Tag Archives: predictive gene testing

DNA instruments?

Photo: Jan Chipchase
What would a straw designed for collecting DNA samples look like? What kinds of drinks would be compatible with collecting that sample i.e. not contaminate the sample? Is there a point when accepting a drink + straw is the equivalent of contractually agreeing to have a DNA sample collected?

links for 2010-02-09

  • When the Dor Yeshorim organisation was set up in New York and Israel in 1983, Tay-Sachs disease was rife in the Jewish community. The mutated gene that causes the disorder, is more common among Ashkenazi Jews than most other ethnic groups. Jewish marriage customs made it likely that two carriers would start a family together, with a 1 in 4 risk that every child would be affected.
    Of ten babies born with the condition in usa in 2003, none was Jewish, and only one child with Tay-Sachs was born in Israel that year. The reason was Dor Yeshorim’s genetic screening initiative. Jewish people are now tested for Tay-Sachs status, and the community’s matchmakers do not pair carriers together. The new genetic test by Counsyl is now attempting to do for more than a hundred other genetic conditions what Dor Yeshorim did for Tay-Sachs. By informing prospective parents about the recessive mutations they carry, it should substantially reduce their risk of having children with an inherited disease.
  • British couples are to be offered a groundbreaking genetic test that would virtually eliminate their chances of having a baby with one of more than 100 inherited diseases.The simple saliva test, which identifies whether prospective parents carry genetic mutations that could cause life-threatening disorders such as cystic fibrosis, spinal muscular atrophy or sickle-cell anaemia in their children, is to be launched within weeks in Britain, The Times has learnt. If the procedure, which will cost about £400 per person or £700 for a couple, is widely adopted, it could dramatically reduce the incidence of 109 serious inherited conditions that collectively affect one in every 280 births.

HGC develop principles to regulate genetic tests sold to public in UK

The UK’s Human Genetics Commission (HGC), the Government’s advisory body on new developments in human genetics and how they impact on individuals’ lives, is seeking views on a ‘Common Framework of Principles’ for direct-to-consumer genetic tests. The Principles were developed by an international expert working group that was convened and supported by the HGC.

Direct-to-consumer genetic tests can significantly influence choices that may profoundly affect the lives of an individual and their family. Genetic tests that can provide information about health can heighten anxieties, leading individuals to make inappropriate requests for further tests, or alternatively encourage a complacent disregard for the effects of an unhealthy lifestyle. Other tests can also provoke anxieties, such as ancestry tests that offer fundamental information about identity and ethnicity. Yet, in the majority of countries, there is very little regulation of this steadily growing market and so the quality of service and the provision of support to accompany testing are determined by the test provider.

via BioNews and FT

Predictive Genome Scientist Face Off

Mapping the Epigenome

Mapping the Epigenome

Mapping the Human ‘Diseasome’

Mapping the Human ‘Diseasome’

Lewis Wolpert
“I have entered into this wager with Rupert Sheldrake because of my interest in the details of how embryos develop, and how our understanding of this process will progress. In my latest book, How We Live and Why We Die, I suggest that it will one day be possible to predict from an embryo’s genome how it will develop, and I believe it is possible for this to happen in the next 20 years.”

Rupert Sheldrake
“Lewis Wolpert’s faith in the predictive power of the genome is misplaced. Genes enable organisms to make proteins, but do not contain programs or blueprints, or explain the development of embryos.”

Lewis Wolpert (developmental biologist) & Rupert Sheldrake (parapsycholgist) have set themselvesa a face-off challenge via the RS  that “By 1 May 2029, given the genome of a fertilised egg of an animal or plant, we will be able to predict in at least one case all the details of the organism that develops from it, including any abnormalities.”

——

The Diagrams: (top) This radial diagram produced by The New York Times and Martin Krzywinski, the developer of Circos, represents the number of small molecules, called methyl groups, attached to segments of chromosome 22 across seven different types of human tissue. Methyl groups are one part of the epigenome, which controls how genes are expressed in different types of cells. (bottom) Dr. Butte, an assistant professor of medicine at Stanford, is trying to redefine how diseases are classified by looking not at their symptoms or physiological measurements, but at their genetic underpinnings. This map links different diseases, represented by circles, to the genes they have in common, represented by squares. Each circle represents a disease or disorder and is scaled in proportion to the number of genes associated with that disease.

Illumina launches own website and MyGenome iPhone application

How similar is my genome to Bill Gates.. what a scary thought.

How similar is my genome to Bill Gates.. what a scary thought.

At the recent Consumer Genetics Show, Illumina, a genomics technology provider of second-generation sequencing instruments (the Genome Analyzer II),  is launching a personal genome sequencing service via a new website; everygenome.com. The website discusses the processes of genotyping and DNA sequencing for individuals, doctors and scientists and will offer its service for $48,000 on its Genome Analyzer II platform.  It will conduct the sequencing at its laboratory  providing customers with a list of SNPs (single-nucleotide polymorphism) and structural variations in their genomes.

Illumina is the first sequencing-technology provider to open its service business to individual customers for non-research purposes and to consider how interpretation and comparison of ones genome could exist on the Iphone.

However Illumina does not provide interpretation services. The analysis and evaluation is where the spin begins, the disease- risk assessments, ancestry analyses and information about inherited traits.  It has instead  partnered with direct-to-consumer interpretative services offered by  23andMe, Navigenics, Decode Genetics, and Knome. Customers can select from these partners to receive interpretative packages of their data for an additional fee.

As it will only be a few years until the technologies that are being invested in will enable the the sequencing of our genomes to be cheap enough to buy in Boots, very cheap sequencing will rapidly result in a depletion of the sequence generation market as people will only need to get their genome sequenced once to have all the data they need in the world. So it is here that interpretation of this data that will be the “gift that keeps on giving…as new research uncovers more details about the functional portions of the genome and their interactions with environmental risk factors customers will always need their reports updated and re-analysed in increasingly more sophisticated ways.” This analysis will be a constantly evolving self-knowledge portal that can be tapped into as and when for the individual – creating a consistent re-reading of data. (via GenomicFutures)

The FATE perspective

  • The FATE institute recognize that this ability to learn more and more about ones genetic makeup and future health can consistently be updated and soon it wil be like reading your own horoscope in the Metro paper. The more and more we learn about ourselves the more we will only listen to what we want to hear, a DNA sequence interpretation will become very much like a coldreading, a form of mentalism wheer you listen out for what you want to hear. And in doing so it may or maynot motivate you to change the way you live.
  • The FATE Institute believes that the more personal genome sequencing companies choose to invest in interpretations of SNP data as well as the technology the easier it will be for individuals to be able to choose how and by whom they want their future to be interpreted.
  • Those start-ups and corporations who interpret their future each have their own motivations, branding and perspectives that taint the outcomes.They currently offer interpretative services that offer individuals a subscription to a fountain of their own self-knowledge that will continue to provide analysis about their own future lives indefinitely.
  • However how will this change as the technology develops further and becomes accessible to all?
  • What will be the impacts of an open source democratic approach to personal genome sequencing?
  • How will this technology be harnessed if it leaves the large private sector laboratories and enters individuals homes and makeshift laboratories similar to those that are occurring in response to the synbiobrick era?
  • Will citizen geneticists be able to sequence their genome and interpret the data in their own home, patent it using Science Commons licenses and sell their services on ebay or Amazon?
  • What similarities and differences can we see between this possible future  and the open source approach in the software industry and the abilities for the web 2.0 to provide platforms for amateur activists and social entrepreneurs that exists outside of traditional corporations, start ups or  top down state structures?

Personal Genome Project Entrance Exam

In 2001, the Human Genome Project published a working draft of the human genome sequence, thus providing unprecedented advances in our knowledge of how a human works. The PGP makes sequencing personal. Just like the personal computer brought information technology to individuals, the PGP brings DNA sequencing to individuals.

So a while back I registered to the Personal Genome Project after they initally decoded the genome of their first ten participants and called for 10,000 volunteers to sign up for the potential to share their genome sequence and other personal information with the scientific community and the general public. (View example public profile pages here) To be considered, volunteers must pass an entrance exam to ensure a clear understanding of what it is they are getting themselves into and have an understanding of genomes and DNA and the bigger ethical picture of the Personal Genome Project.

I am currently working my way through the PGP study guide provided by the Alan and Priscilla Oppenheimer Foundation and hoping to fill in the gaps about the DNA and genome sequencing basics as well as use this as an insight into the PGP’s ethical considerations and risk legislation of sharing  personal details to the public. I am not too sure if I really am aware of the implications and would say that this process is informing my ethical and moral position on predicitve gene testing and the PGP.

Question: Why do I have to take an exam to participate in the PGP?
Answer: The PGP takes informed consent very seriously and believes that an exam is the best way to ensure that you have the knowledge necessary to understand the benefits and risks associated with participating in the project.

For those interested in contributing their genetic material to the PGP check out their participation page

Crowdsourcing/Opensource genomics

This past September, Silicon Valley startup 23andMe took another step in its self-described mission of “democratizing personal genetics” when it slashed the price of its gene-scanning service from $999 to $399. Increasing its user base is part of the company’s goal of becoming a robust platform for web-based genetic research. And by starting to collect, compile, and compare phenotypic and environmental data from these users, 23andMe is catalyzing DNA’s move from labs to Facebook tabs.

23andMe.com has the feel of a social-networking website, but its users are sharing genetic information rather than photographs. For $399, you don’t get a full genome scan, but rather a look at 580,000 different single nucleotide polymorphisms (SNPs): the genetic variants most often tied to distinctive personal traits. Users can elect to share this information with family and friends via their site-based profiles. 23andMe’s competitors, deCODEme and Navigenics, have different price structures and focus on different selections of SNPs, but the basic premise of their services is the same.

via Seed