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How to sequence your own DNA at home

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Re: How to sequence your own DNA at home

#81

Post by kriro »

colechristensen wrote: post #53
brikym wrote: post #52

With such cheap costs every city should be sequencing dog turds and sending out big fines. The pay back would be very quick.

It's quite a bit more difficult with poop. A rather large proportion of the DNA in poop isn't from the creature that pooped it. (mostly bacteria)

And you'd need the DNA of all dogs to boot (unless they are already somehow stored when a dog is registered). But generally speaking, I do like the idea. Also for horse poop which is pretty common on roads here in the countryside.

Re: How to sequence your own DNA at home

#82

Post by vintermann »

jdmoreira wrote: post #57

I don't want to sequence at home. But I do want to sequence it using a third-party that gives me all the raw data. I live in Europe and I'm just a simple consumer. Does anyone know how I can do this? What service would I use / you can recommend? Them not keeping it on their side would be a huge bonus of course but not sure I can ask for that much.

YSEQ is basically a mom- and pop shop, two German scientists who helped set up Family Tree DNA's labs in Texas then went home to start a small competitor (I think there was some sort of disagreement or conflict) in the space of high-resolution Y DNA sequencing for genealogists.

They also do high resolution full genome sequencing on request. But be warned, it takes a long time, and they reserve the right to cancel your order if you complain about how long it takes!

They're not the cheapest option, but when it comes to privacy for Europeans, I think they're as good as they come. You want a bit of "difficult to work with" when it comes to privacy.

Re: How to sequence your own DNA at home

#84

Post by epgui »

mjg59 wrote: post #75

As someone with experience (albeit almost 20 years out of date) experience of wet lab DNA collection and sequencing - this stuff is hard, you will fail a lot, and you will fail a lot more if you don't have an extremely clean environment to do this in. And once you have data, you should be asking yourself how accurate it is given the environment you collected it in, you should be looking at correlated sequence errors…

Nanopore data is a lot easier to analyze than short read sequencing data. You just don’t get the same alignment/assembly issues: these things sequence incredibly long reads.

(also a biochemist, MSc)

Re: How to sequence your own DNA at home

#86

Post by vintermann »

stymaar wrote: post #62
jdmoreira wrote: post #57

I don't want to sequence at home. But I do want to sequence it using a third-party that gives me all the raw data. I live in Europe and I'm just a simple consumer. Does anyone know how I can do this? What service would I use / you can recommend? Them not keeping it on their side would be a huge bonus of course but not sure I can ask for that much.

> But I do want to sequence it using a third-party Don't forget to change your DNA when the third party's database will eventually leak. (see the 21andMe's data leak: https://en.wikipedia.org/wiki/23andMe_data_leak )

They did not leak their database, the attacker guessed some user passwords and scraped those people's match lists.

I don't think they even got their hacked user's test results - you can download those from 23andMe, as GDPR requires, but it's a "request your data" process which isn't so easy to do at scale without people noticing.

23andMe is also not NGS sequencing, so you get only a couple of 100000 letters randomly* distributed across your whole genome.

Re: How to sequence your own DNA at home

#87

Post by eps »

sergey-a wrote: post #60
jdmoreira wrote: post #57

I don't want to sequence at home. But I do want to sequence it using a third-party that gives me all the raw data. I live in Europe and I'm just a simple consumer. Does anyone know how I can do this? What service would I use / you can recommend? Them not keeping it on their side would be a huge bonus of course but not sure I can ask for that much.

Sequencing dot com. TellmeGen DNA Complete. Unless you live in Germany (in Germany it seems to be illegal to send saliva to other countries).

Can you get raw data from Tellmegen?

Can't seem to find any info on this on their website.

Re: How to sequence your own DNA at home

#88

Post by mbeavitt »

Jules-Bertholet wrote: post #9
whatever1 wrote: post #3

What is the accuracy in this ? Aka if I run the experiment 10 times how many differences will i get? I don’t have a physical sense on what would be a good number.

Oxford Nanopore unfortunately has a high error rate (3-5%) compared to other sequencing technologies. And the errors are non-random

This is simply not true, advances in basecalling and using Duplex give you >Q25

Re: How to sequence your own DNA at home

#89

Post by vintermann »

sergey-a wrote: post #38
armanj wrote: post #21

one main marketing leverage of 23andMe, AncestryDNA, etc are fulfilling the curiosity of people who want to know which part of the world their genes are from. I guess that dataset should be preparatory.

Problem with those providers - they only check 700K positions out of 3 billion and there is no mapping quality or allelic depth data in those dataset and this is critical for assessing whether the detected variant is a false positive or real. It's not suitable for health investigations since most of DNA is not sequenced and genotyping technology is known to produce high rate of false positive for rare mutations. (I'm…

It's a bit ironic, since FTDNA and MyHeritage (which uses FTDNA's lab) have switched to NGS now, so they presumably could deliver those notorious "health insights", at least better than 23andMe. But they aren't in that market, and 23andMe shows no inclination to switch. They're probably licking their wounds after the user hack and buyout fiasco.
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