
‘Key player’ identified in genetic link to psychiatric conditions - elorant
https://www.cardiff.ac.uk/news/view/1566294-key-player-identified-in-genetic-link-to-psychiatric-conditions
======
oferzelig
According to GeneCards, these diseases are related to this gene for quite some
time:

[https://www.genecards.org/cgi-
bin/carddisp.pl?gene=CYFIP1](https://www.genecards.org/cgi-
bin/carddisp.pl?gene=CYFIP1)

~~~
yohann305
First time I stumble upon this website (GenesCard). It shows how extensive the
shared human knowledge is about genes and how little I know! And also this
website is full of useful data HN people can use for playing with ML. Thanks
for sharing !

~~~
amelius
Well, if you want to use this data to "play" with ML, then you also need an
annotated dataset for at least say 100 individuals.

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dooglius
In rats.

[https://www.nature.com/articles/s41467-019-11119-7](https://www.nature.com/articles/s41467-019-11119-7)

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dekhn
yawn, another overreaching PR piece. psychiatric conditions are massively
polygenic and even the idea of driver causal mutations is suspect.

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7532yahoogmail
Suppose I learn person X is missing CYFIP1. Could on use crisper to put it
back? Where would I get a CYFIP1 for X? Are the dna bases really the same
person to person?

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patientplatypus
Dollars to donuts industry will use this to screen employees, insurance
companies will use it to deny coverage, and people won’t date you without a
prescreen. I’m almost to the point that I fear any new technology by default
because I immediately think of all the ways society could turn it towards
evil.

Paraphrasing Einstein our capacity for increases in human knowledge far
outweighs our capacity for increases in human compassion.

~~~
extra88
> people won’t date you without a prescreen

Most people don't do that for STIs today so why would they do it for genetic
predisposition of heritable diseases?

~~~
mieseratte
Hell, pre-screening as a concept was taught to me in a biology class 10+ years
ago with one example being (some) Jewish communities implementing genetic
counseling as a pre-screen before marriage to avoid unwell offspring, e.g.
Tay-Sachs. Organizations[0] exist for this purpose already.

The ethics of this as a situation was taught by watching and discussing
Gattaca, a movie from 1997.

Certainly not a new idea nor concern. It is a reality, though not quite
widespread. Perhaps we will open new societal cans of worm through mass-
market, rapid screening. As I write this, somewhat reminds me of the internet.

[0] -
[https://en.wikipedia.org/wiki/Dor_Yeshorim](https://en.wikipedia.org/wiki/Dor_Yeshorim)

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bschne
There was a post on slatestarcodex [1] a while back that talked about various
models/conceptions of both schizophrenia and autism as well as the associated
personality traits etc., which I found quite interesting.

1\. [https://slatestarcodex.com/2018/12/11/diametrical-model-
of-a...](https://slatestarcodex.com/2018/12/11/diametrical-model-of-autism-
and-schizophrenia/)

~~~
SolaceQuantum
Not sure how I feel about this implication that schizophrenia and autism are
opposite issues on the same axis; there's existing evidence that schizotypy
and autism are actually considered quite similar. The schizotypal personality
disorder mentioned must actually be diagnosed via a ruling out of autism, as
they both have similar symptoms and score similarly in socio-cognitive testing
(eg. facial emotion recognition).

EDIT: Also, given that schizotypal personality disorder scores similarly to
autism in recognizing human facial expressions, I'm not entirely sure where
the author in the link is getting the depiction of a schizotypal person being
particularly socially insightful through an examination of facial feature (the
provided example being how to extrapolate from an eye twitch).

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leemailll
The title is quite an exaggeration for the paper.

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gingabriska
Can we use 23andme data to see if we've this gene?

~~~
dekhn
It really depends. In this article, they describe a complex genetic
architecture, with copy number variations (the entire gene exists in multiple
copies along the genome) as well as deletions and insertions. 23andme data,
being based on microarrays, probably gives a misleading read on this because
the complex genetic architecture is not encoded into the microarray.

I generally recommend against reading primary liuterature or the PR around it
and immediately checking genetic tests to see if you "have this disorder". IN
complex diseases, many genotypes have low penetrance (IE, the genotype
variable is only weakly correlated with the phenotype label), and diseases
like this are complex, polygenic, and any individual mutations only partially
explain the visible phenotype.

~~~
filoleg
Perhaps a stupid question (as I am neither very educated on the topic of
genetics nor have I used 23andme myself), but isn't there a way to download
the dump of your raw genome data (that is compatible with all the other
genetic analysis tools out there) from 23andme that would allow you to find
it?

Btw fully agreed with you on the points of complexity and regular people
misinterpreting their results following the PR hype.

~~~
dekhn
When you download that dump from 23andme, _unless you signed up for whole
genome sequencing, and even then_ , the dump will not include high resolution
data which would allow you to analyze these results in the context of the
paper.

If you did WGS (whole genome sequencing), you _might_ be able to take the VCF
files (or the FASTQ) and, hopefully, their mapping process did an accurate job
computing your individual genotype. However, in cases like this with CNVs and
indels, I wouldn't really trust the assembly. MOst of the tools that we built
to produce genotypes get a lot of the details of the mapping or assembly
wrong. You could do a lot better if you had your genome sequencing using both
long and short read tech, and used the long reads to make a reliable scaffold
and then mapped the short reads, but with CNVs, much of that is still
guesswork.

~~~
filoleg
Ah, that clarifies it, thank you. I didn't realize that the raw dumps on
23andme would differ depending on which version of the product you paid for,
as well as the inherent imprecision of those.

~~~
dekhn
If you want a high quality genome (ilumina UYG) to start with, it's
[https://my.pgp-hms.org/profile/hu80855C](https://my.pgp-
hms.org/profile/hu80855C) which includes the original BAM files (so you can
try your own mapping) as well as called variants (conveniently[?] segregated
into SNPs and indels).

I would expect "everything" you need (except for long reads) is here for you
to determine if the owner of that genotype (I can vouch for them...) has the
genetic alterations described in this article
([https://www.nature.com/articles/s41467-019-11119-7](https://www.nature.com/articles/s41467-019-11119-7))
after performing some sort of magical rat/human remapping (tricky) or
referencing off of
[https://www.omim.org/entry/615656](https://www.omim.org/entry/615656)

I would be impressed if somebody could actually make a clinically actionable
recommendation for this genome, as Illumina described it as have zero known
risk.

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yakshaving_jgt
If the results of this study are confirmed, I sincerely hope CYFIP1 becomes at
least colloquially known as The Andrew Wakefield Gene.

~~~
king_panic
Explain

~~~
yakshaving_jgt
Andrew Wakefield[0] is a disgraced and discredited former doctor who authored
a fraudulent research paper in prestigious medical journal _The Lancet_ which
claimed a link between the MMR vaccine and autism.

Wakefield's "study" led to a decline in vaccination rates in the US, the UK,
and likely several other countries, and has resulted in serious illnesses and
deaths.

[0]:
[https://en.wikipedia.org/wiki/Andrew_Wakefield](https://en.wikipedia.org/wiki/Andrew_Wakefield)

~~~
lifeisstillgood
I am guessing that naming the gene after him is a sort of sarcastic rejoinder
- a bit like naming a line of meridian after a flat earther?

I get it but there are dozens of not hundreds of people who have put in
decades of work each to discover and enhance our understanding of this gene
and its medical links - they would be better candidates. Or perhaps they could
choose to name it.

But celebrating a fraud and "fake news" founder ... even sarcastically does
not sit right with me.

Happily I saw a dog turd on the street a while back - we could name that after
Wakefield. Perhaps put it on Google maps.

~~~
senectus1
It would be more than that. Wakefield is a guiding light name in the anti-vacc
community. This would severely water down the effectiveness of his name...

And especially in todays search engine driven world of "self education" that
could be amazingly effective.

