Data will be co-located with the computational engine (at the Google empire??)
c) DELIVER: The analyzed results or query results (usually much smaller) will be delivered to the consumer via the Internet.

Will it work? I think so.

Jan 5, 2008

Consumer Education through Video Clips

WSJ has discussed the use of YouTube in consumer advertisement.

There is another use of YouTube: to educate consumers on exotic products, such as genomic testing.

deCode Genetics, a biotech company (NASDAQ: DCGN), has experimented it on YouTube.

The results? A bit discouraging.

332 views so far (as of 1/5/08) after it was posted on November 17, 2007. I will keep tracking it...

Date NumberOfViews
11/17/2007 0
1/5/2008 332
3/9/08 698

As a separate note, here is a collection of 10 YouTube videos on genetic conditions:

Jan 3, 2008

Glossary of Consumer Genomics


  • a gene is the basic functional unit of heredity. Genes are made up of DNA.


  • the study of a single gene and its effect on human health. For example, a mutation of the CFTR gene causes cystic fibrosis.


  • the study of all human genes, including their interaction with environment factors such as smoking and diet.

Single Nucleotide Polymorphism (SNP):

  • a single basepair variation in the DNA that might differ from person to person. SNPs can be used to profile a person’s genomic information. Currently, up to 2 millions of SNPs can be measured on a single microarray.


  • a technology to measure SNPs or mRNAs.


  • most diseases are caused by the interaction of the genome and the environment.

Genomic Testing:

  • the measurement of a person’s SNPs using microarray or other technologies. Sometimes, it is also called genetic testing in the mass media.

What is Consumer Genomics

Anne Wojcicki & Linda Avey (founders of 23andme) interview on PBS

About Me and this Consumer Genomics Blog

I was trained as a physician. Eleven years ago, I started to conduct medical research. In my day job, I am a bioinformatics scientist. I have been tracking direct-to-consumer genomic products since 2005. Earlier 2007, I started using "consumer genomics" and "consumer bioinformatics" in an academic grant to describe the paradigm shift of genomics and bioinformatics from the lab to the consumers.

Now my academic research interest also includes consumer education, access, and interpretation of genomic testing results -- an activity I called "consumer bioinformatics".

I will address the consumer, science, and business aspects of direct-to-consumer genomics in this blog.

I am going to discuss the following issues:
  • The importance of data portability in consumer genomics
  • The consumer aspect of consumer genomics
  • and much more ...