[KerryOdair]

This is from Vadim Urasin co founder of YFull:

"We have registered ID YF10000 yesterday. A milestone. Thank you all for orders. By the way, in this batch we have added about a hundred samples from scientific papers of this year (later I will write references to papers). They have a lot of new SNPs. This is a main reason of delay with results."

This is a remarkable accomplishment in my mind which represents 10,000 samples in the Ytree database. This is a remarkable effort that represents citizen scientists, scientific studies and universities contributing this information in a public forum for everyone to see.

This I think brings to conclusion this thread and yes we can sequence the Y for all to see. Its been a great ride and it will continue with new data from current and ancient populations. A well done by everyone involved and thanks to SEQanswers that gave me a podium to discuss these issues.

[KerryOdair]

New test available for whole genome to general public from FullGenomes as a pilot project.

New from Justin Loe at FullGenomes

FGC has a new offering, offered as a pilot project, the long read whole genome, which has 10 Mb haplotype blocks. This is a dramatic improvement on the current short-read whole genome technology of 150 bp. Our offering is currently $2750 per sample.

https://www.fullgenomes.com/purchases/61/?

Our offering will also provide advanced ancestry information as well as significant improvements in the data for other applications. We can also refer you to appropriate teams for sophisticated health analysis (FGC does not provide health reports).

See (technology used)

http://www.10xgenomics.com/news/10x-genomics-new-chromium-system-enables-full-access-to-critical-molecular-and-cellular-information/

Features from 10xgenomics on full genome testing:

Solution Features
Complete genomic information from a single universal library
Call variants and resolve long-range information from a single library that is compatible with all Illumina sequencers
Multi-megabase phase blocks
Greater than 10 Mb haplotype blocks with phased SNVs, indels, and structural variants
Low DNA input
High quality libraries from 1 ng of genomic DNA
Turn-key analysis pipeline and visualization tools
Powerful algorithms and software for phasing, variant calling and structural variant analysis

[KerryOdair]

This is a very nice announcement and shows how far we have come in products available to the public.

PUBLIC RELEASE: 28-JAN-2016
Full GenomesTM Corporation collaborates with Novogene to offer low-cost whole genome ancestry test
Comprehensive GenomeGuide now available at $895

It will be in the range of 15x - 20x, since our results that is the range that gives good Y chromosome coverage. 20x is equivalent to Y Elite, in terms of the Callable Loci metric. So, its not fixed at specific number but we'll target it in that range as we get more data.

From other beta data:

Callable loci
20x: 13,888,138

Mapped Y coverage
20x: 22,818,005

The various Y Elite tests all average approx 14 million Callable Loci, however, the purpose here isn't to replace the Y Elite product, although ultimately, it is possible that a whole genome test will be no more expensive.
--
Justin Loe, M.S. Bioinformatics

NOVOGENE CORPORATION

SHARE PRINT E-MAIL
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 $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.

[KerryOdair]

Whole Genome Sequencing and Y Chromosome Sequencing

There has been an interesting discussion at Rootsweb about Whole Genome Sequencing and Y sequencing. The entire thread can be read there.

http://archiver.rootsweb.ancestry.com/th/index/GENEALOGY-DNA/2016-01

I have distilled some of the conversation into three points of information coming from Justin Loe Fullgenomes, Thomas Krahn and Tim Janzen. All three of these folks have been leaders in the area of testing over the years. We are coming eventually to a price point where Whole Genome Sequencing will probably replace sequencing the Y. The conversations below will make this more clear.

FullGenomes
Whole Genome Sequencing 2x $280
Whole Genome Sequencing 4x $395
Whole Genome Sequencing 10x $725
Whole Genome Sequencing 15x $895
Whole Genome Sequencing 20x $1,200
Whole Genome Sequencing 30x $1,650
Ultimate 100x Whole Genome $5,350
Y Elite 2.0 Sequencing $775


The largest cost factor for Y chromosome tests is not the sequencing, but the enrichment procedure. With enrichment the price will never drop far below $400, so you might as well sequence with sufficient coverage.

On the long run there is no future for BigY and FGCs Y tests since the WGS tests keep dropping in the price, but Y tests don't.

Thomas Krahn

Justin Loe from FullGenomes just posted the information below on another list:


Mapped Y coverage
30x 22,856,938
10x 22,025,697
4x 17,678,170
2x 13,755,442

Average Callable Loci
30x 14,558,001
10x 8,046,540
4x 1,050,996
2x 349,397

Y Elite 2.0:
14,000,000 Callable Loci approximately on average"

It thus appears that one needs to order at least the 30x whole genome sequence from FullGenomes to get the same number of callable Y chromosome loci as you can get from the Y Elite 2.0 test.

I would like to point out that even Full Genomes' Ultimate 100x Whole Genome is not the Holy Grail in whole genome sequencing because the data is unphased. What we are still waiting for is a company to generate phased whole genome sequencing data with an extremely high level of accuracy. I know that companies are working on this, but so far it has been challenging for the companies to do.

Sincerely,
Tim Janzen

[KerryOdair]

YTree 1200 Sardinian samples from Paolo Francalacci's article

This is some very exciting news that I was lucky enough to be involved in a small way. Many new samples from Paolo Francalacci's paper are being added to the YFull tree. More information and comments can be seen at the Yfull Facebook page. I would like to thank Paolo and Vadim for their efforts in this endeavor. I hope this is the beginning of academic data being brought into a public forum for all to see. Current Technical requirements: .FASTQ or .BAM file; coverage min 25X; read length min 100 bp for determining age estimations. Currently the YTree at YFull is at revision 3.17.

Vadim Urasin YFull Principle
17 hrs · Edited
"We started to add in our YTree 1200 Sardinian samples from Paolo Francalacci's article http://www.ncbi.nlm.nih.gov/pubmed/23908240 Kerry O'Dair thank you for help with first communication with Paolo. At first we will add 49 samples. They have ids 4399-4401, 4411, 4416, 4592-4632 (numbers of 3 samples indefined yet). Later we create special page with list of samples anf their subclades and we will change way to show them in our YTree and add reference to Paolo's article.
Unfortunately we can not add these samples in any group for reason of keeping privacy. Also we will not use these sample for age estimation because of their low quality. But you will see changes in our YTree. I think we will define many new subclades. Each batch we plan to add about 60 Sardinian samples.
We don't promise to add all of 1200 samples but we will add many of them."

Breakdown of subclades in study:

http://imgur.com/pKVZW93

[KerryOdair]

This was just published by YFull for SNP Lists

Full Y-SNP list now here - http://www.yfull.com/snp-list/
"Y" series - http://www.yfull.com/yf/snp-list/
"YP" series - http://www.yfull.com/yp/snp-list/

[KerryOdair]

Nice to see that this issue is beginning to be addressed for other researchers. www.yfull.com is now up to version 3.12 of their database.

Data bank launched for global access to ancient DNA

Medical and other researchers and science teachers around the world will be able to compare ancient DNA from humans from thousands of years ago with the genetics of modern day humans, thanks to a new world-first open access databank at the University of Adelaide's Australian Centre for Ancient DNA (ACAD).

The Online Ancient Genome Repository (OAGR) (https://www.oagr.org.au/) catalogues a significant collection of DNA data from ancient human skeletons and microbes found in their dental plaque. Both raw and analysed data, along with details about the individual humans such as where they were found and how the data was produced, will be freely accessible in a searchable format.

Full Article

http://www.sciencedaily.com/releases/2015/06/150617091631.htm

Facebook page

https://www.facebook.com/ACAD.Adelaide?fref=ts

Another interesting ancient DNA Facebook page

https://www.facebook.com/groups/249055928471080/

[KerryOdair]

Looking forward to seeing this paper when available. This is right in my wheel house dealing with the E haplogroup and the E-M35 subclade. This is what the sequencing of the Y is all about. Mr Cruciani is an author of this paper and has always been a leader in this kind of anaylsis. Really looking forward to reading this paper.

http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=fd6e251e-5448-4f9d-95cf-a1d3cef7476c&cKey=18c7dfd4-027e-49ae-90d3-b34103109e36&mKey=cabdedda-497c-457e-8481-34a866ab3681

[KerryOdair]

Full Text PDF and additional files available for viewing and downloading. We are progressing along nicely with research since this thread was first started. Thanks to this forum I believe we have received a much wider audience.

Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample

http://www.biomedcentral.com/1756-0500/8/174/abstract

Background Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. Methods DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. Results From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. Conclusions The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.

[KerryOdair]

Here is an exchange with Yfull people on samples in their database on Facebook.

What is the total number of samples in the database today? This number would include all sources of sequenced data FullGenomes, FTDNA, 1000 Genomes Etc. Are there other sources besides the three I have named?

Vadim Urasin about 3300 samples. Almost all samples are from those 3 sources. Several samples are from scientific articles also. Version 3.9 of experimental tree to be released soon.

Also some stats from FullGenomes Folks

Here's our latest progress. Done by a team of 3 people.

Our latest numbers:

1. Total SNP discovery: 35,000 SNPs
2. Total FGC SNPs listed or in investigation status in ISOGG: 630
3. Total R1b SNPs from FGC in ISOGG: 133
4. Total FGC SNPs in YSEQ: 2,803 (as of April 14)
5. Total kits sequenced or analyzed: approximately 1,000 (10 mb (Big Y) or 14 mb (FGC/BGI)

The progress in the last 12 months has been amazing. A great deal of this effort is coming from the citizen scientists who are not waiting for the big companies to take some action to interpret the data.

[KerryOdair]

Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data

Two important advances: 1) the accumulation of BigY and FGC test data, and 2) the publication of Y-chromosome sequences for three ancient samples (Anzick-1, Ust-Ishim, and K14), have made it possible to estimate the average rate of basesubstitutions (SNPs). The authors of this study have developed a new method of selecting true mutations in modern and ancient samples, and have defined with high accuracy the rate constant of SNP mutations: 0.82 · 10-9 per year per bp (95% CI: (0.70 - 0.94) · 10-9).


Link to paper:

http://rjgg.molgen.org/index.php/RJGGRE/article/view/151/175

[KerryOdair]

This is information released by Yfull with version 3.4 of their Ytree which has age estimations for subclades and TMRCA. These will be refined over time with new samples. My particular results certainly are in line with previous estimations of time made independently by myself and others. This really is a significant step forward in dating the Y Chromosome with so many samples. Many thanks to the people at YFull. Below their statement on snp dating.


Vadim Urasin YFull.com: Y-Chr Sequence Interpretation Service


In the version 3.4 of Y-Tree we plan to show an estimation of age for all subclades with at least one Big Y or Y Elite. The algorythm of estimation by SNP count we will explain later in an article written by Adamov, Vladimir Gurianov, Sergey Karzhavin, Vadim Urasin We have checked our estimation by information of common ancestors our clients. For 12 of 14 subclades estimated age is inside 95% confidence interval. But estimated age of I-YP1012 and I-A379 is not. In the chart you can see all 14 subclades with known ancestors. For all subclades in the Y-Tree a confidence interval depends from number of samples. For subclades with 1 sample a bounds of 95% confidence interval of age estimation are -48.8% +61.6% in the average, for subclades with 2 samples a bounds of 95% confidence interval are -43.3% +50.1% in the average, for 3 samples: -34.6% +37,3%, for 4 samples: -28,9% +32,2%. More samples - better estimation

[KerryOdair]

New open source paper with supplemental files on:

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Abstract

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

http://mbe.oxfordjournals.org/content/early/2014/12/13/molbev.msu327.full

[KerryOdair]

Statistics for version 2.31 of Y-Tree is adding 321 SNPs, 22 subclades by haplogroups:

https://www.yfull.com

A1a: 1 SNP
B: 2 SNPs
E: 1 SNP, 1 subclade
H: 17 SNPs
I1: 21 SNPs, 2 subclades
I2: 51 SNPs, 1 subclade
J2: 38 SNPs
T: 96 SNPs, 6 subclades
N: 3 SNPs
R1a: 40 SNPs, 7 subclades
R1b: 50 SNPs, 5 subclades
others: 1 SNP

[KerryOdair]

This certainly needs to be accomplished soon and adopted by both commercial, academic and private groups. These groups have tried to force their designations on other groups to the confusion of all.


Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era

H.D. Larmuseau Maartenemail, Van Geystelen Anneleen, Kayser Manfred, van Oven Mannis, Decorte Ronny
Received: July 30, 2014; Received in revised form: November 7, 2014; Accepted: November 9, 2014; Published Online: November 14, 2014
DOI: http://dx.doi.org/10.1016/j.fsigen.2014.11.012
Publication stage: In Press Accepted Manuscript
Abstract
Full Text
References
Highlights
•An overview of four defined categories of currently used Y-chromosomal phylogenies.
•A reduced consensus tree is the most appropriate reference resource for forensics.
•Initiatives to reach an international consensus phylogeny are highly recommended.
Abstract
Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended.

http://www.fsigenetics.com/article/S1872-4973(14)00252-X/fulltext