7 ms·

This is very cool. Are there by chance any associated projects that could evolve into something like 23andme but remain entirely within a private network meani

This is very cool. Are there by chance any associated projects that could evolve into something like 23andme but remain entirely within a private network meaning that the data is entirely in the hands of the individual?

netizen-936824 5y ago
Sounds like a fediverse project?
- Malp 5y ago
  Oh God, I would not want a distributed group of actors with limited trust to sequence my DNA. Maybe it's a project for close group of friends that would be interested?
  - netizen-936824 5y ago
    I wasn't thinking sequencing but rather comparison. Could even hash data for comparison to enforce privacy (unsure how effective that would be) But this could enable things like finding relatives which is what I got out of the comment about 23andme. Instead of all the data being centralized, storage and comparison could be distributed
    - Malp 5y ago
      Ah, thanks for clarifying. I misunderstood the main idea behind your comment.
  - inciampati 5y ago
    Your DNA is almost exactly the same as other people's, just a unique mix. Not sure what you are concerned about. What would you expect a bad actor to do with your DNA sequences? I'm genuinely curious.
    - fragmede 5y ago
      A very practical reason not to want your DNA out there, unrestricted, is insurance costs. From car insurance, to health insurance, to mortgage lending rates, and life insurance, and while GINA from 2008 is supposed to protect that information, there are loopholes with the interpretation of that law that should give everybody pause.
    - snovv_crash 5y ago
      Using that analogy, all the 1s and 0s in your private key are the same as everyone else's as well. Genetic data can be used for all kinds of things, the worst of which would be things like targeted diseases or planting your DNA at a crime scene.
      - inciampati 5y ago
        Actually it's like your private key is made up of ~1000 1 mb pieces that each have 1/1000 rate of difference with any other similar piece. Oh, and the order of the pieces is almost always exactly the same. No, genomes are not "almost the same" because they are all in base-4 sequences and this made up of the same 0s 1s 2s and 3s. We are astoundingly similar, even unusually so for a large mammalian species.
    - LinuxBender 5y ago
      Your DNA is almost exactly the same as other people's, just a unique mix. Music is exactly the same notes, just a unique mix. So why is Sony upset that I want to stream their entire library? But jokes aside... A few decades ago I fought the military on collecting my DNA. I stalled them long enough to get my honorable discharge and avoid that all together. It's funny you ask because the commander asked the same thing and joked "Are you afraid we are going to clone you?!" to which I replied, "No sir, you should be afraid you are going to clone me." and we both had a laugh because he knew I was right. The military are not fond of critical/free thinkers. One of me was plenty. I explained that insurance companies were already using this data to retroactively cancel peoples policies even if they were not actively afflicted by something. The commander showed me how to use the FOIA request system. Laws have evolved a little since then but there are plenty of other risks. For starters, I can't easily change my DNA like I can change my debit card. That data can be used to tie me to others or guilt by association which is undesirable drama. It can also be used to try to sell me things. It can also be used to target biological weapons against specific groups of people. There appears to be an imbalance of data sharing in this regard. [1] Then there is simply the matter of privacy. If I want to share my DNA with some lab that is in turn going to sell it out to hundreds of other companies over and over forever, I should at very least be getting paid a vast amount of money and land and have legally binding contracts and NDA's that cover what is and is not allowed to be done with my data and how long it may be retained. That contract and the laws enforcing the contract must have some serious teeth with very serious ramifications for anyone violating it whether intentionally or by mistake. [1] - https://www.youtube.com/watch?v=biNxl7tiVSY https://www.youtube.com/watch?v=biNxl7tiVSY
mylons 5y ago
yes. if you wanted to annotate your genome you could “easily” do it on your brand new macbook (this is ram intensive, you probably need 32G). you’d need a reference genome, like https://www.nist.gov/programs-projects/genome-bottle https://www.nist.gov/programs-projects/genome-bottle then you’d need a program like bwa http://bio-bwa.sourceforge.net/ http://bio-bwa.sourceforge.net/ to map your data. then use https://samtools.github.io/bcftools/howtos/variant-calling.html https://samtools.github.io/bcftools/howtos/variant-calling.h... or something else to produce variants from the mapping results. then compare your resultant vcf file to something like dbSNP: https://www.ncbi.nlm.nih.gov/snp/ https://www.ncbi.nlm.nih.gov/snp/ at this point you can start generating a raw version of a 23andMe report.
- LinuxBender 5y ago
  Nice! Thankyou for the links. I will research all of this.
  - mylons 5y ago
    good luck! it’s not that tough, just a lot of new vocabulary.
- tootie 5y ago
  I'm unclear from this what kind of equipment you need to extract and analyze the material?
  - mylons 5y ago
    you’d likely to have to get the nanopore sequencer in the article or find a lab using Next Generation Sequencing to sequence your DNA and give you “raw data” which are usually fastq files
- pas 5y ago
  Could you please explain how this mapping works? Why it needs so much RAM? Is it doing a fuzzy search of sorts for known sequences (genes)? Why can't it do so one by one?
ampdepolymerase 5y ago
A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.
- mylons 5y ago
  wow i didn’t know they were that “cheap” now. i used to work for a major competitor to the sequencer you linked, the SOLiD. and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off.
  - joshuamcginnis 5y ago
    What do you mean by it's always a few years off? Nanopore will allow you to do high-quality genomic sequencing _now_, in a home lab if you wanted, for less than $3K. If you amortize the 3K by the number of genomes you can sequence on the same flow cell, the price per base or per genome falls precipitously, depending on the size of the genome of course.
  - ampdepolymerase 5y ago
    The one I linked to is a decade out of date and OEM discontinued.
    - mylons 5y ago
      ya my first thought was how hard are reagents to get, but probably not that hard. i wasn’t in the lab, i was in bioinformatics so i’m generally clueless on reagent acquisition.
  - divbzero 5y ago
    > and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off. Is this also true for nanopores in protein sequencing? This HN comment from a few weeks back [1] pointed out recent progress but perhaps the tech is still not quite there. [1]: https://news.ycombinator.com/item?id=29481075 https://news.ycombinator.com/item?id=29481075

netizen-936824 5y ago

Sounds like a fediverse project?

Malp 5y ago
Oh God, I would not want a distributed group of actors with limited trust to sequence my DNA. Maybe it's a project for close group of friends that would be interested?
- netizen-936824 5y ago
  I wasn't thinking sequencing but rather comparison. Could even hash data for comparison to enforce privacy (unsure how effective that would be) But this could enable things like finding relatives which is what I got out of the comment about 23andme. Instead of all the data being centralized, storage and comparison could be distributed
  - Malp 5y ago
    Ah, thanks for clarifying. I misunderstood the main idea behind your comment.
- inciampati 5y ago
  Your DNA is almost exactly the same as other people's, just a unique mix. Not sure what you are concerned about. What would you expect a bad actor to do with your DNA sequences? I'm genuinely curious.
  - fragmede 5y ago
    A very practical reason not to want your DNA out there, unrestricted, is insurance costs. From car insurance, to health insurance, to mortgage lending rates, and life insurance, and while GINA from 2008 is supposed to protect that information, there are loopholes with the interpretation of that law that should give everybody pause.
  - snovv_crash 5y ago
    Using that analogy, all the 1s and 0s in your private key are the same as everyone else's as well. Genetic data can be used for all kinds of things, the worst of which would be things like targeted diseases or planting your DNA at a crime scene.
    - inciampati 5y ago
      Actually it's like your private key is made up of ~1000 1 mb pieces that each have 1/1000 rate of difference with any other similar piece. Oh, and the order of the pieces is almost always exactly the same. No, genomes are not "almost the same" because they are all in base-4 sequences and this made up of the same 0s 1s 2s and 3s. We are astoundingly similar, even unusually so for a large mammalian species.
  - LinuxBender 5y ago
    Your DNA is almost exactly the same as other people's, just a unique mix. Music is exactly the same notes, just a unique mix. So why is Sony upset that I want to stream their entire library? But jokes aside... A few decades ago I fought the military on collecting my DNA. I stalled them long enough to get my honorable discharge and avoid that all together. It's funny you ask because the commander asked the same thing and joked "Are you afraid we are going to clone you?!" to which I replied, "No sir, you should be afraid you are going to clone me." and we both had a laugh because he knew I was right. The military are not fond of critical/free thinkers. One of me was plenty. I explained that insurance companies were already using this data to retroactively cancel peoples policies even if they were not actively afflicted by something. The commander showed me how to use the FOIA request system. Laws have evolved a little since then but there are plenty of other risks. For starters, I can't easily change my DNA like I can change my debit card. That data can be used to tie me to others or guilt by association which is undesirable drama. It can also be used to try to sell me things. It can also be used to target biological weapons against specific groups of people. There appears to be an imbalance of data sharing in this regard. [1] Then there is simply the matter of privacy. If I want to share my DNA with some lab that is in turn going to sell it out to hundreds of other companies over and over forever, I should at very least be getting paid a vast amount of money and land and have legally binding contracts and NDA's that cover what is and is not allowed to be done with my data and how long it may be retained. That contract and the laws enforcing the contract must have some serious teeth with very serious ramifications for anyone violating it whether intentionally or by mistake. [1] - https://www.youtube.com/watch?v=biNxl7tiVSY https://www.youtube.com/watch?v=biNxl7tiVSY

mylons 5y ago

yes. if you wanted to annotate your genome you could “easily” do it on your brand new macbook (this is ram intensive, you probably need 32G). you’d need a reference genome, like https://www.nist.gov/programs-projects/genome-bottle https://www.nist.gov/programs-projects/genome-bottle then you’d need a program like bwa http://bio-bwa.sourceforge.net/ http://bio-bwa.sourceforge.net/ to map your data. then use https://samtools.github.io/bcftools/howtos/variant-calling.html https://samtools.github.io/bcftools/howtos/variant-calling.h... or something else to produce variants from the mapping results. then compare your resultant vcf file to something like dbSNP: https://www.ncbi.nlm.nih.gov/snp/ https://www.ncbi.nlm.nih.gov/snp/ at this point you can start generating a raw version of a 23andMe report.

LinuxBender 5y ago
Nice! Thankyou for the links. I will research all of this.
- mylons 5y ago
  good luck! it’s not that tough, just a lot of new vocabulary.
tootie 5y ago
I'm unclear from this what kind of equipment you need to extract and analyze the material?
- mylons 5y ago
  you’d likely to have to get the nanopore sequencer in the article or find a lab using Next Generation Sequencing to sequence your DNA and give you “raw data” which are usually fastq files
pas 5y ago
Could you please explain how this mapping works? Why it needs so much RAM? Is it doing a fuzzy search of sorts for known sequences (genes)? Why can't it do so one by one?

ampdepolymerase 5y ago

A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

mylons 5y ago
wow i didn’t know they were that “cheap” now. i used to work for a major competitor to the sequencer you linked, the SOLiD. and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off.
- joshuamcginnis 5y ago
  What do you mean by it's always a few years off? Nanopore will allow you to do high-quality genomic sequencing _now_, in a home lab if you wanted, for less than $3K. If you amortize the 3K by the number of genomes you can sequence on the same flow cell, the price per base or per genome falls precipitously, depending on the size of the genome of course.
- ampdepolymerase 5y ago
  The one I linked to is a decade out of date and OEM discontinued.
  - mylons 5y ago
    ya my first thought was how hard are reagents to get, but probably not that hard. i wasn’t in the lab, i was in bioinformatics so i’m generally clueless on reagent acquisition.
- divbzero 5y ago
  > and i feel like nanopore is the VR of dna sequencing. it’s always just another few years off. Is this also true for nanopores in protein sequencing? This HN comment from a few weeks back [1] pointed out recent progress but perhaps the tech is still not quite there. [1]: https://news.ycombinator.com/item?id=29481075 https://news.ycombinator.com/item?id=29481075