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Author Topic: Nanopore genome sequencing  (Read 18267 times)

Simon Dresner

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Nanopore genome sequencing
« on: February 18, 2012, 05:11:58 AM »

A new kind of genome sequencer has been demonstrated. The significance is that it can  read indivdual strands of DNA and in much longer sequences (thousands of bases) than existing sequencers can. That means that it can work with very little material because there isn't the need to amplify the DNA like there is with current technology and the sequences can be reassembled much more easily. This technology has been in prospect for a long time, but it seems to have finally been got to work. Does this offer the possibility that the human DNA found in the remaining fecal material from the Seven site could be sequenced and identified in the near future?

The article from New Scientist below describes the technology in more detail. It concentrates on the portable version (MinION), but the lab version (GridION) is the one that would be used for a task like this.

http://www.newscientist.com/article/dn21495-usb-stick-can-sequence-dna-in-seconds.html

The article from Nature emphasises that the technique has only been demonstrated for a sequence of a few thousand base pairs and it still needs to be proven for longer genomes.

http://www.nature.com/news/nanopore-genome-sequencer-makes-its-debut-1.10051
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Ric Gillespie

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Re: Nanopore genome sequencing
« Reply #1 on: February 18, 2012, 06:06:16 AM »

Does this offer the possibility that the human DNA found in the remaining fecal material from the Seven site could be sequenced and identified in the near future?

Possibly.  The University of Toronto's Donnelly Centre for Celluar & Biomolecular Research is currently trying to sequence the human DNA in the material. 
A little history:
The Oklahoma University Molecular Biology Laboratories found mitochondrial DNA from two individuals but the amounts were too small to sequence. They also found bacteria that are common in human feces and other bacteria that are common in soil. "Next generation" (Roche 454) examination of the material revealed significant quantities of rodent DNA.  Oklahoma concluded that the material is probably clumps of soil from a "rodent run" - a route along the ground frequently used by rodents.  The only rodents on Nikumaroro are Polynesian rats - Rattus exulans - and they do seem to have set routes that they follow, but that doesn't explain the presence of human DNA and the physical appearance of the clumps seems to indicate that, although they are now hard and brittle, they were originally soft enough to be flat on the bottom.  In short, they look like dried out poop.  Toronto wanted to take a crack at the stuff.  We said, "Go for it."
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Simon Dresner

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Re: Nanopore genome sequencing
« Reply #2 on: February 18, 2012, 09:00:29 AM »

It's interesting to hear that another lab is trying to sequence the material now. Presumably Toronto are using a more advanced technique than Oklahoma did? How much of the material was left for them to use? Have you kept any more in reserve? If the stuff was carried by rodents that would seem to imply there will be more of it scattered along their runs. I'd thought it was meant to be human faeces, but from what you're saying it sounds like it might be rat faeces with human DNA in it because they ate something human. Or the human DNA could have been modern DNA contamination? I've been intrigued since the DNA test result was announced last year that material from two individuals was found. That would seem to imply Fred Noonan survived long enough to get to the Seven site.
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Ric Gillespie

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Re: Nanopore genome sequencing
« Reply #3 on: February 18, 2012, 09:20:10 AM »

Presumably Toronto are using a more advanced technique than Oklahoma did?

Yes.

How much of the material was left for them to use?

In a relatives sense, lots.  Only tiny amounts are needed for analysis.

Have you kept any more in reserve?

They'll only use what they need. I kept one small "clump" here for non-DNA research.  That proved to be a smart move. The DNA scientists were so focused on the hi-tech procedures that nobody thought to wonder why the clump was flat on the bottom.

If the stuff was carried by rodents that would seem to imply there will be more of it scattered along their runs.

But there wasn't.  A large area has been excavated and no other material like this has turned up.

I'd thought it was meant to be human faeces, but from what you're saying it sounds like it might be rat faeces with human DNA in it because they ate something human.

The clumps are way too big to be rat poop - or, if it is, I never want to meet that rat.

Or the human DNA could have been modern DNA contamination?

Possibly, although the lab in Oklahoma went to extraordinary lengths to reduce that possibility.

I've been intrigued since the DNA test result was announced last year that material from two individuals was found. That would seem to imply Fred Noonan survived long enough to get to the Seven site.

IF the material is human faeces, and IF the two individuals represented by the DNA in the poop are Amelia and Fred (we have a sample of Earhart's mtDNA but still no luck finding a reference sample for Fred) THEN we get to puzzle over how the DNA from two people get into one piece of poop.
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Monty Fowler

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Re: Nanopore genome sequencing
« Reply #4 on: February 18, 2012, 01:44:10 PM »

"THEN we get to puzzle over how the DNA from two people get into one piece of poop."

*cough* I vote for just  continuing the search for the plane. Don't even want to go there. Nope.

Love to Mother, but who doesn't revel in poop, putative or otherwise,
Monty Fowler, TIGHAR No. 2189 CER
Ex-TIGHAR member No. 2189 E C R SP, 1998-2016
 
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Chris Johnson

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Re: Nanopore genome sequencing
« Reply #5 on: February 18, 2012, 02:03:22 PM »

Latrine area of camp? If I was one of two people stranded then I'd try and set up some kind of protocol ref waste such as a slit trench where both of you would void.

Rat DNA, well rats are into most things.
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Harry Howe, Jr.

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Re: Nanopore genome sequencing
« Reply #6 on: February 18, 2012, 02:44:05 PM »


When I was in Scouts, then as a Leader, then in Army Survival School, then when into wilderness camping, canoeing, fishing, etc.  I always dug a hole , went, covered it up, and marked the spot with an "X" (crossed sticks, stones in X shape, etc) so noone would step  on it.

I always thought that it was standard practice.
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LTM   Harry (TIGHAR #3244R)
 
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Chris Johnson

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Re: Nanopore genome sequencing
« Reply #7 on: February 18, 2012, 02:49:14 PM »


When I was in Scouts, then as a Leader, then in Army Survival School, then when into wilderness camping, canoeing, fishing, etc.  I always dug a hole , went, covered it up, and marked the spot with an "X" (crossed sticks, stones in X shape, etc) so noone would step  on it.

I always thought that it was standard practice.

Beleive most TIGHAR digs are only in the 10CM range of the surface but would welcome being put right.
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Ric Gillespie

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Re: Nanopore genome sequencing
« Reply #8 on: February 18, 2012, 05:13:11 PM »

Beleive most TIGHAR digs are only in the 10CM range of the surface but would welcome being put right.

That's correct.
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Harry Howe, Jr.

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Re: Nanopore genome sequencing
« Reply #9 on: February 18, 2012, 08:09:21 PM »


Don't get the connection between the depth of a TIGHAR dig (about 4 inches) and the DNA indications.

Re:rodent DNA in human excrement:  I'm castaway on a deserted island, I'm hungry, Rats on run, parachute string for a snare,  roast rodent, food!  not bad.
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Chris Johnson

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Re: Nanopore genome sequencing
« Reply #10 on: February 19, 2012, 12:52:51 AM »

Harry,

I was referencing it as some kind of latrine pit, 4" isn't deep but it could be the only depth they could dig too.
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Harry Howe, Jr.

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Re: Nanopore genome sequencing
« Reply #11 on: February 19, 2012, 10:03:25 AM »


Chris
Gotcha, I was a bit dense there  LOL
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LTM   Harry (TIGHAR #3244R)
 
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Tom Swearengen

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Re: Nanopore genome sequencing
« Reply #12 on: February 19, 2012, 03:22:52 PM »

4 inches isnt deep , but what is the makup of the soil? Coral, maybe some lava deeper?
Tom Swearengen TIGHAR # 3297
 
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Chris Johnson

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Re: Nanopore genome sequencing
« Reply #13 on: February 20, 2012, 04:21:09 AM »

How deep are crab burrows in the area?

Woke up wondering if a crab pulled some viscera such as a bowl into its burrow
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Andrew M McKenna

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Re: Nanopore genome sequencing
« Reply #14 on: February 21, 2012, 03:08:01 AM »

4 inches isnt deep , but what is the makup of the soil? Coral, maybe some lava deeper?

"Soil" such as it is, is basically coral rubble with bits of organic material that has filtered down into the voids between the rubble. 

Coral atolls typically sit on top of a seamount, or extinct volcano, but it is way down there, and there is no volcanic rock to be found on Niku unless it was brought there by someone from afar.

Andrew
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