Re: [DIYbio] Re: Karyotyping? etc

-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: GnuPG v1.4.12 (GNU/Linux)
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=wOG4
-----END PGP PUBLIC KEY BLOCK-----
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.12 (GNU/Linux)
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=XvcG
-----END PGP SIGNATURE-----
Genotyping by SNP (a la 23andpatentme) will not identify chromosomal
translocations, and might even miss some kinds of chromosomal number
abnormality (i.e. two X chromosomes, if they are the same parental
chromosome? Lemme think about that..).

So, given that many intersex or sex-developmental conditions are caused
by chromosome-level oddities, if you have for example a
clean-translocation you may only observe it by sequencing if you
sequence the point at which translocation occurred, which probably
varies a lot.

Now, quantitative or real-time PCR might pick up copy number variation,
so you could use that; there might even be someone on campus who'll do
it as a favour if you identify the areas you'd like to check for copy
number (start with marker genes on both sex chromosomes, for example)
and buy the primers in?

On 25/09/14 13:51, Alexey Zaytsev wrote:
> Hey.
>
> Not to say that you should not do karyotyping if you'd really like to,
> but it might be easier (and a lot more reliable) to rather look at the
> DNA sequence. There are companies that do genotyping for just 100
> dollars, and that gives you a lot of additional fun and medical
> information. Or if you like DIY, and have access to a PCR machine,
> doing a few PCRs with primers specific to Y chromosome should be very
> easy, cheap and reliable.
>
> On Thu, Sep 25, 2014 at 11:43 AM, jem <jemmaredmond@gmail.com> wrote:
>> coolio
>>
>> Thanks for the info, it looks like one very convoluted process and perhaps
>> time critical? I'd have to steal er borrow stuff from the other labs/groups
>> plus I would need to book time on the microscopes.. It would be good to see
>> this process being done in minute detail like a video or something. I'll
>> have a gander and see if I can find some more info later...
>>
>> On Tuesday, September 23, 2014 7:49:23 PM UTC+1, Nathan McCorkle wrote:
>>>
>>> Check out colchicine and giemsa stain, the first sets up cultured
>>> cells for karyotyping and the latter stains the chromosomes.
>>>
>>> www.pitt.edu/~super7/31011-32001/31081.ppt
>>>
>>> If you don't have the time:
>>> https://www.scienceexchange.com/services/karyotyping
>>>
>>>
>>>
>>> On Sep 23, 2014 7:03 AM, "jem" <jemmar...@gmail.com> wrote:
>>>>
>>>> Hi dakota,
>>>>
>>>> I've had a lot of weird medical problems, the details of which I shan't
>>>> go into. Yes I had surgeries when I was too young to remember and surgery
>>>> later when I did remember but discovered later that they were doing
>>>> something else.. The surgeries probably explain the development issues I had
>>>> and medical problems encountered later on. I've had multiple scans, nothing
>>>> too strange encountered, just minor stuff related to development issues, its
>>>> been suggested I have an mri but I expect nothing significant will be found
>>>> and again its another cost I can't really afford and another test I don't
>>>> really want (I'm pretty sick of hospitals, pun intended)
>>>>
>>>> For me this is more out of curiosity and eliminating a possibility.
>>>>
>>>> One endro suggested a probable scenario and he could be right but I kind
>>>> of disagree, he was speculating, and I would like to see proof, so I gave
>>>> bloods for analysis, a karyotype test was supposed to have been carried out
>>>> but it was either 1. not done or 2. they lost the paperwork (which is quite
>>>> normal here).
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Tuesday, September 23, 2014 12:59:23 PM UTC+1, Dakota wrote:
>>>>>
>>>>> Yes it is unfortunately sometimes difficult to find a doctor who will
>>>>> listen to what you have to say with an open mind, and not just an open ear.
>>>>> I've had the best luck at teaching hospitals, although that can differ I am
>>>>> sure. I'd say showing up with knowledge in hand ready to propose a
>>>>> hypothesis and subsequent specific test might be your best bet in some
>>>>> cases. I've had the best luck showing up with knowledge in hand or head
>>>>> and approaching the subject with delivery in medical or chemical terms, and
>>>>> in general have gotten a good response once the doctor realizes you aren't
>>>>> another Joe Smoe reading WebMD and convincing yourself you have cancer and
>>>>> 100 other diseases.
>>>>>
>>>>> Or, maybe they are silently still thinking they know better but will
>>>>> appease the patient to give the illusion of them being cooperative and
>>>>> believing anything you just said.
>>>>>
>>>>> I don't know medicine so I can't comment fully, but I would say that
>>>>> scientists would probably make pretty damn good doctors. The lack of
>>>>> analysis and data sets gathered prior to a diagnosis and treatment regiment
>>>>> I've experienced is pretty scary. At least at the teaching hospital, the
>>>>> specialist wanted 3 sets of tests spaced 1 week apart to get an average of
>>>>> levels, whereas another one took one set of tests and said here, take this
>>>>> forever.
>>>>>
>>>>> There is also the problem of waiting months in between seeing
>>>>> specialists, and if one sucks, you still have to pay!
>>>>>
>>>>> But anyway, for your specific case, just keep googling and finding tons
>>>>> of papers relating to what it is you want to do. I think a lot of the
>>>>> legwork is going to have to be done by you, if you want something bad
>>>>> enough, you'll figure out a way to do it. Obviously having a personal
>>>>> relationship to the cause is an even bigger motivator.
>>>>>
>>>>> I guess I'm still not entirely sure what exactly you want to come up
>>>>> with a test for, just gonadal dysgensis or other intersex conditions in
>>>>> general?
>>>>>
>>>>> When you say hide surgeries, do you mean you had procedures done when
>>>>> you were to young to remember and your doctors/parents didn't want you to
>>>>> know about them for fear they might impact your perception of yourself?
>>>>>
>>>>> Sorry if that's a personal question but I'm just trying to understand
>>>>> where you're coming from.
>>>>>
>>>>>
>>>>>
>>>> --
>>>> -- You received this message because you are subscribed to the Google
>>>> Groups DIYbio group. To post to this group, send email to
>>>> diy...@googlegroups.com. To unsubscribe from this group, send email to
>>>> diybio+un...@googlegroups.com. For more options, visit this group at
>>>> https://groups.google.com/d/forum/diybio?hl=en
>>>> Learn more at www.diybio.org
>>>> ---
>>>> You received this message because you are subscribed to the Google
>>>> Groups "DIYbio" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to diybio+un...@googlegroups.com.
>>>> To post to this group, send email to diy...@googlegroups.com.
>>>> Visit this group at http://groups.google.com/group/diybio.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/diybio/b15b4d50-7954-49ea-85cc-21e5446481a7%40googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>
>> --
>> -- You received this message because you are subscribed to the Google Groups
>> DIYbio group. To post to this group, send email to diybio@googlegroups.com.
>> To unsubscribe from this group, send email to
>> diybio+unsubscribe@googlegroups.com. For more options, visit this group at
>> https://groups.google.com/d/forum/diybio?hl=en
>> Learn more at www.diybio.org
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "DIYbio" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to diybio+unsubscribe@googlegroups.com.
>> To post to this group, send email to diybio@googlegroups.com.
>> Visit this group at http://groups.google.com/group/diybio.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/diybio/1717e021-0fa0-41b6-857a-ec4ed01e6174%40googlegroups.com.
>>
>> For more options, visit https://groups.google.com/d/optout.
>

--
Twitter: @onetruecathal, @formabiolabs
Phone: +353876363185
Blog: http://indiebiotech.com
miniLock.io: JjmYYngs7akLZUjkvFkuYdsZ3PyPHSZRBKNm6qTYKZfAM