[KerryOdair]

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.

Hello Krobison,

I understand your point about psedoautosomal regions and not being terribly useful for tracing the male lineage. When I started this thread it was not clear to me if there were viable methods to separate chromosomes for sequencing from the whole genome without full genome sequencing. Again I am not an expert and have no experience in sequencing machines and there use.

So far I have discovered that methods do exist.

1. The 1000 genomes project is using a method for separating the chromosomes
2. There are flow shorter machines that separate chromosomes.
3. In this article there is Fluorescence activated cell sorting technology
4. Illumina Inc. also uses a process for separating the chromosomes in their whole genome sequencing.

The process for sorting of the chromosomes and sequencing machines are in the market place today. Is there a business model that meets a commercial need that people will pay for that can sustain a viable commercial business? My personal answer to this is yes. I have stated earlier in this thread about the numbers and why people would be interested in this kind of testing.

Let me give you examples of the market place dictating new products. Until companies such as Decodeme and 23andme a genealogy company such as Familytreedna had no interest in autosomal tests on chips. Because of the success in the market place today of the 23andme product Familytreedna has their own chip and test for this now. Ethnoancestry was first to the market place for the testing of individual snp’s. Again the market demand made Familytreedna create products for this kind of testing.

I believe that sequencing companies today are so focused on health issues, animal husbandry, and agriculture advances in genome testing that the market place I describe is not even given consideration. It may be niche market. But I think it is a moneymaking niche market not on the scale of these other markets but still a large market in its own right.

I have seen no indication as of yet that sequencing the Y would fall under the regulations of the CLIA certification at this point in time. Just a side note, I have had a telephone conversation with an Associate at Illumina Inc. who will get back to me after the new year when he has had time to discuss this idea with his company. They have not thrown me under the bus as of yet with this concept.

In a perfect world it would be a swab or spit test for the sample. If it requires blood for the process we can live with that. We must first get the sequence. Then the second part to this equation is the library and other software to complement and compare the results.

[krobison]

Unless there is a lot of effort focused on driving the cost down, the cost of separating out a specific chromosome is likely to far exceed the cost of just sequencing the whole mess & sifting out what you want. Groups interested in haplotyping (and it is interesting that another proposed method has not yet been implemented).

If you really wanted to focus on Y, easier way is hybridization capture (e.g. SureSelect, OLink, EZCap). The technology exists now, is easily automatable & doesn't require additional high-capital equipment (such as a flow sorter), but you probably are looking at no less than $1K-$1.5K per Y-chromosome targeted -- IF you can get a lot of orders. Otherwise, it starts looking more like $2-3K per Y-chromosome.

But I'm still very skeptical that a market exists between the current array-based tests ($0.1K) & full genome sequencing ($5K-$12K) for a Y-specific test. Are there really going to be enough people curious about their genetic history who are willing to pay 10X the cost for a bit more resolution? Still, a clever operator could set this up & certainly a research group could access any of the existing service providers to do this.

[Joann]

Interesting

I think it would be very interesting to explore the non-coding regions of the Y, in addition to gene sequence variation, in order to chart ancestry, especially where biological evidence can be aligned with paper evidence obtained from written history.

Perhaps in an extension of the methods discussed above, the whole human Y can be tagged and then separated out from other chromosomes by buoyant density or other physical techniques previously applied to subcellular fractionation. It might be an investment to set up the protocol, but then it should simplify and lower the cost of sequencing.

[krobison]

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.

I don't doubt that people will be interested in the challenge, but given that this is a tiny bit of genetic machinery that half the population lacks & seems to have very little useful for the other half, it's hard to see much value beyond tracing histories.

Given that thousands of public Y chromosomes will be available in the near future, it's hard to imagine many groups focusing on this -- and if they do there are established methods (as I listed above, plus Fluidigm & RainDance and other PCR approaches) for targeting sequencing.

[KerryOdair]

I don't doubt that people will be interested in the challenge, but given that this is a tiny bit of genetic machinery that half the population lacks & seems to have very little useful for the other half, it's hard to see much value beyond tracing histories.

Tracing the history of mankind seems interesting to me and others as well. I would think there are a number of population geneticists who might take exception to your comment. Not only do we have the opportunity to study todays populations but methods are also being developed to sequence ancient DNA as well. How much of our DNA is perhaps archaic DNA from other species of mankind? They are in the process now of sequencing the hobbit people from the Philippines. There are many samples in storage to be tested to give us insights of population makeup from the Iron, Bronze, and earlier ages. With different scientific disciplines many gaps in pre history can be better understood. This is the latest study by Cruciani that just came out today on our E1b1 haplogroup.

http://www.plosone.org/article/slideshow.action?uri=info:doi/10.1371/journal.pone.0016073&imageURI=info:doi/10.1371/journal.pone.0016073.g001

based on this paper : http://www.plosone.org/article/info:...l.pone.0016073

To make these new discoveries he used sequencing of the Y to find these new snp's

Given that thousands of public Y chromosomes will be available in the near future, it's hard to imagine many groups focusing on this -- and if they do there are established methods (as I listed above, plus Fluidigm & RainDance and other PCR approaches) for targeting sequencing.

I am not convinced at this point in time that there are going to be thousands of public Y chromosomes in the near future. This will only happen if the complete genome is sequenced based on whats happening today. That expense is two great I think to accomplish that goal in the near future. Sequencing just the Y could be cost effective enough to get the thousands we are looking for in a public format for all to study.

[krobison]

Note that from ancient remains none of the whole chromosome isolation techniques are likely to work; the chromatin is probably already quite degraded. Another reason for developing hybridization & PCR-based methods; they don't care.

It's not that I think nobody is interested in the Y; it's just that truly developing a technology for isolating Y chromosomes is a serious undertaking for a niche area. There may be groups working on isolation, but it's doing a lot of work for a modest gain.

Again, the cost of data generation for one human genome really is around $10K, perhaps lower with Complete Genomics. Data generation for Y chromosome via SureSelect or RainDance or similar would be on order of $2K per genome -- of which $1K is the sequencing and $1K is the selection. So another method is either going to need to do something more interesting (such as haplotyping a diploid chromosome) or cost much less than $1K.

You could, for example, use Quake's method to separate chromosomes, use qPCR to identify which well had the Y & then just sequence that well. So in a sense, the technology exists -- but it isn't currently commercially available. Perhaps Quake could be interested in undertaking a wide survey of Y

So I'm making it badly, but the argument I'm making is two fold: (1) technology exists now to sequence the Y for $1K-$2K, so any group wishing to target Y-chromosome information could have data in about 2 months (if they have the DNA) and (2) huge numbers of public Y data is looming. So perhaps this thread should be renamed "Yes, we can sequence the Y-chromosome & it's being done".

[KerryOdair]

It's not that I think nobody is interested in the Y; it's just that truly developing a technology for isolating Y chromosomes is a serious undertaking for a niche area. There may be groups working on isolation, but it's doing a lot of work for a modest gain.

I have read articles that deal with targeting specific areas on specific chromosomes for medical tests at low costs. Maybe this avenue of research will allow a technique that will be viable for the Y chromosome.

Again, the cost of data generation for one human genome really is around $10K, perhaps lower with Complete Genomics. Data generation for Y chromosome via SureSelect or RainDance or similar would be on order of $2K per genome -- of which $1K is the sequencing and $1K is the selection. So another method is either going to need to do something more interesting (such as haplotyping a diploid chromosome) or cost much less than $1K.

You could, for example, use Quake's method to separate chromosomes, use qPCR to identify which well had the Y & then just sequence that well. So in a sense, the technology exists -- but it isn't currently commercially available. Perhaps Quake could be interested in undertaking a wide survey of Y

I wish Quake was interested in doing this. But I do not see the academic environment having the resources to do this on a wide enough scale. It will take a commercial effort in my mind.

So I'm making it badly, but the argument I'm making is two fold: (1) technology exists now to sequence the Y for $1K-$2K, so any group wishing to target Y-chromosome information could have data in about 2 months (if they have the DNA)

We are currently spending $700 to sequence approximately 120K BP today on the hope of finding new snps. Then we spend $30 per snp testing for placement in the tree. So we are currently almost spending $1000 just on the hope of finding new snps. So your cost for sequencing the whole Y chromosome is not far from what we are spending today. This whole debate is brought up very well by an article today in Genome Web Daily below. From my posts you most realize I am in the camp of us not having a $1000 genome and its interpretation via software. I am in the camp of the Genetic future article link below.

The $1,000 Genome Debate is 'Already ... Irrelevant'
January 12, 2011


Matthew Herper and Daniel MacArthur are at odds over the $1,000 genome. Forbes' Herper argues that even though sequencing is becoming cheaper, analyzing a genome still costs much more than $1,000. Over at Genetic Future, MacArthur responds that as sequencing costs continue to fall, "a substantial niche will develop for innovators providing affordable, intuitive, accurate interpretation tools."
On his blog, John Hawks says that "the inevitability of the $1,000 genome has already made it irrelevant." He expects a $1,000 genome will be announced sometime this year and whole-genome sequencing at 4x coverage for less than $100 by the end of 2014. "I think there's a good chance they will be less than $50 at that time," Hawks says of human genomes. As sequencing gets cheaper, he adds, there will be "an expensive, professional class of genome interpretation" for everything from medical applications to personalized genealogical consultation services. "Genomes may not be literally too cheap to meter, but they'll certainly be, as George Church has suggested, free with additional purchase," Hawks says Matthew Herper and Daniel MacArthur are at odds over the $1,000 genome. Forbes' Herper argues that even though sequencing is becoming cheaper, analyzing a genome still costs much more than $1,000. Over at Genetic Future, MacArthur responds that as sequencing costs continue to fall, "a substantial niche will develop for innovators providing affordable, intuitive, accurate interpretation tools."
On his blog, John Hawks says that "the inevitability of the $1,000 genome has already made it irrelevant." He expects a $1,000 genome will be announced sometime this year and whole-genome sequencing at 4x coverage for less than $100 by the end of 2014. "I think there's a good chance they will be less than $50 at that time," Hawks says of human genomes. As sequencing gets cheaper, he adds, there will be "an expensive, professional class of genome interpretation" for everything from medical applications to personalized genealogical consultation services. "Genomes may not be literally too cheap to meter, but they'll certainly be, as George Church has suggested, free with additional purchase," Hawks says.

http://blogs.forbes.com/matthewherper/2011/01/06/why-you-cant-have-your-1000-genome/

http://scienceblogs.com/geneticfuture/2011/01/why_you_can_have_your_1000_gen.php

http://johnhawks.net/weblog/topics/biotech/whole-genome/sequencing-1000-dollar-genomes-2011.html

(2) huge numbers of public Y data is looming. So perhaps this thread should be renamed "Yes, we can sequence the Y-chromosome & it's being done".

Your statement here reminds me of an old tv commercial about hamburger chains. Its tag line was "Where's the Beef" I am still looking for all these huge numbers of public Y data is looming as you say. I would possibly rename the thread this way if you want.

We can sequence the Y but who is doing it and where is the data?

PS. It seems the 1000 genomes project is slowing down due to funding from what I understand.

[Joann]

Newborn screening and next gen sequencing

In her recent talk at the Genomics and Public Health conference, Sharon Terry suggested that our current genetic testing platform for newborns (check your state department of public health for its panel of genetic tests administered at birth) might soon give way to a genomic profile returned to the individual at no charge. That data (in sequence form) could certainly serve to provide material for extended Y chromosome analysis for those who were interested.

https://www.cmpinc.net/2010PHGConference/presentations/Terry.pdf

See slide 5

[krobison]

Complete Genomics releases 40 genomes; 20 more in March. Multiple ethnicities. Presumably about 1/2 male.

[KerryOdair]

Affymetrix Releases Comprehensive Validated Data from AxiomT Genomic Database

http://www.tradershuddle.com/20110303177524/Press-Releases/Affymetrix-Releases-Comprehensive-Validated-Data-from-the-Axiom%E2%84%A2-Genomic-Database.html

Written by TradersHuddle Staff
Thursday, 03 March 2011 03:05
SANTA CLARA, Calif.-( Business Wire )-

Affymetrix, Inc. (NASDAQ: AFFX) today announced the release of a complete data set of 5 million variants on its website. The genotyping data set, part of the Axiom™ Genomic Database, is based on extensive validation of genomic variants from the Single Nucleotide Polymorphism Database (dbSNP), 1000 Genomes Project, NHGRI Database of Published Associations, and collaborations that have led to the discovery of novel SNPs and insertion/deletions (indels). The data set includes genotyping data for more than 2 million validated rare and common genomic variants that Affymetrix recently contributed to the 1000 Genomes Project, many of which were not previously available from any source. The data will be incorporated into the 1000 Genomes Project’s public data repository.

[GregRM]

Analysis of next-gen ChrY data at DNA-Forums

Over the last several months, several of us at DNA-Forums have been mining the publicly-available next-gen ChrY data (mainly 1000 Genomes Project data, and some Complete Genomics data), similar to the approach that Keith suggested earlier in this thread. Here is the link to the section of the site where most of the discussion is occurring: http://dna-forums.org/index.php?/forum/143-1k-genomes/ . At this point, we have looked closely at haplogroups R and I, but we have preliminary classifications (based on known variants) for many of the other 1000 Genomes males with "low_coverage" data. So far, we have identified ~300 novel candidate variants (SNPs and short indels) that seem to be present in two or more samples under haplogroups R and I, and, with some outside help, 3 have been confirmed by conventional sequencing (more are in the pipeline; we're tracking our progress using this spreadsheet: https://spreadsheets.google.com/ccc?...thkey=CIOag_UD). In the process, we've also been discovering potential new phylogenetic structure to the Y-tree. An example showing a proposed phylogeny under R-U106 is here: http://www.box.net/shared/4x1fqatlqb . Kerry, if you're interested in joining the effort, feel free to chime in at DNA-Forums...there seem to be plenty of Haplogroup E samples to look at.

[SeqAA]

You realize it's a pain in the .... to isolate y chromosomes?
I'm not sure what your gameplan is for sequencing just the Y chromosome. Platform really isn't your problem here, it's flow cytometry.

[KerryOdair]

Over the last several months, several of us at DNA-Forums have been mining the publicly-available next-gen ChrY data (mainly 1000 Genomes Project data, and some Complete Genomics data), similar to the approach that Keith suggested earlier in this thread. Here is the link to the section of the site where most of the discussion is occurring: http://dna-forums.org/index.php?/forum/143-1k-genomes/ . At this point, we have looked closely at haplogroups R and I, but we have preliminary classifications (based on known variants) for many of the other 1000 Genomes males with "low_coverage" data. So far, we have identified ~300 novel candidate variants (SNPs and short indels) that seem to be present in two or more samples under haplogroups R and I, and, with some outside help, 3 have been confirmed by conventional sequencing (more are in the pipeline; we're tracking our progress using this spreadsheet: https://spreadsheets.google.com/ccc?...thkey=CIOag_UD). In the process, we've also been discovering potential new phylogenetic structure to the Y-tree. An example showing a proposed phylogeny under R-U106 is here: http://www.box.net/shared/4x1fqatlqb . Kerry, if you're interested in joining the effort, feel free to chime in at DNA-Forums...there seem to be plenty of Haplogroup E samples to look at.

Hello,

I am sorry for not responding earlier but times have been busy. I have read about the good work you are doing over at DNA-Forums along with other subclades. Currently in the E-M35 project we are getting new results from some new Walk on the Y tests for our group. We are getting new snp's with these tests. Since our group was the first to test WOY, newer tests by Thomas are sequencing more base pairs than our original tests in 2009.

We currently have no one to dedicate time to the 1000 Genome data. Hopefully someone soon will take up that cause and champion the effort in our group. I have brought this to the attention of our members in the project. Hopefully we will be able to put our full attention into this data soon.

Regards,
Kerry O'Dair

[KerryOdair]

You realize it's a pain in the .... to isolate y chromosomes?
I'm not sure what your gameplan is for sequencing just the Y chromosome. Platform really isn't your problem here, it's flow cytometry.

Yes, I understand the flow cytometry is the basic problem. Steven Quake at Stanford is still working on this issue. Here is the latest article on that front.

http://www.technologyreview.com/biomedicine/37204/?mod=related

There is also a startup company Noblegen that is developing a simplified version of nanopore genome sequencing technology. This may lead to getting the Y along with the rest of the genome at a cost for the man on the street.

http://www.technologyreview.com/biomedicine/37551/?mod=chfeatured

Another person I am working with on this issue has had contact with a company in China. They are looking at the problem from two different angles. One being a chip for testing 10 to 25 million base pairs on the Y. The other if we can get enough people together is just to use existing technology to sequence the Y and create the library. The second solution pricing would be about half the cost of current sequencing of the genome done by Illumina and Complete Genomes.

[KerryOdair]

Here is an update on the 1K genome mining project for snp’s being done by researchers at DNA-FORUMS. They have isolated 1200+ Z snp’s and 26 have been verified to date. This group of Z snp’s is more than twice the size of any other snp development category. Hundreds of primers are now available through Familytreedna for testing of these snp’s.

I am still searching for a cost effective solution for sequencing the Y. The genetic genealogy people are beginning to be acknowledged by the academic community for the contributions we have found and advancing our knowledge. We are a group of people who are motivated to advance our knowledge of the human genome and our genetic population travels.

This is a list from the Isogg website that denotes what the SNP letters stand for. This is a handy list if you have not seen it before.

SNPs development indicated by beginning letters:
DF = anonymous researcher using publicly available full-genome-sequence data, including 1000 Genomes Project data; named in honor of the DNA-Forums.org genetic genealogy community
IMS-JST = Institute of Medical Science-Japan Science and Technology Agency
KL = Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
L = Thomas Krahn, MSc (Dipl.-Ing.) of Family Tree DNA's Genomics Research Center; snps named in honor of the late Leo Little
M = Peter Underhill, Ph.D. of Stanford University
N = The Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing
P = Michael Hammer, Ph.D. of University of Arizona
Page, PAGES or PS = David C. Page, Whitehead Institute for Biomedical Research
PK = Biomedical and Genetic Engineering Laboratories, Islamabad, Pakistan
S = James F. Wilson, D.Phil. at Edinburgh University
U = Lynn M. Sims, University of Central Florida; Dennis Garvey, Ph.D. Gonzaga University; and Jack Ballantyne, Ph.D., University of Central Florida
V = Rosaria Scozzari and Fulvio Cruciani, Università "La Sapienza", Rome, Italy
Z = G. Magoon, Richard Rocca, David F. Reynolds, Bonnie Schrack, Peter M. Op den Velde Boots, and an anonymous individual, independent researchers of 1000 Genomes Project data and Thomas Krahn, MSc (Dipl.-Ing.) of Family Tree DNA's Genomics Research Center, with support from the DNA-Forums.org genetic genealogy community


Ancient DNA reveals secrets of human history
Modern humans may have picked up key genes from extinct relatives.

Pääbo is amazed at how quickly the Neanderthal genome has been mined.

http://www.nature.com/news/2011/110809/full/476136a.html