The following information was provided by Full Genomes Corporation. With thanks to Justin Loe.
Full GenomesTM Corporation, the first company to offer a high-resolution and comprehensive Y chromosome test in January 2013, announced today that it is collaborating with Novogene, a leading genomics solution provider with the largest Illumina-based sequencing capacity in China, to offer GenomeGuide, one of the first whole genome tests for ancestry purposes, for under $1,000.
GenomeGuide, now available to consumers at US $895, includes raw data (BAM file), variant summary reports from SnpEff and VEP that are compatible with third party tools, such as Promethease, autosomal and X-chromosomal variant identification (Variant Call Format) files, and mitochondrial and Y chromosome reports (for males). As with other Full Genomes products, GenomeGuide is intended for ancestry/research-use only, and should not be relied upon for medical or diagnostic purposes.
Novogene, the only Illumina Genome Network partner in China, will deliver high-quality WGS data using the Illumina Hi-Seq X Ten system capable of sequencing up to 18,000 human genomes per year at the lowest cost per genome, and will apply its advanced bioinformatics capabilities and expertise to provide variant analysis.
"The advent of new technology has enabled Full Genomes to offer GenomeGuide, a new whole genome ancestry test which will be the most comprehensive ancestry test on the market today," stated Justin Loe, CEO of Full Genomes. "Full Genomes is committed to providing responsible and detailed genetic reports to the customer," he added, "and we are incorporating the latest technology to enable the consumer to receive comprehensive information on their ancestry. With their advanced Illumina technology, outstanding informatics/analysis, and highly responsive and effective support, we are confident that Novogene will deliver the high-quality WGS results our customers expect."
"We look forward to collaborating with Full Genomes and to helping enable the delivery of this highly cost competitive ancestry research to consumers," stated Dr. Ruiqiang Li, Founder and Chief Executive Officer of Novogene. "As one of the first companies in the world to purchase Illumina's HiSeq X Ten in early 2014, we have extensive experience with the system and are uniquely positioned to provide Full Genomes and its customers with the highest quality WGS data."
About Full Genomes Corporation
Full Genomes incorporated in 2012 for the purpose of making full genomic sequencing for genealogical use available to the general public at a leading price point. Full Genomes introduced Y Elite, a comprehensive (next generation sequencing) of the Y chromosome in 2013 to the genetic genealogy market. Since then, a variety of customers in the U.S. and overseas, as well as a number of institutions have used FGC's Y chromosome product. Full Genomes' proprietary DNA analysis capabilities for the Y chromosome have been recognized and have been used for a variety of research projects. Full Genomes has partnered with various vendors and organizations for sequencing and chip development with the goal of advancing new products and DNA services addressing additional markets.
About Novogene
Novogene Bioinformatics Technology Company, Ltd., headquartered in Beijing with branches in the US and UK, is a leading genomics solution provider with cutting edge bioinformatics expertise and the largest Illumina-based sequencing capacity in China. Committed to quality service and scientific excellence, Novogene has achieved rapid growth and industry recognition by working in partnership with diverse healthcare, educational and research institutions around the globe to realize the unlimited potential of the rapidly evolving world of genomics. The company has completed numerous major service projects with findings published by top-ranked journals such as Science and Nature. Novogene is the first company in China to purchase Illumina's HiSeq X 10 system and is the only Illumina Genome Network partner in China. Novogene Corporation is Novogene's U.S. subsidiary, based in San Diego, CA. To learn more, visit http://en.novogene.com.
For more information, contact:
Justin Loe
Chief Executive Officer
424-333-8537
justin.loe@fullgenomes.com
Full Genomes Corporation
Joyce Peng, Ph.D.
Global Marketing Director and General Manager
1-626-222-5584
joyce.peng@novogene.com
Novogene Corporation
Showing posts with label Full Genomes. Show all posts
Showing posts with label Full Genomes. Show all posts
Thursday, 28 January 2016
Friday, 27 November 2015
Full Genomes winter discount
Full Genomes Corporation have announced a winter sale (or summer sale if you're in the southern hemisphere!). The tests offered by this company are suitable for the very advanced genetic genealogists in our community.
There is a $100 discount on the Y Elite test if you use the following code:
This brings the price down to US $675.
The Y Elite is a comprehensive Y-chromosome sequencing test, which is used for the discovery of new SNPs. It is currently the most advanced Y-DNA test on the market, and the only next generation sequencing Y-DNA test which offers a read length of 250 bps.
If you're thinking of taking a Y Elite test it's best to make sure that you join the appropriate Y-DNA haplogroup project so that you can share your results with the volunteer admins.
There are also discounts on the whole genome sequencing tests from Full Genomes. A report on the Y-chromosome is included with this test, but the autosomal DNA results are provided without medical interpretation or advice. However, users can upload their data to third party tools such as Promethease, which accepts VCF files from Full Genomes.
The 30x whole genome is now $1600 (reduced from $1850), a saving of 13.5%
There is a 10% reduction on the other whole genome sequencing tests:
10x is $670 instead of $745
4x is $337 instead of $375
2x is $225 instead of $250
These offers are only available for a limited time so if you are thinking of ordering don't delay.
There is a $100 discount on the Y Elite test if you use the following code:
Winter15FGC
This brings the price down to US $675.
The Y Elite is a comprehensive Y-chromosome sequencing test, which is used for the discovery of new SNPs. It is currently the most advanced Y-DNA test on the market, and the only next generation sequencing Y-DNA test which offers a read length of 250 bps.
If you're thinking of taking a Y Elite test it's best to make sure that you join the appropriate Y-DNA haplogroup project so that you can share your results with the volunteer admins.
There are also discounts on the whole genome sequencing tests from Full Genomes. A report on the Y-chromosome is included with this test, but the autosomal DNA results are provided without medical interpretation or advice. However, users can upload their data to third party tools such as Promethease, which accepts VCF files from Full Genomes.
The 30x whole genome is now $1600 (reduced from $1850), a saving of 13.5%
There is a 10% reduction on the other whole genome sequencing tests:
10x is $670 instead of $745
4x is $337 instead of $375
2x is $225 instead of $250
These offers are only available for a limited time so if you are thinking of ordering don't delay.
For further information about any of these tests contact Full Genomes via their website at www.fullgenomes.com.
For a comparison of the different SNP testing options see the ISOGG Y-SNP testing chart.
Wednesday, 6 May 2015
New Y Elite 2.0 test from Full Genomes Corporation
The technical details are as follows:
Length coverage: 13.2+ megabases (a conservative estimate)
Read length: 250 base pairs
Coverage: 30x
Supplier: Omega Bioservices
Features: better SNP calling and better STR calling quality
Cost: US $750
This new product replaces the earlier Y Elite test sourced through BGI Genomics and the Y Prime (100 bp) test. It is the only commercial next generation sequencing test which offers a 250 bp read length, and is also the only NGS test which includes mtDNA results.
For further details contact the company via their website:
https://www.fullgenomes.com
For information on the currently available SNP tests see the Y-DNA SNP testing chart in the ISOGG Wiki. The chart has not yet been updated to include the new Y Elite 2.0 test but should be updated in the next few days.
With thanks to Justin Loe of Full Genomes Corporation.
Monday, 1 September 2014
A big price reduction on the Y Elite test from Full Genomes Corporation
As of today's date Full Genomes Corporation (FGC) has reduced the price of their Y Elite test from US $999 to $850. The FGC Y Elite is currently the most comprehensive Y-chromosome sequencing test on the market. The Y Elite sequences around 23 million bases, of which between 12 and 16 million are in mappable regions. There are nearly 60 million base pairs in the entire Y-chromosome, around half of which are in highly repetitive regions, but with currently available technology it is not yet possible to sequence the entire Y-chromosome.
For a comparison of all the available Y-SNP tests see the ISOGG Y-DNA SNP testing chart.
FGC also has a whole genome pilot which is due to launch very soon. The pilot programme was announced on the Anthrogenica Forum on 25th August. The test has a read length of 150 base pairs and will cost US $1850 per sample. The read length will be for 150 base pairs.
For a comparison of all the available Y-SNP tests see the ISOGG Y-DNA SNP testing chart.
FGC also has a whole genome pilot which is due to launch very soon. The pilot programme was announced on the Anthrogenica Forum on 25th August. The test has a read length of 150 base pairs and will cost US $1850 per sample. The read length will be for 150 base pairs.
Saturday, 26 July 2014
Full Genomes launches Y Prime - a new Y chromosome sequencing product
The following press release has been written by Full Genomes Corporation.
Full Genomes Corporation (FGC) is announcing today the introduction of a new Y chromosome sequencing product, dubbed Y Prime. The Y Prime test leverages recent technology advances to economically sequence large portions of a male's Y chromosome, enabling advanced, high-resolution tracing of direct paternal line ancestry.
FGC has worked with industry leaders to develop a new Y chromosome capture approach and has combined it with Illumina "next-gen" sequencing. The resulting data will be processed with the latest alignment algorithms to improve read mapping. The overall result is a cutting-edge product with Y chromosome coverage breadth that is close to that of FGC's original comprehensive Y sequencing product (now termed Y Elite), at a much lower cost. Additionally, the new product is priced lower than the leading competitor, while retaining a significant advantage in terms of quality and comprehensiveness.
FGC is releasing the following comparison statistics as estimates of test coverage based on Y Prime pilot results.
Y Prime will be offered at a standard price of $625. An introductory price of $599 is available for orders placed by August 31, 2014. Y Prime is currently available at the discounted introductory price through the Full Genomes website by ordering the Comprehensive Y test using the coupon code "YPRIME".
The new product is also expected to offer significant improvements in turnaround time for results. Testing will be performed by a U.S.-based sequencing facility.
Additionally, FGC has recently been developing new sample collection protocols, designed to reduce the frequency of delays due to the need for repeat sample collection.
Justin Loe, CEO of FGC, commented, "Our new product is consistent with our mission to deliver the best quality Y sequencing products at the most affordable prices possible, and to continue to innovate with new products targeted to the genetic genealogy community."
FGC will continue to offer the original comprehensive Y sequencing product, with sequencing performed at BGI, under the new name Y Elite. To help customers decide which product is right for them, FGC is releasing BED files to indicate the regions covered by representative tests; these are available at http://goo.gl/pcq6FE and can be used to determine whether a particular site or SNP of interest is likely to be covered by the test. Customers with questions may contact orders@fullgenomes.com.
DAK note: I am advised that Greg Magoon has further technical comparisons available, which are the raw data files from the pilot samples (BAM files and FGC analytical reports), that are also available for comparison for specialists.
Update 29 July 2014
Full Genomes have announced that the Y Prime test will be offered at a new low price of $589.
Full Genomes Corporation (FGC) is announcing today the introduction of a new Y chromosome sequencing product, dubbed Y Prime. The Y Prime test leverages recent technology advances to economically sequence large portions of a male's Y chromosome, enabling advanced, high-resolution tracing of direct paternal line ancestry.
FGC has worked with industry leaders to develop a new Y chromosome capture approach and has combined it with Illumina "next-gen" sequencing. The resulting data will be processed with the latest alignment algorithms to improve read mapping. The overall result is a cutting-edge product with Y chromosome coverage breadth that is close to that of FGC's original comprehensive Y sequencing product (now termed Y Elite), at a much lower cost. Additionally, the new product is priced lower than the leading competitor, while retaining a significant advantage in terms of quality and comprehensiveness.
FGC is releasing the following comparison statistics as estimates of test coverage based on Y Prime pilot results.
Y Prime will be offered at a standard price of $625. An introductory price of $599 is available for orders placed by August 31, 2014. Y Prime is currently available at the discounted introductory price through the Full Genomes website by ordering the Comprehensive Y test using the coupon code "YPRIME".
The new product is also expected to offer significant improvements in turnaround time for results. Testing will be performed by a U.S.-based sequencing facility.
Additionally, FGC has recently been developing new sample collection protocols, designed to reduce the frequency of delays due to the need for repeat sample collection.
Justin Loe, CEO of FGC, commented, "Our new product is consistent with our mission to deliver the best quality Y sequencing products at the most affordable prices possible, and to continue to innovate with new products targeted to the genetic genealogy community."
FGC will continue to offer the original comprehensive Y sequencing product, with sequencing performed at BGI, under the new name Y Elite. To help customers decide which product is right for them, FGC is releasing BED files to indicate the regions covered by representative tests; these are available at http://goo.gl/pcq6FE and can be used to determine whether a particular site or SNP of interest is likely to be covered by the test. Customers with questions may contact orders@fullgenomes.com.
DAK note: I am advised that Greg Magoon has further technical comparisons available, which are the raw data files from the pilot samples (BAM files and FGC analytical reports), that are also available for comparison for specialists.
Update 29 July 2014
Full Genomes have announced that the Y Prime test will be offered at a new low price of $589.
Saturday, 26 April 2014
A new BAM file analysis service from Full Genomes Corporation and a special offer on the FGC test
The following message is posted on behalf of Full Genomes Corporation:
Full Genomes Corporation (FGC) is announcing the official launch of a service to analyze BAM files from Family Tree DNA's Big Y product. The analysis is being launched at a price of $50 per kit. Recently, FGC had offered the Big Y analysis for a limited time, as a beta product, at no charge. FGC will continue to allow individuals to contribute their BAM files to the Full Genomes database without charge, so that their results may be used in kit cross-comparisons. The offering is designed to provide broader access to FGC's proprietary Y chromosome analysis services and to build FGC's database for purposes of kit comparisons.
The analysis will include the same reports as provided to customers of the Full Genomes sequencing product, with the exception of the mitochondrial DNA analysis, which will use the Yoruba reference sequence for Big Y kits. So, the analysis will consider Y-STRs and INDELs, in addition to Y-SNPs. To be clear, however, the results won't be able to achieve the same resolution as the Full Genomes sequencing product due to limitations with the underlying data from the Big Y test.
Interested individuals should first obtain access to their Big Y BAM file by contacting Family Tree DNA customer service. Those interested in ordering analysis can follow the instructions here to set up a Full Genomes account, make payment, and upload their BAM file; analysis will be performed in weekly batches. Those who are only interested in contributing their results to the Full Genomes comparison database may send the download link to fgcfilesharing@gmail.com, while also indicating their interest in donating their results and optionally providing a name (like FTDNA Kit Number) to associate with the results.
According to Dr. Greg Magoon, Y chromosome data analysis consultant for FGC, "I think the FGC analysis will address many of the needs that have been expressed by members of the genetic genealogy community who have been looking at Big Y results in recent weeks. In my view, the main strengths of the FGC analysis include its cross-kit comparisons and its SNP reliability classifications. We have put a lot of R&D into separating the wheat from the chaff to allow customers and researchers to quickly focus on the most reliable, phylogenetically-useful variants. I think the FGC analysis will help to significantly speed the interpretation of results and decrease the burden on busy genetic genealogists."
Separately, FGC is announcing a beta-stage referral program, which will provide customers with access to advanced analyses of their Full Genomes "next-gen" sequencing data. A Full Genomes customer who refers at least three other individuals to order the Full Genomes test will be entitled to a bleeding-edge, advanced analysis of their choosing. Potential analysis options include:
-Remapping of results to the newer, build 38 human genome reference sequence
-Remapping of results with a new and improved alignment algorithm/approach
-Y-STR analysis using a newer, larger STR database
-Phylogenetic analysis for portions of the Y tree
-Variant calling (SNPs and INDELs) for autosomal and X-chromosome data
Interested customers are advised to contact sales@fullgenomes.com to supply documentation of referrals and to discuss custom analysis options.
Dr Magoon said: "From a research perspective, I'm very excited about the potential for the referral program to push the boundaries of Y-chromosome analysis. We've already been able to work with customers on a case-by-case basis to do some very interesting customized analyses with the Full Genomes results, including the identification of large duplications and deletions through copy-number variation (CNV) analysis."
Speaking about FGC's next-gen sequencing test, CEO Justin Loe said: "The FGC Y chromosome product is the most comprehensive in the market today but it is also, as we recognize, expensive for many potential customers. Over the near term, we expect to be able to make this product more affordable. Additionally, with the advent of new sequencing technologies other products will also be offered."
In fact, in honor of DNA Day, Full Genomes is currently offering a limited-time discount of 20% off the normal price for their comprehensive Y chromosome sequencing test (using coupon code "FGCDNA").
Dr Magoon commented: "I think what we're seeing across genetic genealogy is that companies are finding a niche with products focused on particular areas. For example, 23andMe has been a pioneer in autosomal DNA. We have seen that BritainsDNA has been making great advances in developing innovative chip-based tests for Y chromosome (and other) markers. Family Tree DNA has established a leadership role in Y-STRs and in full mitochondrial DNA sequencing. YSEQ, with Dr. Thomas Krahn, is the world leader in developing Y chromosome marker tests using Sanger sequencing. I am very excited to see FGC working hard to establish a similar role here in the field of "next-gen" Y chromosome sequencing."
Related blog posts
- A confusion of SNPs
The analysis will include the same reports as provided to customers of the Full Genomes sequencing product, with the exception of the mitochondrial DNA analysis, which will use the Yoruba reference sequence for Big Y kits. So, the analysis will consider Y-STRs and INDELs, in addition to Y-SNPs. To be clear, however, the results won't be able to achieve the same resolution as the Full Genomes sequencing product due to limitations with the underlying data from the Big Y test.
Interested individuals should first obtain access to their Big Y BAM file by contacting Family Tree DNA customer service. Those interested in ordering analysis can follow the instructions here to set up a Full Genomes account, make payment, and upload their BAM file; analysis will be performed in weekly batches. Those who are only interested in contributing their results to the Full Genomes comparison database may send the download link to fgcfilesharing@gmail.com, while also indicating their interest in donating their results and optionally providing a name (like FTDNA Kit Number) to associate with the results.
According to Dr. Greg Magoon, Y chromosome data analysis consultant for FGC, "I think the FGC analysis will address many of the needs that have been expressed by members of the genetic genealogy community who have been looking at Big Y results in recent weeks. In my view, the main strengths of the FGC analysis include its cross-kit comparisons and its SNP reliability classifications. We have put a lot of R&D into separating the wheat from the chaff to allow customers and researchers to quickly focus on the most reliable, phylogenetically-useful variants. I think the FGC analysis will help to significantly speed the interpretation of results and decrease the burden on busy genetic genealogists."
Separately, FGC is announcing a beta-stage referral program, which will provide customers with access to advanced analyses of their Full Genomes "next-gen" sequencing data. A Full Genomes customer who refers at least three other individuals to order the Full Genomes test will be entitled to a bleeding-edge, advanced analysis of their choosing. Potential analysis options include:
-Remapping of results to the newer, build 38 human genome reference sequence
-Remapping of results with a new and improved alignment algorithm/approach
-Y-STR analysis using a newer, larger STR database
-Phylogenetic analysis for portions of the Y tree
-Variant calling (SNPs and INDELs) for autosomal and X-chromosome data
Interested customers are advised to contact sales@fullgenomes.com to supply documentation of referrals and to discuss custom analysis options.
Dr Magoon said: "From a research perspective, I'm very excited about the potential for the referral program to push the boundaries of Y-chromosome analysis. We've already been able to work with customers on a case-by-case basis to do some very interesting customized analyses with the Full Genomes results, including the identification of large duplications and deletions through copy-number variation (CNV) analysis."
Speaking about FGC's next-gen sequencing test, CEO Justin Loe said: "The FGC Y chromosome product is the most comprehensive in the market today but it is also, as we recognize, expensive for many potential customers. Over the near term, we expect to be able to make this product more affordable. Additionally, with the advent of new sequencing technologies other products will also be offered."
In fact, in honor of DNA Day, Full Genomes is currently offering a limited-time discount of 20% off the normal price for their comprehensive Y chromosome sequencing test (using coupon code "FGCDNA").
Dr Magoon commented: "I think what we're seeing across genetic genealogy is that companies are finding a niche with products focused on particular areas. For example, 23andMe has been a pioneer in autosomal DNA. We have seen that BritainsDNA has been making great advances in developing innovative chip-based tests for Y chromosome (and other) markers. Family Tree DNA has established a leadership role in Y-STRs and in full mitochondrial DNA sequencing. YSEQ, with Dr. Thomas Krahn, is the world leader in developing Y chromosome marker tests using Sanger sequencing. I am very excited to see FGC working hard to establish a similar role here in the field of "next-gen" Y chromosome sequencing."
Related blog posts
- A confusion of SNPs
Sunday, 17 November 2013
The Y-chromosome sequence interpretation service from YFull.com
This article is for advanced genetic genealogists who have had their Y-chromosome sequenced or who are interested in doing so.
With the forthcoming SNP tsunami, the analysis and interpretation of the Y-chromosome results provided by the various companies will be one of the key determining factors in the success of their products. Fortunately within the genetic genealogy community we have a number of intrepid pioneers who have volunteered to serve as guinea pigs by testing at all the companies so that we will eventually be able to do comparisons between all the products. David Hollister, who runs the Hollister one-name study and is the co-administrator of the Hollister DNA Project, is one of our brave guinea pigs. He has already had his Y-chromosome sequenced with Full Genomes Corporation. He has previously tested with the Genographic Project, and has had STR testing at Family Tree DNA. David is now waiting for his results from the Chromo 2 test from BritainsDNA and the BIG Y test from Family Tree DNA. Another genetic genealogist Itaï Perez has already provided a comprehensive look at the Full Genomes Y-sequencing results in a guest post on CeCe Moore's blog so I see no point in covering the same ground. However, David has recently submitted his Full Genomes data to another service by the name of YFull.com for an alternative interpretation. David was really excited by his results and was so "blown away" by the reports he received from YFull that I asked him if he might be able to share some screenshots so that other genetic genealogists might get a feel for what to expect from this service. David has very kindly agreed and has also obtained the consent of the YFull team for me to publish these screenshots. You will need to click on each image to see larger versions of the screenshots.
This is David's home page on his YFull account. Note that according to YFull there are 41,828 known Y-SNPs and 478 short tandem repeats (Y-STRs).
This report shows David's position on the Y-haplotree and his results for all the SNPs tested on his branch of tree. Separate reports are available for "controversial" SNPs and no calls.
This report provides a list of private and unknown SNPs. 247 private and unknown SNPs were found in David's sequence: 66 were deemed to be of best quality, 10 were of acceptable quality, and 13 were of low quality. For 111 SNPs only one reading could be obtained. A temporary internal ID system is used to identify the private SNPs and they all bear the prefix YFS, an abbreviation for YFull Singleton.
This report shows results for the Indels. Indel is the term used to describe insertions and deletions - positions in the sequence where extra As, Cs, Ts and Gs have been inserted or where they are absent.
There is a handy SNP index that allows you to query your results by SNP name.
Here is the report showing results for the 478 STRs tested.
This pie chart shows the percentage of "good" and "uncertain" alleles. 90.2% of the alleles were classified as "good". Note that next generation sequencing with a read length of 100 bps does not pick up some of the longer STRs in the sequence.
YFull have recently introduced a group feature. There are currently groups available for haplogroups R1a and G2a.
YFull are based in Moscow in Russia. They are currently providing a free service for a limited period, but I understand that they will at some point start charging a small fee. They are able to use data for any Y-chromosome which has been sequenced at a minimum 25X coverage and with a read length of at least 100 base pairs. Data needs to be provided in the form of a BAM file. If you have tested with Full Genomes they will provide you with your BAM file on request. Results are not yet available from Family Tree DNA's BIG Y test but I understand that they will also make the BAM files available. It remains to be seen what level of analysis and interpretation FTDNA will provide.
We can expect the interpretation of Y-chromosome sequencing results to change over time as our knowledge improves, and as more comparative results become available. In the meantime YFull certainly provides an interesting complement to the service provided by Full Genomes. No doubt we can expect other similar services to appear on the scene in the coming months as more sequences become available.
See also
- ISOGG Y-DNA SNP testing chart
- The new Big Y test from Family Tree DNA
- A confusion of SNPs
- A simplified Y-tree and a common standard for Y-DNA haplogroup and SNP nomenclature
With the forthcoming SNP tsunami, the analysis and interpretation of the Y-chromosome results provided by the various companies will be one of the key determining factors in the success of their products. Fortunately within the genetic genealogy community we have a number of intrepid pioneers who have volunteered to serve as guinea pigs by testing at all the companies so that we will eventually be able to do comparisons between all the products. David Hollister, who runs the Hollister one-name study and is the co-administrator of the Hollister DNA Project, is one of our brave guinea pigs. He has already had his Y-chromosome sequenced with Full Genomes Corporation. He has previously tested with the Genographic Project, and has had STR testing at Family Tree DNA. David is now waiting for his results from the Chromo 2 test from BritainsDNA and the BIG Y test from Family Tree DNA. Another genetic genealogist Itaï Perez has already provided a comprehensive look at the Full Genomes Y-sequencing results in a guest post on CeCe Moore's blog so I see no point in covering the same ground. However, David has recently submitted his Full Genomes data to another service by the name of YFull.com for an alternative interpretation. David was really excited by his results and was so "blown away" by the reports he received from YFull that I asked him if he might be able to share some screenshots so that other genetic genealogists might get a feel for what to expect from this service. David has very kindly agreed and has also obtained the consent of the YFull team for me to publish these screenshots. You will need to click on each image to see larger versions of the screenshots.
This is David's home page on his YFull account. Note that according to YFull there are 41,828 known Y-SNPs and 478 short tandem repeats (Y-STRs).
This report shows David's position on the Y-haplotree and his results for all the SNPs tested on his branch of tree. Separate reports are available for "controversial" SNPs and no calls.
This report provides a list of private and unknown SNPs. 247 private and unknown SNPs were found in David's sequence: 66 were deemed to be of best quality, 10 were of acceptable quality, and 13 were of low quality. For 111 SNPs only one reading could be obtained. A temporary internal ID system is used to identify the private SNPs and they all bear the prefix YFS, an abbreviation for YFull Singleton.
This report shows results for the Indels. Indel is the term used to describe insertions and deletions - positions in the sequence where extra As, Cs, Ts and Gs have been inserted or where they are absent.
There is a handy SNP index that allows you to query your results by SNP name.
Here is the report showing results for the 478 STRs tested.
This pie chart shows the percentage of "good" and "uncertain" alleles. 90.2% of the alleles were classified as "good". Note that next generation sequencing with a read length of 100 bps does not pick up some of the longer STRs in the sequence.
YFull have recently introduced a group feature. There are currently groups available for haplogroups R1a and G2a.
YFull are based in Moscow in Russia. They are currently providing a free service for a limited period, but I understand that they will at some point start charging a small fee. They are able to use data for any Y-chromosome which has been sequenced at a minimum 25X coverage and with a read length of at least 100 base pairs. Data needs to be provided in the form of a BAM file. If you have tested with Full Genomes they will provide you with your BAM file on request. Results are not yet available from Family Tree DNA's BIG Y test but I understand that they will also make the BAM files available. It remains to be seen what level of analysis and interpretation FTDNA will provide.
We can expect the interpretation of Y-chromosome sequencing results to change over time as our knowledge improves, and as more comparative results become available. In the meantime YFull certainly provides an interesting complement to the service provided by Full Genomes. No doubt we can expect other similar services to appear on the scene in the coming months as more sequences become available.
See also
- ISOGG Y-DNA SNP testing chart
- The new Big Y test from Family Tree DNA
- A confusion of SNPs
- A simplified Y-tree and a common standard for Y-DNA haplogroup and SNP nomenclature
Friday, 15 November 2013
A confusion of SNPs
This article is for experienced genetic genealogists and requires a reasonable understanding of SNPs and haplogroups.
The launch of the new Big Y test from Family Tree DNA has brought to light the difficulties in comparing the offerings of the different testing companies. We have a chart in the ISOGG Wiki which compares the various Y-SNP tests on the market but it is clear that we are not always comparing apples with apples. One of the major difficulties relates to the claims by the companies about the number of Y-SNPs on their chip. A SNP is a change or a mutation in the DNA alphabet at a single position on the Y-chromosome (eg, a C changing to a T). There are around 59 million base pairs in the Y-chromosome. However, surprising as it might be in this genomic era, there are still large sections of the Y-chromosome that have not yet been explored. Build 37, the current build of the human genome reference sequence, has only mapped out the positions of around 25 million base pairs – less than half of the Y-chromosome.1 The discovery of new SNPs is therefore limited to the parts of the Y-chromosome that can be sequenced using current technology. These areas represent just over 40% of the Y-chromosome. In theory, therefore, a SNP could be found on any one of the 25 million bases that can be sequenced.
The exact number of SNPs on the Y-chromosome is not yet known. There is no central resource listing all known SNPs because there is fierce competition and the companies are keen to keep knowledge of the SNPs that they have discovered from their competitors for as long as possible. We therefore have some SNPs that are in the public domain, some unpublished SNPs that are known only to Family Tree DNA/the Genographic Project, some SNPs that are known only to Full Genomes Corporation and some SNPs that are known only to BritainsDNA. To make matters worse all three companies use different naming systems for their SNPs. Full Genomes SNPs are prefixed by the letters FG, and BritainsDNA SNPs bear the prefix S. I understand from the reports from the Family Tree DNA 2013 Conference that the Genographic Project will be publishing a paper some time in the New Year with the new 2014 Y-SNP tree. It therefore remains to be seen what naming system they will use for their SNPs. There will undoubtedly be considerable overlap in the SNPs offered by the different testing companies but until they release their data or until we have comparative results available we will not be able to work out which SNPs are equivalent (synonymous) – in other words which SNPs occur at the same position but which have been given different names by different companies. For example U106 and S21 are alternative names for a single SNP which defines one of the major branches of the R1b haplogroup.
The problem is well illustrated by the recent developments in R1b-M222, a subclade which predominates in Ireland and Scotland, and is seen in many of the surnames that are associated with the clans reputed to descend from the semi-legendary Irish historical figure Niall of the Nine Hostages.2 According to the early results from the Chromo 2 testing at BritainsDNA 27 new SNPs have been discovered downstream of M222.3 Yet at the Family Tree DNA Conference last weekend Miguel Vilar from the Genographic Project advised that they have identified 22 SNPS below M222. Do any of the Geno 2.0 SNPs correspond with the SNPs found by BritainsDNA? The answer is we simply do not know. Neither company releases the full raw data that will allow the participant to determine the genome reference position of the SNPs for which he has tested positive so the results from the two companies cannot be compared. Few results are in any case available at present from the Chromo 2 testing. The Genographic Project are presenting the results of their Gathering the Mayo Genes Project at a public event in Castlebar on Sunday so it may be that further information will be forthcoming then.
So where can we find out about SNPs and their position on the Y-DNA haplotree? By far the most important source is the Y-SNP tree maintained by ISOGG - the International Society of Genetic Genealogy. The tree was launched on 10th April 2006. By the end of the year there were 436 SNPs on the tree. By September 2013 there were 3610 SNPs on the ISOGG tree. According to Roberta Estes' report from Day 2 of the FTDNA conference the new 2014 Y-SNP tree, which will be published by the Genographic Project in 2014, will have 6200 SNPS and 1000 branches.4 This effectively doubles the size of the existing tree and will represent a significant workload for the team of volunteer project administrators who maintain the tree.
However, the ISOGG tree only documents the SNPs whose precise location on the Y-haplotree is known – in other words SNPs that define particular branches of the human family tree on the Y-line. There are thousands more known SNPs. For these SNPs we know that a mutation has been found on the Y-chromosome at the position in question but we do not know if it has any phylogenetic significance, that is, if these SNPs define branches on the Y-tree or if they are unique to the individual.
ISOGG have a SNP index that lists not just the SNPs that are on the haplotree but also those which "are or have been under active investigation and consideration for addition to the Y Haplotree." ISOGG further state that the "SNPs listed here are less than 10% of the currently known SNPs". To supplement the SNP index ISOGG member David Reynolds maintains the ISOGG SNP Compendium Spreadsheet. This was last updated about a month ago and contains a list of 47,680 SNPs which have yet to be added to the ISOGG tree and the SNP index. A small minority of these SNPs are alternative names for previously known SNPs that are already on the tree (for example, some S series SNPs correspond with some of the Z series SNPs that have already been placed on the tree). Most of the rest are SNPs whose position on the Y-chromosome is known but where we do not as yet know where they belong on the Y-tree. David Reynolds reported back in September that he had about another 5000 SNPs to process. He is "curating and combining duplicates" as he goes along so it is a time-consuming process.
There are no doubt many more SNPs that are being published in scientific papers and I don't know if anyone in the genetic genealogy community is currently keeping track of these. In one recent paper uploaded to the ArXiv preprint server two Chinese researchers discovered 25,000 new phylogenetically relevant SNPs.5
Let's now have a look at the offerings of the various testing companies in the light of these numbers. I'm discussing the companies in chronological order based on the dates when their tests were launched. Some companies offer chip-based SNP tests. These tests can only test for previously known SNPs, but the companies can customise the chips to include their own proprietary SNPs for investigation. The new gold standard tests are those which use next-generation sequencing technology. These have the potential to discover thousands of new SNPs.
The Geno 2.0 test from the Genographic Project
The Geno 2.0 test from the Genographic Project was launched in July 2012 and was the first chip test to come on the market with a comprehensive panel of Y-SNPs. The Genographic Consortium published a paper earlier this year with all the technical details of their new GenoChip.6 The supplementary data tell us that the Genographic Project started with "a raw SNP candidate database of approximately 27,500 SNPs" though some of these were duplicates. The original target was to produce a chip with 15,000 SNPs but according to the paper the chip includes around 12,000 SNPs. Customers can download a CSV file with a list of the SNPs. There were 12,059 SNPs in the most recent file that I downloaded for one of my project members. The Genographic Project do not currently provide the genome reference positions of the SNPs on their chip, and it seems likely that this information is being withheld pending publication of the 2014 tree.
The Chromo 2 test from BritainsDNA/ScotlandsDNA
The Chromo 2 test from BritainsDNA/ScotlandsDNA was launched in June 2013. It uses a customised Illumina chip which is advertised as "covering over 15,000 Y chromosome markers, carefully selected to be most informative, and as free from duplication as possible". Only a limited number of results have been released from this test so far, but a flood of results is expected in the next couple of weeks. Customers receive an Excel spreadsheet with a list of all the markers that have been tested. In the one spreadsheet that I've seen there was a list of 14,184 SNPs. Of these, 8,682 SNPs had the S prefix. On the current ISOGG 2013 Y-SNP index the S series SNPs stop at S530. In the list of SNPs that I saw there were 8385 S series SNPs with numbers higher than S530. Many of these SNPs will probably define new branches on the Y-tree but many more could simply be alternative names for currently known SNPs. We do know that the BritainsDNA chip includes SNPs found in the Genomes of the Netherlands Project, and also many SNPs that are likely to be informative for people of British descent. However, BritainsDNA, in common with the Genographic Project, do not publish the genome reference positions of their SNPs. Unless they provide ISOGG with the positions of their SNPs we will have no way of knowing where they fit on the tree and which of their SNPs correspond with those identified by other testing companies.
Full Genomes
Full Genomes is a new start-up company which made a quiet entry onto the market some time towards the end of 2012. They only began advertising their services publicly towards the end of March 2013.7 They currently offer the most comprehensive Y-DNA test on the market covering about 20 to 25 million base pairs representing around 42% of the Y-chromosome. Full Genomes claim to cover 47,000 of the known SNPs on the ISOGG tree and in the ISOGG SNP Compendium. This is after removing "ambiguous results, and synonyms from consideration".8 Around 14 million of the SNPs are reported to be within mappable regions. However, their test is also uncovering many new private SNPs which have not as yet been made public, and the number of new SNPs discovered can be expected to rise as more and more people get tested. At present each testee in one of the common haplogroups can probably expect to find between 25 and 40 private high-quality SNPs. Full Genomes make the raw data available in a BAM file so that customers will have access to the genome reference numbers and can check the ISOGG tree for alternative SNP names as and when new SNPs are placed on the tree.
The Big Y test from Family TreeDNA
The new Big Y test from Family Tree DNA was launched at the weekend at Family Tree DNA's Conference. I've provided preliminary details in a previous blog post. As this is a new test, no results are yet available, and proper comparisons with the other available tests cannot be done. The FTDNA FAQs tell us that the test covers "at least 10 million base-pairs of reliably mapped positions of non-recombining Y-Chromosome", though the exact number of base pairs sequenced has not been disclosed. One conference attendee who spoke to the FTDNA staff was told that "the number of bp [base pairs] analysed will be at least 10 million, but could in some samples go up to 12 million".9 FTDNA claim that their test provides more coverage "than any Y-DNA test on the market". However, the test is clearly not quite so comprehensive as the Full Genomes test but it does have the virtue of being considerably cheaper which will make testing multiple people within a single subclade a feasible proposition. Confusingly FTDNA claim that the test will cover "nearly 25,000 known SNPs placing you deep on the haplotree". I can only think they've taken their figure of 25,000 known SNPs from the research into the Geno 2.0 chip and that they are seemingly unaware of the ISOGG SNP Compendium Index which, as discussed above, lists over 47,000 SNPs. If they are covering over 10 million SNPs then they will surely test most of the SNPs in the Compendium. Fortunately FTDNA have confirmed that they will make the raw data in the form of BAM files available to their customers so we will eventually be able to make comparisons.
Is next generation sequencing SNP testing for you?
Next generation sequencing is clearly becoming the gold standard for SNP testing. The Genographic Project have announced that they will be introducing a new test within the next seven to 12 months and I would imagine that their new test will use next generation sequencing. No doubt a rival new NGS test is in the works from BritainsDNA too.
The new next generation sequencing Y-SNP tests do have the potential in the long run to be genealogically relevant. There is supposedly a new SNP roughly every one and a half generations. In other words, if there's no SNP found in a son then there will more than likely be a SNP in the grandson. One day the SNPs will effectively allow us to draw complete trees for Y-lines within a genealogical a timeframe. As with any DNA test, a full Y-chromosome SNP test is only useful if you can compare your results with large numbers of other people so that we can work out the chronological order of the more recent SNPs and establish which ones are unique to specific lineages. With the Full Genomes test people in the common haplogroups are reportedly getting between 25 and 40 private SNPs. I imagine the numbers will be pretty similar for the Big Y test from FTDNA.
The numbers of people taking these tests are still relatively small – probably in the hundreds rather than the thousands. Even at $495 a time large-scale testing within a surname project is not going to be a practical proposition. However, if low-hanging SNPs are found that are specific to particular surname lineages then, if these SNPs are added to the a la carte menu, people could test for these single SNPs at $39 a time. STR markers can be used in combination with SNPs to predict who will be positive for which SNP, but ideally you need to be tested to at least 67 markers to make a confident prediction.
The potential problem is that FTDNA are only likely to want to invest money developing single SNPs if there are a reasonable number of people who would be willing to pay for such a test. The more recent the SNPs the fewer people will share them and consequently there will be less chance of the custom SNP tests being developed. FTDNA also only currently have the capacity to offer an additional 2000 custom SNPs. However, they have indicated that they will be re-introducing some form of static deep clade test, probably in the first quarter of 2014, which will be at a much more affordable price. SNPs found in the first phase of the Big Y testing will be candidates for inclusion on these chips so there is possibly some incentive for selected representatives of the various subclades to be tested to ensure that the key new SNPs are included in these tests. Full Genomes have also indicated that they hope to offer single SNPs, and a more economically priced SNP test, but it remains to be seen what they will offer. At the current prices NGS full Y testing is really only for people who wish to contribute to our scientific knowledge and to help delineate all the branches on the Y-tree. No doubt the costs will come down in time. Perhaps in five years or ten years the full Y test will be the norm but we're not there yet.
If you are interested in SNP testing the choice of testing company will be down to the individual and will depend on your budget and your objectives. The ISOGG SNP Testing Chart in the ISOGG Wiki provides a comparison between all the testing companies and is updated as new information becomes available. There will inevitably be new products coming onto the market in the next year with each new test appearing to have a slight advantage over its competitors until the next big thing comes along. I strongly recommend that you join the relevant haplogroup project. The group administrators are all very knowledgeable and will be able to offer good advice. There is a list of Y-DNA haplogroups in the ISOGG Wiki. Most of the projects have associated mailing lists which are currently buzzing with activity, and these will often be the best source of information and commentary.
The SNP tsunami
The large number of SNPs that will be generated in what has been described as the SNP tsunami will represent a significant challenge for the haplogroup project admins and the citizen scientists who are trying to interpret these data. The new 2014 SNP tree from the Genographic Project, with a mere 6000 or so SNPs, will be something of an irrelevance, and by the time it is published it will be massively out of date, though it will at least lay the foundations for a new nomenclature. The volunteers who maintain the ISOGG tree will have their work cut out to keep up with the new developments. One of the team, David Dowell, has already commented: "It is clear that our processes need to be reorganized and streamlined if we are going to be able to continue to serve the genetic genealogy community and researchers in related disciplines in a timely basis."10
It seems likely that the current confusion will prevail for several months. As one poster on the U106 list has commented, the now infamous quote by Donald Rumsfeld is a very good summary of the current SNP situation:
2. Moore LT, McEvoy B, Cape E et al. A Y-chromosome signature of hegemony in Gaelic Ireland. American Journal of Human Genetics 2006 78(2): 334–338. Note, however, that this study only used 59 low-resolution STR haplotypes, and many people disagree with the conclusions, both in age and origins.
4. Estes R. 2013 Family Tree DNA Conference Day 2. DNAeXplained blog, 12 November 2013.
5. Wang C-C, Li H. Discovery of phylogenetic relevant Y-chromosome variants in 1000 Genomes Project data. ArXiv preprint server. Submitted 24 October 2013.
6. Elhaik E, Greenspan E, Staats S et al. The GenoChip: a new tool for genetic anthropology. Genome Biology and Evolution 2013; 5(5): 1021-31.
7. See the thread entitled Full Y chromosome sequencing: Phase III Pilot on the Anthrogenica Forum.
8. Magoon G. Message posted in the R1b-U06 mailing list, 11 November 2013.
9. See the comment thread in the private ISOGG Facebook group at https://www.facebook.com/groups/isogg/permalink/10152015234637922/.
10. Dowell D. ISOGG group gears up for SNP tsunami. Dr D Digs Up Ancestors blog, 13 November 2013.
11. For the background to the quote see the entry for Donald Rumsfeld at Wikiquote: https://en.wikiquote.org/wiki/Donald_Rumsfeld.
© 2013 Debbie Kennett
The launch of the new Big Y test from Family Tree DNA has brought to light the difficulties in comparing the offerings of the different testing companies. We have a chart in the ISOGG Wiki which compares the various Y-SNP tests on the market but it is clear that we are not always comparing apples with apples. One of the major difficulties relates to the claims by the companies about the number of Y-SNPs on their chip. A SNP is a change or a mutation in the DNA alphabet at a single position on the Y-chromosome (eg, a C changing to a T). There are around 59 million base pairs in the Y-chromosome. However, surprising as it might be in this genomic era, there are still large sections of the Y-chromosome that have not yet been explored. Build 37, the current build of the human genome reference sequence, has only mapped out the positions of around 25 million base pairs – less than half of the Y-chromosome.1 The discovery of new SNPs is therefore limited to the parts of the Y-chromosome that can be sequenced using current technology. These areas represent just over 40% of the Y-chromosome. In theory, therefore, a SNP could be found on any one of the 25 million bases that can be sequenced.
The exact number of SNPs on the Y-chromosome is not yet known. There is no central resource listing all known SNPs because there is fierce competition and the companies are keen to keep knowledge of the SNPs that they have discovered from their competitors for as long as possible. We therefore have some SNPs that are in the public domain, some unpublished SNPs that are known only to Family Tree DNA/the Genographic Project, some SNPs that are known only to Full Genomes Corporation and some SNPs that are known only to BritainsDNA. To make matters worse all three companies use different naming systems for their SNPs. Full Genomes SNPs are prefixed by the letters FG, and BritainsDNA SNPs bear the prefix S. I understand from the reports from the Family Tree DNA 2013 Conference that the Genographic Project will be publishing a paper some time in the New Year with the new 2014 Y-SNP tree. It therefore remains to be seen what naming system they will use for their SNPs. There will undoubtedly be considerable overlap in the SNPs offered by the different testing companies but until they release their data or until we have comparative results available we will not be able to work out which SNPs are equivalent (synonymous) – in other words which SNPs occur at the same position but which have been given different names by different companies. For example U106 and S21 are alternative names for a single SNP which defines one of the major branches of the R1b haplogroup.
The problem is well illustrated by the recent developments in R1b-M222, a subclade which predominates in Ireland and Scotland, and is seen in many of the surnames that are associated with the clans reputed to descend from the semi-legendary Irish historical figure Niall of the Nine Hostages.2 According to the early results from the Chromo 2 testing at BritainsDNA 27 new SNPs have been discovered downstream of M222.3 Yet at the Family Tree DNA Conference last weekend Miguel Vilar from the Genographic Project advised that they have identified 22 SNPS below M222. Do any of the Geno 2.0 SNPs correspond with the SNPs found by BritainsDNA? The answer is we simply do not know. Neither company releases the full raw data that will allow the participant to determine the genome reference position of the SNPs for which he has tested positive so the results from the two companies cannot be compared. Few results are in any case available at present from the Chromo 2 testing. The Genographic Project are presenting the results of their Gathering the Mayo Genes Project at a public event in Castlebar on Sunday so it may be that further information will be forthcoming then.
So where can we find out about SNPs and their position on the Y-DNA haplotree? By far the most important source is the Y-SNP tree maintained by ISOGG - the International Society of Genetic Genealogy. The tree was launched on 10th April 2006. By the end of the year there were 436 SNPs on the tree. By September 2013 there were 3610 SNPs on the ISOGG tree. According to Roberta Estes' report from Day 2 of the FTDNA conference the new 2014 Y-SNP tree, which will be published by the Genographic Project in 2014, will have 6200 SNPS and 1000 branches.4 This effectively doubles the size of the existing tree and will represent a significant workload for the team of volunteer project administrators who maintain the tree.
However, the ISOGG tree only documents the SNPs whose precise location on the Y-haplotree is known – in other words SNPs that define particular branches of the human family tree on the Y-line. There are thousands more known SNPs. For these SNPs we know that a mutation has been found on the Y-chromosome at the position in question but we do not know if it has any phylogenetic significance, that is, if these SNPs define branches on the Y-tree or if they are unique to the individual.
ISOGG have a SNP index that lists not just the SNPs that are on the haplotree but also those which "are or have been under active investigation and consideration for addition to the Y Haplotree." ISOGG further state that the "SNPs listed here are less than 10% of the currently known SNPs". To supplement the SNP index ISOGG member David Reynolds maintains the ISOGG SNP Compendium Spreadsheet. This was last updated about a month ago and contains a list of 47,680 SNPs which have yet to be added to the ISOGG tree and the SNP index. A small minority of these SNPs are alternative names for previously known SNPs that are already on the tree (for example, some S series SNPs correspond with some of the Z series SNPs that have already been placed on the tree). Most of the rest are SNPs whose position on the Y-chromosome is known but where we do not as yet know where they belong on the Y-tree. David Reynolds reported back in September that he had about another 5000 SNPs to process. He is "curating and combining duplicates" as he goes along so it is a time-consuming process.
There are no doubt many more SNPs that are being published in scientific papers and I don't know if anyone in the genetic genealogy community is currently keeping track of these. In one recent paper uploaded to the ArXiv preprint server two Chinese researchers discovered 25,000 new phylogenetically relevant SNPs.5
Let's now have a look at the offerings of the various testing companies in the light of these numbers. I'm discussing the companies in chronological order based on the dates when their tests were launched. Some companies offer chip-based SNP tests. These tests can only test for previously known SNPs, but the companies can customise the chips to include their own proprietary SNPs for investigation. The new gold standard tests are those which use next-generation sequencing technology. These have the potential to discover thousands of new SNPs.
The Geno 2.0 test from the Genographic Project
The Geno 2.0 test from the Genographic Project was launched in July 2012 and was the first chip test to come on the market with a comprehensive panel of Y-SNPs. The Genographic Consortium published a paper earlier this year with all the technical details of their new GenoChip.6 The supplementary data tell us that the Genographic Project started with "a raw SNP candidate database of approximately 27,500 SNPs" though some of these were duplicates. The original target was to produce a chip with 15,000 SNPs but according to the paper the chip includes around 12,000 SNPs. Customers can download a CSV file with a list of the SNPs. There were 12,059 SNPs in the most recent file that I downloaded for one of my project members. The Genographic Project do not currently provide the genome reference positions of the SNPs on their chip, and it seems likely that this information is being withheld pending publication of the 2014 tree.
The Chromo 2 test from BritainsDNA/ScotlandsDNA
The Chromo 2 test from BritainsDNA/ScotlandsDNA was launched in June 2013. It uses a customised Illumina chip which is advertised as "covering over 15,000 Y chromosome markers, carefully selected to be most informative, and as free from duplication as possible". Only a limited number of results have been released from this test so far, but a flood of results is expected in the next couple of weeks. Customers receive an Excel spreadsheet with a list of all the markers that have been tested. In the one spreadsheet that I've seen there was a list of 14,184 SNPs. Of these, 8,682 SNPs had the S prefix. On the current ISOGG 2013 Y-SNP index the S series SNPs stop at S530. In the list of SNPs that I saw there were 8385 S series SNPs with numbers higher than S530. Many of these SNPs will probably define new branches on the Y-tree but many more could simply be alternative names for currently known SNPs. We do know that the BritainsDNA chip includes SNPs found in the Genomes of the Netherlands Project, and also many SNPs that are likely to be informative for people of British descent. However, BritainsDNA, in common with the Genographic Project, do not publish the genome reference positions of their SNPs. Unless they provide ISOGG with the positions of their SNPs we will have no way of knowing where they fit on the tree and which of their SNPs correspond with those identified by other testing companies.
Full Genomes
Full Genomes is a new start-up company which made a quiet entry onto the market some time towards the end of 2012. They only began advertising their services publicly towards the end of March 2013.7 They currently offer the most comprehensive Y-DNA test on the market covering about 20 to 25 million base pairs representing around 42% of the Y-chromosome. Full Genomes claim to cover 47,000 of the known SNPs on the ISOGG tree and in the ISOGG SNP Compendium. This is after removing "ambiguous results, and synonyms from consideration".8 Around 14 million of the SNPs are reported to be within mappable regions. However, their test is also uncovering many new private SNPs which have not as yet been made public, and the number of new SNPs discovered can be expected to rise as more and more people get tested. At present each testee in one of the common haplogroups can probably expect to find between 25 and 40 private high-quality SNPs. Full Genomes make the raw data available in a BAM file so that customers will have access to the genome reference numbers and can check the ISOGG tree for alternative SNP names as and when new SNPs are placed on the tree.
The Big Y test from Family TreeDNA
The new Big Y test from Family Tree DNA was launched at the weekend at Family Tree DNA's Conference. I've provided preliminary details in a previous blog post. As this is a new test, no results are yet available, and proper comparisons with the other available tests cannot be done. The FTDNA FAQs tell us that the test covers "at least 10 million base-pairs of reliably mapped positions of non-recombining Y-Chromosome", though the exact number of base pairs sequenced has not been disclosed. One conference attendee who spoke to the FTDNA staff was told that "the number of bp [base pairs] analysed will be at least 10 million, but could in some samples go up to 12 million".9 FTDNA claim that their test provides more coverage "than any Y-DNA test on the market". However, the test is clearly not quite so comprehensive as the Full Genomes test but it does have the virtue of being considerably cheaper which will make testing multiple people within a single subclade a feasible proposition. Confusingly FTDNA claim that the test will cover "nearly 25,000 known SNPs placing you deep on the haplotree". I can only think they've taken their figure of 25,000 known SNPs from the research into the Geno 2.0 chip and that they are seemingly unaware of the ISOGG SNP Compendium Index which, as discussed above, lists over 47,000 SNPs. If they are covering over 10 million SNPs then they will surely test most of the SNPs in the Compendium. Fortunately FTDNA have confirmed that they will make the raw data in the form of BAM files available to their customers so we will eventually be able to make comparisons.
Is next generation sequencing SNP testing for you?
Next generation sequencing is clearly becoming the gold standard for SNP testing. The Genographic Project have announced that they will be introducing a new test within the next seven to 12 months and I would imagine that their new test will use next generation sequencing. No doubt a rival new NGS test is in the works from BritainsDNA too.
The new next generation sequencing Y-SNP tests do have the potential in the long run to be genealogically relevant. There is supposedly a new SNP roughly every one and a half generations. In other words, if there's no SNP found in a son then there will more than likely be a SNP in the grandson. One day the SNPs will effectively allow us to draw complete trees for Y-lines within a genealogical a timeframe. As with any DNA test, a full Y-chromosome SNP test is only useful if you can compare your results with large numbers of other people so that we can work out the chronological order of the more recent SNPs and establish which ones are unique to specific lineages. With the Full Genomes test people in the common haplogroups are reportedly getting between 25 and 40 private SNPs. I imagine the numbers will be pretty similar for the Big Y test from FTDNA.
The numbers of people taking these tests are still relatively small – probably in the hundreds rather than the thousands. Even at $495 a time large-scale testing within a surname project is not going to be a practical proposition. However, if low-hanging SNPs are found that are specific to particular surname lineages then, if these SNPs are added to the a la carte menu, people could test for these single SNPs at $39 a time. STR markers can be used in combination with SNPs to predict who will be positive for which SNP, but ideally you need to be tested to at least 67 markers to make a confident prediction.
The potential problem is that FTDNA are only likely to want to invest money developing single SNPs if there are a reasonable number of people who would be willing to pay for such a test. The more recent the SNPs the fewer people will share them and consequently there will be less chance of the custom SNP tests being developed. FTDNA also only currently have the capacity to offer an additional 2000 custom SNPs. However, they have indicated that they will be re-introducing some form of static deep clade test, probably in the first quarter of 2014, which will be at a much more affordable price. SNPs found in the first phase of the Big Y testing will be candidates for inclusion on these chips so there is possibly some incentive for selected representatives of the various subclades to be tested to ensure that the key new SNPs are included in these tests. Full Genomes have also indicated that they hope to offer single SNPs, and a more economically priced SNP test, but it remains to be seen what they will offer. At the current prices NGS full Y testing is really only for people who wish to contribute to our scientific knowledge and to help delineate all the branches on the Y-tree. No doubt the costs will come down in time. Perhaps in five years or ten years the full Y test will be the norm but we're not there yet.
If you are interested in SNP testing the choice of testing company will be down to the individual and will depend on your budget and your objectives. The ISOGG SNP Testing Chart in the ISOGG Wiki provides a comparison between all the testing companies and is updated as new information becomes available. There will inevitably be new products coming onto the market in the next year with each new test appearing to have a slight advantage over its competitors until the next big thing comes along. I strongly recommend that you join the relevant haplogroup project. The group administrators are all very knowledgeable and will be able to offer good advice. There is a list of Y-DNA haplogroups in the ISOGG Wiki. Most of the projects have associated mailing lists which are currently buzzing with activity, and these will often be the best source of information and commentary.
The SNP tsunami
The large number of SNPs that will be generated in what has been described as the SNP tsunami will represent a significant challenge for the haplogroup project admins and the citizen scientists who are trying to interpret these data. The new 2014 SNP tree from the Genographic Project, with a mere 6000 or so SNPs, will be something of an irrelevance, and by the time it is published it will be massively out of date, though it will at least lay the foundations for a new nomenclature. The volunteers who maintain the ISOGG tree will have their work cut out to keep up with the new developments. One of the team, David Dowell, has already commented: "It is clear that our processes need to be reorganized and streamlined if we are going to be able to continue to serve the genetic genealogy community and researchers in related disciplines in a timely basis."10
It seems likely that the current confusion will prevail for several months. As one poster on the U106 list has commented, the now infamous quote by Donald Rumsfeld is a very good summary of the current SNP situation:
"There are known knowns; there are things we know that we know.There will be confusion, there will be chaos and there will be competition in the coming months, but from this confusion, chaos and competition many important new discoveries will emerge. I predict that as far as Y-chromosome research is concerned 2014 will be the Year of the SNP.
There are known unknowns; that is to say, there are things that we now know we don't know.
But there are also unknown unknowns – there are things we do not know we don't know."11
Updates
Vince Tilroe advises in a comment on Roberta Estes' blog that the 1.5 Y-SNPs per generation was based on the hypothetical presumption that "the entire 60 megabases [60 million bases] of the Y-chromosome could be sequenced. This is not the case by any means, and consequently a more realistic expectation should be closer to 1 Y-SNP per every 4 to 6 generations". Preliminary results from the Full Genomes testing suggest that there is around one Y-SNP every 3 to 4 generations.
Jim Wilson, the Chief Scientist from BritainsDNA, has provided a list of equivalent SNP names for some of the SNPs on the Chromo 2 chip. He has also advised that in due course he will be sharing the genome co-ordinates to allow comparisons with comprehensive Y-chromosome sequences. See CeCe Moore's blog post A list of alternate names for the Y-SNPs from BritainsDNA's Chromo 2 test for further details.
See also
- A simplified Y-tree and a common standard for Y-DNA haplogroup and SNP nomenclature
- The Y-chromosome sequence interpretation service from YFull
- YSEQ.net - a new company offering a single SNP testing service
References and notes
1. For further information see the ISOGG Wiki article on the Y-chromosome:
www.isogg.org/wiki/Y_chromosomeVince Tilroe advises in a comment on Roberta Estes' blog that the 1.5 Y-SNPs per generation was based on the hypothetical presumption that "the entire 60 megabases [60 million bases] of the Y-chromosome could be sequenced. This is not the case by any means, and consequently a more realistic expectation should be closer to 1 Y-SNP per every 4 to 6 generations". Preliminary results from the Full Genomes testing suggest that there is around one Y-SNP every 3 to 4 generations.
Jim Wilson, the Chief Scientist from BritainsDNA, has provided a list of equivalent SNP names for some of the SNPs on the Chromo 2 chip. He has also advised that in due course he will be sharing the genome co-ordinates to allow comparisons with comprehensive Y-chromosome sequences. See CeCe Moore's blog post A list of alternate names for the Y-SNPs from BritainsDNA's Chromo 2 test for further details.
See also
- A simplified Y-tree and a common standard for Y-DNA haplogroup and SNP nomenclature
- The Y-chromosome sequence interpretation service from YFull
- YSEQ.net - a new company offering a single SNP testing service
References and notes
2. Moore LT, McEvoy B, Cape E et al. A Y-chromosome signature of hegemony in Gaelic Ireland. American Journal of Human Genetics 2006 78(2): 334–338. Note, however, that this study only used 59 low-resolution STR haplotypes, and many people disagree with the conclusions, both in age and origins.
4. Estes R. 2013 Family Tree DNA Conference Day 2. DNAeXplained blog, 12 November 2013.
5. Wang C-C, Li H. Discovery of phylogenetic relevant Y-chromosome variants in 1000 Genomes Project data. ArXiv preprint server. Submitted 24 October 2013.
6. Elhaik E, Greenspan E, Staats S et al. The GenoChip: a new tool for genetic anthropology. Genome Biology and Evolution 2013; 5(5): 1021-31.
7. See the thread entitled Full Y chromosome sequencing: Phase III Pilot on the Anthrogenica Forum.
8. Magoon G. Message posted in the R1b-U06 mailing list, 11 November 2013.
9. See the comment thread in the private ISOGG Facebook group at https://www.facebook.com/groups/isogg/permalink/10152015234637922/.
10. Dowell D. ISOGG group gears up for SNP tsunami. Dr D Digs Up Ancestors blog, 13 November 2013.
11. For the background to the quote see the entry for Donald Rumsfeld at Wikiquote: https://en.wikiquote.org/wiki/Donald_Rumsfeld.
© 2013 Debbie Kennett
Friday, 8 November 2013
A simplified Y-tree and a common standard for Y-DNA haplogroup and SNP nomenclature
This article is for experienced genetic genealogists and requires an understanding of SNPs and haplogroups.
A very useful online resource for Y-chromosome researchers in the form of a simplified version of the Y-chromosome SNP tree has come online this week. The new pared-down version of the Y-tree is introduced in a paper by Mannis Van Oven, Anneleen Van Geystelen, Manfred Kayser, Ronny Decorte and Maarten H D Larmuseau entitled Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome. The paper has been accepted for publication in the scientific journal Human Mutation but has yet to go through the full editorial process. Mannis Van Oven's name is already well known to mitochondrial DNA researchers because he maintains the Phylotree website which hosts the definitive mtDNA tree. The simplified Y-tree is conveniently being maintained on the same website and can be found at www.phylotree.org/Y
The new Phylotree version of the Y-tree will serve as a complement to the full Y-SNP tree which is maintained by ISOGG (the International Society of Genetic Genealogy). The Y-tree is now a very complicated structure and is set to become even more detailed in the coming months with the flood of new Y-SNPs that are being discovered from academic projects and through commercial testing with Full Genomes Corp, the Genographic Project (Geno 2.0) and BritainsDNA/ScotlandsDNA (Chromo 2). There will always be a need to have the fine detail of the full high-resolution tree, especially when one is trying to drill right down to the low-hanging branches. However, sometimes it's useful to get an overview of the structure of the tree as a whole without the complication of all the addition sub-branches, twigs and twiglets, and this is something that the new Phylotree Y-tree does very nicely.
I'm very pleased to see that the paper acknowledges the contributions made by the many "independent researchers" within the genetic genealogy community. The resources that the authors used to compile their reference phylogeny included "a large number of websites maintained by independent researchers", all of whom are named in the acknowledgements.
An important innovation in this paper is a very welcome attempt to introduce a much-needed common standard for Y-SNP and Y-haplogroup nomenclature. As the authors explain "Due to multiple independent discovery events, a considerable number of Y-SNPs are known by multiple names". This diversity of names is a source of considerable confusion for both academic researchers and genetic genealogists. For example, haplogroup R1b1a2, the predominant European haplogroup, has two major branches. The markers that define these branches are known as P312 and U106 at the Genographic Project and Family Tree DNA but have the alternative names S116 and S21 at BritainsDNA/ScotlandsDNA. All four of these marker names appear in the scientific literature but the scientists often don't provide the alternative names. ISOGG provides a Y-SNP index which allows the researcher to check for other SNP names but not every researcher will know of this resource. The solution proposed by Van Oven et al is to decide on "one default name depending on which of the aliases is most frequently used in the literature", and these are the names which appear in the Phylotree Y-tree, though the alternative names are given in the accompanying spreadsheet.
It does of course remain to be seen if the scientists and testing companies will adopt the recommended nomenclature for the 417 SNPs included on the simplified Y-tree, but we can certainly hope that they will do so. Most of the names are already in use at Family Tree DNA and within the various FTDNA haplogroup projects. The one SNP name on the tree which will probably cause the most difficulties is R-M529, which is currently better known as L21 and sometimes S145. The name M529 seems to have been chosen because it was cited in an academic paper published in 2011 by Myres et al.1 However, the name L21 is now so ingrained in the collective genetic genealogy consciousness that I suspect that the proposed new name will probably not catch on. BritainsDNA have always used their own proprietary S series naming system but I hope that they will at least consider adopting the new nomenclature for the core SNPs included on the Phylotree Y-tree so that we can all speak a common language.
In the coming months we can expect an explosion of new Y-SNPs now that the first results have started to come in for the Chromo 2 test from BritainsDNA/Scotlands DNA and from the full Y-chromosome sequencing tests at Full Genomes. However, the nomenclature will continue to be a big problem as each company tries to maintain a competitive advantage. Full Genomes have already indicated that they will be offering custom single SNPs for sale to compete with FTDNA. We can probably expect to see a flood of FG SNPs being made available in the next few months. The positions of the new FG SNPs on the tree are not yet known so no other companies will be able to offer these new SNPs. So far I've only seen one data file from the BritainsDNA Chromo 2 test. This file contains over 14,000 Y-SNPs, of which around 8000 or more are proprietary S series SNPs, only a tiny percentage of which are listed in the ISOGG Y-SNP index. It may be that many of the BritainsDNA SNPs will turn out to be equivalent to the SNPs that are already on the ISOGG tree or included on the Geno 2.0 chip, and these SNPs will almost certainly be included in the Full Genomes test. However, neither BritainsDNA nor the Genographic Project provide the genome reference positions for the SNPs on their chips so there is currently no way of knowing which S series SNPs are already known about and which ones are new. Fortunately there are many pioneers with large pockets in the genetic genealogy community who can afford to have their DNA tested at Full Genomes, BritainsDNA and the Genographic Project. With data available for comparison from two or more companies it should then be possible for the volunteer haplogroup project administrators to compare the results and establish the positions of any newly discovered SNPs on the Y-tree.
The other unknown is whether or not Family Tree DNA will be responding to the competition from Full Genomes and BritainsDNA. Their group administrators' conference is taking place this weekend in Houston, Texas, and the conference schedule has now been made available online. Miguel Vilar from the Genographic Project will be providing a Geno 2.0 update and talking about the Y-2014 tree, and Michael Hammer will be talking about the "implications of the 2014 Y-tree". FTDNA usually make a big announcement at the conference and the speculation is that they will perhaps be announcing the launch of a new Geno chip and/or the introduction of a full Y-chromosome test. Spencer Wells has already indicated that a new Geno chip might be on the way as early as 2014.2
Unfortunately, all three currently available Y-SNP tests are very expensive and well beyond the means of the average genetic genealogist. I'm rather hoping that at some point one of the companies will introduce a cheaper Y-SNP test that will allow a customer to have a refined haplogroup designation sufficient to rule out false positive matches but without breaking the bank.
For the moment I would advise anyone considering ordering a Y-SNP test to wait and see what the results are from the tests taken by the early adopters. If you want to join the pioneers and experiment with one of the new SNP tests then you can see a chart comparing the services offered by the main testing companies in the ISOGG Wiki.
With so many exciting new developments I wonder what the Y-chromosome tree will look like in 2014. The ISOGG SNP Index lists all the SNPs that are either on the Y-tree or which are under investigation, but these SNPs represent less than 10% of the known Y-SNPs. David Reynolds maintains the ISOGG Y-SNP Compendium Spreadsheet which currently contains almost 40,000 additional Y-SNPs, and has indicated that he still has over 12,000 SNPs to add, time permitting. The SNPs in this spreadsheet have not all been validated and many are not available for testing at any commercial company. It may well be that the tree will increase in size ten-fold or more in the next twelve months which will represent a significant challenge for the volunteer ISOGG Y-SNP team who maintain the tree in their own free time.
Chris Tyler-Smith cautioned us in February at a special ISOGG presentation at the Sanger Institute in Cambridge that the Y-tree nomenclature system was set to break down in 2013, and indeed that already seems to be the case. He raised the possibility of using an ancestral reference sequence for the Y-chromosome along the lines of the RSRS (Reconstructed Sapiens Reference Sequence) introduced for mitochondrial DNA in 2012.3 I wonder if that is something that we will see implemented in 2014.
Whatever the future has in store it is certainly a very exciting time for Y-chromosome researchers and, as Chris Tyler-Smith commented in February, there will be "more opportunities than ever for computer-literate citizen scientists".
References
1. Myres NM, Rootsi S, Lin AA et al. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. European Journal of Human Genetics 2011; 19 (1); 95-101.
2. Petrone J. National Geographic considering move to new SNP chip for Genographic Project. GenomeWeb, 13 August 2013.
3. Behar DM, Van Oven M, Rosset S et al. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. American Journal of Human Genetics 2012; 90 (5): 936.
Resources
- The ISOGG Y-DNA SNP testing comparison chart
- A list of Y-DNA haplogroup projects
- BritainsDNA haplogroup nicknames
See also
- A confusion of SNPs
© 2013 Debbie Kennett
A very useful online resource for Y-chromosome researchers in the form of a simplified version of the Y-chromosome SNP tree has come online this week. The new pared-down version of the Y-tree is introduced in a paper by Mannis Van Oven, Anneleen Van Geystelen, Manfred Kayser, Ronny Decorte and Maarten H D Larmuseau entitled Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome. The paper has been accepted for publication in the scientific journal Human Mutation but has yet to go through the full editorial process. Mannis Van Oven's name is already well known to mitochondrial DNA researchers because he maintains the Phylotree website which hosts the definitive mtDNA tree. The simplified Y-tree is conveniently being maintained on the same website and can be found at www.phylotree.org/Y
The new Phylotree version of the Y-tree will serve as a complement to the full Y-SNP tree which is maintained by ISOGG (the International Society of Genetic Genealogy). The Y-tree is now a very complicated structure and is set to become even more detailed in the coming months with the flood of new Y-SNPs that are being discovered from academic projects and through commercial testing with Full Genomes Corp, the Genographic Project (Geno 2.0) and BritainsDNA/ScotlandsDNA (Chromo 2). There will always be a need to have the fine detail of the full high-resolution tree, especially when one is trying to drill right down to the low-hanging branches. However, sometimes it's useful to get an overview of the structure of the tree as a whole without the complication of all the addition sub-branches, twigs and twiglets, and this is something that the new Phylotree Y-tree does very nicely.
I'm very pleased to see that the paper acknowledges the contributions made by the many "independent researchers" within the genetic genealogy community. The resources that the authors used to compile their reference phylogeny included "a large number of websites maintained by independent researchers", all of whom are named in the acknowledgements.
An important innovation in this paper is a very welcome attempt to introduce a much-needed common standard for Y-SNP and Y-haplogroup nomenclature. As the authors explain "Due to multiple independent discovery events, a considerable number of Y-SNPs are known by multiple names". This diversity of names is a source of considerable confusion for both academic researchers and genetic genealogists. For example, haplogroup R1b1a2, the predominant European haplogroup, has two major branches. The markers that define these branches are known as P312 and U106 at the Genographic Project and Family Tree DNA but have the alternative names S116 and S21 at BritainsDNA/ScotlandsDNA. All four of these marker names appear in the scientific literature but the scientists often don't provide the alternative names. ISOGG provides a Y-SNP index which allows the researcher to check for other SNP names but not every researcher will know of this resource. The solution proposed by Van Oven et al is to decide on "one default name depending on which of the aliases is most frequently used in the literature", and these are the names which appear in the Phylotree Y-tree, though the alternative names are given in the accompanying spreadsheet.
It does of course remain to be seen if the scientists and testing companies will adopt the recommended nomenclature for the 417 SNPs included on the simplified Y-tree, but we can certainly hope that they will do so. Most of the names are already in use at Family Tree DNA and within the various FTDNA haplogroup projects. The one SNP name on the tree which will probably cause the most difficulties is R-M529, which is currently better known as L21 and sometimes S145. The name M529 seems to have been chosen because it was cited in an academic paper published in 2011 by Myres et al.1 However, the name L21 is now so ingrained in the collective genetic genealogy consciousness that I suspect that the proposed new name will probably not catch on. BritainsDNA have always used their own proprietary S series naming system but I hope that they will at least consider adopting the new nomenclature for the core SNPs included on the Phylotree Y-tree so that we can all speak a common language.
In the coming months we can expect an explosion of new Y-SNPs now that the first results have started to come in for the Chromo 2 test from BritainsDNA/Scotlands DNA and from the full Y-chromosome sequencing tests at Full Genomes. However, the nomenclature will continue to be a big problem as each company tries to maintain a competitive advantage. Full Genomes have already indicated that they will be offering custom single SNPs for sale to compete with FTDNA. We can probably expect to see a flood of FG SNPs being made available in the next few months. The positions of the new FG SNPs on the tree are not yet known so no other companies will be able to offer these new SNPs. So far I've only seen one data file from the BritainsDNA Chromo 2 test. This file contains over 14,000 Y-SNPs, of which around 8000 or more are proprietary S series SNPs, only a tiny percentage of which are listed in the ISOGG Y-SNP index. It may be that many of the BritainsDNA SNPs will turn out to be equivalent to the SNPs that are already on the ISOGG tree or included on the Geno 2.0 chip, and these SNPs will almost certainly be included in the Full Genomes test. However, neither BritainsDNA nor the Genographic Project provide the genome reference positions for the SNPs on their chips so there is currently no way of knowing which S series SNPs are already known about and which ones are new. Fortunately there are many pioneers with large pockets in the genetic genealogy community who can afford to have their DNA tested at Full Genomes, BritainsDNA and the Genographic Project. With data available for comparison from two or more companies it should then be possible for the volunteer haplogroup project administrators to compare the results and establish the positions of any newly discovered SNPs on the Y-tree.
The other unknown is whether or not Family Tree DNA will be responding to the competition from Full Genomes and BritainsDNA. Their group administrators' conference is taking place this weekend in Houston, Texas, and the conference schedule has now been made available online. Miguel Vilar from the Genographic Project will be providing a Geno 2.0 update and talking about the Y-2014 tree, and Michael Hammer will be talking about the "implications of the 2014 Y-tree". FTDNA usually make a big announcement at the conference and the speculation is that they will perhaps be announcing the launch of a new Geno chip and/or the introduction of a full Y-chromosome test. Spencer Wells has already indicated that a new Geno chip might be on the way as early as 2014.2
Unfortunately, all three currently available Y-SNP tests are very expensive and well beyond the means of the average genetic genealogist. I'm rather hoping that at some point one of the companies will introduce a cheaper Y-SNP test that will allow a customer to have a refined haplogroup designation sufficient to rule out false positive matches but without breaking the bank.
For the moment I would advise anyone considering ordering a Y-SNP test to wait and see what the results are from the tests taken by the early adopters. If you want to join the pioneers and experiment with one of the new SNP tests then you can see a chart comparing the services offered by the main testing companies in the ISOGG Wiki.
With so many exciting new developments I wonder what the Y-chromosome tree will look like in 2014. The ISOGG SNP Index lists all the SNPs that are either on the Y-tree or which are under investigation, but these SNPs represent less than 10% of the known Y-SNPs. David Reynolds maintains the ISOGG Y-SNP Compendium Spreadsheet which currently contains almost 40,000 additional Y-SNPs, and has indicated that he still has over 12,000 SNPs to add, time permitting. The SNPs in this spreadsheet have not all been validated and many are not available for testing at any commercial company. It may well be that the tree will increase in size ten-fold or more in the next twelve months which will represent a significant challenge for the volunteer ISOGG Y-SNP team who maintain the tree in their own free time.
Whatever the future has in store it is certainly a very exciting time for Y-chromosome researchers and, as Chris Tyler-Smith commented in February, there will be "more opportunities than ever for computer-literate citizen scientists".
References
1. Myres NM, Rootsi S, Lin AA et al. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. European Journal of Human Genetics 2011; 19 (1); 95-101.
2. Petrone J. National Geographic considering move to new SNP chip for Genographic Project. GenomeWeb, 13 August 2013.
3. Behar DM, Van Oven M, Rosset S et al. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. American Journal of Human Genetics 2012; 90 (5): 936.
Resources
- The ISOGG Y-DNA SNP testing comparison chart
- A list of Y-DNA haplogroup projects
- BritainsDNA haplogroup nicknames
See also
- A confusion of SNPs
© 2013 Debbie Kennett
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