Whole Genome Sequencing – Next Step?

The first human genome was sequenced in April 2003: Human Genome Project

This achievement is celebrated annually on DNA DAY, 25th April. Also celebrated on DNA DAY is the discovery of the double-helix structure of the chromosome by Francis Crick and James Watson in 1953. Rosalind Franklin, although not acknowledged in the awarding of the Nobel Prize to Crick and Watson, was associated with the discovery.

dna

The first Irish Genome was sequenced in 2010:

Irish Genome Sequenced, Revealing Early Celtic Origins

In 2015, the first Ancient Irish Genome was sequenced:

Scientists Sequence First Ancient Irish Human Genomes

The cost of Whole Genome Sequencing (WGS) has come down to under $1000 by 2017.

Picture1

Image courtesy of the NIH.

Until recently, we genetic genealogists thought about yDNA (y-chromosome DNA) testing, atDNA (autosomal DNA)  testing, mtDNA (mitochondrial DNA) testing and not forgetting X-DNA testing, as separate types of DNA testing. They are all distinct types of DNA but with whole genome sequencing, these could now all be purchased in one package.

In fact, www.YSEQ.net is doing just this with its latest offering “YSEQ’s Whole Genome Test (15x)”.

The quality of the sequencing and balancing this with the cost per genome will be important factors for genetic genealogists. Being able to use pre-existing sites for comparing results with those of other people will also be a factor. I have some learning to do on all of this!

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Is yDNA Going out of Fashion?

 

We have 23 pairs of chromosomes in each cell. 22 pairs of chromosomes are autosomal (atDNA) and one pair is sex chromosomes. Two X’s for female and one X and one Y for male.

chromosomes

I see a huge swell of interest in autosomal DNA testing, especially since the cost has gone down so much. There is a lot of competition among the various testing companies, which is helping to lower costs.  Do your swab or saliva test and boom, a few weeks later you get relatives and ethnic origins presented to you. It is as if there is no effort involved other than doing the test. However, this is not true, as it can require a lot of effort to understand the results fully, especially if you have gaps on your family tree or your tree doesn’t go back far enough to make the connection. Autosomal DNA matching has limitations too (another blog post?).

When DNA became available for testing by the public around the year 2000, it was yDNA (y-chromosome DNA) which was used most ubiquitously. ySTRS (short tandem repeats on the y-chromosome) were used and still are, although the number of ySTRs tested has increased hugely since the early days. Mitochondrial DNA (mtDNA) was also available back then and still is,  but it was not until many years later circa 2010, that autosomal DNA testing became available to the public. Only one main stream DNA testing company now does ySTR testing which can now be combined with extensive SNP (single-nucleotide polymorphisms)  testing. However, I think that yDNA testing is being pushed into the background by the extensive promotion of autosomal DNA testing..

For men, yDNA used in conjunction with autosomal DNA testing can be very powerful when the yDNA aligns with the autosomal DNA. Finding biological fathers for males can be made easier using both yDNA and autosomal DNA.

yDNA testing is tending to become the pursuit of surname enthusiasts and dedicated researchers. SNP testing and next-generation sequencing (NGS) have become the preserve of those who know of its existence, and  who have  a historic allegiance to yDNA testing. Having been a voluntary yDNA project administrator for many years, I love the pursuit of yDNA testing. Matching other people at more and more intricate levels is like looking for the Holy Grail and it is exciting as you make new discoveries using tests like the Big Y at Family Tree DNA. The dedicated citizen scientists are hugely important in all of this endeavour.

There seems to be a need to impress  the public of the value of yDNA testing in family history research. Of course only men can do this test but women can find men on suitable ancestral lines to contribute their yDNA to the research and provide the DNA for such tests.

In the past, headlines were made using Genghis Khan, Niall of the Nine Hostage and Brian Boru in terms of their supposed yDNA trails to the present day. The diaspora felt the excitement of yDNA testing to see if they too were part of this wave. Some of the associations with well-known male figures, such as the above, have been debunked but there is research which is still ongoing to connect manuscripts, annals and historic documents to certain male lines. Members of clans get tested to see if they match the clan male line , or if indeed that male line can actually be ascertained. Non paternity events (fathers not being who they were thought to be) get shown up in the male line.

So, should we be interested in male lines? I think we should be, as there is plenty to be learned from this research. Likewise, tools for autosomal DNA analysis should be provided  by the testing companies to make it possible to get as much out of the test as possible. It is not magic!

Perhaps, with the cost of testing the full genome coming way down, this is the future of genetic testing.

 

 

 

 

 

 

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Spreading your Autosomal DNA Around

genealogy-and-dnaGedmatch
DNA.LandMYHeritageLiving_DNA

As I write in March 2017, I can say that I have done autosomal DNA testing with Family Tree DNA (2011), Ancestry (2015) and 23andme (2016). I have uploaded my autosomal raw data to Gedmatch (2011), DNA Land (2016), My Heritage (2017) for free. Also, Living DNA have my raw data and I am awaiting their analysis of my ethnic make up. Hopefully, I have covered all bases.

However,  I am still trying to identify my late father’s mother using DNA. In another posting I outlined how I eventually identified his father in 2013, using a combination of yDNA (2003-2009) and autosomal DNA. My father’s autosomal DNA was originally processed by Family Tree DNA in 2013. I  uploaded his raw data to Gedmatch.com, DNA.Land and recently to MyHeritage.com.

I use whatever tools are available on each site to help with the analysis. Having a CHROMOSOME BROWSER to use is very important for analysis of matches.

chromosome_browser

The diagram above, shows the 22 autosomal chromosomes and the X-chromosome. In another posting, I’ll talk about the software  and sites I use for analysis purposes.

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My Ancestry Estimates

Just for the fun of it, I have posted screen shots of the estimates of my ethnicity from three testing companies. For the record, I describe myself as half Irish and half Welsh (UK) as my father was Irish and my mother was Welsh.

(i) Family Tree DNA

family_tree_dna

Family Tree DNA

 

(ii) Ancestry.com

Ancestry.com

Ancestry.com

 

 

Ancestry.com map

Ancestry.com map

(iii) 23andMe.com

23andMe.com

23andMe.com

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Genetic Genealogy – my personal update

Having been involved in using DNA or genetic genealogy (as it is termed these days) in family history for over 16 years, I haven’t blogged very much on the topic but I hope to change that in 2017!

As we approach the end of 2016, I am reflecting on the year I have had in genetic genealogy both as a voluntary administrator of DNA projects and my own personal genetic genealogy research.

On the former (DNA Projects), I am involved in voluntarily managing three projects. The biggest of these is the Ireland yDNA Project which has grown to well over 7000 members as we approach the 11th year of its existence. It keeps me busy and requires daily attention! Secondly, the O’Shea yDNA Project, which is over 13 years old,  has almost 200 members. Thirdly, the NW Co. Cork Family Finder Project is much newer and smaller with under 100 members. On yDNA, the SNP avalanche continues apace with new SNPs being added to the y-haplotree all the time. Genetic genealogy is a fast moving, exciting interest to have and I love keeping up with it online using message boards, Facebook Groups, videos, blog posts and research papers. Citizen scientists provide a huge amount of resources to the genetic genealogy  community for which I am very grateful.

On my own personal research, having already tested with Family Tree DNA and AncestryDNA, in 2016, I also decided to test with 23andMe. These three main testing companies combined with Gedmatch form the basis for my autosomal DNA analysis. Note, that Gedmatch.com is a free database which is provided by enthusiasts.  This site features very highly in my research. I have also uploaded my DNA data to DNA.LAND. I also utilize blogs,  websites and software freely provided by enthusiastic researchers. I also download statistical charts etc., which are kindly provided by genetic genealogy enthusiasts.

I will write another blog post soon, as a follow up to my blog post of 2014, where I shared the fact that I had successfully utilized genetic genealogy to identify my father’s paternal family. See Personal DNA Success Story, for details.

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More on Cork RC Parish records

This posting is a follow up to previous postings relating to the “black hole” in availability of online church records for genealogical purposes, in Cork City and surrounds. I decided to write this post because I feel that people are confused by what is available  and where it can be found and what is not available online.

The chart below is my effort to untangle what is available online and what is not. I am focusing on the parishes of the deanery of Cork.

parishes

1836-1901* in the chart above, refers to Watergrasshill & Glenville as per the Watergrasshill parish website.
Glounthane** in the chart above, or “New Glanmire” as it is called on the National Library (NLI) of Ireland parish listing.
1775-1880*** includes earlier marriage banns according to the NLI.

From the chart, you can see that until the National Library of Ireland (NLI ) uploaded images in 2015,of the parishes listed, there was no online availability of baptisms and marriages for Ballincollig, Blackrock, Glanmire, Glounthane, Passage West, Ss Mary & Anne (North Parish) and St. Patrick’s RC Parishes. Even now, you have to wade through the online scanned records although these have been transcribed many years ago using tax payers’ money. But, as I mentioned in my previous post, it is wonderful to have the NLI images online despite the fact that they have already been transcribed by the Cork Ancestral Project which is sitting on these transcriptions (a long story).

Note, that the dates listed above, are approximate and do not allow for gaps in the records etc. Please check them.

Irishgen = www.irishgenealogy.ie which is a free site which has records for many of the parishes in the Diocese of Cork and Ross in Co. Cork and many other parishes in Ireland.

NLI = www.nli.ie which provides images of microfilmed RC registers in their possession as well as maps showing the locations of the parishes.

CAP = Cork Ancestry Project based in the Cork Co. Library  does not provides any online access to the RC records which they transcribed many years ago.

FT= Frank Thompson (private individual) who voluntarily transcribed 5 parishes in South Cork.

“Own Parish website” refers to Watergrasshill Parish website.

MHC=  Mallow Heritage Centre which is a payong site which has primarily transcribed the RC records for the diocese of Cloyne in Co. Cork and a huge number of parishes in the rest of Ireland. It is a paying site and is now linking transcriptions to the images on the NLI website.

A few things which I should mention are that there is a hard copy of the baptismal and marriage index for Ss Mary  & Anne available to be inspected  onsite at the Cork Co. Library. There is also a bound copy of the transcriptions which  was completed voluntarily by Frank Thompson many years ago, available to be viewed in the Cork Co. Library.

Other points to be mentioned are that the images provided by irishgenealogy.ie are of the registers while the images provided by the National Library are of the microfilmed registers. The national Library of Ireland provides invaluable maps of the parishes too.

Also, it appears that there are no marriage records for the time frame for Watergrasshill, which is otherwise well served for baptismal records. It is edifying to see that the Watergrasshill Parish provide transcriptions of their baptismal records.

ADDENDUM (added 20th Jan 2016)

The following image is an article which appeared in the Cork News on the 7th September 2012. It relates to the church records which were transcribed by the Cork Ancestral Project which are still not online.

ADDENDUM (added 11th February 2016)

Findmypast (paying site)is to release a collection of 10 million indexed records from Irish Catholic parish registers, in March 2016. This release is based on transcriptions of the microfilm church records which the National Library of Ireland (NLI) put online in 2015 and will link to the image of the page on the register, on the NLI website.

ADDENDUM (added 2nd March 2016). Ancestry.com has also transcribed the Catholic church records and now offers them online.

cork_news_article

 

 

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A Giant Step Forward for Irish Genealogy

I am so thrilled that the National Library of Ireland has seen fit to provide online, free access to the images of the microfilm of the Catholic Church records, which it has in its archives.

These online church records can now be accessed through Church Registers at NLI.

While these records are not a complete set of records for several (if not many) parishes, they represent a huge step forward. We can now see images of the actual pages of the registers for parishes which are provided as transcriptions by Rootsireland.ie (paying site) which we could not see prior to this. Irishgenealogy.ie provides images of registers to complement its transcriptions for the more recently transcribed parishes but not for those done many years ago (long story).

Some parishes in Ireland, for example the records for the “black hole” in Cork City, are now online. As a campaigner over many years to get these (Cork) transcribed records online (long story), I am delighted to see that the NLI has bypassed the ongoing and petty blockages in providing these to the global diaspora.

It is wonderful to see records in their original context. The joy in seeing an image of the actual record, no matter how faded or illegible cannot be replaced, by careful transcription. It is just a shame that the tax payers’ money was not better spent over the years. Duplication, competition and several disparate online sources for the Catholic Church records is not helpful to the amateur genealogist. Hopefully, petty politics and religious interests can now be put aside as we see an openness emerging from the years of secrecy and obfuscation relating to records pertaining to Irish genealogy.

As I said this is a huge step forward. Genealogists everywhere can combine all the sources mentioned above, to maximize the benefit for their own research. Thank you NLI!

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