Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    The buzz from her talk in the spring is that she gives quite an informative & entertaining talk.

    Comment


    • #17
      A little googling around revealed that you can access many of the published personal genomes on Penn State's modification of the UCSC Genome Browser; perhaps you could snag some more Y chromosome SNPs there.

      For example, try entering the coordinates chrY:2,700,000-9,000,000

      Make sure you have the "Individual Genotypes" track on under "Personal Genomes"

      Comment


      • #18
        Originally posted by krobison View Post
        A little googling around revealed that you can access many of the published personal genomes on Penn State's modification of the UCSC Genome Browser; perhaps you could snag some more Y chromosome SNPs there.

        For example, try entering the coordinates chrY:2,700,000-9,000,000

        Make sure you have the "Individual Genotypes" track on under "Personal Genomes"
        The Y Chromosome Consortium is our strongest organization for research on the Y Chromosome. Our guru’s in this area are at this link: http://ycc.biosci.arizona.edu/contributors.html

        Certainly Hammer, Karafet, and Underhill are major players in this endeavor. Cruciani has been the biggest contributor in the study of the M35 haplogorup which our website studies.

        Our dataset in the M35 project I think could be matched up against any data set in the world for this group. To use our group as a base before whole genome testing on the subset of the Y chromosome seems to make sense to me. Lets take a small bite of the apple without trying to swallow the whole apple in one bite. If we can deal with this 60 to 80 million base pairs and develop the tools to compare the data this might help in the larger picture. This would seem to be a good proving ground for sequencing and tool development. But first things first we need to sequence the data on the Y chromosome. I believe we have the numbers, resources to finance and the necessary releases of private information to make a go of this from our members.

        I appreciate your insights and information. Maybe I am ahead of the power curve on this issue. But this M35 group and project has been a leader in breaking new ground in this area of study. Since the V13 snp discovery and paper by Cruciani we have discovered 11 new subclades for V13 alone in this one subclade of M35. We have broken new ground and wish to continue to do so and think big.

        This is the browser link they use at this site.




        Link to Consortium website:

        Last edited by KerryOdair; 10-05-2010, 11:59 AM.
        FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

        Comment


        • #19
          Some companies or institutions are getting considerable data somewhere.

          Complete Genomics Sequences Over 300 Human Genomes in Q3, Order Backlog Grows to 800
          October 05, 2010

          According to an amended S-1 form filed with the Securities and Exchange Commission this week, the company had an order backlog of more than 800 human genomes, an increase of 300 genomes compared to mid-July.
          FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

          Comment


          • #20
            This looks like a good start in the right direction for personal genomes.

            Our genomes, unzipped
            11/10/2010
            Categories: Uncategorized
            Written by Daniel MacArthur
            When we launched this website back in June, I welcomed readers with a promise that Genomes Unzipped would “ultimately be much more than just a group blog”. Indeed, the last four months of blogging have really just been a prelude of sorts to what comes next: the real Genomes Unzipped.

            Today we’re launching an exciting new phase of the project. Although we’re not entirely sure where this journey will take us, we’re looking forward to finding out – and to bringing you along with us.

            What are we doing?
            Over the last year, all the members of Genomes Unzipped have had genome scans performed by personal genomics company 23andMe; several of us have also had additional tests done by other genetic testing companies (Counsyl, deCODEme). From today, we’ll be making all of our raw genetic data and the reports generated from these tests freely available online. As the project proceeds, we aim to obtain data from an ever larger array of tests – ultimately extending to whole-genome sequencing – and release it openly. Right now you can freely download the 23andMe data from everyone in the project from this website.

            Over the next few weeks, each of the members will be writing about their own experiences with genetic testing, and what they’ve learnt from their own genetic data. We’ll be discussing analyses we’ve performed on our own raw data, using software written both by group members and other collaborators; and we’ll be releasing the code for that software in our new code repository. We’ll also be talking about the process of deciding to release our genetic data publicly, and how we discussed this decision with our families.

            To make it easier for us (and you) to explore our genomes, we have assembled a custom genome browser using JBrowse – this provides a visual interface that allows our 23andMe (and later, complete sequence) data to be viewed in the context of genes and other features. It’s still in prototype form, but we’ll be refining it and adding more data as the project proceeds.

            Link:
            We strive to provide the most in-depth reviews and guides on DNA tests, ancestry kits, and so much more. 
            FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

            Comment


            • #21
              More questions

              Thanks Kerry. Now I would appreciate some futher comment from you on what this group's approach does or doesn't (will or won't) do for the genealogy special interest groups working with online data. For example, how accessible do you find the Y chromosome data?

              Comment


              • #22
                Originally posted by Joann View Post
                Thanks Kerry. Now I would appreciate some futher comment from you on what this group's approach does or doesn't (will or won't) do for the genealogy special interest groups working with online data. For example, how accessible do you find the Y chromosome data?
                Hello Joann,

                These are big questions you have asked. I have not contacted these people directly as of yet but intend to do so. On the surface it looks like they are using autosomal data to compare at first with the ability to move on to sequenced data in the future. This would represent results from 23andme, DeCodeMe, and Familytreedna Family Finder results. This just came out on 10-11-10 about this site. Dienekes blog has already discussed and done some comparison of their data already. This can be found at the link below:

                Physical Anthropology, Human Genetics, Archaeology, History, etc.


                We need some way to have a public repository of this information somewhere that everyone can use. Right now the data is being controlled by companies and academic institutions.

                We have already established a collective of information from 23andMe and DeCodeMe tests in our community. It compares the data from their tests. The data can be downloaded from the zip file at the link below.

                Adriano Asquecco files for 23andMe Data

                Below are the links for all testing done with 23andMe by different haplogroups




                We have exhausted most of the new snp discoveries from this endeavor. We did not find as many new snp’s as we hoped due to the fact that the testing chips were designed with known snp’s. Testing chips can only test for known snp’s. We must move on to sequencing for complete data information. Autosomal data will only move us back 5 to 6 generations at best.

                Currently today we use STR and SNP data. The largest STR public database is Ysearch which has its problems but it the best we have.

                Link: http://www.ysearch.org/

                Familytreedna has the largest selection for snp testing in the market place today. But this type of testing is difficult trying to establish a new snp placement in the Y tree. However, it is the best we have today. Many new L series snp’s have been established. Below is a link for a great utility looking at these new snp’s. It has the last 2008 release of the Y tree along with a draft tree which shows all the newly discovered snp’s. Using this utility you can click on the new snp and go directly to a Y mapper. There are a considerable number of haplogroup projects trying to find new snp’s in their particular haplogroup designation ours being the M35 project. This utility was developed by Thomas Krahn at Familytreedna. He also has a X mapper as well

                Discover your DNA story and unlock the secrets of your ancestry and genealogy with our autosomal DNA, Y-DNA, and mtDNA tests.




                Well enough for this post maybe you will have some follow up questions. Hopefully I have answered your questions. I certainly do not have all the answers. My goal is to try and get the players together to make this Y Chromosome sequencing happen.
                Last edited by KerryOdair; 10-12-2010, 10:54 AM.
                FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

                Comment


                • #23
                  There's always more questions

                  What kind of consent problems do you forsee as a prelude to requesting individuals to grant the release their Y sequence data to a genealogy community?

                  Comment


                  • #24
                    Originally posted by Joann View Post
                    What kind of consent problems do you forsee as a prelude to requesting individuals to grant the release their Y sequence data to a genealogy community?
                    This is another big question. However, I will start with ISOGG and Katherine Borges response as the Director of ISOGG. I will supply some other information and thoughts beyond the Y chromosome as well in the near future.


                    Katherine Borges is the Director of ISOGG, the International Society of Genetic Genealogy, a non-profit organization of over 7,000 members spread throughout the US and 60 other countries. She also serves as co-admin of the Portugal Project as well as several other surname Projects at FTDNA. Here is the essence of her statement before the FDA hearing earlier today:

                    "......Our (ISOGG's) mission is to promote and educate members and the general public about the use of DNA testing for genealogical and ancestry purposes. We are comprised of serious enthusiasts who represent an active core of the estimated one million people who have taken DTC (direct to consumer) tests for genealogy and ancestry purposes since their inception about ten years ago.

                    As the name of our society implies, our focus is primarily upon using DTC tests for genealogy, but a growing segment of our membership also use personal genome tests to trace health-related information within their families. However, testing for ancestry and anthropology is far and away the largest segment of the DTC genetic testing market. This clearly does not fall under FDA's area of responsibility. Our concern is that FDA should not attempt to expand its regulatory authority beyond its proper domain of medical applications, and it should assure that its actions in the medical area do not inadvertently impact the non-medical applications.

                    ISOGG is a dues-free society with no funding sources. The organization has no direct financial stake in any proposed regulation, and is not affiliated with or financially supported by the companies offering these tests. However, our members understand that they would bear the impact and resultant costs of any regulatory matrix imposed upon testing companies, first as taxpayers, and secondarily as consumers of the services they offer.

                    Our membership is not opposed to regulation that works to protect or help consumers where a clear need for legislation is evident and an agreed-upon national purpose is fulfilled. In 2008, we supported GINA, and many of our members wrote to their legislators to urge them to pass this important bill.

                    Additionally in 2008, ISOGG encouraged and facilitated the development of Y-chromosome nomenclature standards for Short Tandem Repeats or STRs by the National Institutes of Standards and Technology, and their subsequent adoption by the ancestral DNA companies and labs. These standards were published in the Fall edition of the free-access online Journal of Genetic Genealogy. This initiative for voluntary standards by a private organization is similar to the implementation of voluntary standards such as those of UL and NEMA in the electrical industry, and ANSI standards in many others.

                    The great majority of our ISOGG membership feels strongly that any expansion of FDA regulatory authority that would have the effect of preventing consumers from ordering DTC tests would be unwise and unnecessary. At a minimum, no action of that sort should be taken without credible, compelling scientific data to support such a move. Relevant studies of this nature and quality are currently being conducted.

                    In making these statements I have in mind the role of the media and certain written academic opinions that over the past few years have sought to impact this issue. Sensationalistic media articles that relate anecdotal cases should not be used as a basis to regulate. Many of the articles I've read have been biased, reflecting the author's views without presenting voices from both sides of the issue. For example, just last week, a DC area reporter was looking for stories from consumers of DTC testing for an article to be published in anticipation of this meeting. He was contacted by several individuals who had positive testing experiences, but he did not follow up on these contacts. He told another consumer that he was specifically seeking negative experiences.

                    Even more seriously, we see a tendency towards a paternalistic attitude by certain groups in the medical professions who seek to limit access to medical information that is not directly under their control. Their arguments often express an extremely low opinion of the ability of people outside of their own professions to comprehend any genetic information or come to terms with its implications. Yet, we heard Col. Magill of Walter Reed state here yesterday that sometimes he sees a patient who knows more about a medical issue than he does, just from personal research. A mandated intermediary would impose yet another cost to consumers.

                    Additionally, over-regulation can even negatively impact participation in scientific studies. My own mother signed up to participate in Kaiser Permanente's genome study, but then backed out for the very reason that the results will not be returned to her. A barrier to access to one's own genetic information also seems contrary to the intent of HIPAA law, and to the new rules issued last week by the White House requiring health insurance companies to provide free coverage for screenings, laboratory tests and other preventative care.

                    The general view of ISOGG's members is that regulatory agencies should not stand between a consumer who wishes to collect data on their own genome, and labs that can provide that service. The genome of an individual consists fundamentally of information, and every individual in a free society has an absolute right to information about their own genome from a source of their choosing.

                    Our membership base consists of many MDs, PhDs, and other specialists who are willing to volunteer their time to assist with the development of industry standards, good practices, and advisory panels. These concepts could be developed in collaboration with federal agencies like NIST and the FTC. And FDA's regulatory requirements for DTCs could be met with something as simple as full and adequate disclosures of the limitations of the tests by the testing companies.

                    The result could be a happy medium to the benefit of consumers, the laboratories, the testing companies, the government and to taxpayers."


                    The full, edited, statement in final form will be filed with the records of the conference within the next two weeks. It will vary somewhat from the above.
                    FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

                    Comment


                    • #25
                      Here is a link to the genomesunzipped consent form. It looks like a well thought out form for release of personalized genome information.

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

                      Comment


                      • #26
                        not good enough

                        I don't think this version of informed consent is good enough. See one of my earliest remarks on this forum at the at the SeqAnswers thread:

                        DDBJ dealing with mass data produced by the second generation sequencer.

                        Nucleic Acids Res. 2008 Oct 16;

                        Authors: Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y


                        My comment focuses on these authors' stated concerns about individual genomes in public databases. While we are all products of evolution we are furthermore relatives of individual ancestors, not one generic "model organism". As you well know, Kerry, current genetic genealogy technique is already a very powerful trace back to deep ancestry. It crosses past many generations of our individual forebears, identifying them and linking them--and us--in detail not yet fully appreciated, in my opinion.

                        Comment


                        • #27
                          Originally posted by Joann View Post
                          I don't think this version of informed consent is good enough. See one of my earliest remarks on this forum at the at the SeqAnswers thread:

                          DDBJ dealing with mass data produced by the second generation sequencer.

                          Nucleic Acids Res. 2008 Oct 16;

                          Authors: Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y


                          My comment focuses on these authors' stated concerns about individual genomes in public databases. While we are all products of evolution we are furthermore relatives of individual ancestors, not one generic "model organism". As you well know, Kerry, current genetic genealogy technique is already a very powerful trace back to deep ancestry. It crosses past many generations of our individual forebears, identifying them and linking them--and us--in detail not yet fully appreciated, in my opinion.
                          They suggest approval from relatives before entering into this consent form. How would you improve their comments? Or do you feel we cannot at this point in time put this information into public format?
                          FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

                          Comment


                          • #28
                            Within the context of whole genome sequencing, living relatives' approval is rather close to irrelevant. Furthermore, consent documents should never be used as a technical band-aid. The ethical budens should shift from relying on such consent documents to gated whole genome databases in order for research-relevant sections to be made consistently available from general genome databases. Quite frankly, the rules and order established by paper archivists (and in particular medical records archivists) already go a long way in serving as a model protocol. Sections of gene-centric, identity markers and ancestry markers can be bioinfomatically extracted from the whole genome data of a given individual volunteer (or group) and viewed in the context of a study or search.

                            Comment


                            • #29
                              The 1000 Genomes Project Consortium

                              The 1000 Genomes has published information on its pilot project. Lots of good information on this at the links below. Mutation rate discoveries could be the most interesting part of this new information. I was surprised at how much supplemental information was released in the publication. The Y Chromosome information is still lacking for what I would like to see. Baby steps I guess at this point. Even with the pilot project a tremendous amount of data involved.




                              NIH-supported work produces tool for research into genetic contributors to human disease.

                              Physical Anthropology, Human Genetics, Archaeology, History, etc.
                              FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

                              Comment


                              • #30
                                Blogger Luke Jostins apparently did the Y-chromosome analysis -- you might contact him to get more info.

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Current Approaches to Protein Sequencing
                                  by seqadmin


                                  Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                                  04-04-2024, 04:25 PM
                                • seqadmin
                                  Strategies for Sequencing Challenging Samples
                                  by seqadmin


                                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                  03-22-2024, 06:39 AM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, 04-11-2024, 12:08 PM
                                0 responses
                                13 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 04-10-2024, 10:19 PM
                                0 responses
                                19 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 04-10-2024, 09:21 AM
                                0 responses
                                15 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 04-04-2024, 09:00 AM
                                0 responses
                                43 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X