Tuesday 13 December 2016

GEDmatch - where to start


GEDmatch is a free website.
(there are few more tools available for a subscription option, but not neccessary)

The goal of the website is to be able to help identify your DNA matches and which segment(s) of the Chromosome(s) you match.

From there you can identify others sharing the same segment(s), and hopefully from there you can identify a shared ancestor, and from there attribute that segment of DNA to that ancestor, which then helps you work out how your other matches match.

All a bit complicated?

Ancestry shows you only your matches, it does give you an idea of how much DNA you share, according to their algorithm, and a suggestion of how close that relationship is.

For example


GEDmatch will pin down this information more precisely allowing you to find your cousins easier.
For example, here is the same match after running a "One-to-One compare"


It tells me which Chromosome and where, how long and how many SNPs match, and gives an estimate of how many generations back to the MRCA - "most recent common ancestor".

From here I can run a "People who match 1 or both of two kits" and this will show me if anyone matches the same segment, in the example below I have now found 4 others who appear to share the same DNA segment.


Now, to be sure that you all share the same ancestor you will need to run the "One-One compare" for each match on the list to each other match. Some may not actually match the others - this is because for each SNP we have 1 part paternal and one maternal, so the matches that don't match each other will be from your other side.

Once you have found a group of 3 or more (distant from each other ie not including close family members) that do match, then this is called a Triangulation Group. From here it comes back to the paper trail to verify the actual connection. So you will need to have a properly proven tree back as many generations as possible.

Sound good?
So, how do you get onto GEDmatch...
Firstly login to your Ancestry account and go to your DNA Results Summary.
On the right hand side of this page is a grey box with cog icon marked Settings.
Click this and then you can click on Download Raw DNA data

You will be sent an email with a link, save the file somewhere you can find it. 

Now, go to www.GEDmatch.com and register for an account

Now you will have a start page with the following

Click on the AncestryDNA.com option, and upload your file.
You will be given a kit number, take note of this.

It will take some time for your matches to load (4hours-2days), but if you know any other person's kit number you will be able to run a one-to-one compare whilst you wait.
Also a good idea is to upload your gedcom file, and read the help files.



Once your file is "tokenised" you can run the One-to-many matches




You will see something like this

Your matches are ordered from best to worst
By clicking on the "A" button this will take you to a one-to-one compare and you can go from there - as above.

As a guide you need to be looking first at those who share more than 10cM, and more than 1200 SNPs.

Matches can be false as DNA is totally random, so the higher the cM and the SNPs the more likely it is to be a real match. Anything higher than 15cM is pretty definite, or 1800 SNPs for a 10cM match.
For a 7cM match about 1500 SNPs is around 50% likely of being a true match.



Good luck!
Here are some links that can guide you further

http://smithplanet.com/stuff/gedmatch.htm


http://www.genie1.com.au/blog/78-tips-for-using-gedmatch


Thursday 17 November 2016

Health report from your DNA test

So, do you want to delve into the scary world of your genes and what it might or might not tell you about your health and future health?

Firstly, be VERY aware that you need to speak to your Doctor about any concerns, your genes may tell you what you are predisposed to but it all depends on so many factors of environment, nutrition, exercise, lifestyle etc. However if we know what we may be predisposed to then we are armed with the power to change some of these factors and hopefully reduce or eliminate their influence :)

http://www.y-str.org/2015/02/variant-report.html

Use this program to print a basic report on health, just go with the default files.
You will probably get red genes flagged up. Start with those and use several sites to lookup the RS numbers.

http://www.snpedia.com/index.php/SNPedia

https://www.selfdecode.com/snp/Rs6323/

and of course Google.

Basically I just searched and searched until I was able to make sense of what the CURRENT medical interpretation of the effect of the gene is, of course bearing in mind it all depends on the effectiveness of the research.

Once I felt I could interpret the red flagged genes I moved on to the yellow ones.

This WILL take quite a while.

Once you have documented your genes and you feel you understand about homozygous, heterozygous, and risk alleles then you are probably ready to use the Promethease website.

 https://promethease.com/

It costs US$5 and you will get an extensive, interpreted report.
It is so big it is overwhelming and quite difficult to actually find the meaning for yourself.
(see Addenda below)

That's why I think the first exercise is best completed :)

I do however think that the genes that affect how your body metabolizes medication are important, and if you have any of these genes it would be a very good idea to discuss this with your Doctor.

There are lots and lots of other websites I came across whilst researching, this was just my experience.

You may find these links of interest
http://suzycohen.com/articles/snpsmethylation/comment-page-2/

https://www.snpedia.com/index.php/Yasko_Methylation

https://selfhacked.com/2014/12/07/about-mao-a-and-what-to-do-if-you-have-the-warrior-gene/

Stay healthy!

Addenda



Reading your Promethease Report
The main section shows your 'genos', i.e. your genotypes and genosets. 

Each Geno is colour coded around the edge: Green=Good, Grey=Not Set, Red=Bad - this is called Repute
Many genos have a bit of good and a bit of bad. These remain 'Not Set' (the grey ones). Sometimes that's because they're not distinctly Good or Bad, but usually it means no human/scientist has determined a classification yet.


The rs number (example rs61750595) in the top left of the Geno box identifies a specific location in your DNA, and is known as a SNP. Clicking on this 

will take you out of your report and into SNPedia where you can read more.

The two letters next to the SNP (example T;C) are known as the Orientation - each letter is known as an Allelle and  needs to be identified when interpreting the consequences of each genotype. Clicking the Orientation will lead you to this information.

Magnitude - a subjective measure of interest :

Also refer to Max Magnitude across all genotypes for this SNP

Geno time - timestamp of last modification of page

Frequency - how common is this genotype in your chosen population
Choosing a different ethnicity will change the population 'Frequency' for each genotype.

Gene - is the name given to the segment of DNA to which the Genos belong.

How to Print
A printout of everything would be thousands of pages, so here are suggestions how-to
http://snpedia.com/index.php/Promethease/Learn_More

Another suggestion as to how to take the report to your Medical Professional would be to save it to a USB stick

Sunday 13 November 2016

Ancestry DNA matches - What to do next?

So, your Ancestry DNA test has come back, and you are faced with a heap of matches - what next?

Firstly, open Chrome and install the Snavely Ancestry DNA helper extension at the link below,
this enables more functionality from your results.
https://chrome.google.com/webstore/detail/ancestrydna-helper/hjflmfphflaeehhpdiggobllgffelfee

Secondly, download your raw dna data file - on your DNA start page
https://www.ancestry.com.au/dna/
you will see a cog on the right hand side of the screen labelled Settings.
Click here, and click on download raw DNA data.

You can then upload this to the free website Gedmatch.
 https://www.gedmatch.com
You will need to register an account, and click on AncestryDNA.com under File Uploads.
This will enable further analysis of your data, but we will return to this later.

Now, return to the Ancestry DNA start page, and click on View All DNA Matches.
They are organised in order of closest relationship by default.


First look at any Hints you may have by clicking on the Hints button with the green leaf, you will only get these if Ancestry thinks two people are identical, one from your tree and one from the matched tree.
Now, return back to the matches page.
You will notice that many matches have no trees, very small trees or private trees.
Many people have actually taken the DNA test for other reasons than family history, and are not interested in matches, or they have not linked their tree to the results. For the time being ignore these matches.

Now, let's look at the matches with trees, starting at the top.
Click on View Match
You will see two or three tabs:
1) Pedigree and Surnames (this is the default)
2) Shared matches (if there are any)

3) Map and Locations



After an initial glance at the common names, unless you have a really rare name I find most of the time it is easier to start via the Map and Locations tab.

At the top right of the map is a little black square with a white box marked inside, click this to open a larger screen. Now zoom in to the areas you are interested in.
Your family will be shown in blue, your matches' family in orange, and where you both have people in the same location these are shown in green.




When you click on a green marker, you will first see your ancestor's in that location, and secondly your matches' ancestors. Blue shows only yours, and orange only theirs. By looking around at the surnames, dates and places, this may give you an idea of how you may be connected.

By clicking on a name and the View Details  , this will pop up the family and from there you can click on View Full Tree.
Then, you can start researching further to see if you can extend your tree so that you find a link.

There is no "filing system" for your matches, and you will soon get lost, so just above the tabs and below the Predicted Relationship is a Notepad icon - type yourself a note in here and click Save.
You can use the Star button as a toggle for yourself as well.

Of some use is the information on the Predicted Relationship Confidence, there is a little "i" button, clicking this will show you an "estimate" of how much DNA you share, unfortunately Ancestry use an algorithm to calculate this figure, and apart from inaccuracies it does not show the size of segments shared, nor the locations, which is where Gedmatch comes in (detail shown in the right picture).



The more of your matches that have uploaded to Gedmatch the better as it gives a far better indication of the strength and location of the relationship.

Meanwhile keep going through your matches trying to find links, to contact a tree owner it has been found that the best way is to click on the owners name and then use the orange Contact button, rather than the send message button on the previous page, for some reason Ancestry appears to get glitches in their messaging system and the orange button appears to be more reliable. However, be prepared for a lack of response of about 80% :( You will be able to see how long the tree owner has been a member of ancestry and when they were last online, this may give you an indication about the chance of a reply.

Once you get to 5-8th cousins the link is quite distant, and can involve way too much work on the off chance of finding a precarious connection. I only look at these if they come up in a search or shared matches.

Lastly a couple of handy downloads:
7th generation template here http://www.genealogyjunkie.net/downloads.html 
X-DNA chart here http://www.genie1.com.au/blog/63-x-dna

Any questions, anything I missed, please let me know.
Gedmatch next!






Sunday 23 October 2016

Ancestry DNA and Ancestors

Find me on Ancestry here
http://connect.ancestry.com.au/Profile/0064b90f-0001-0000-0000-000000000000

Tree here:
http://trees.ancestry.com/tree/104053075/family/pedigree?cfpid=290038259757&selnode=1

My ancestors - map of places and names:

Addy, Alice
Addy, Elizabeth Beatrice
Addy, John
Addy, Jonathan
Addy, Joseph
Addy, Joseph
Addy, Joseph
Addy, William
Allot, George
Allot, John
Allot, John
Allot, John
Allot, Martha
Altham, Christopher
Altham, Mary
Attwell, James
Attwell, John
Attwell, John
Attwell, Samuel
Atwell, James
Atwill, John
Atwill, Mary
Atwill, Richard
Atwill, William
Barnes, Hargreaves
Barnes, John
Barnes, Martha Ellen
Baron, Mary
Bate, Edward
Bate, Enoch
Bate, Jane
Bate, Matthew
Beckley, Grace
Berry, Hannah
Berry, Joshua
Berry, Matthew
Berry, Matthew
Bever, Mary
Billsbury, Ralph
Bilsbury, Hannah
Bilsbury, Margaret
Bilsbury, Ralph
Birchall, Jane
Birchall, William
Booth, Mary
Booth, Mary Elizabeth
Booth, Samuel
Booth, Thomas
Booth, Thomas
Booth, William
Bradshaw, Ann
Bradshaw, Elizabeth
Bradshaw, Ellen
Bradshaw, Margaret
Bray, Grace
Bridge, Margaret
Briggs, Mary Ann
Briggs, Robert
Briggs, Robert
Brock, Catherine
Brohan, Mary
Brooks, Leah
Buckley, George Edward
Buckley, Joseph
Buckley, Rosamund
Buckley, Thomas
Buckley, Thomas
Butterworth, Betty
Castell, Christopher
Castle, Barnabas
Castle, Christopher
Castle, Elizabeth
Castle, Elizabeth Anne
Castle, Henry
Castle, John
Champion, George
Charlton, Sarah
Cheetham, Ann
Collings, Ann
Collings, John
Coop, James
Coop, John
Coultas, Elizabeth
Crews, Joan
Crook, Betty
Crowther, Elizabeth
Crowther, Grace
Crowther, John
Dearden, Fanny
Dillen, Grace
Done, Ann
Done, Richard
Done, Thomas
Done, Thomas
Duckworth, Anne
Duckworth, James
Dugdale, Mary Anne
Dugdale, William
Ellison, Elizabeth
Ellison, Hamlet
English, Henry Samuel
English, Joseph Henry
English, Nellie
English, William
Farley, Elizabeth
Ffolland, Michael
Ffolly, Simon
Folland, Hugh
Folland, Mary
Folland, Richard
Folland, Simon
Fort, Henry
Fort, Peggy
Fort, Robert
Gibbons, Ann
Gibbons, Francis
Goldthorp, John
Goldthorp, Jonathan
Goldthorp, Mary
Gowling, Robert
Graham, John
Gray, Jane
Gresty, Sarah
Hall, William
Hamer, James
Hamer, Joseph
Hamer, Leah
Hamer, Martha
Hamer, Richard
Hargreaves, Alice
Harvey, Thomasine Mary
Harvey, William
Haslam, Abigail
Haslam, Thomas
Haworth, Agnes
Haworth, Mary
Haynes, Charlotte Susannah
Hellawell, Charles
Heywood, Betty
Heywood, Thomas
Hilton, Sarah
Hodge, John
Hodge, Mary
Holt, Elizabeth
Holt, Ellen
Holt, Henry
Hooper, Eliza
Hooper, John
Hooper, John
Hooper, Thomas
Hooper, Thomas jun.
Hooper, William
Horrocks, Alice
Hotham, Ann
Hotham, William
Houghton, Hannah
Howarth, John
Hutchinson, Ann
Hutchinson, Mary Brooks
Jackson, Susannah
Kenworthy, Mary
Kenworthy, Sarah
Kershaw, Charles
Kershaw, Charles
Kershaw, James
Kershaw, John
Kershaw, Sarah
Lee, Sarah
Lees, Abraham
Lees, Sally
Lightfoot, John
Lightfoot, John
Lightfoot, Joseph
Lightfoot, Mary
Lightfoot, Ralph
Lightfoot, Richard
Livesey, Charles
Livesey, Elizabeth
Livesey, Peter
Livesey, Richard
Livesey, Richard
Livesey, Richard
Livsay, Robert
Lomax, Ann
Lomax, Hannah
Lomax, John
Lord, Betty
Lord, James
Mallalieu, Sarah
Marcroft, Ann
Marcroft, Robert
Markes, Anne
Moxworthy, Elizabeth
Munkes, Jane
Nichols, Isaac
Nichols, Sarah
Nuttall, Andrew
Nuttall, Jane
Nuttall, Richard
Nuttall, William
Openshaw, Susan
Openshey, James
Orm, James
Orm, James
Orme, Ann
Partridge, Betty
Petty, George
Petty, Jane
Platt, Alice
Platt, Dorothie
Platt, John
Pope, James
Pope, Martha
Radcliffe, Alexander
Radcliffe, Edmund
Radcliffe, Jerry
Radcliffe, Nancy
Radcliffe, Robert
Radcliffe, Samuel
Radcliffe, Thomas
Radcliffe, William
Radly, Hannah
Reeve, Grace
Reeve, Nathaniel
Richardson, Ann
Richardson, Geo.
Richardson, Susannah
Richardson, Thomas
Riley, Anne
Rogerson, Abraham
Rogerson, Ann
Rogerson, William
Roobotham, Sarah
Rooney, Christopher
Rooney, James
Rooney, John
Rooney, John William
Rowley, Sarah
Schofield, Hannah
Shaw, Eliza Ann
Shaw, John
Shore, Betty
Shore, John
Shorrock, Ann
Shorrock, Meadowcroft
Shorrock, Roger
Simpson, Hannah
Simpson, Thomas
Smith, Alice
Smith, John
Smith, Judith
Smith, Richard
Smith, Robert
Stock, Benjamin
Stock, Elizabeth
Stock, John
Stonely, Ann
Storey, Susanah
Storey, Thomas
Story, Thomas
Story, Thomas
Story, William
Sykes, Abraham
Sykes, Caroline
Tarring, Arthur
Tarring, Emblin
Taylor, Leah
Taylor, Nancy
Thompson, Sarah
Thompson, William
Thompson, William
Todd, Abraham
Todd, John
Todd, John
Todd, John
Todd, Mary Ann
Torring, William
Turner, Ann
Turner, Betty
Turner, Thomas
Venison, Edward
Venison, Rebecca
Venison, Robert
Walch, Betty
Walker, Ann
Walker, Harry
Walker, James Coop
Walker, John
Walling, Lilian
Waterhouse, Mary
Webster, Elizabeth
Whewall, Mary
Whitaker, Henry
Whittaker, Abraham
Whittaker, James
Whittaker, Mary Ann
Whittaker, Mary Ann
Wild, Ellen
Wild, James
Williamson, Robert
Williamson, Susannah
Wilme, Anne
Wilson, Jane
Winterbotham, Mary
Woolley, Ann
Woolley, Daniel
Woolley, Daniel
Woolley, John
Woolley, Nancy
Woolley, William
Wright, Isabella
Wright, Robert