jm + genomics   8

Rossa McMahon re GMI
Rossa McMahon with a twitter thread on the legality of GMI's genomic data collection program in Ireland:
GMI is a big, expensive company. It announced planned investment injection of $400m last year. It is engaged in a hot industry - hot because of investor interest and hot because of regulatory/ethics concerns.

GDPR is not new. It has been known since 2016. Data protection law is not new. It has been known since 1988. The impact of these laws on genetic data collection & use is not a surprise. So if you have a $400m+ business and this is a key business issue, you have taken advice. And you have, no doubt, been in a position to take that advice from some of the best and/or most expensive advisors available. Assumptions are dangerous, but I think it is fair to assume this has happened.

So read the story again.

Would you be looking for repeated meetings with [Department of Health], answers to questions on regulatory matters and assurances from the State, if you had legal advice of your own to the effect that you are operating or can operate as your currently are?
gmi  genomics  genetics  data-privacy  privacy  gdpr  ireland 
5 weeks ago by jm
Ireland putting profit before people with genomic medicine strategy
From David McConnell and Orla Hardiman at TCD:
Much of the medical information sought by GMI [Genomics Medicine Ireland] has been collected from patients in public hospitals funded by the exchequer at great expense [...]. Clinicians are being contracted and asked to obtain consent from their patients to transfer clinical information to GMI, along with a tissue sample for WGS [Whole Genome Sequencing]. We understand GMI will pay for the additional hospital clinical costs required for the project. It will obtain the full genetic code for each patient (WGS), and it will analyse all the data. For the most part .... there is minimal tangible benefit to the patient who participates in this programme.

It is important to realise that GMI will own all the clinical and WGS data that they have acquired from the health service, which is of considerable commercial value. GMI will also have complete control over the research and any outcomes. Participating patients do not appear to have access to their data held by GMI – and there does not seem to be a “right to be forgotten”, despite the commercial nature of the enterprise. Moreover, the genomic and clinical data may also be transmitted outside of the European Union, and thus will not be protected by the stringent data-protection laws within the EU.[....]

The Government has made a very big investment in GMI. There may be a view that it is not necessary to provide any additional public investments in genomic medicine in Ireland. However, to those of us who care about the longer-term development of genomic medicine in Ireland, this would be a seriously short-sighted approach. One person in 20 will develop a genetic disorder in their lifetime and half of the Irish population will experience a form of cancer. These and many other patients should be able to benefit from a publicly-available genomics project that can drive new medical care in Ireland.

Genomic medicine is here to stay. We urgently need a properly governed genomics programme in Ireland that will ensure that Irish genomics remains within the public (non-commercial) domain, and that data obtained from Irish citizens will be used to benefit the entire Irish population.

(via Aoife McLysaght)
gmi  wgs  genome  open-data  data-privacy  gdpr  privacy  health  medicine  ireland  genomics 
5 weeks ago by jm
Crumlin hospital sent DNA off without consent
a company called WuXi NextCODE owning the genome data for a large part of Ireland's population is very cyberpunk
wuxi-nextcode  genomics  genomes  data-privacy  privacy  crumlin-hospital  genes  ireland  gdpr 
january 2019 by jm
Building a Regex Search Engine for DNA | Hacker News
The original post is pretty mediocre -- a search engine which handles a corpus of "thousands" of plasmids from "a scientist's personal library", and which doesn't handle fuzzy matches? I think that's called grep -- but the HN comments are good
grep  regular-expressions  hacker-news  strings  dna  genomics  search  elasticsearch 
april 2016 by jm
The impact of Docker containers on the performance of genomic pipelines [PeerJ]
In this paper, we have assessed the impact of Docker containers technology on the performance of genomic pipelines, showing that container “virtualization” has a negligible overhead on pipeline performance when it is composed of medium/long running tasks, which is the most common scenario in computational genomic pipelines.

Interestingly for these tasks the observed standard deviation is smaller when running with Docker. This suggests that the execution with containers is more “homogeneous,” presumably due to the isolation provided by the container environment.

The performance degradation is more significant for pipelines where most of the tasks have a fine or very fine granularity (a few seconds or milliseconds). In this case, the container instantiation time, though small, cannot be ignored and produces a perceptible loss of performance.
performance  docker  ops  genomics  papers 
november 2015 by jm
Can we have medical privacy, cloud computing and genomics all at the same time?
Today sees the publication of a report I [Ross Anderson] helped to write for the Nuffield Bioethics Council on what happens to medical ethics in a world of cloud-based medical records and pervasive genomics.

As the information we gave to our doctors in private to help them treat us is now collected and treated as an industrial raw material, there has been scandal after scandal. From failures of anonymisation through unethical sales to the care.data catastrophe, things just seem to get worse. Where is it all going, and what must a medical data user do to behave ethically?

We put forward four principles. First, respect persons; do not treat their confidential data like were coal or bauxite. Second, respect established human-rights and data-protection law, rather than trying to find ways round it. Third, consult people who’ll be affected or who have morally relevant interests. And fourth, tell them what you’ve done – including errors and security breaches.
ethics  medicine  health  data  care.data  privacy  healthcare  ross-anderson  genomics  data-protection  human-rights 
february 2015 by jm
How I decoded the human genome - Salon.com
classic long-read article from John Sundman: 'We are becoming the masters of our own DNA. But does that give us the right to decide that my children should never have been born?' part two at http://www.salon.com/2003/10/22/genome_two/
human  genome  genomics  eugenics  politics  life  john-sundman  disability  health  dna  medicine  salon  long-reads  children 
may 2013 by jm

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