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  • Joann
    replied
    Kerry, do you expect to post your full Y sequence, and if so, where?

    Leave a comment:


  • KerryOdair
    replied
    Full Y sequence product

    The product is now available and the people are coming to order the Y sequence. Some comments from facebook page with people ordering from all different areas of the Y tree. Five people in the E-m35 group alone have ordered this product.

    Link:

    Leave a comment:


  • KerryOdair
    replied
    Here is additonal information on this new company sequencing the Y Chomosome:

    Note:  This blog post outlines upcoming changes to Google Currents for Workspace users. For information on the previous deprecation of Googl...

    Leave a comment:


  • KerryOdair
    replied
    Originally posted by krobison View Post
    Perhaps they will be acquired by 23andme; otherwise they may not be around very long.
    Thanks for the insight on some questions for the company, but I addressed those during my investigation. 23andMe has made it pretty clear that they are not interested in the Y side of the business. They clearly are in this for medical implications and not geneology. Geneology is a by product they have to put up with in my mind to get testers. For autosomal data at $99 you cannot beat their offering. But their 3.0 update version of their chip did not enhance the number of Y SNP's. Still many incorrect calls at least in the E-M35 area of the tree.

    The company doing the sequencing is significant in the industry but people can contact FullGenomes and make their own decision on the matter.

    Leave a comment:


  • krobison
    replied
    Originally posted by KerryOdair View Post
    The sample is saliva. I suggest you go to the FullGenomes website and contact them via their sales representative.

    Based on my own personal investigation I am satisfied with this company and placed an order with them. They have passed my litmus test through various sources.

    Based on prior posts you have made, you have been skeptical of the market place for this product. It fills a void that is not being addressed by either Familytreedna or the Genographic project. I guess we will see over time how big the market will be. I say big enough.
    I'd suggest you inquire deeper about how they are obtaining your Y; probably hybrid capture. Read length & library prep method matter too. The quality of the data & what you infer from it is critically dependent on how they do this.

    One measure you should apply when you get the data is the distribution of coverage across the Y. Getting uniform capture is not easy, especially with lots of repeats.

    On the business side, I'm glad someone is making a go at it & would be happy to see a market. Perhaps they have a very low cost business model, serving primarily as a pass-through to a large sequencing provider. Just that realistically the number of men willing to pay $1.3K for this information is not 0 (clearly!) but unlikely to support a big business. Perhaps they will be acquired by 23andme; otherwise they may not be around very long.

    Leave a comment:


  • KerryOdair
    replied
    Originally posted by krobison View Post
    Have they described what technology they are using to pull the Y? What sort of sample do you submit?

    Interesting that someone thinks there is a business to be had here, given the low medical utility of the Y. I'm not objecting to genealogical research, just wondering how big the market will be & if this company can stay afloat.
    The sample is saliva. I suggest you go to the FullGenomes website and contact them via their sales representative.

    Based on my own personal investigation I am satisfied with this company and placed an order with them. They have passed my litmus test through various sources.

    Based on prior posts you have made, you have been skeptical of the market place for this product. It fills a void that is not being addressed by either Familytreedna or the Genographic project. I guess we will see over time how big the market will be. I say big enough.

    Everyone will have to make a personal decision on the value of this test for themselves. I am tired of waiting for cheap nanopore sequencing that seems to be more vapor ware than reality these days. I am older and this sequence can happen today not sometime in the unknown future.

    Leave a comment:


  • krobison
    replied
    Have they described what technology they are using to pull the Y? What sort of sample do you submit?

    Interesting that someone thinks there is a business to be had here, given the low medical utility of the Y. I'm not objecting to genealogical research, just wondering how big the market will be & if this company can stay afloat.

    Leave a comment:


  • KerryOdair
    replied
    I started this thread in September of 2010 in a quest for Y Chromosome sequencing. I have found a company in this business and I have placed an order to have my Y Chromosome fully sequenced. I am confident that this new test will be the beginning of a new era for citizen science and development of a more precise phylogenic tree.

    I am going to have the raw data to work with in any venue that might further my knowledge about my Y heritage.

    Leave a comment:


  • KerryOdair
    replied
    This company has been brought to my attention. Maybe we now have the real deal. Can anyone add any further information on this new company and details.

    FullGenomes

    We are currently offering a one of a kind test—not available elsewhere—that will sequence your FULL Y-DNA chromosome. This is the DNA you inherit from your father, and his father and so on, back in time. It will allow you to determine the exact SNP's and STR's you have and how you are related to other family members and members of your community.

    Last edited by KerryOdair; 05-01-2013, 11:20 AM.

    Leave a comment:


  • KerryOdair
    replied
    This is a slide presentation by Bonnie Schrack who is the Admin of the A haplogroup study at FTDNA. This is a quote from her on the slides.

    "It's awesome to finally be able to discuss our research! I'm not totally free yet, though, until our paper has been submitted to a journal. Mike Hammer would prefer that we not divulge absolutely all the details, but for now, here's a link to my presentation. Soon I'll post the speaking notes, but for now it's just the slides."



    Meanwhile, look into Iwo Eleru, Nigeria. See: http://www.bbc.co.uk/news/science-environment-14947363


    " Prof Stringer thinks that ancient humans did not die away once they had given rise to modern humans.


    They may have continued to live alongside their descendants in Africa, perhaps exchanging genes with them, until more recently than had been thought."

    Thomas said that they have once again upgraded their equipment, doubling their capacity again. This gives 4 times the coverage of the original Walk the Y, covering more than 5 million bases. To date, they have run 494 pre-qualified participants and of those, 198 did not find a new SNP.

    There are changes coming in how the palindromic region is scored which will change the matches shown. Palindromic mismatches will now be scored as one mutation event, not multiples. Microalleles will able be reported in the next rollout version, expected probably in January. The problem with microalleles is not the display, but the matching routine.

    Of importance, there has not been an individual WTY tested from haplogroups B, M, D or S, and we need one. So if you know of anyone, please contact Thomas.

    Thomas has put his Powerpoint presentation online at http://www.dna-fingerprint.com/stati...lkThroughY.pdf
    Last edited by KerryOdair; 11-13-2012, 11:02 PM. Reason: Add information

    Leave a comment:


  • KerryOdair
    replied
    This is the significant news from the FTDNA admin conference in Houston TX 2012. A paper to be published in the near term about this. Also a link to slides by Thomas Krahn.

    Dr. Mike Hammer has been talking about A00, the new most basal clade of the human Y-chromosome phylogeny. Apparently, >338ky old Y-chromosome ancestor for modern humans, at 98% confidence, with most basal clade found in western Cameroon and in African Americans separated by ~500 years from Cameroonian chromosome.

    Root of human Y-chromosome phylogeny is now much older than both mtDNA Eve and first modern human fossils.

    Slides: http://prezi.com/kz2c-q4b-_m1/a00-on...plogroup-tree/

    "A00 on the Y Haplogroup Tree
    A new view on African origins from a Y chromosome perspective
    by Thomas Krahn on 12 November 2012"

    Leave a comment:


  • KerryOdair
    replied
    Originally posted by KerryOdair View Post
    This is the latest Walk Through the Y Project information from the FTDNA conference October 2011 Houston TX from Thomas Krahn.

    http://www.dna-fingerprint.com/stati...lkThroughY.pdf
    This is additional information supplied by Tim Janzen at the conference in regards to Y chromosome testing.

    Thomas Krahn summarized the latest Roche 454 sequencer Y chromosome sequencing results. He is doing Y chromosome enrichment of the DNA prior to sequencing so that he can maximize the Y chromosome sequence data from each sequencing run. In his latest run he tested 8 samples, but only 2 came out reasonably well. He plans to reduce the number of beads he uses in the sequencer and he hopes that will improve the quality of his data. In the latest experiment he got about 19,000 reads from one sample, of which about 48% of the reads were from the Y chromosome after Y enrichment. The average read length was in the 400-600 base pair range. Thomas plans to put the latest sequencing results on his FTP server as a downloadable file of about 300 million megabytes of data for Y SNP hunters to review. Thomas plans to continue to work on Y sequencing until he can perfect the sequencing. Thomas said that there are about 20 million base pairs on the Y that are worthwhile sequencing. The first 2 million base pairs on the p arm are pseudoautosomal and thus aren't helpful from a Y SNP search prospective. The palindromic regions also generally don't have many Y SNPs. The new 454 sequencer will allow about 20 times as many bases to be sequenced as can be done with the WTY project currently. Now the WTY results generally include about 400,000 base pairs. Thus Thomas anticipates at least 6-8 million base pairs of the Y chromosome can be sequenced with the new 454 sequencer in the short term and hopefully about 20 million base pairs can be sequenced in the long term.

    Leave a comment:


  • KerryOdair
    replied
    This is the latest Walk Through the Y Project information from the FTDNA conference October 2011 Houston TX from Thomas Krahn.

    Leave a comment:


  • KerryOdair
    replied
    This is a significant marriage of venture capital. Maybe 23andMe will be the first to offer full genomes that go beyond the scope of what Knome and Illumina provide today.

    DNAnexus Raises $15 Million, Teams With Google To Host Massive DNA DatabaseIn addition to the funding, the company is also announcing a key partnership: it’s's teamed with Google to give a long-term home to the Short/Sequence Read Archive (SRA) database. This immense dataset, which spans 400 terabytes at this point, includes publically available whole-genome sequences that scientists can use for research purposes. The data has previously been housed by the government at the NCBI, but federal cuts mean that organization can no longer shoulder the burden, which is where DNA Nexus and Google are stepping in.

    It was only a few years ago that 23andMe and other personal genomics companies began to fulfill the futurisitic promise of allowing consumers to test their own DNA for hundreds (rather than hundreds of thousands) of dollars. And now it won't be long until these screens become far more exhaustive, with such tests comprising your entire genome, rather than just specific portions of it. Society still has plenty of thinking to do when it comes to the privacy and ethical issues involved — but from a straight logistical perspective there's another thing we need to consider: every person's DNA sequence represents a huge chunk of data spanning hundreds of gigabytes. Today a company called DNAnexus is announcing that it's raised $15 million from Google Ventures and TPG Biotech to help help scientists and genome-related services host and manage this data. Also participating in the round are First Round Capital, SoftTech VC, K9 Ventures, and Felicis Ventures.


    Leave a comment:


  • Joann
    replied
    chromosome ultrastructure in a single cell: beyond sequencing

    Kerry,
    Thanks for posting this paper which brings into focus the ultrastructure of a single chromosome from a single cell. And no statistical analysis whatsoever... I should also point out that even here, it is fixed material that is examined. Can't predict whether these techniques could help with gross isolation of Y chromosomes for large-scale sequencing projects.

    Leave a comment:

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