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Power77
05-02-2018, 11:15 AM
Does anyone here know if such tests exist? Personally, I’d like to be screened for the kind of chromosomal abnormalities that would show up in a karyotype. I’m 99.9% sure I don’t have any problems, but I’m still a worrier:D.

I thought a DNA test could’ve been a way to kill two birds with one stone. I love 23andme, but it appears that their testing is strictly SNP genotyping, and apparently they can’t even tell if someone is intersex or not (at least this is what Alex Khomenko [who’s a leading 23andme geneticist] told me in a private message despite contradictory statements from his part on the matter (https://www.quora.com/What-intersex-conditions-can-or-cannot-be-detected-by-23andMe/answer/Alex-Khomenko):lol::doh:. Is mere SNP genotyping standard as far as DTC DNA tests go? Are there any tests out there that both provide admixture information and count your chromosomes? Or are there at least any that provide the kind of raw data that a third party could look at in order to screen for chromosomal abnormalities?

If the answer is “no”, does that mean I’d have to go through doctors (ya know, those people who’d refuse anything that would make their own patients feel better about themselves, be it via hormonal therapy [except if you’re a mentally ill transsexual] and/or DNA tests [except if you’re an hermaphrodite]) in order to resquest such analyses? Also, what would be the most affordable chromosome counting service?

FGC Corp
05-02-2018, 07:29 PM
We can do it.
A whole genome test and analysis could determine karyotype.

Power77
05-02-2018, 10:35 PM
We can do it.
A whole genome test and analysis could determine karyotype.

Really? Thanks for your answer FGC Corp! Which company would you recommend then?
Would such a test provide me my Y-DNA haplogroup again? Also, I guess we can safely say that I have a Y chromosome since both FTDNA and 23andme identified my Y-DNA marker.

FGC Corp
05-02-2018, 11:37 PM
Really? Thanks for your answer FGC Corp! Which company would you recommend then?
Would such a test provide me my Y-DNA haplogroup again? Also, I guess we can safely say that I have a Y chromosome since both FTDNA and 23andme identified my Y-DNA marker.

Karyotype tests aren't really necessary unless you have some reason to believe that you have a condition that would be caused by it.

They are rare:
https://www.yourgenome.org/facts/what-is-a-chromosome-disorder

Syndrome Abnormality ----Incidence
Down’s Trisomy 21 ---------15 in 10,000
Edwards’ Trisomy 18 --------3 in 10,000
Patau’s Trisomy 13 ----------2 in 10,000
Turner Monosomy X ---------2 in 10,000 (female births)
Klinefelter’s XXY ------------10 in 10,000 (male births)
XXX XXX --------------------10 in 10,000 (female births)
XYY XYY ---------------------10 in 10,000 (male births)

22931

These are serious disorders, so you would already know that you have them without genetic testing. In my view, I don't believe such testing would be a good idea unless you have strong evidence that you would need it.

Power77
05-03-2018, 01:35 AM
Karyotype tests aren't really necessary unless you have some reason to believe that you have a condition that would be caused by it.

They are rare:
https://www.yourgenome.org/facts/what-is-a-chromosome-disorder

Syndrome Abnormality ----Incidence
Down’s Trisomy 21 ---------15 in 10,000
Edwards’ Trisomy 18 --------3 in 10,000
Patau’s Trisomy 13 ----------2 in 10,000
Turner Monosomy X ---------2 in 10,000 (female births)
Klinefelter’s XXY ------------10 in 10,000 (male births)
XXX XXX --------------------10 in 10,000 (female births)
XYY XYY ---------------------10 in 10,000 (male births)

22931

Thanks again FGC Corp!

Would Fullgenomes be able to detect some of the conditions listed above? Also, would you recommend this specific test? Is it better than 23andme and/or FTDNA as far as health reports are of concern?

FGC Corp
05-03-2018, 01:39 AM
Thanks again FGC Corp!

Would Fullgenomes be able to detect some of the conditions listed above? Also, would you recommend this specific test? Is it better than 23andme and/or FTDNA as far as health reports are of concern?

We don't do clinical genetic testing. A whole genome test, properly analyzed, would be very useful.

However, I can't recommend it because in an adult the symptoms would already have presented themselves. If you don't have any symptoms associated with those conditions, I don't think it would be an effective use of money.

Power77
05-03-2018, 01:50 AM
We don't do clinical genetic testing.

That means FGS won’t detect them anyway:\?


A whole genome test, properly analyzed, would be very useful.

Where is it possible to get a properly analyzed WGS test then?


However, I can't recommend it because in an adult the symptoms would already have presented themselves. If you don't have any symptoms associated with those conditions, I don't think it would be an effective use of money.

Some people lack symptoms. Moreover, I’m interrested in those tests for the simple reason that I think it’s cool (and therefore useful) to know about yourself in the most accurate way possible;).

FGC Corp
05-03-2018, 03:19 AM
Some people lack symptoms. Moreover, I’m interrested in those tests for the simple reason that I think it’s cool (and therefore useful) to know about yourself in the most accurate way possible;).

We offer whole genome sequencing. However, we would not be able to provide a medical report. We do provide a list of variants that can be analyzed via a variety of tools.

See:
http://www.fullgenomes.com/news/

"SNP and INDEL variants are given with amino acid, intron/exon, protein, etc. information using VEP and SNPeff. Additional data is provided in BAM format, and/or FASTQ."

Power77
05-03-2018, 08:30 AM
We offer whole genome sequencing. However, we would not be able to provide a medical report. We do provide a list of variants that can be analyzed via a variety of tools.

See:
http://www.fullgenomes.com/news/

"SNP and INDEL variants are given with amino acid, intron/exon, protein, etc. information using VEP and SNPeff. Additional data is provided in BAM format, and/or FASTQ."

Apparently, you do offer clinical whole genome sequencing:


We can now offer a whole genome clinical report service in collaboration with a partner as a pilot offering. Cost of the pilot is $900 per whole genome sample. You receive a clinically valid report in compliance with FDA and CLIA standards. Note that we require a doctor's order.

BTW, wouldn’t people with an extra chromosome get more variants than normal at a concerned specific location? Also, what are INDEL variants?

FGC Corp
05-03-2018, 02:10 PM
Apparently, you do offer clinical whole genome sequencing:



BTW, wouldn’t people with an extra chromosome get more variants than normal at a concerned specific location? Also, what are INDEL variants?


Apparently, you do offer clinical whole genome sequencing:


Quote Originally Posted by FGC Corp
We can now offer a whole genome clinical report service in collaboration with a partner as a pilot offering. Cost of the pilot is $900 per whole genome sample. You receive a clinically valid report in compliance with FDA and CLIA standards. Note that we require a doctor's order.

We decided not to work with that company so we don't offer that clinical report or service.

FGC Corp
05-03-2018, 02:18 PM
BTW, wouldn’t people with an extra chromosome get more variants than normal at a concerned specific location? Also, what are INDEL variants?

The read depth is a measure that can be used (number of reads mapped).


The number of reads that align to a given 5–10-kb window of a reference genome will give a measure called read-depth. “Simply look for how many reads are placed in that window versus how many should place there if it’s a diploid genome,” says Evan Eichler, professor of genome sciences at the University of Washington. With 25-fold coverage, you can reliably detect deletions (fewer or missing reads) and duplications (an overabundance of reads) down to 2–3 kb, he notes — far beyond other molecular cytogenetic methods by at least an order of magnitude. Read-depth is the only sequencing analysis able to determine the absolute copy number,
https://www.biocompare.com/Editorial-Articles/157466-Molecular-Cytogenetics-Using-Next-Gen-Sequencing/

Power77
05-03-2018, 03:15 PM
The read depth is a measure that can be used (number of reads mapped).


https://www.biocompare.com/Editorial-Articles/157466-Molecular-Cytogenetics-Using-Next-Gen-Sequencing/

Interresting. Does Fullgenomes use such a NGS tool when sequencing and analyzing a customer’s genome? If “yes”, I guess that means the customer in question could in theory detect an abnormality from looking at his/her raw data even if the test doesn’t directly report it, right?

PS: I’m still wondering what are INDEL variants:).

FGC Corp
05-03-2018, 07:20 PM
Interresting. Does Fullgenomes use such a NGS tool when sequencing and analyzing a customer’s genome? If “yes”, I guess that means the customer in question could in theory detect an abnormality from looking at his/her raw data even if the test doesn’t directly report it, right?


Yes, that's right.

FGC Corp
05-03-2018, 08:55 PM
PS: I’m still wondering what are INDEL variants:).


Indel is a molecular biology term for an insertion or deletion of bases in the genome of an organism. It is classified among small genetic variations, measuring from 1 to 10 000 base pairs in length,[1][2][3][4][5][6][7] including insertion and deletion events that may be separated by many years, and may not be related to each other in any way.[8] A microindel is defined as an indel that results in a net change of 1 to 50 nucleotides.[9]

ref:
https://en.wikipedia.org/wiki/Indel


An INDEL (INsertion/DELetion) is where a single base has been deleted, or inserted into one genome relative to another. It is a symmetrical relationship, as a deletion in one corresponds to an insertion in another.

http://thegenomefactory.blogspot.com/2013/10/understanding-snps-and-indels-in.html