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I'd like to see the cost of bioinformatics cloud computing come down by several orders of magnitude as well. The ideal scenario seems to be a global network of

I'd like to see the cost of bioinformatics cloud computing come down by several orders of magnitude as well. The ideal scenario seems to be a global network of in-field mobile clinical units that can collect samples, run diagnostic tests and sequence genome data. Then upload that collected real time data to public data stores on AWS S3 or Google Cloud Genomics. Which a team of researchers can then access from their own labs around the world.

jackcosgrove 10y ago
Genomic data needs very strong privacy controls. HIPAA would probably prohibit making entire genomes public without patient consent, even if they have been de-identified. Just sequencing a fraction of the patient's genome subsequently could make identifying the entire public genome easy.
- tosseraccount 10y ago
  Not all countries have HIPAA style privacy restrictions. Public whole genomes are available.
- gumberculese 10y ago
  Here are 1000 whole genomes: http://www.1000genomes.org/ http://www.1000genomes.org/ The VCF files are reasonably formatted, the raw sequencing data is in the FASTQs, which are huge and hard to deal with. Go nuts!
  - jackcosgrove 10y ago
    The About page says, "The 1000 Genomes Project developed guidelines on ethical considerations for investigators doing sampling, outlined in the Informed Consent Background Document and the Informed Consent Form Template. All collections included in the Project followed these ethical guidelines and model informed consent language." Here is the consent template: http://www.1000genomes.org/sites/1000genomes.org/files/docs/Informed%20Consent%20Form%20Template.pdf http://www.1000genomes.org/sites/1000genomes.org/files/docs/... The post I responded to sounded like the genomic data would be uploaded without consent to a giant public database. Even with consent the greater concern is that employers, medical providers, national health services, and health insurance companies could, by sequencing part of your genome, match it to a public database identifying you and your entire genome. This could then be used to raise prices, deny health care, or deny employment. De-identification is not enough if the material is indicative enough that efforts to re-identify it can succeed. Kudos to those advancing science by making their genomes public, but it's a risk I would not take.
    - bduerst 10y ago
      Except it is illegal for employers and insurance companies to do such discriminatory practices. With new technology comes new responsibility - we shouldn't shy away from the tech because we don't want the burden of enforcing regulation.
- dekhn 10y ago
  Hi, my genome is public. Feel free to do any privacy analysis on it. https://my.pgp-hms.org/profile/hu80855C https://my.pgp-hms.org/profile/hu80855C You should have no problem deidentifying me.
lunula 10y ago
I'm not sure if the pendulum can swing any more in the direction of centralization. I expect genomic appliances that are disconnected from the internet to become common with advances in sequencing tech like nanopore sequencing. Imagine a lab that buys disposable sequencing based diagnostics. Open the package, drop in the sample, and get the answer anywhere and anytime without the need for a HiFi internet connection or HIPPA compliance woes.
dekhn 10y ago
The cost of bioinformatics cloud computing isn't going to come down by several orders of magnitude: it already tracks the raw hardware costs + cost of running a cloud data center + a tiny margin on top.

jackcosgrove 10y ago

Genomic data needs very strong privacy controls. HIPAA would probably prohibit making entire genomes public without patient consent, even if they have been de-identified. Just sequencing a fraction of the patient's genome subsequently could make identifying the entire public genome easy.

tosseraccount 10y ago
Not all countries have HIPAA style privacy restrictions. Public whole genomes are available.
gumberculese 10y ago
Here are 1000 whole genomes: http://www.1000genomes.org/ http://www.1000genomes.org/ The VCF files are reasonably formatted, the raw sequencing data is in the FASTQs, which are huge and hard to deal with. Go nuts!
- jackcosgrove 10y ago
  The About page says, "The 1000 Genomes Project developed guidelines on ethical considerations for investigators doing sampling, outlined in the Informed Consent Background Document and the Informed Consent Form Template. All collections included in the Project followed these ethical guidelines and model informed consent language." Here is the consent template: http://www.1000genomes.org/sites/1000genomes.org/files/docs/Informed%20Consent%20Form%20Template.pdf http://www.1000genomes.org/sites/1000genomes.org/files/docs/... The post I responded to sounded like the genomic data would be uploaded without consent to a giant public database. Even with consent the greater concern is that employers, medical providers, national health services, and health insurance companies could, by sequencing part of your genome, match it to a public database identifying you and your entire genome. This could then be used to raise prices, deny health care, or deny employment. De-identification is not enough if the material is indicative enough that efforts to re-identify it can succeed. Kudos to those advancing science by making their genomes public, but it's a risk I would not take.
  - bduerst 10y ago
    Except it is illegal for employers and insurance companies to do such discriminatory practices. With new technology comes new responsibility - we shouldn't shy away from the tech because we don't want the burden of enforcing regulation.
dekhn 10y ago
Hi, my genome is public. Feel free to do any privacy analysis on it. https://my.pgp-hms.org/profile/hu80855C https://my.pgp-hms.org/profile/hu80855C You should have no problem deidentifying me.

lunula 10y ago

I'm not sure if the pendulum can swing any more in the direction of centralization. I expect genomic appliances that are disconnected from the internet to become common with advances in sequencing tech like nanopore sequencing. Imagine a lab that buys disposable sequencing based diagnostics. Open the package, drop in the sample, and get the answer anywhere and anytime without the need for a HiFi internet connection or HIPPA compliance woes.

dekhn 10y ago

The cost of bioinformatics cloud computing isn't going to come down by several orders of magnitude: it already tracks the raw hardware costs + cost of running a cloud data center + a tiny margin on top.