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Sequencing your DNA with a USB dongle and open source code

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Re: Sequencing your DNA with a USB dongle and open source code

#131

Post by gww »

tomjakubowski wrote: post #124
mylons wrote: post #118

Earlier quoted context omitted.

bwa specifically performs a burrows wheeler transform of a 3GB string. other mapping algorithms usually rely on some sort of indexing of the genome. the program then loads this into memory and queries that index for each “read” (a dna fragment from the dna sequencer). when i worked on https://github.com/iontorrent/tmap we thought it would be a good idea to do something like a “local alignment” (using https://en.wikip…

Human DNA contains roughly 3.2 billion nucleotides. A 3 GB string suggests an encoding with one byte per nucleotide. I'm curious: since there are only 4 bases in DNA, for genomic data, this seems rather inefficient. Is there any advantage in encoding the DNA with two bits per nucleotide? source for 3.2 billion: https://www.ncbi.nlm.nih.gov/books/NBK21134/#!po=0.485437

It's very common to use 2 bits per nucleotide despite the human genome having ambiguous bases on top of the 4 letters. These tools typically encode the ambiguous base as a random nucleotide but keep track of them and then convert them to a random nucleotide later.

In practice BWT alignment based tools may use a forward-index and a mirror-index of the reversed genome string (not reverse complemented). This dual index approach is important for dealing with mismatches strings. There's a nice example explaining this for an older tool named Bowtie [2]

With a two bit encoding and both indices it isn't uncommon for a genome index to take up several GB of RAM. For example, BWA uses 2-3 GB for its index [3].

[1] https://en.wikipedia.org/wiki/FM-index [2] https://academic.oup.com/bioinformatics/article/25/14/1754/2... [3] https://academic.oup.com/bioinformatics/article/25/14/1754/2...

There are some great computational benefits using 2 bit encoding for the BWT

Re: Sequencing your DNA with a USB dongle and open source code

#132

Post by koeng »

andrewon wrote: post #98
joshuamcginnis wrote: post #78

Earlier quoted context omitted.

I did a HMW extraction kit on the DNA and used a gel to estimate the volume of HMW DNA. Yes, you need to be able to run a gel, but I'm not sure what the expectation is from folks; that you just place a random piece of non-sterile tissue on a chip and have it do the extraction, sequencing and assembly? That seems like an unrealistic expectation.

They do work on an extraction flowcell that can be added on top. I’m hoping they can make it as easy as adding sample to a well, at least for blood or saliva.

If you're talking about the voltrax, you still need to pipette reagents in at the right times. They don't really talk about it in their advertising, but it's basically just to make mixing consistent when you have under-trained techs. Definitely will get there eventually, but I don't know if they are working on that right now.

Re: Sequencing your DNA with a USB dongle and open source code

#133

Post by lostlogin »

m12k wrote: post #18

I'm really curious about what I could learn by getting my DNA sequenced, but I'm worried about my rights to not have it recorded and shared without my consent if I got someone else to do it for me - so any advance toward an affordable home test setup is very welcome.

It’s out the bag now - you can be identified via relatives DNA.

https://www.latimes.com/california/story/2020-12-08/man-in-t...

Re: Sequencing your DNA with a USB dongle and open source code

#134

Post by lawrenceyan »

joshuamcginnis wrote: post #40
ampdepolymerase wrote: post #6

Earlier quoted context omitted.

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

That's not true. I just did a high-quality sequence and assembly of a new species of fungus from my home lab using nanopore. You can see all my code used for assembly and analysis that will be referenced in a paper I plan to publish in Jan here: https://github.com/EverymanBio/pestalotiopsis

Given that the decoder is machine-learned and depends on a training set to go from squiggle -> ATGC..., how do you ensure that sequences which haven't been seen before (not in the training set) are still accurately accounted for?

Re: Sequencing your DNA with a USB dongle and open source code

#135

Post by refurb »

biophysboy wrote: post #21
m12k wrote: post #18

I'm really curious about what I could learn by getting my DNA sequenced, but I'm worried about my rights to not have it recorded and shared without my consent if I got someone else to do it for me - so any advance toward an affordable home test setup is very welcome.

Its only valuable if somebody also interprets it for you, such as telling you whether you have a genetic predisposition for certain diseases.

That's Prometheus, no? They got acquired however, but prior to that you could upload data anonymously and then browse the analysis. It was very rough though, just linking sequences to risk, but a lot of it was inconclusive.

Re: Sequencing your DNA with a USB dongle and open source code

#136

Post by greggman3 »

haihaibye wrote: post #73
foobarbecue wrote: post #39

Earlier quoted context omitted.

If you haven't seen Gattaca, you should

There should be a directors cut where the mission fails because of Vincent's hidden heart condition. Gattaca shows eugenics has been so vilified that the audience will root for a character who selfishly commits fraud, risking lives and scientific progress for his own vanity. The really scary fact is that there would be no need for a police state and segregation. The genetically enhanced would just completely dominate…

100% Agree. Gattaca actually showed A SPACE PROGRAM running similar to the real space programs. I don't know about now but the first astronauts needed certain genes or they weren't allowed in. AFAIK that used to be true for fighter pilots. Want to be one you needed perfect eye sight. Bad genes = selected out.

Re: Sequencing your DNA with a USB dongle and open source code

#137

Post by jcims »

tekproxy wrote: post #130
adabaed wrote: post #36

Earlier quoted context omitted.

Imagine insurers refusing to give you a service due to your predisposition to certain diseases...

Imagine gene therapy to fix the problems. After a few generations, many diseases will be extinct. There's a guy on YouTube doing diy gene therapy to treat his lactose intolerance so it's not exactly science fiction.

The Thought Emporium

https://youtube.com/c/thethoughtemporium

He’s got a ton of other interesting projects, the DIY gene therapy is just one that stands out because it seems so risky.

Re: Sequencing your DNA with a USB dongle and open source code

#138

Post by jcims »

dekhn wrote: post #52
shukantpal wrote: post #50

Earlier quoted context omitted.

At scale?

Sure. I've worked with and know people who could carry this out at scale, although obviously individual sample collection isn't highly scalable. Edit: I used to help Google fund researchers like Joe Derisi and others who develop technology to do this, and some of the people I worked with in my academic career are quite good at identifying serial killers from 30 year old DNA. If you're downvoting because you think I'm…

It seems very unlikely to me that there isnt at least *some* genetic information that would be of direct value in advertising. Like if Google took five years of personalized ad performance info and filtered that through the associated individual’s known DNA to develop a predictive model.

Re: Sequencing your DNA with a USB dongle and open source code

#139

Post by jcims »

josters wrote: post #100
hourislate wrote: post #70

Earlier quoted context omitted.

I'm curious whether a Covid PCR test could be used to sequence your DNA. Is there enough of a specimen in the process.

I read a story[1] about a UK-based Covid testing firm who was planning on collecting and selling their customers' DNA samples. > Its "research programme information sheet", last updated on October 21, says the company retains data including "biological samples" and "the DNA obtained from such samples", as well as "genetic information derived from processing your DNA sample ... using various technologies such as genot…

This reads like the lead-in to an episode of Black Mirror.

Re: Sequencing your DNA with a USB dongle and open source code

#140

Post by andrewxdiamond »

jrumbut wrote: post #81
toomuchtodo wrote: post #65

Earlier quoted context omitted.

“Passed in 2008, a federal law called the Genetic Information Nondiscrimination Act (GINA) made it illegal for health insurance providers in the United States to use genetic information in decisions about a person's health insurance eligibility or coverage.” Also prevents employment discrimination based on genetics. https://www.genome.gov/about-genomics/policy-issues/Genetic-... (disclosure: have had my DNA sequenced…

What I worry about is having this data laundered through a couple of vendors. "How could we know our vendor's vendor was using genetic information in their proprietary risk score?" "How could we know our client's client was using our score for life, health, or auto insurance/employment/lending/etc decisions?" It's a "can't unring a bell" situation and the gaps in the regulations and the incentives for bad behavior ar…

Because insurance is regulated against this. They can’t just Willy-nilly get data and “scores” from uncontrolled sources.
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