Genomics. Personalized medicine. Math.

[Brian-E]

As an addition to posting #2 (DNA advances solving many cold cases), it's a sobering thought that the same new technology is also exonerating many innocent people who have been spending years in prison convicted of a serious crime which they did not in fact commit. DNA analysis is proving that these people could not possibly have been the perpetrator of the crime. I don't have any particular link, but there are now many examples worldwide. Criminal justice systems all over the world are being shown by advances in forensic analysis of DNA samples to be more fallible than used to be thought.

[xilman]

Originally Posted by Brian-E

As an addition to posting #2 (DNA advances solving many cold cases), it's a sobering thought that the same new technology is also exonerating many innocent people who have been spending years in prison convicted of a serious crime which they did not in fact commit. DNA analysis is proving that these people could not possibly have been the perpetrator of the crime. I don't have any particular link, but there are now many examples worldwide. Criminal justice systems all over the world are being shown by advances in forensic analysis of DNA samples to be more fallible than used to be thought.

Very true but there is a darker side to the use of DNA evidence in court proceedings. Judges, lawyers and, especially, juries do not by and large understand Bayesian statistics and have only a tenuous grasp of what is meant by false positives and false negatives.

[Brian-E]

Originally Posted by xilman

Very true but there is a darker side to the use of DNA evidence in court proceedings. Judges, lawyers and, especially, juries do not by and large understand Bayesian statistics and have only a tenuous grasp of what is meant by false positives and false negatives.

Yes, this is very well known here in The Netherlands. We had a terrible miscarriage of justice here not very along ago where a nurse was convicted of murdering patients on the basis of statistics of when she had been on duty and which patients had subsequently died. There was no other serious evidence against her. She spent several years in prison and had one unsuccessful appeal against her conviction before it was shown that the statistical argument was sheer nonsense.
https://en.wikipedia.org/wiki/Lucia_de_Berk

EDIT: I should add that this case had nothing to do with DNA. I have got sidetracked by what you say about judicial misunderstanding of Bayesian statistics.

[retina]

Originally Posted by Brian-E

Yes, this is very well known here in The Netherlands. We had a terrible miscarriage of justice here not very along ago where a nurse was convicted of murdering patients on the basis of statistics of when she had been on duty and which patients had subsequently died. There was no other serious evidence against her. She spent several years in prison and had one unsuccessful appeal against her conviction before it was shown that the statistical argument was sheer nonsense.
https://en.wikipedia.org/wiki/Lucia_de_Berk

From the link:

Lucia de Berk's diary also played a role in her conviction. On the day of death of one of her patients (an elderly lady in a terminal stage of cancer) she wrote that she had 'given in to her compulsion'. She wrote on other occasions that she had a 'very great secret' and that she was concerned about 'her tendency to give in to her compulsion'. De Berk has stated that these were references to her passion for reading tarot cards, which she explains she did secretly because she did not believe it appropriate to the clinical setting of a hospital. However, the court decided they were evidence that she had euthanised the patients. According to the court, the reading of cards does not accord with a 'compulsion' nor with 'perhaps an expression of fatigue', as she described it at the time. De Berk's daughter Fabiënne stated in an interview on the television program Pauw & Witteman that some of her mother's notes in the diaries are 'pure fiction' which she intended to use in writing a thriller.

So this was before FB was around. But with so much nonsense people post to FB it wouldn't be very difficult to find something that can be deliberately accidentally misconstrued as some sort of confession or proof of wrongdoing when no such thing has happened.

If they are on a witch-hunt then they'll find something to get you. This is why mass surveillance should be a crime. No one should be able to read/see/use information you posted in private without your permission. For any reason, no exceptions. It is far too easy to re-interpret it and make it say whatever anyone wants it to say.

Sorry [/rant]

[Batalov]

Statistics, damned lies...
There was an urban myth about a hospital cat that would totally accurately predict death of patients. I remember that I googled this when the writers of the House MD series wrote the cat in. At least in House the explanation was found.

Anyway, in DNA sequencing process the statistics used as I already mentioned is of a benign, solid nature - the sampling is a Poisson process. But more about this later.

[Batalov]

Originally Posted by tServo

In case you haven't heard about CRISPR-Cas, it is a method that allows the editing of DNA & RNA to be done very much easier. Initial enthusiasm about how this could be used to cure so many diseases has run up against the reality of the complexity of Genomics itself as well as moral & ethical issues.
I am aware of a Chinese scientist who has claimed 2 girls exist whose DNA was edited when they were but an embryo. He tried to make them immune to AIDS, but failed.

Still, the prospect that this could go terribly wrong and produce some run-away virus that causes a pandemic haunts me.

We will only venture into only how to read the (read-only) memory which is the DNA code.

I will not touch upon writing or editing, even though this research exists; it is a huge can of worms. It is true that some countries have less strict rules than others; that's why cloning and germline gene editing reports come preliminarily from China. In US, UK and EU, even research is entirely walled-in by tons of regulations.

However, I will say that our organisms as they are - already naturally copy, edit, repair (single base errors are repaired, twists and kinks in the double helix, and so on), splice and reorganize its own DNA (and then predominantly discard all errors of copying and manipulation of DNA). CRISPR is but one of the methods of tweaking those natural mechanisms. Some other methods (example) have already passed the arc of being unspeakable, then controversial, then arcane and rare and then into accepted medical practice.

[chalsall]

Originally Posted by Batalov

However, I will say that our organisms as they are - already naturally copy, edit, repair (single base errors are repaired, twists and kinks in the double helix, and so on), splice and reorganize its own DNA (and then predominantly discard all errors of copying and manipulation of DNA). CRISPR is but one of the methods of tweaking those natural mechanisms.

Just to put this out there...

As someone who lives in the tropics and who has had both Dengue and Chikungunya, I follow the research into "Gene Drives" very closely.

I hate mosquitos! They are evil little things! Personally, if I could I would wipe them off the face of the earth in a minute if I had the choice!

But, at the same time, I appreciate that such an action might have unexpected consequences, and so I'm thankful the current research and experiments are being done very carefully and with a lot of oversight.

And, further, such research could be misused for evil against other humans -- a selective attack vector against certain variants of humans, for example.

P.S. If anyone travels to the tropics and gets Dengue, DO NOT take aspirin for the pain. The headache is amazing and can last for days, but introducing a painkiller into your system which is also a blood thinner is seriously ill-advised...

[Batalov]

In my past work, I had worked extensively in ID (infectious diseases), a decade ago and more. Sequencer's yields were small (really needed several instrument runs to sequence a human DNA dataset), but for malaria and M.tuberculosis - fairly adequate (because their genomes are a thousand times smaller). We sequenced hundreds of isolates of malaria and TB. It was a fairly academic research; we did closer to some answers about drug resistance and genome plasticity in these organisms, but we never expected to get to a cure, back then.

There are sequencing-based solutions that are reaching usability now, - to quickly sequence and identify the main pathogen(s) in a given patient, and get to precise treatment fast, but that's done on organism level. You sequence everything (that's metagenomics) and check what organisms' DNA is present. You can find some leads into which subspecies or a strain is there; but apparently one doesn't search for SNPs in that particular sample. Among other things - the variants would be diluted and averaged.

We did find a specific pathogen in a child's blood some time ago, but that is not a typical event. We wrote it up, so unusual it was. ...We saved that child, literally.

[chalsall]

Originally Posted by Batalov

We saved that child, literally.

That must feel really good!

Congratulations. Sincerely!

[LaurV]

Originally Posted by Brian-E

same new technology is also exonerating many innocent people who have been spending years in prison convicted of a serious crime which they did not in fact commit

There is not much "new" here, the technology is old and when you have the DNA and you have the guy it is easy to see if there is a match or not. What is "new" and in fashion in all these articles is when you have the DNA and you have no guy -- how to find him? This is where the "new" is, which comes with the DNA data bases and innovative algorithms to search them and find the guy or his genealogy from the close or far relatives who are in the DB already.

Which is commendable, of course, I would be the first who, if I could, I would hang those guys from their thingies in the middle of the town and let them there for a while so the people could see them, but on the other hand, it smells to me like a lot of propaganda too, for the people to record themselves in such DBs. Not that such thing would be bad, at the end, we have nothing to hide...

[Brian-E]

Originally Posted by LaurV

There is not much "new" here, the technology is old and when you have the DNA and you have the guy it is easy to see if there is a match or not. What is "new" and in fashion in all these articles is when you have the DNA and you have no guy -- how to find him? This is where the "new" is, which comes with the DNA data bases and innovative algorithms to search them and find the guy or his genealogy from the close or far relatives who are in the DB already.
[...]

The part which I have understood is "new" (say, last 20 years) is that DNA which can positively identify an individual, or be shown not to belong to someone, can now be extracted from much tinier traces than was possible before.