You can browse by chromosome or gene name, it includes data on all kinds of genetic variants from SNPs to CNVs and it gives each variant a score according to the strength of the evidence. I haven't had a chance to really tell how useful these scores are, but there's an option to create your own score based on how much weight you give different kinds of evidence. The dataset is huge although it doesn't seem to have been updated for a few months.
Overall, it's a new tool and there's sure to be bugs to iron out, but it seems like it could be very useful. I do worry though that this kind of database encourages misleading ways of thinking about autism genetics.
There are numerous genetic variants which have been strongly linked to autism, although none of them account for more a small proportion of cases because these variants are rare. But many (most, actually, is my impression) of them have also been observed in people with other symptoms ranging from ADHD to epilepsy to schizophrenia.
So searching a database of "autism genes" could encourage you to think that these were only autism genes, which is far from true. Genetics, it is becoming increasingly clear, doesn't respect our current concepts of psychiatric illness or our academic specialities. There are few (if any) parts of the genome that can be neatly fenced off and declared exclusive to ADHD experts, schizophrenia researchers or whatever.
But disease-specific databases encourage the illusion that they do exist. It's the same old problem of the filter bubble which many people have warned about in the context of general purpose search engines. Scientists have filter bubbles too.
This is not of course a criticism of AutismKB in particular - the same goes for any similar "disease-gene" database. And to be fair AutismKB does provide links to a schizophrenia database, and a couple of others but you have to dig quite deep to get there. The "main page" of results for any given variant is pure autism.
That's the whole problem with filter bubbles - they make it too easy to hear what you want to hear, compared to getting a new perspective, so you don't even think to look outside the filter.
Xu LM, Li JR, Huang Y, Zhao M, Tang X, and Wei L (2011). AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic acids research PMID: 22139918
21 comments:
Of course none of the three CNVs that my kids have are included in the database. I guess I shouldn't be surprised though, if their mutations are so rare that even their identical twin doesn't have it, what is the chance that it would appear in another child?
But seriously, I have to wonder at how useful this sort of information is if the mutations are so rare that they have only been found in a couple of cases. It seems to me that most of these mutations would have to be random noise rather than a clinically significant finding.
Yeah, that's a good point. Many of them probably will turn out to be noise although some of them (e.g. 15q11-13) are highly replicated and rare in controls.
The problem, as you say, is the mutations that are so rare that it's impossible to compare them between patients and controls. I think eventually we might be able to predict which mutations will cause symptoms, based on the function of the gene, and that would help us to decide about very rare mutations... but we're a long way from being able to do that at present.
Neuroskeptic,
One should put a S to autism if one really wants to do some valid analysis of any work on autism.
or indeed want to do any “neuroscientific” study ethically and economically worth doing-
One should keep in mind that there is not even agreement on what the symptoms leading to the autisms diagnostic are .
I am so sorry about it because it also makes every clinical trial expensive and difficult and little people like I cannot put together a clean study worth doing even for the private fun of it.
Those clinical studies being even more difficult since what is generally admitted as the “core symptoms” is showing no marked benefit from Big Pharma medication –and we all know how biased in favor of Big Pharma are the published trials and the French homeopaths pretending to treat autism like Dr philippe Servais are crooks.
It seems to me that –for now- to advise clients on diagnosis and treatments in a broad sense using genetic results is a fraud
and to select samples on a genetic” classification basis” to do good studies expecting better sensibility is unrealistic
since the same genetic variation gives various clinical picture from “sane” to severely autistic even in the same families and the genetic variation are so numerous.
neuroskeptic,
only 5% of the autism cases can be attributed to a genetic cause.
One – if a scientist and even if he has a rule for a certain number of word - should always remember it.
I personally had the honor but also suffer the deep shame to hear
the honorable Rt. Hon. John Bercow MP, Speaker of the House of Commons,
and father of an autistic son protest
and silence a scientist
by putting briskly to perspective with a quiet but impressive authority what geneticist results had offered the world until now
at an Autism Research Lorna Wing Conference.
I am sick to be unable to explain that 5% to parents of autistic persons and to the clients and to be obliged to change subject with a soothing reminder that anyway genetic transmission in itself do not means disease or undesirable and that nothing is more genetically transmitted than blue eyes and most people find it attractive nowadays -omg does- when poets in France and Russia used to celebrate love brown eyes who were rarer in Napoleonic times.
omg,
I think France and Italy should have their fair share of the British MP (and ours can learn a thing or two in GB from the gutter press making enquiries in their finances) since one cannot ask for political asylum in GB for persecution by the psychoanalysts and the French medical Gestapo and Italy need that kind of people to prevent crooks taking again power at the next election after technical honest people had been allow to govern and do good work.
It is a matter of heated family debate around pasta dishes and some of my opponents think we should import British voters
instead of my mandatory exchange of MP proposal but everybody agree that Italy will lose its cultural identity with too many voters against wooden fire to make pizze on ecological ground. What can you expect of people disgustingly bad mannered enough to impose to Italian customers in Italy their revolting and nauseating habit of drinking capuccini out of breakfasts and putting grated cheese on fish pasta sauce?
If I don't have my cappucino I die. I'm not a fan of European politics, of late the fascist uprisings repels me almost completely. Unless the EU succeeds as a political conglomerate, each country is way too homogenous to be like GB or a fully fledged democracy. Also GB has a functioning monarchy and retains a relatively classy power decorum. America lacks that, countries outside the Commonwealth like most parts of Europe, lack that. This is off topic though. Even though it could be genetic, autism can be rehabilitated without medication. If autism is a disorder then it should stand on its own because it doesn't look to conform to the rehabilitating patterns of other disorders unless it's comorbid that's a different matter. Correct me if I'm wrong. Cool if there was a database matching genes in terms of rehabilitation.
Can we try to keep the discussion on topic, please.
omg,
You wrote:
"Cool if there was a database matching genes in terms of rehabilitation."
But it is not going to happen soon and probably never will.
This post gave you a hope that the motivated and clever fathers like the honorable Rt. Hon. John Bercow MP, Speaker of the House of Commons and MJ 7 December 2011 20:13 are not buying it anymore.
As MJ commented:
"I have to wonder at how useful this sort of information is if the mutations are so rare that they have only been found in a couple of cases."
If you read his blog you will find a clever and sobering discussion about folic acid as a putative causation of autism. Worth studying and also smoking in mothers since the blood vessels in placenta of smoking mothers have been shown to be of a poor quality etc...
Mj blog is also worth reading for the clinical pictures: he describes for example how one morning one of his autistic young daughters delighted and surprised her father by asking with three correct sentences- he was not aware she could produce- her parents to wake up and let her go out and play with a new snow.
How could you find the best treatment with such strong variability of symptoms in the same person one day from another?
The answer is easy:
You have to have a very large number of person in each of your different treatment groups and control group.
Too bad that her mutation is so rare.
Too bad that nobody agree about diagnosis criteria in the autisms.
And the "spectrum DSM 5 proposal "look to me like a screen between the public and nude scientists and a recipe for disaster.
The spectrum DSM 5 proposal include many more individuals with a given genetic variation even if the clinical picture of many seems not worrying for a psychiatrist.
It is very difficult to tell what is normal behavior -be it for a toddler or for an adult - when you are looking for mild forms of autism.
Example: A lot of adult male English citizens show an impressive obsession with soccer. Should we look for other telling signs of Asperger in those as soon as we found a genetic variation with a severely autistic person of his family?
omg,
Thanks for being fairplay-the britixsh women are known for that.
if you read French , a neuroscientist François Gonon has chosen an intelectual journal a lot of politicians read to write about the need to forgot about the neurosciences leading the way to new treatments and new diagnostic methods in psychiatry.
Like super British MP he insist on the "famous 5%.
http://www.esprit.presse.fr/archive/review/detail.php?code=2011_11
It is not to say researchers should not receive funding and jobs. One never know: a wonderful anecdote from the Luxembourg born french Nobel laureat for medecine 2011 is that when he was re'ceived at the French academy of science, a physicist ask him what research on immunity in insects was worth doing unless one was looking for insecticides. it is now established that the part of the immune system that researcher chose to study in insects has been preserved in humans. He didn't found any insecticide to fight malaria but rich countries did not fund much research against the killer N°1 in the world before Bill gate was pouring big chunks of his fortune(and friends' fortune) on research to advance in that field.
Ivana,
I'm not British and I don't read intellectual journals. I read cook books.
Politicians don't read intellectual journals. Elsevier hire think tanks to summarize key articles and email politicians and their assistants delete it.
I thought malaria was a black market thing - they have better drugs and lots of different kinds than legit big pharmas from what I recall. Having lived in malaria prone region for years.. lathering myself with mosquitoe repellant at nights (antimalarials were crap) I believe the major concern was resistance.
Locals have better resistance /immunity to malaria so they worry about the mosquitoes themselves. The mosquitoes have evolved? last time I spoke to CDC on the ground.
Falciparum was the most common when we ran tests. I kept a diligent record of malaria stuff and smuggled treatment drugs back home because the local stuff were better.. most of the treatment tabs seemed to be manufactured from India, really potent stuff! Didn't see the Sanofis and fancies on the ground..
omg,
As much as you admire scientists omg, you cannot let them sell anything they believe in on the internet without critics aiming at controlling false claims!
– false claims like: a genetic screening of your autistic child will help you get for the child more suitable drug treatments or education methods.
Scientists can believe a little too much in the worth of their discoveries and/or they can love too much fame and money.
You are also too kind with the politicians and unfair with their advisors
- politicians and their advisors are lacking more often morals and political courage than knowledge in our western countries.
Pr Dave Nutt- a Britsh pharmacologist who lose a political appointment of advisor of the health minister to speak his mind against alcohol dangerosity compared to cannabis and horse riding - is an exception.
I bet that a lot of French MPs know that psychoanalysis theory about autism is a fraud
Those French MP are well-travelled at the expenses of the taxpayers and they know that France is an exception in the treatment of autism and a red lantern in the rights of the mentally ill
but they give the voters what they think necessary to get themselves reelected.
The worst of the American right wing politicians -for another example- know very well that the earth is not flat and that Darwin theory has very few holes in it
and pollution and bad diet and excesses of Big Pharma drugs kill- but they choose to ignore it publicly to gain red necks into voting for them. Full stop to my mind.
it is anyway useful to educate the politicians and let them know your view- better not to add in your letter that you do not vote though!
Politicians have a lot of power in sciences and research and not only because they fund public research by grants and by civil servants salaries.
They also can decide that some research is forbidden (stem cell) or protect the persons undergoing treatments in research protocols by consent laws, protect vulnerable persons from fraudsters using the internet to sell them useless genetic tests or unproven treatments at a very high financial cost for those who can afford it and culpability for those who can’t etc...
NB: In Ghana the newest and more efficient treatment against malaria cost an average monthly salary and many cannot afford it. Idem the newest AIDS drugs are too expensive for many Africans. Unlike psychiatric drugs it seems that against AIDS and malaria the best option is the most expensive.
Of course, on the internet and the African market places you find many fake drugs which may explain why you found Indian generics treatments more potent I guess.
I think we need politicians and yhe voters well informed about science and that some activists are dangerously simplistic in their views and propaganda.
Actually we did try the fancy malaria drugs in prestigious ex-pat hospital and it wasn't as effective. I think India and Asia are ahead of Western countries in terms of treatments plus cheaper. Not only do they have more skilled practioners but they have more treatment experience. But of course there are equally as many scams and counterfeits. I get my medicals / dentals done in Asia. Tried here - crap. I'm the one telling the doc what I need. Perhaps research doesn't necessarily equate to superior practice.
Science is a profession like many others: you have good scientists, bad scientists, broad-minded scientists, narrow-minded scientists, science pioneers, science detractors... I'm not so much a fan of scientists as I am of certain political leaders, only because I've interacted with both. Like I've met well known scientists and they didn't wow me or come off as extraordinarily insightful human beings, whereas some leaders I've met left me in awe. I remember one time a professor sent a 50? page thesis about a complaint.. typically an MP might get 200 letters a day.. the assistant read the cover then threw it in the trash. Scrawny letter about abuse in nursing home, letter went straight to MP. Would the same have happened in the Ivory Tower? Probably not. Who is more impartial? Requires more wisdom, integrity and leadership skills? Probably the office higher up the pyramid.
Politicians don't think about science and research unless it's nuclear but they have army scientists for that. Do jocks care what nerds write? Providing job security, clean water in some cases, healthy economy, security etc. takes most of their mental space I assume. There probably needs to be more awareness about autism in France before it can be lobbied for stuff. For that to happen there needs to be more advocacy groups and protests. If you can get hundreds of people to protest then at least one MP will take advantage of the situation - also gives lobbyists something to work with. Big pharma spend billions on lobbyists each year who dine with politicians and their advisors. A lot of that money funds advocacy groups, charities, awareness, awareness, so they can show the advisor there's a demand. Look at the epidemic, awareness groups, this clause needs to be scrapped, this Bill has to be reinacted. They use public office as marketing avenue, subsidize costs etc.
omg,
The persons I know in the western world are often very much concerned about health care or at least their own and family and significant.
You are right many can be victims from Big Pharma lobbying and false science (and also in France from the very potent political Psychoanalysis lobbying plus the only ABA for autistic education lobby)
But the same persons can be easy prey from simplistic and demagogic activists or from biased presentation of scientific pieces of work.
May be the journalists are to blame to some extent but also some of the scientists.
Some scientists are misleading the public about the importance and immediate usefulness of a "discovery" of theirs or a tool the world own them.
And some scientists are very good at recruiting activists around their name to give a strong voice to premature claims.
The need for funds is not an excuse for the geneticians boasting prematurely about their discoveries about a shrank-or whatever- gene at conferences organized by families and autistic persons associations without telling their vulenrable public the truth:
their discovery is fascinating and a hope may for the future but that shrank -or whatever- gene is for now only one of many genes suposedly involved in wiring a brain in an autistic way
and all those genes together account for only around 5% of the cases.
presenting those genetic findings in autism in a fancy way do not change the reality of that 5%.
Also dear omg,
NS might censure me for being out of topic but if the Indians are making generic galenic forms that works better than the initially patented antimalaria drugs.
Those drugs are not generic presentation drugs but "me-too drugs' and you can patent them and make much more money than by selling generics.
In Africa some Indians are doing much good - like some Cinese and some Americans and Europeans etc..but some Indians have also decided to make big bucks by running private hospital aiming at making money from the African middle class on the advertissment that the medical staff is 100% Indian.
Nb: Indians have very good med schools for sure but they are humans: Indians gave the modern world the mahatma Gandhi but also Gandhi's killer and from the same religion background - hindu extremism is to blame.
I'd like to see how scientists 'recruit' activists. Never heard of it in my life.
The media misleads the public like they do with every other profession - science is no exception.
Indians trade kosher. Plenty of Italians in Africa running underage s-e-x trade. The French are known for human trafficking and organ harvesting. I have human rights reports about these networks.
Illicit meds, UN officials and private militias raping natural resources, drug barons, land grabbers, corrupt officials coffering, blackmailing, backstabbing. How do you advise an African leader to handle such issues?
omg,
May be some activist are recruiting scientists but for sure the British surgeon who accused vaccination to cause autism has many folloowers -in America at least- to my knowledge and for some is close to an heroic figure.
Trouble is that some of the underdog might have had a good intuition and we might find established someday in the future that the mothers where right in some cases by reporting that -negative biological test or not for gluten allergy -their autistic child(ren) is improved by a glutenfree diet, or a dairy free diet or by eating a lot of oily fish etc..
To my mind it is more likely that we will obtain thoses informations by good clinical trials and epidemiologic studies but the geneticists might give us breaking news od that sort some day.
I see what you mean. Everyone has the right to believe in something right? People usually think their profession is something meaningful, like they have to do something, say something, make it the absolute, the omega. I blame Hollywood. If I inject some random person with vaccines, will they become autistic? I think though scientists are the easiest to manipulate. People have some common sense but maybe nerds have a hero complex.
omg,
OK.
:)
I like the colors on that database. It could totally be android app if they changed the title to 'ARE YOU CRAZY? IS HE CRAZY? ARE YOU TWO GENETICALLY COMPATIBLE?' Of course it'll have NOTHING to do with life like those pop psychology quizzes but you could rank outcomes with false positives attached to congratulations senorita you have 25% chance of producing autistic baby.
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