Saturday, May 28, 2016

Jamboree



Additional Resources since the Jamboree Syllabus published: 

DNA Day morning session:

"NextGen Y-SNP DNA Testing Can Illuminate Your Paternal Line"

 


John Cleary, "Using SNP Testing & STRs to enhance a genetic genealogy research project." Rerecorded from Who Do You Think You Are Live 2016, Birmingham, England to enhance audio: 





DNA Day afternoon session:

"When Technology Conflicts with Human Values"


Harari (2015):



Haidt (2013):



Mukherjee (2016):


M

Tuesday, May 24, 2016

More Family Finder Matches?



FTDNA project administrators should be getting notices soon that announce the following changes in the threshold Family Finder customers must meet in order to be matched with each other. For those of you who like to monitor how such changes impact the number of matches you are shown, you better document your baseline data quickly. Your number of matches should change soon. 




You asked for it - we listened!

For several years the genetic genealogy community has asked for adjustments to the matching thresholds in the Family Finder autosomal test. After months of research and testing, we have implemented some exciting changes effective very soon.
Currently, the current matching thresholds - the minimum amount of shared DNA required for two people to show as a match are:

       Minimum longest block of at least 7.69 cM for 99% of testers, 5.5 cM for the other one percent
       Minimum 20 total shared centiMorgans 

Some people believed those thresholds to be too restrictive, and through the years requested changes that would loosen those restrictions.

Soon, the following changes will have been implemented to the matching program.

       No minimum shared centiMorgans, but if the cM total is less than 20, at least one segment must be 9 cM or longer.
       If the longest block of shared DNA is greater than 9 cM, the match will show regardless of total shared cM or the number of matching segments.
The entire existing database has been rerun using the new matching criteria, and all new matches have been calculated with the new thresholds. 
Most people will see only minor changes in their matches, mostly in the speculative range. They may lose some matches but gain others.  

I am assuming that most of you will get additional matches -- particularly those formed by single shared segments between 9 and 19 cMs. This will not be close relatives but potentially could be with family members in the 4th to 6th cousin range. Such matches have been suppressed because the shared cMs totaled less than 20. They can be detected in comparisons run at GEDmatch on FTDNA data.

Some die hard genetic genealogists love to analyze the changes in matches reported when adjustments are made such as the one that is imminent from FTDNA. Yesterday Jason Lee reported in a ISOGG Facebook post: "Two thirds of my matches at AncestryDNA are single segment matches under 9 cM." Those wishing to dissect the differences between databases and differences in a single database before and after screening criteria is changed will have a field day as FTDNA rolls out the above change.


If you want to be able to compare your "before" matches with the "after" ones, you better move fast. This change may start rolling out very soon.


Thursday, April 21, 2016

DNA Day Sales & a Birthday Party




Many of you know that we celebrate DNA Day on April 25th to commemorate the 63rd anniversary of the publication of the Nature article that detailed the structure of DNA. It's a little late to enter ASHG's DNA Day essay contest this year, but you still may want to contemplate your own response to the assigned topic. Read the next paragraph before you guess what my position might be. 

A few of you may know that this day has a special significance for the Dowells of Nashville. It will be the 2nd birthday of our 2014 DNA Day miracle. Benjamin was born 9 months AFTER he had part of his DNA screened to select a healthy fertilized egg that did not contain his mother's heritable mutated and potentially deadly Brugada gene.



DNA SALES!!!

To help us celebrate Benjamin's 2nd birthday this weekend, at least two of the big three US DNA labs are having sales from now until April 26th.


1. Last night CeCe Moore spread the word about the DNA Day sale at AncestryDNA 
- $79 and free shipping if you use the FREESHIPDNA code -
DNA.ANCESTRY.COM


2. 10 AM Central time today is the kickoff of a big DNA Weekend sale at Family Tree DNA



Ancestry's sale price is for the only product in the company's line of DNA tests. FTDNA's sale includes many but not all of the company's tests -- some of them discounted more than they often are during sales. 

I'm going to a 2 year old's birthday party this weekend dressed as -- (did you guess it?) -- a carnival barker.

So come one, come all and let the spitting and swabbing begin!! 


Sunday, April 17, 2016

My 10th great-grandfather is my 9th great-grandfather?



I was stimulated to write this post by reading Lara Diamond's blog today which has the clever title: My Pedigree Has Collapsed! I figured that anything the Ashkenazi could do us WASPs could  do better. Nothing like a little ethnic rivalry. The other granddad of my three Dowell grandsons is Ashkenazi.

According to my RootsMagic software, my immigrant ancestor Richard CURRIER is my tenth great grandfather. But wait he is also my ninth great grandfather:


Yes, Nathaniel Currier of Currier and Ives fame was a 4th great-grandson of immigrant Richard. Thank you for asking. But back to my main point.

 If you insist in trying to read all the details, your browser may open a somewhat clearer image if you click on each page. All the individuals below the line of type projecting to the left halfway down each page are identical in each line. Only their generation number is different.



So one could theorize that I should have inherited some atDNA from these early Puritan ancestors since my pedigree collapsed under their weight. But that was a long time ago and many generations to pass the segments down. By now they would be well traveled, well worn and often recombined. Thank God for those thorough and well preserved New England vital records. As a result I know that my 10th great grandfather is also my 9th great grandfather is also my 9th great grandfather.

Saturday, March 5, 2016

SNP Tsunami Continues Into Third Year




Many of us spend a great deal of time, energy and money attempting to document that a particular ancestor of ours belonged to a particular tribe or ethnic group. We all get very excited when we find a family Bible or a diary of an ancestor that dates back two or three hundred years.

Don’t you wish your ancestors had carried a passport which got stamped at every branching point of their intercontinental migration route as they trudged through prehistory? Actually they did. In some cases our genomes have recorded more than a hundred thousand years of travel.

This travel is documented in the mitochondrial DNA of all of us. A separate and more detailed path is documented in the yDNA of men. Many call this anthropology. In Chapter 6 of my most recent book, NextGen Genealogy: The DNA Connection, I call this extreme genealogy. In either case it is the study of haplogroups – or the ancient clans to which our ancestors belonged.

Women ancestors were somewhat limited in what they could communicate to distant descendants because our mitochondrial DNA (mtDNA) contains only 16,569 locations in which they can record the presence of one of the four chemical bases that make up our DNA. Their paths through prehistory can be traced for our female lines using mtDNA test results. mtDNA was the basis for Bryan Sykes’ pioneering Seven Daughters of Eve.

Our men ancestors had tens of millions of additional locations where such information could be logged. What we look for today is where on our genomes these ySNPs occurred in this transcribed travel record. Once such a permanent change has occurred, it is passed down to all male descendants.

What are ySNPs and how do they differ from the ySTRs we have been testing since 2000?


Short Tandem Repeat (STR)
Pronounced "stir." This is a repeating pattern of genetic code letters at a location on the genome. The value is the number of times that pattern is repeated at that location.
Single Nucleotide Polymorphism (SNP)
Pronounced "snip." A single and permanent change in the DNA bases at a given location.

Consumer DNA testing to discover family history information began in 2000 with the focus on the Y chromosome (yDNA) which only males possess. Mitochondrial DNA testing for both genders soon followed but is somewhat limited because it has ONLY 16,569 locations to store a single bit of information. By 2010 autosomal DNA testing burst on to the scene and has become the most popular test.

By 2013 a new testing cycle for yDNA became available to genealogists. While the previous cycle had focused on testing ySTRs, the new wave examines ySNPs.

However, yDNA can record 3,500 times the data that mtDNA can. Therefore, it has the power to record a much more detailed migratory history.
Most of yDNA testing to date has been conducted on Short Tandem Repeats (ySTRs). When we talk about 12, 25, 37, 67 and 111 marker tests, we are referring to how many ySTRs were tested. STR testing is analogous to dispatching a census taker to a village which is known to have 12, 25… residences. In our scenario the locations of these residences have been defined by geneticists as being accessible and having a rate of mutation that is somewhat predictable. At each location our census taker records how many STRs are currently in residence.

In NextGen testing the focus shifts to Single Nucleotide Polymorphisms (SNPs). Instead of dispatching probes to specific, predefined locations, NextGen ySNP testing is more analogous to take satellite images along the entire Y-chromosome. Although the chromosome contains almost sixty million identifiable locations, current technology allows us to get reliable data from only about a fourth of those locations. Still this is an overwhelming amount of data. The computing power to analyze it has only recently become available.

At present ySNP chasing is only in its infancy. A vast majority of the SNPs we know today have been discovered in the last two years. The statistics in the chart below represent the number that had been placed on the International Society of Genetic Genealogists (ISOGG) yTree committee chaired by Alice Fairhurst:

Cumulative SNPs placed on the ISOGG yTree

Another way to look at this SNP tsunami is to view the new SNPs identified in a two year period (2013-2015) for R1b-L21, the most common male haplogroup in Western Europe today:

Known SNPs in R-L21 haplogroup in mid-2013 (Mike Walsh)

Known SNPs in R-L21 haplogroup in mid-2015 (Mike Walsh)

We are still working to find the exact location and sequence for many of them. In some ways our knowledge today would be like getting a SNP passport with several dozen “check point” stamps on it but in random order. We know that our genomes passed through all those points but are still trying to decipher in what sequence that journey occurred. The charts above for R1b-L21 represent ySNPs that we have been able to arrange in evolutional order. As more men are tested and we can document where they exited the main SNP trail, we can refine our chronology for all of us.

The chart below for sub-clade R-1026 is an expansion of the seven pale pink SNPs clustered at the bottom of the chart above. This subclade was unknown when the previous chart was drawn in 2013.


Courtesy of Alex Williamson -- www.ytree.net 

Even with this deluge there are many more thousands of SNPs to come. The NextGen curve is where the ySTR was in 2003 when 10,000 tests had been sold by FTDNA. Ironically, that is the number of BIG Y tests Bennett Greenspan reports FTDNA has sold to date. Full Genomes report their company has sold 1,500 NextGen tests. 

Most of the ySNPs that have been discovered have yet to be specifically placed and more will be discovered as testing numbers increase. The entire recently discovered R-S1026 haplogroup above is not yet integrated into the ISOGG ytree. It is only partially integrated into the FTDNA ytree. The R-S1026 chart contains many blocks or boxes that group newly discovered SNPs. At this point we believe we have the blocks in the correct chronological order of their appearance. However, we have yet to sort the SNPs within boxes into their correct order of appearance. And more remain to be discovered. Other haplogroups are in a similar state of discovery and growth. The SNP tsunami shows no sign of receding anytime soon. 


Saturday, February 20, 2016

Family Health History: TapGenes




When the possibility of DNA testing for identifying possible health issues is raised, a sizable segment of the medical community responds that such testing is unnecessary because a family health history is more useful. Fortunately, I believe the number of practitioners espousing this belief is diminishing. Actually, it’s not either/or. Genetic testing should be part of a comprehensive family health history.

Those of us who have been serious family historians for a while, recognize that we rarely have a complete health history of three or more generations of our family. Even if we have been able to collect death certificates for our parents, grandparents and great-grandparents (along with their siblings), really don’t have detailed information upon which medical diagnoses can be based. Some of our relatives died in wars, childbirth, epidemics or other causes before their underlying health conditions manifested themselves. In addition, many the causes of demise listed on many death certificates are too vague to add much guidance to present day diagnoses. Most patients, when asked to fill out family health histories in a clinician’s office, have far less reliable information than those of us who are genealogists.

DNA testing, even if is of whole genomes, also represents other challenges. Many medical practitioners are not knowledgeable about DNA and may feel threatened to admit this to their patients. This avenue to information within our bodies was not available when most of them received their professional training. Much as we might wish it were the case, DNA testing cannot provide information on all the causes of our current or future states of health. Environmental factors still contribute significantly.  The long running “nature” versus “nurture” debate rages on.

Part of RootsTech 2016, which I attended earlier this month, was an Innovator Showdown competition for a prize pot of $100,000. An international field of 46 competitors was narrowed to 12 prior to the conference. At the Media Dinner on Wednesday, that group was narrowed to 6 finalists. On Friday these remaining competitors were interviewed before thousands of attendees. The panel of judges then selected the winners with participation of the audience who voted on their smartphones. First place went to TapGenes. The winners received $20,000 in cash and additional in kind awards that more than doubled that amount.   


Yes, the eagle eyes of some readers have identified Judy Russell, The Legal Genealogist, seated in the lower left background, who was a member of the distinguished panel of judges.


TapGenes offers you the convenience of keeping all your family health history in one safe and secure place.
A visit to the TapGenes website will explain what this prizewinning app has to offer you and your family. If you wish to signup right away please use this link.

Wednesday, December 16, 2015

Promethease: For Your Health & Insomnia



On Sunday The Legal Genealogist, also known as Judy Russell, posted "All you want for Christmas..." is a DNA test kit. Her post began:
So… if that’s you this year, if what you really want for Christmas is a DNA test kit … which one do you get?
Her answer was very thorough and I will not try to duplicate it here. However, you would do well to read her thoughts. Her analysis of the options is sound, genealogically speaking, and she left very little to be added. Except....


Testing only for health related information:

All of us should know by now DNA testing is definitely not a case where "one size fits all." Judy knew this and she provided many viable options, but she left one out and I believe she did that on purpose. We will get back to what her purpose may have been later in this post.

In the last several days I have been approached three times by individuals asking what DNA test I would recommend for gaining health related information. Two wish to self test and the other is looking for holiday gift ideas for two sons. All of the would-be test takers are middle-aged. If they test they would become the kind of test takers all serious genetic genealogists love to hate. They all know little and claim no interest in knowing more about their ancestry except for how their genes may impact their own health. In addition they all claim not to be concerned about their carrier status for diseases that the FDA now permits 23andMe to report to clients. That really doesn't leave much from which to choose. 

Some information about prescription drug interactions with an individual's genome can purchased through a test offered by Healthspek which I have discussed in previous posts. However, that is only one part of the health related information inquiring minds would like to know about what is recorded within their personal genomes.

Several years ago I took a quick look at Promethease but found it to be not as user friendly as similar information presented by 23andMe. Since the reports generated by both companies were coming from the same source data, I opted to concentrate on those on my site at 23andMe


Hemochromatosis Carriers:

During the holiday season three years ago we offered to gift our children and their significant others with 23andMe test kits. One of the things we learned from this was that both one son and his wife were carriers for hemochromatosis -- which causes one's body to accumulate too much iron. The parents were not flagged as being at risk for developing this disorder but their offspring -- our young grandchildren -- were at elevated risk. I discussed this finding with my daughter-in-law who is a gynecological surgeon and medical school faculty member. I recommended that she relay this information to the boys' pediatrician so that he could make note of it in their files and monitor this possibility. My MD daughter-in-law asked if I would write a long email to the pediatrician that explained this development to him.

I did so but I found this to be ironic (pun intended) since I'm an information doctor not a medical professional. Some of you know that I have never had a biological science course of any description in my life. My insatiable curiosity about DNA was God's punishment of me when She read my transcript and realized my academic deficiency. So much for needing medical professionals to protect and guide us uninitiated civilians as we are introduced to the information in our own genomes. But I digress.


Promethease:

Back in September The Legal Genealogist wrote "A Healthy Choice" as a post to her popular blog. In it she presented a very thorough introduction to Promethease as a source for health related information from our genes.



Rather than trying to repeat her succinct prose my intent is to expand on the personal experiment she reported. Until recently I was unaware that self downloaded raw atDNA results from any of the big three testing companies can be uploaded and processed through Promethease. However, the 23andMe test chip has significantly more health related SNPs than the chips of the other two companies. FTDNA has made conscious decision to stay away to the extent possible from SNPs thought to be health related. This decision was made years ago in order to minimize the potential for regulatory problems with the FDA. As we learn more about our genomes, it is increasingly difficult to avoid SNPs with known health consequences. Ancestry discloses little about its rationale for selecting the SNPs on its chip.


Raw data from each of the major U.S. testing companies when processed through Promethease for three different users: 

23andMe Ancestry Family Finder
Legal Genealogist
Gray 17,613 11,225 10,070
Green 5,281 1,538 1,261
Red 413 255 166
Total 23,307 13,018 11,497
Dr. D
Gray 19,049 11,609 10,348
Green 5,580 1,572 1,296
Red 388 248 153
Total 25,017 13,429 11,797
Dr. D's wife
Gray 18,414 11,245 10,384
Green 5,519 1,491 1,265
Red 429 276 177
Total 24,362 13,012 11,826

Clearly customers get reports on about twice as many SNPs from 23andMe raw data than from the data from competitors. My little study has replicated Judy's. So if your only objective in taking an autosomal DNA test is to learn more about how your genetic component may contribute your future health, 23andMe raw data will give you more to analyze and analyze and analyze. That is what you will be doing if you go this route. Processing raw data from 23andMe or Ancestry only costs $5. Family Finder data costs $7 because xDNA must be downloaded separately and added to the mix to get the most complete picture that can be extracted from those data. If you have raw data from all three companies as does The Legal Genealogist and Dr. D., all your data can be loaded into Promethease at one time and processed for a total of $11.


Alzheimer's risk:

It is easy to drown in the data. In my own report Alzheimer's was associated with 156 SNPs: 56 good; 11 bad and 89 with small associations that have yet to be classified as either good or bad. You cannot look at the predictive power of a single SNP and be confident that you know something about how your genome may affect your future health. The human genome is far to complex for this kind of intellectual short cut.


SNPs currently thought to be related to Dr. D's Alzheimer's risk
If you have that obsessive-compulsive gene and love to pour over all the known data, this may be the test for you. If you have already done an atDNA test, for an additional investment of only $5 or $11 dollars, you can entertain yourself all night!


Holiday sale:

As most of you know 23andMe recently raised the price of its test kit to $199 for U.S. customers. If you are already a 23andMe customer, you recently should have received an offer to order kits for $149. This price is good for purchases completed through 11:59 pm PST on January 8, 2016. What you may not have noticed in the fine print is that you can place up to three separate orders. Each order can be for up to ten kits. This allows one to order as many as thirty kits at this sale price.


Caveat:  

If you are at all interested in using DNA testing to learn ancestry information for genealogical purposes, read Judy's December 6th blog post "Now... and not now" before you order any kit from 23andMe.


Tuesday, December 8, 2015

Ancestry to drop Family Tree Maker software. RootsMagic benefits?



The Ancestry blog announced today that the company would stop selling its desktop software program Family Tree Maker (FTM) as of the last day of this month. The company says it will continue to support current owners of Family Tree Maker at least through January 1, 2017. 


Our subscription business and website, on the other hand, continue to grow and we are doubling down our efforts to make that experience even better for our Ancestry community.

If the past is any guide to the present, it will be a waste of time for the genealogical community to try to influence Ancestry to reverse course on this matter. 

This behavior, while it may make business sense, does not enamor customers to trust Ancestry to be there for them in the long run. Ancestry has a history of buying or acquiring products and then abandoning them often with the loss of massive amounts of useful data lost in the process.

I was a user of FTM once upon a time. Then I moved to Family Origins. At the time I was thrilled because I thought this would mean Ancestry's marketing know how would increase the reach of Family Origins. WRONG. In retrospect it appears that Family Origins was acquired to get rid of competition for FTM. Family Origins was allowed to die a quiet death. Fortunately the programming team behind Family Origins came together soon after their non-competition clause of their sales contract expired and produced RootsMagic now in version 7.0.8.0.


RootsMagic along with Legacy on the Windows platform would seem to be among the companies best able to benefit from Ancestry's recent announcement. RootsMagic is already moving into the breach this evening with a special offer to FTM users.



Reunion is in a position to have a similar opportunity for those using FTM on the Mac platform. 


This decision by Ancestry should not lead to the destruction of useful genealogical data as the corporation's previous decisions to withdraw access to MyFamily.com sites did a couple of years ago. Access to yDNA and mtDNA test data conducted by Ancestry and by Sorenson Molecular Genealogy Foundation (SMGF) was also lost to the genealogical community and those who had contributed it when Ancestry decided to concentrate on autosomal DNA.

Taken by itself the decision announced today does not seem to be as damaging to the genealogy community as some of Ancestry's previous actions. However, it leaves this blogger wondering what if anything we should expect when Ancestry acquires former competitors such as Fold3, and Find A Grave? What should we expect from Ancestry's strategic alliances to make other databases available to its customer base?