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  • #31
    Familytreedna Administrators conference:

    October 31, 2010 Walk Through the Y Paper by Thomas Krahn in Houston Texas. Possible enrichment strategy for Y chromosome. We are getting closer but we are not there yet. Waiting for someone to take the next big step.



    2009 paper and prototype testing using our E-M35 project members for Walk Through the Y.

    Last edited by KerryOdair; 11-01-2010, 08:29 AM.
    FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

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    • #32
      Crowd-source gene analysis circa Oct. 11, 2010

      Originally posted by ECO View Post
      This is very cool and inspiring. I wonder if the collective we could volunteer to help with this dataset. We have enough experts in assembly, annotation, SNP discovery, etc, that 4 human genomes (better yet a family) could be a very interesting data set.

      I'll have to think on it a little more, but I would love to collaborate with her and her family to open up the dataset to SEQanswers users. Perhaps I could secure or fund a donation of some compute resources for the product.

      Thanks for posting it Kerry!

      edit: Looks like we'd be a little late to the party...
      Maybe not ECO...

      See comments at Forbes, Oct 11, 2010--Rober Langreth

      Comment


      • #33
        Originally posted by Joann View Post
        Maybe not ECO...

        See comments at Forbes, Oct 11, 2010--Rober Langreth
        http://blogs.forbes.com/robertlangre...iads-monopoly/
        Which part "maybe not"...helping with the analysis or being late to the party.

        Not sure how I see Myriad's inevitable wave of lawsuits would effect this type of community analysis.

        Comment


        • #34
          no accusations of infringement

          According to the NY Times:

          In its brief to the appellate court, Myriad argued that the plaintiffs did not have standing to sue because Myriad was not accusing them of infringement.

          See page 20 (internal document number) of Myriad appellate brief:
          The College of American Pathologists is the world's leading organization of board-certified pathologists.



          So right now, there is no indication from Myriad that there will be such infringement accusations made in the future....

          .......But I mainly wanted to point out the crowd source capabilities that you had elucidated in a prior published SEQanswers post.
          Last edited by Joann; 11-04-2010, 05:04 AM. Reason: clarification

          Comment


          • #35
            Well until the Y is fully sequenced this seems to be a significant article for finding new snp's that people match.

            PRESS RELEASE
            Nov. 3, 2010, 8:00 a.m. EDT
            Affymetrix to Provide Data Set of Millions of Genotypes to 1000 Genomes Project
            These Variants Will Empower Future Genotyping Studies and Genetic Characterizations of Human Disease and Health

            In addition, Affymetrix will release a larger data set of approximately 5 million variants on its website, www.Affymetrix.com, before the end of 2010. The new data includes approximately 3 million human SNPs discovered by the 1000 Genomes Project that were not found in the HapMap Project or the NCBI's Single Nucleotide Polymorphism Database (dbSNP, release 130). This information, which was generated by Affymetrix using the Axiom(TM) Genotyping Solution, will allow scientists to create customized Axiom Genotyping Arrays containing 50,000 to as many as 2.6 million markers. The entire Axiom Genomic Database provides an extensive selection of ready-to-use variants for custom array designs and enables an unprecedented level of success in assay conversion.

            FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

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            • #36
              Presentations from The 6th International Conference on Genetic Genealogy from Familytreedna

              Family Finder: Looking Under the Hood


              Family Finder & Population Finder


              "Inferring Genetic Ancestry: Oppourtunities, Challenges, and Implications"


              IT Roadmap 2010


              Predicting Individual Ancestry Using Genome-wide Genetic Data


              Summarizing and Anticipating the Next Decade with NRY, mtDNA, and Autosomal DNA


              Walk Through the Y Project
              FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

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              • #37
                Article on full genome sequencing around the world with maps.

                Genomes by the thousand
                FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

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                • #38
                  Kerry those were really informative posts in this thread.. though could not read them all, but a list of bookmarks for weekend reading!

                  thanks
                  --
                  bioinfosm

                  Comment


                  • #39
                    Originally posted by bioinfosm View Post
                    Kerry those were really informative posts in this thread.. though could not read them all, but a list of bookmarks for weekend reading!

                    thanks
                    Thanks,

                    Just trying to show whats going on in the Y chromosome world today. Looking forward to see who wins the race in the sequencing of the Y chromosome. I hope someday to be able to track the paternal wanderings of my line in the world. At present its looks like my line is on course to be one of extinction. No other similar surname has my particular haplotype designation at this point in time and my line will daughter out. My paternal journey starts in Egypt and ends in the Pacific Northwest in the U.S. It would be nice to fill in the map along the way to the Pacific ocean. My surname is validated in genealogy to Pennsylvania starting in 1755. So how does this Irish name go from Egypt to the British Isles? I am not sure I have the total story in the U.S. and I certainly do not have any answers between the British Isles to Egypt. Many sequenced Y chromosomes would certainly give a degree of confidence as to how it all came about. It certainly would make a great story to pass on to place a timeline for the locations on the map of the paternal travels over time.
                    FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

                    Comment


                    • #40
                      Top Ten Innovations 2010
                      Innovative products that have the life science community buzzing.

                      Pacbio named #1 innovation for products in 2010

                      The long awaited “third-generation” sequencer from Pacific Biosciences takes first place in this year’s Top 10 Innovations contest. The technology qualifies as belonging to a new era because it’s “the first single-molecule real-time sequencer,” says Stephen Turner, the machine’s coinventor and the company’s chief technology officer, speaking to a packed auditorium at this year’s American Society of Human Genetics meeting.

                      Link:
                      FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

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                      • #41
                        Sequencing a Single Chromosome

                        This looks very interesting for isolating the Y chromosome for sequencing.

                        Now two teams have devised ways to determine these groupings—known as the haplotype—in an individual. Stephen Quake and collaborators at Stanford University developed a way to physically separate the chromosome pairs and sequence each strand of DNA individually. Jay Shendure and colleagues at the University of Washington in Seattle sequenced DNA from single chromosomes in specially selected pools and used this information to piece together the genome. Both projects were published this week in Nature Biotechnology.

                        FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

                        Comment


                        • #42
                          Originally posted by KerryOdair View Post
                          This looks very interesting for isolating the Y chromosome for sequencing.

                          Now two teams have devised ways to determine these groupings—known as the haplotype—in an individual. Stephen Quake and collaborators at Stanford University developed a way to physically separate the chromosome pairs and sequence each strand of DNA individually. Jay Shendure and colleagues at the University of Washington in Seattle sequenced DNA from single chromosomes in specially selected pools and used this information to piece together the genome. Both projects were published this week in Nature Biotechnology.

                          http://www.technologyreview.com/biomedicine/26973/
                          This method has been looked at by Thomas Krahn at Familytreedna. These are his remarks regarding this process. I was hoping for a more positive response than this. Still looking for more comments and solutions in this forum.

                          Thanks for your notification.

                          "Yes, it is possible to separate single chromosomes with this technology or also with an instrument called flow sorter.
                          This technology has been used extensively during the Human Genome Project to make sure that the reads are mapped on the correct chromosome.

                          However this technology requires the generation of cell lines, so swabs are out and we'd need to collect fresh blood.
                          Then if we only have a single chromosome it is difficult to get the complete chromosome sequence amplified up to run a sequencing chemistry on it.
                          Likely there will be multiple gaps and we'd need to sequence several single chromosome isolates to get the complete sequence.
                          All in all this is quite expensive and I'm not sure if it will ever reach a point when it can be marketed commercially.
                          However it's good that people at least try to find solutions. We have considered flow sorting before, but we've excluded it because of the cost factor."

                          Thomas
                          FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

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                          • #43
                            Y-specific

                            Wet lab developments could head in two directions--refining methods now used for single cell sequencing to enhance successful single chromosome sequencing. Or improved chromosome isolation methods to collect enough Y chromosome sample for one good sequencing run.

                            The third is continued advances in and applications of whole genome sequencing.

                            In all these cases, advances in computational techniques targeted to Y chromosome assembly and annotation is win-win-win and an excellent focus of scientific resources.

                            Comment


                            • #44
                              DNA tags let us sequence the genome from a single parent

                              Three researchers at Stanford, Hong Yang, Xi Chen, and Wing Hung Wong, have developed a way to piece sequence fragments back into the discrete chromosomes from whence they came. They call it Phase-Seq, because now the genomic sequences are phased.

                              First they adapted Fluorescence Activated Cell Sorting technology to isolate single chromosomes based on their unique signatures when stained with certain dyes. Once they isolated a chromosome—in this case, chromosome 19—they chopped them into small fragments, as usual. But then they added a chromosome-specific tag to each fragment. After sequencing the fragments, they used the tags to reconstruct the separate maternal and paternal haploid genome sequences.

                              Link to article:



                              Full Article:
                              Last edited by KerryOdair; 12-23-2010, 09:14 AM.
                              FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

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                              • #45
                                Haplotyping the Y in most males is VERY easy -- you look for Y sequences. Only in an XYY male would there be any point to applying these new technologies for the Y -- and the expectation there is both Y will be identical.

                                Exception would be if you are interested in some pseudoautosomal regions where confusion with Y is possible -- but these won't be terribly useful for tracing the male lineage anyway.

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