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  • krobison
    replied
    Have you looked in the 1000 Genomes data at chrY? Perhaps they have some useful variants there - -quite a lot of data is online. How many new SNPs for Y showed up in the Bushman or Asian whole genome sequences?

    For the sort of high-throughput approach you are describing, one of the targeted sequencing technologies could make sense. For example, you might try designing a RainDance or OLink primer library to amplify the Y. Or, perhaps a SureSelect/Nimblegen approach.

    A big question would be what cost per sample are you really willing to take on and how many samples? That would really affect the choice of technology.

    Leave a comment:


  • KerryOdair
    replied
    Originally posted by Joann View Post
    Hi Kerry,
    Welcome to seqanswers! While your questions target the very interesting intersection between cytogenetics and next gen sequencing, I cannot answer any of them directly. However I encourage you to do more literature research for yourself on this topic taking advantage of public databases. For example at the USPTO patent search site, under the advanced search for Y chromosome (enter abst/"Y chromosome" as your search term, you will note less than 80 published patents and applications--most dealing with physical methods for sperm cell separation on the basis of the Y chromosome. Then you can check Google scholar for chromosome fractionation and see where the most current research in that literature leads you. Perhaps you will be able to locate a commercial laboratory or research program currently engaged in this task.
    Thanks for the information on USPTO patent search site and the Google scholar. My goal is to find a commercial laboratory who might take on this task. I am hoping exposure in this forum might lead to potential companies interested in such an endeavor. Your site is very valuable in this vain. Your bioinformatics section listing software and google map of next generation sequencing service providers have all been very helpful looking into this matter. Obviously the next step after finding a company to sequence the data is finding viable tools to interpret the data.

    We have already been involved in a commercial investigation of the Y chromosome. We had eight people with 100k BP sequenced in a region of the Y with a high incidence of SNP discovery. We had mixed results finding new SNP’s. This particular company is not ready as of yet to take a commercial product sequencing the Y to the market place. We were the alpha test for this company on Y chromosome sequence testing. However, this company has contributed many new snp’s doing these tests. Any L series snp’s are a result of this testing. However, we are just seeing the tip of the iceberg with this testing.

    With sequencing we would see all snp’s, CNV’s, insertions and deletions, and transposons. The goal being able to develop a complete Y phylogeny tree. Another goal would be to develop a good snp molecular clock. STR’s mutation rates based on father and son studies are few and these str’s mutate more rapidly than snp’s. This would be the holy grail of ancient paternal ancestry with complete y chromosome testing.

    Ancient ancestry has a very strong following in the geneological community. Most sequencing is geared to medical and agricultural activities at the moment. In our project we have gone beyond a well studied haplogroup done by Cruciani in the E-M35 haplogroup. Our haplogroup represents about 4% of the population. We currently have close to 1800 members in this project and represents about 1/3 of the total number who have actually been tested in this group. The R1B1 haplogroup will never be fully understood without sequencing and represents a much larger per cent of the population. Thanks again for your great forum.

    Regards,
    Kerry O’Dair

    Leave a comment:


  • krobison
    replied
    First off, what's wrong with the sequence we already have? Y is not a total wasteland.

    One group has reported specifically capturing a specific mammalian chromosome by flow cytometry & getting sequences highly enriched for the targeted chromosome.

    Leave a comment:


  • Joann
    replied
    some directions

    Hi Kerry,
    Welcome to seqanswers! While your questions target the very interesting intersection between cytogenetics and next gen sequencing, I cannot answer any of them directly. However I encourage you to do more literature research for yourself on this topic taking advantage of public databases. For example at the USPTO patent search site, under the advanced search for Y chromosome (enter abst/"Y chromosome" as your search term, you will note less than 80 published patents and applications--most dealing with physical methods for sperm cell separation on the basis of the Y chromosome. Then you can check Google scholar for chromosome fractionation and see where the most current research in that literature leads you. Perhaps you will be able to locate a commercial laboratory or research program currently engaged in this task.

    Leave a comment:


  • KerryOdair
    started a topic Can we sequence the Y Chromosome

    Can we sequence the Y Chromosome

    Hello,

    I am a newbie in this forum who has had extensive testing for STR, SNP, and chip technology by 23andMe. I have been following the developments in the third generation sequence machines such as PacBio, Ion Torrrent and others in the past couple of years.

    Are we getting closer to being able to actually sequence the Y-Chromosome? Technical questions such as can we easily isolate the Y-Chromosome for sequencing? I had hoped that Ion Torrent was a machine that could do this possibly until they were bought out by Life.

    With everyone talking about the $1000 genome at 3 billion BP why can't we sequence the Y-Chromosome at a reasonable cost at 80 million BP?

    To do the Y-Chromosome the need for long reads and multiple reads for accuracy would seem to be necessary. I do not have a science background so I am looking for the overview on this subject.

    Regards,
    Kerry O'Dair

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