My Personal Genome Project report has now arrived

Personal Genome Project Logo

I discovered the Personal Genome Project in September 2014 and immediately tried to sign up. They weren't taking new volunteers.

In December 2015 (15 months later) I finally did succeed in registering, but no-one was very interested in taking a spit-sample.

In May 2016, my sample collection kit arrived and I duly spat for science. I returned my sample for sequencing, at which point they stored it .. and nothing whatsoever happened.

It is now August 2017. Fifteen further months have passed and this morning I received an email from the PGP. I have been sequenced!

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My genome will now be released for research. Was there anything interesting in the report? No. Was it different in any important respect than that which I already received from 23andMe? No.

As usual, the report is mostly centred around SNPs. Unfortunately most interesting phenotypic traits are polygenic, the full connections with genomic variation yet to be unravelled. The SNPs - taken individually - simply adjust your odds ratio up or down for various conditions. Example: some of my SNPs elevate my odds for baldness; others lower it.

Insofar as the science centres around connecting my personal genome with my own phenotype characteristics, research should now focus on the latter.

I look forward to the first request for the promised punch biopsy.

In which I sign up with the PGP

Back in September 2014, I tried to sign up with the Personal Genome Project, based at UCL in its UK incarnation (Harvard Medical School in the States). Sadly, this proved so popular that admissions had closed by the time I tried. But now they're open again and I've signed up!

It's a process which selects for both intelligence and perseverance. An online exam has to be passed testing your understanding of their ethics policy, the risks and dangers as well as your basic understanding of genetics. The whole thing took me an hour and a half.

They try to scare you off:

"Unanticipated uses of your data and cell lines

"The list of potential uses of your data and cell lines by other individuals is diverse and sometimes worrisome. The benefit of these things is that other researchers will use them in their own work, greatly facilitating the process of scientific research. Other researchers might also create their own interpretations of your genetic data -- and these could make incorrect claims regarding your predisposition to traits and diseases that we cannot control.

"Someone might match your public data against other genetic databases to find matches for yourself or relatives - this includes criminal and forensic DNA fingerprinting databases as well as other genetic research studies.

"More nefarious uses are also possible, if unlikely. DNA is commonly used to identify individuals in criminal investigations. Someone could plant samples of DNA, created from genome data or cell lines, to falsely implicate you in a crime.

"It’s currently science fiction -- but it’s possible that someone could use your DNA or cells for in vitro fertilization to create children without your knowledge or permission, or to create human clones."

Anyway, I'm good with all that.

Hopefully the UCL process will now run and at some point I will be asked to provide a DNA sample.

"You may be invited to provide additional tissues or other specimens as approved by the study and the UCL REC ...

"Description of certain specimen sample collection procedures:

"(i) A skin punch biopsy (about 3–4 mm in diameter) is collected from the underside of the upper arm or hip and requires local anaesthesia. Anaesthetic cream is applied and covered with a bandage for 45–60 minutes then wiped off and swabbed with alcohol to sterilise the area. Then a 3‒4 mm skin biopsy is obtained. A bandage and antibiotic ointment is applied.
...
"The ... skin biopsy may involve pain, bleeding and/or fainting, and may also cause temporary bruising and/or infection at the site of puncture. Some degree of permanent scarring can be expected from the skin biopsy procedure."

Under 'Benefits' the documentation states:

"ARTICLE VII: Benefits

"7.1 No benefits to you

"You are not likely to benefit in any way as a result of your participation in the PGP-UK."

So cool.

The Personal Genome Project

The Economist this week (in Technology Quarterly) covered - in a profile of Harvard's Prof. George Church - the global Personal Genome Project. Here is what Wikipedia has to say.

"The Personal Genome Project (PGP) is a long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personal genomics and personalized medicine. It was initiated by Harvard University's George M. Church and announced in 2005. As of August 1, 2014, more than 3,500 volunteers have joined the project. Volunteers are currently accepted if they are permanent residents of the US, Canada or the UK, and are able to submit tissue and/or genetic samples. The Project is planned to launch for Europe and in development for South America and Asia.

The project will publish the genotype (the full DNA sequence of all 46 chromosomes) of the volunteers, along with extensive information about their phenotype: medical records, various measurements, MRI images, etc. All data will be placed within the public domain and made available over the Internet so that researchers can test various hypotheses about the relationships among genotype, environment and phenotype.

An important part of the project will be the exploration of the resulting risks to the participants, such as possible discrimination by insurers and employers if the genome shows a predisposition for certain diseases.

The Harvard Medical School Institutional Review Board requested that the first set of volunteers include the principal investigator George Church and other diverse stakeholders in the scientific, medical, and social implications of personal genomes, because they are well positioned to give highly informed consent. As sequencing technology becomes cheaper, and the societal issues mentioned above are worked out, it is hoped that a large number of volunteers from all walks of life will participate. The long-term goal is that every person have access to his or her genotype to be used for personalized medical decisions.

The first ten volunteers are referred to as the "PGP-10". These volunteers are:

Misha Angrist, Duke Institute for Genome Sciences and Policy
Keith Batchelder, Genomic Healthcare Strategies
George M. Church, Harvard
Esther Dyson, EDventure Holdings
Rosalynn Gill-Garrison, Sciona
John Halamka, Harvard Medical School
Stan Lapidus, Helicos BioSciences
Kirk Maxey, Cayman Chemical
James Sherley, Boston stem cell researcher.
Steven Pinker, Harvard

In order to enroll each participant must pass a series of short online tests to ensure that they are providing informed consent. By the end of 2012, more than 2000 participants had enrolled in the Harvard PGP. As of August 1, 2014, more than 3,500 volunteers have joined the project."

I'm naturally very keen to get my entire genome sequenced and interpreted, and relaxed about the privacy issues. The PGP disclaimer document you have to sign is pretty lurid - here are some of the dangers you're warned against.

"(ii) Anyone with sufficient knowledge and resources could take your DNA sequence data and/or posted trait information and use that data, with or without changes, to:

(A) accurately or inaccurately reveal to you or a member of your family the possibility of a disease or other trait or propensity for a disease or other trait;

(B) claim statistical evidence, including with respect to your genetic predisposition to certain diseases or other traits, that could affect the ability of you and/or your family to obtain or maintain employment, insurance or financial services;

(C) claim relatedness to criminals or other notorious figures or groups on the part of you and/or your family;

(D) correctly or incorrectly associate you and/or your relatives with ongoing or unsolved criminal investigations on the basis of your publicly available genetic data; or

(E) make synthetic DNA and plant it at a crime scene, or otherwise use it to falsely identify or implicate you and/or your family."

and, a little later,

"More nefarious uses are also possible, if unlikely. DNA is commonly used to identify individuals in criminal investigations. Someone could plant samples of DNA, created from genome data or cell lines, to falsely implicate you in a crime. It’s currently science fiction -- but it’s possible that someone could use your DNA or cells for in vitro fertilization to create children without your knowledge or permission, or to create human clones."

In any event, my attempts to sign up were met with this response.

"Dear PGP-UK Volunteer,

The response to our recent request for enrolment has been fantastic and the first available 1,000 slots have now all been assigned. To help us establish a smooth running of the entire process, we have temporarily paused the enrolment to focus our limited resources on the first 1000 volunteers.

We will open the enrolment again as soon as we can. In the meantime, you can follow our progress on the PGP-UK web site (http://www.personalgenomes.org/uk) and social media (http://blog.personalgenomes.org) of the international PGP Community.

Thank you for your patience and continued support,

PGP-UK Team"

So I'll just have to wait my turn. Watch this space.