What about the personal sequencing of fecal matter to determine the composition and species of bacteria in a person's own stool? This test could be done routinely for monitoring and could generate a serious amount of revenue. Each poop is an opportunity for NGS sms lån

Already done at secon dgenome. stool anlysis (fecal fats etc...) has been done for years by all the ref labs)

Fill us in on the details - what are you going to diagnose? how much will it cost per test? what is your patient pool sms lån

High-throughput screening.....microarrays.......next gen sequencing. Billions and billions have been spent, but when I go for my physical, the doctor is still sticking her finger up my ass to check my prostate. How much longer can it be before an army of taxpayers shows up at the gates of NIH to ask for their money back. I'll be amongst them.

Sequencing or Nextgen sequencing IS POOP. Sequencing always was and will always be an academic R and D full of errors project. The reason for the next was because the first stunk...and so will the next. Wasted money, the reason why the NIH funda are getting cut!! LIFE, Illumina and the rest of the sequencing frauds have cheated the world and 401K accounts.

"There are at least a dozen disorders which can be diagnosed by sequencing poop. This is a powerful test which allows the entire spectrum of microbial disorders and cancer to be assessed."

enllighten us. In nearly 150 posts no one has yet come up with anything that stands up.

There are at least a dozen disorders which can be diagnosed by sequencing poop. This is a powerful test which allows the entire spectrum of microbial disorders and cancer to be assessed.

How many different diseases and syndromes can be diagnosed by sequencing poop?

You should poop at least once per day!

After reaching my 40s I'm only pooping once per week. Is this normal?

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"I'm not concerned about the corn in my poop, I'm worried about the black tar looking regions."

If you're that worried I'd recommend getting the black regions of your poop sequenced.

I'm not concerned about the corn in my poop, I'm worried about the black tar looking regions.

"I usually eat corn at least twice per week. Why do you ask?"

Because, if you have corn in your poop it is likely because you ate corn!

I usually eat corn at least twice per week. Why do you ask?

"I'm not sure if this is a problem but lately parts of my poop are dark in color like black tar with the lighter brown regions containing little nuggets of corn. Is this normal?"

It depends, have you eaten corn recently?

I'm not sure if this is a problem but lately parts of my poop are dark in color like black tar with the lighter brown regions containing little nuggets of corn. Is this normal?

Today I found out from my doctor that the mucus and pus in my stool was due to Irritable Bowel Syndrome. I didn't need to get my stool sequenced to find this out.

"Why does coffee make me poop?"

You probably have a mutation in one of the genes in your protein kinase pathway. I would recommend getting your exome sequenced to find the mutation. Since it is likely inherited you could get by with low read depth for your NGS exome sequence. 30x coverage should do fine to diagnose your problem. In the meantime, stay away from coffee unless you are near a toilet. Don't drink and drive unless you want to risk pooping in your pants!

Why does coffee make me poop?

no, my numbers are fine. You quote in your paper 70ng human DNA/g feces for a healthy volunteer and 309ng human DNA/g feces for a CRC patient (you don't state the CRC stage). The amount of bacterial DNA/g of feces varies but is always in the ug's/g feces i.e. very much higher than the amount of human DNA.

The numbers you are quoting are completely incorrect!

There is much more human genomic DNA in stool than you are quoting.

Read the following paper from my lab which will give you an education!

http://cebp.aacrjournals.org/content/15/6/1115.full.pdf

You need to read more peer reviewed literature!

"This is a new application idea!!! Hence the title of this post. There is no reason why this wouldn't work. If you are soo smart, provide a technical reason why this wouldn't work! This could be a huge money maker as a clinical diagnostic!"

okay, so you're suggesting shot-gun sequencing of total DNA isolated from a stool sample in order to get the entire microbiome, the patients full genome sequence and 'cancer signatures' as you call them, right?

So let's assume that the $1,000 genome is reality (although it doesn't really include labour, analysis etc but never mind) and that it can be done in 2 days.

From experience, human DNA in stool DNA is less than 1% but let's be generous and call it 1%. That means to get the whole genome sequence from shot-gun sequencing of total stool DNA requires 100x as much sequencing as dedicated genome sequencing. Therefore $100,0000 and 200 days.

Now lets assume you want to see the 'cancer signatures' too. Tumour DNA from bowel cancer is very much less than 1% of the human DNA in stool DNA but again, be generous and assume 1%. So now multiple by 100 again and it's $10,000,000 and 20,000 days or just over 54 years to perform the test. This was what you were suggesting someone should request from their family doctor......

Pardon the pun but you don't know shit!

This is a new application idea!!! Hence the title of this post. There is no reason why this wouldn't work. If you are soo smart, provide a technical reason why this wouldn't work! This could be a huge money maker as a clinical diagnostic!

Apparently sarcasm genes are being under expressed and stupidity genes, over.

"You need to be educated on the applications which are possible with next generation sequencing. This cam easily be done on the HiSeq at a reasonable cost. You need to do some homework and read up on NGS before calling people names. You are ignorant."

show me one published example where both a patient's whole genome sequence has been determined and their microbiome determined in one go, from a stool sample.

"I understand you are suggesting getting a patients entire genome sequence and the make-up of their microbiome in one go, from a stool sample.....you're an idiot."

You need to be educated on the applications which are possible with next generation sequencing. This cam easily be done on the HiSeq at a reasonable cost. You need to do some homework and read up on NGS before calling people names. You are ignorant.

"You obviously don't understand. By sequencing a stool sample you get the human whole genome from intestinal cellular DNA as well as the entire GI tract microbiome. You get both! This is why the sequencing of stool samples is incredibly informative."

I understand you are suggesting getting a patients entire genome sequence and the make-up of their microbiome in one go, from a stool sample.....you're an idiot.

"You're an idiot! sequencing your genome (whole genome sequencing) and sequencing your micorobiome from a stool sample are two completely different things."

You obviously don't understand. By sequencing a stool sample you get the human whole genome from intestinal cellular DNA as well as the entire GI tract microbiome. You get both! This is why the sequencing of stool samples is incredibly informative.

"By sequencing your stool you'll be able to get a complete picture of all the different bacteria in your colon while also detecting signatures associated with cancer. It is the most powerful test available and just because there are negative jealous people on this site making selfish recommendations don't deny yourself the best medical care. Simply demand from your doctor whole genome sequencing of your stool. Life is precious and we all deserve the best. If you have mucus, pus, or blood in your stool please do yourself a favor and get whole genome sequencing. What is your life worth to you?"

You're an idiot! sequencing your genome (whole genome sequencing) and sequencing your micorobiome from a stool sample are two completely different things.

"Agree with the comment below - don't believe some snake-oil seller on the internet, go to your doctor and ASK them about sequencing and see if they think the information would be of any use to them. If you do have sequencing done you will have to pay for it yourself so don't part with any money unless your doctor (not the person selling you the sequencing service) tells you it would be of benefit"

This is good advice - don't self-diagnose using the internet, go to a doctor and get qualified advice.

Agree with the comment below - don't believe some snake-oil seller on the internet, go to your doctor and ASK them about sequencing and see if they think the information would be of any use to them. If you do have sequencing done you will have to pay for it yourself so don't part with any money unless your doctor (not the person selling you the sequencing service) tells you it would be of benefit.

you are talking absolute nonsense! No doctor can, or will, provide whole genome sequencing and no doctor would currently no what to do with the results.

Yes, sequencing a stool sample will give a picture of the make-up of the microbiome but as yet noone knows what this all means - it's very early-stage research.

Similarly with having your own genome sequenced - how to use this in a clinical setting is in the very early stages of research. Linkages to disease susceptibility are generally very weak (with a few exceptions such as CF).

The study of somatic mutations in cancer diagnostics is much better established but this would not apply to having your genome sequenced. This would only be relevent to sequence information obtained from a tumour biopsy.

If you have mucus, pus, blood or anything else unusual in your stools then yes of course, go to you doctor to get a diagnosis and treatment. Sequencing however, will not play any part in that.

By sequencing your stool you'll be able to get a complete picture of all the different bacteria in your colon while also detecting signatures associated with cancer. It is the most powerful test available and just because there are negative jealous people on this site making selfish recommendations don't deny yourself the best medical care. Simply demand from your doctor whole genome sequencing of your stool. Life is precious and we all deserve the best. If you have mucus, pus, or blood in your stool please do yourself a favor and get whole genome sequencing. What is your life worth to you?

"Yes, if you want to get a proper diagnosis and if your life is important to you then I would highly recommend getting whole genome sequencing on your stool. We each deserve the best medical care possible and sequencing is the best."

A proper diagnosis of what?
why would you do whole genome sequencing on stool samples? Are you suggesting sequencing the entire genome of every organism in a stool sample?.....And when did sequencing become 'the best medical care'? when did it become any kind of medical care?

"Thank you! Should I ask my doctor for a sequencing test?"

No! you're doctor wouldn't be able to provide it, nor would he know what to do with the results.

Yes, if you want to get a proper diagnosis and if your life is important to you then I would highly recommend getting whole genome sequencing on your stool. We each deserve the best medical care possible and sequencing is the best.

Thank you! Should I ask my doctor for a sequencing test?

Stool normally contains a small amount of mucus, but passing stools with visible amounts of mucus could be from one of several different diseases or conditions. Mucus in the stool is a common symptom of irritable bowel syndrome (IBS) and ulcerative colitis (a form of inflammatory bowel disease), and is seen to a lesser degree in Crohn's disease. A bacterial infection, anal fissure, or a bowel obstruction may also cause the passage of mucus along with stool. Yes, you should go see your doctor!

I've been having mucus and pus in my stool lately and it is concerning me. Should I see a doctor?

Poop Transplants May Combat Bacterial Infections

http://news.yahoo.com/poop-transplants-may-combat-bacterial-infections-1...

Since poop contains a bacterial representation of your entire GI tract it allows the greatest sensitivity to detect signatures for disease. While poop may sound disgusting it is the second most informative sample type next to whole blood. Poop contains a wealth of diagnostic and prognostic information. Sequencing of poop makes a ton of sense and can help to improve patient care and management.

I don't think you realize the power of sequencing!!! All dumps repeasent on opportunity!!!

Maybe I'm missing something, but how can sequencing the 'Dumpome' differentiate which part of the colon (e.g. ascending or descending) the cells (tumor and normal) found in the poop, originated from?

I just wish someone would sequence my poop!!!

raymond.woo@energizer.com

New Applications for Next Generation Sequencing!!!

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"My company will use sequencing to diagnose the following five conditions:

1. Colorectal cancer
2. Ulcerative colitis
3. Pseudomembranous colitis
4. Diverticulitis
5. Irritable bowel syndrome

There are other disorders of the large intestine and rectum which I'll likely add to the menu but this represents my current thinking"

So you don't actually have tests for those 5 (or any other) conditions currently? There's a lot more to finding a diagnostic for a condition of the digestive tract than merely sequening a stool sample. And then once you believe you have a diagnostic test there's the clinical trials required for FDA approval and/or CE marking.....I hope your VC partners have deep pockets and a lot of patience.

The global market for sequencing products was valued at $2.3 billion in 2010 and nearly $3 billion in 2011. The market is forecast to grow at a compound annual growth rate (CAGR) of 17.5% to reach $6.6 billion by 2016.

Sequencing instruments and consumables made up the largest market segment in 2011, with revenues of nearly $1.6 billion. The segment is expected to grow to $2.2 billion in 2016, a CAGR of 7.3%.

Sequencing services comprise the fastest-growing market segment, totaling $987.6 million in 2011 and expected to each nearly $3.5 billion in 2016, a CAGR of 29.0%.