Re: [DIYbio] Re: Karyotyping? etc

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.
>>>>>
>>>>>
>>>>>
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