Full Y Chromosome Sequencing: Phase III Pilot

[emmental]

This was just posted on FGC's Facebook page about 10:24 this morning:

We should receive the Batch #3 raw data shortly after this Wed Sept 18 with analyses to be done in the days that follow.



I'm batch #4 -- but excited.

[cilldara]

I can't wait to see people's results. It will be really interesting.

[Mikewww]

I imagine a number of volunteers will work diligently comparing the raw results to see what novel SNPs turn up by subclade. Thank you, thank you, thank you!

Right now, that work has been done at the project level using different formats. I suggest that we develop a common or standard format that can incorporate results from FGC and the new Chromo offering as well Geno 2. Obviously there will have to be some transformations of data but I think this could be done by translation indices.

Even if we don't ever store the data from the different projects, if we at least use a standard format and have some controls in the process of storing the data we can eventually combine and analyze the data with automated tools.

Of course, at the rate computing technologies develop we may not need a data center anyway when the day comes to aggregate the data.

[Celtarion]

Mike, do you know more or less how the data will be presented when each of us will receive their result? Will it be something such as a map, then new SNPs discovered, phylogenetic tree showing the new SNPs... Just curious to know

[RobertCasey]

Mike, do you know more or less how the data will be presented when each of us will receive their result? Will it be something such as a map, then new SNPs discovered, phylogenetic tree showing the new SNPs... Just curious to know

We will get two reports: 1) XCEL spreadsheet that summarizes the test results for the known 24,000 YSNPs that FG has in their current database; 2) a second file that can be scanned by more advanced genetic analysis tools. These will be made available to those can analyze further for new mutations. Once discovered, these will be added to the FG database for future reports.

Remember, many of these newly discovered will be yet more duplicate SNPs (SNPs that 100 % track existing YSNPs) and many will be determined to be unstable (mutate too many times, found in areas that are later discovered to unreliable, etc.). So the list will be in a constant state of change. Some will be very private and genealogical YSNPs - hopefully, these will be included as well (but will never qualify for the ISOGG haplotree and will have to be tracked volunteers).

[RobertCasey]

Right now, that work has been done at the project level using different formats. I suggest that we develop a common or standard format that can incorporate results from FGC and the new Chromo offering as well Geno 2. Obviously there will have to be some transformations of data but I think this could be done by translation indices.

Even if we don't ever store the data from the different projects, if we at least use a standard format and have some controls in the process of storing the data we can eventually combine and analyze the data with automated tools.

Of course, at the rate computing technologies develop we may not need a data center anyway when the day comes to aggre
gate the data.

I responded to your request for standardization in another thread:

http://www.anthrogenica.com/showthre...carte-ordering

[warwick]

We will get two reports: 1) XCEL spreadsheet that summarizes the test results for the known 24,000 YSNPs that FG has in their current database; 2) a second file that can be scanned by more advanced genetic analysis tools. These will be made available to those can analyze further for new mutations. Once discovered, these will be added to the FG database for future reports.

Remember, many of these newly discovered will be yet more duplicate SNPs (SNPs that 100 % track existing YSNPs) and many will be determined to be unstable (mutate too many times, found in areas that are later discovered to unreliable, etc.). So the list will be in a constant state of change. Some will be very private and genealogical YSNPs - hopefully, these will be included as well (but will never qualify for the ISOGG haplotree and will have to be tracked volunteers).

You get more than the raw list of SNPs. You'll also get a report of your private SNPs as well as the SNPs shared or not shared with the others in your haplogroup, a report showing the SNPs shared with 1000k participants, and a haplogroup report.

[Acque agitate]

I am part of III batch.
Today I received 3 emails from Full Genomes that activated my profile.
I think it is likely that the data will arrive shortly.

[GailT]

I am part of III batch.
Today I received 3 emails from Full Genomes that activated my profile.
I think it is likely that the data will arrive shortly.

I received the same emails. There are options to share the results with another person, and to create an account to share kit results with multiple people at once.

[lgmayka]

Cognitive Genomics participants are beginning to receive results? Great! But then I wonder why they haven't updated my status, which still says "July."

I have received a response from Cognitive Genomics.
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Whole genome sequencing is complete, but proper postprocessing of the data is taking longer than we had anticipated.

More precisely, I inspected the files we could have returned in June, and found that they did not distinguish between high-confidence reference genome matches and no-calls. This is a common trait of research pipelines handling WGS data, but it would have made for highly incomplete reports from third-party personal genomics tools. We are currently working on fixing this, but I cannot yet give a reliable ETA (at this point, "July" is a placeholder for "I don't know yet").
The website will be updated as soon as I do have a reliable ETA, and you will receive an email when your data is about to be available for download.
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