6 ms·

Real time microRNA detection

21 points by sebst 12y ago

aroch 12y ago
First off, there's probably nothing particularly new or exciting about their "patented biochemistry". Amplifying miRNA and sRNA is relatively easy and takes very little time and is something we've been doing for decades -- polymerases can PCR the entirely of one in 0.5-2 seconds and that "as little as 60mins" claim is a result of this and by no means revolutionary. They're essentially doing qRT-PCR in a plate, which would cost me ~$50-80 to do in my lab. This is another case of the patent office being out of their depth and granting patents to anything that sounds magical but believable to a layperson. Plus I don't need yet another company improperly mining heath data. On top of that, doesn't anyone else think this is a bad idea to try to test everyone for low incidence diseases? miRNA and sRNAs are OK markers for disease, not great and certainly not definitive. You're guaranteeing that most of your positives are false positives.
- cjbprime 12y ago
  I agree with your first paragraph. > On top of that, doesn't anyone else think this is a bad idea to try to test everyone for low incidence diseases? [..] You're guaranteeing that most of your positives are false positives. Hm, it depends on the incidence, and the effect size of the disease you're screening for. Standard healthcare does tests for really low incidence diseases all the time -- for example, amniocentesis is commonly performed to test for a disease (Down's Syndrome) affecting <0.1% of babies, even though the test itself causes increased risk of miscarriage. Is looking for low-probability genetic disease and having to deal with false positives really much different/worse?
  - aroch 12y ago
    The Down's test is definitive, testing for low incidence issues isn't a problem when you can be 99.999....98% confident in your test. Or, more importantly, tests for low incidence occurrences are fine as long as your rate of incidence is substantially higher than your rate of false positive.
- kolinko 12y ago
  Are false positives the real problem, or the fact that the current medical system is not equipped to deal with them?
  - aroch 12y ago
    Yes, false positives on many cancer or organ disease tests would require invasive, exploratory surgery
- noname123 12y ago
  Didn't 23andme start out by offering disease and ancestry information based on SNPs, but then stopped disease prognosis due to liability reasons and the fact that some of the literature on SNP disease markers became controversial/unreliable/outdated? But even genotyping on ancestry data caused problems such as people finding out that their father had an illegitimate child and another sibling they didn't know about, that caused divorces, personal falling out's etc.
  - cjbprime 12y ago
    > Didn't 23andme start out by offering disease and ancestry information based on SNPs, but then stopped disease prognosis due to liability reasons They just stopped because the FDA told them to; AIUI they don't have any liability concerns of their own.
- nmjohn 12y ago
  I think you're missing the point - at least how I'm reading it - the idea is the user friendliness, not that the techniques themselves are novel. You're absolutely correct that PCR and DNA/RNA amplification tech is nothing new and is (relatively) very simple - to the point where I did it in high school biology (AP) 6 years ago and then a number of times in undergrad labs. However I am not aware of anything that makes it this easy for a nurse/doctor to do in the hospital - as they put it "without the need of a specialized technician or expensive lab machinery." There isn't enough information provided to know how useful it will be though. I can see some potentially interesting use cases where a nurse being able to take a blood sample and run a plate with results in an hour could save a lot of time and money. At the same time, it really comes down to the "patented biochemistry" and what specific markers are on the plates. > On top of that, doesn't anyone else think this is a bad idea to try to test everyone for low incidence diseases? miRNA and sRNAs are OK markers for disease, not great and certainly not definitive. You're guaranteeing that most of your positives are false positives. That is highly dependant on the disease in question, no?
  - icegreentea 12y ago
    Given their careful choice of wording, its likely that intermediary processing between getting the blood sample and running the test is needed. In fact, simply be requiring the pipetting, they are already saying that they do no intend doctors or nurses to use this device - this is purely meant to be used in a laboratory context (note: there are lots of hospital labs). This device as it is is clearly meant 'For Research Use' only. The benefit of this device for their use will be relatively narrow. In a patient setting, the benefits of fast, on demand testing is obvious (for certain tests). In a research environment, where they will likely already have bulk PCR processes ready, the benefit is less clear. I work at a company that works in this field - we target DNA instead, and only look at one gene. We have FDA approval for high complexity lab use (https://wwwn.cdc.gov/clia/Resources/TestComplexities.aspx https://wwwn.cdc.gov/clia/Resources/TestComplexities.aspx). From my experience, getting this down to the doctor/nurse level is ridiculously hard, and getting approval for 96 different tests will require a ridiculous amount of capital. My guess is that this is a first gen product designed to work as proof of concept and generate some cash flow so they can bootstrap and move down the complexity chain towards the patient. One thing to note is that 'specialized personnel' are actually pretty cheap given the recent surge in underemployed biochem graduates.
- csirac2 12y ago
  It seems extremely light on actual science. It's been a couple of years since I worked with biologists but dealing with false positives with this type of thing (well, GeneChips anyway), specifying suitable probe sets, getting the experiment right and making sense of the results seemed like an ongoing struggle for the application (measuring bacteria species diversity) - if I remember correctly, comparison with traditional sequencing techniques were required to better understand how the results behaved with eg. species hybridization in these microarrays. But the field moves so fast and I never really grokked the wetlab side of things, so who knows...
deleted 12y ago
[deleted]

21 points by sebst 12y ago

aroch 12y ago

First off, there's probably nothing particularly new or exciting about their "patented biochemistry". Amplifying miRNA and sRNA is relatively easy and takes very little time and is something we've been doing for decades -- polymerases can PCR the entirely of one in 0.5-2 seconds and that "as little as 60mins" claim is a result of this and by no means revolutionary. They're essentially doing qRT-PCR in a plate, which would cost me ~$50-80 to do in my lab. This is another case of the patent office being out of their depth and granting patents to anything that sounds magical but believable to a layperson. Plus I don't need yet another company improperly mining heath data. On top of that, doesn't anyone else think this is a bad idea to try to test everyone for low incidence diseases? miRNA and sRNAs are OK markers for disease, not great and certainly not definitive. You're guaranteeing that most of your positives are false positives.

cjbprime 12y ago
I agree with your first paragraph. > On top of that, doesn't anyone else think this is a bad idea to try to test everyone for low incidence diseases? [..] You're guaranteeing that most of your positives are false positives. Hm, it depends on the incidence, and the effect size of the disease you're screening for. Standard healthcare does tests for really low incidence diseases all the time -- for example, amniocentesis is commonly performed to test for a disease (Down's Syndrome) affecting <0.1% of babies, even though the test itself causes increased risk of miscarriage. Is looking for low-probability genetic disease and having to deal with false positives really much different/worse?
- aroch 12y ago
  The Down's test is definitive, testing for low incidence issues isn't a problem when you can be 99.999....98% confident in your test. Or, more importantly, tests for low incidence occurrences are fine as long as your rate of incidence is substantially higher than your rate of false positive.
kolinko 12y ago
Are false positives the real problem, or the fact that the current medical system is not equipped to deal with them?
- aroch 12y ago
  Yes, false positives on many cancer or organ disease tests would require invasive, exploratory surgery
noname123 12y ago
Didn't 23andme start out by offering disease and ancestry information based on SNPs, but then stopped disease prognosis due to liability reasons and the fact that some of the literature on SNP disease markers became controversial/unreliable/outdated? But even genotyping on ancestry data caused problems such as people finding out that their father had an illegitimate child and another sibling they didn't know about, that caused divorces, personal falling out's etc.
- cjbprime 12y ago
  > Didn't 23andme start out by offering disease and ancestry information based on SNPs, but then stopped disease prognosis due to liability reasons They just stopped because the FDA told them to; AIUI they don't have any liability concerns of their own.
nmjohn 12y ago
I think you're missing the point - at least how I'm reading it - the idea is the user friendliness, not that the techniques themselves are novel. You're absolutely correct that PCR and DNA/RNA amplification tech is nothing new and is (relatively) very simple - to the point where I did it in high school biology (AP) 6 years ago and then a number of times in undergrad labs. However I am not aware of anything that makes it this easy for a nurse/doctor to do in the hospital - as they put it "without the need of a specialized technician or expensive lab machinery." There isn't enough information provided to know how useful it will be though. I can see some potentially interesting use cases where a nurse being able to take a blood sample and run a plate with results in an hour could save a lot of time and money. At the same time, it really comes down to the "patented biochemistry" and what specific markers are on the plates. > On top of that, doesn't anyone else think this is a bad idea to try to test everyone for low incidence diseases? miRNA and sRNAs are OK markers for disease, not great and certainly not definitive. You're guaranteeing that most of your positives are false positives. That is highly dependant on the disease in question, no?
- icegreentea 12y ago
  Given their careful choice of wording, its likely that intermediary processing between getting the blood sample and running the test is needed. In fact, simply be requiring the pipetting, they are already saying that they do no intend doctors or nurses to use this device - this is purely meant to be used in a laboratory context (note: there are lots of hospital labs). This device as it is is clearly meant 'For Research Use' only. The benefit of this device for their use will be relatively narrow. In a patient setting, the benefits of fast, on demand testing is obvious (for certain tests). In a research environment, where they will likely already have bulk PCR processes ready, the benefit is less clear. I work at a company that works in this field - we target DNA instead, and only look at one gene. We have FDA approval for high complexity lab use (https://wwwn.cdc.gov/clia/Resources/TestComplexities.aspx https://wwwn.cdc.gov/clia/Resources/TestComplexities.aspx). From my experience, getting this down to the doctor/nurse level is ridiculously hard, and getting approval for 96 different tests will require a ridiculous amount of capital. My guess is that this is a first gen product designed to work as proof of concept and generate some cash flow so they can bootstrap and move down the complexity chain towards the patient. One thing to note is that 'specialized personnel' are actually pretty cheap given the recent surge in underemployed biochem graduates.
csirac2 12y ago
It seems extremely light on actual science. It's been a couple of years since I worked with biologists but dealing with false positives with this type of thing (well, GeneChips anyway), specifying suitable probe sets, getting the experiment right and making sense of the results seemed like an ongoing struggle for the application (measuring bacteria species diversity) - if I remember correctly, comparison with traditional sequencing techniques were required to better understand how the results behaved with eg. species hybridization in these microarrays. But the field moves so fast and I never really grokked the wetlab side of things, so who knows...

deleted 12y ago

[deleted]