12th International Conference on Genetic Genealogy – Saturday

Genealogy

Genealogy / Genealogy 19 Views 0

Note: It’s been a long day but here are my notes. As always, they are fairly raw so please excuse typos, errors, and omissions. These are essentially my 16 pages of personal notes for the day and I’m sharing them with you. I have some more photos but they are not uploading correctly so this is all I have to share for now. On to the important stuff!

Max opened the morning session with a welcome and thank you to everyone who attended. Max also recognized those who are no longer with us. Bennett said that this is the largest conference we’ve ever had.

Dr. Michael Hammer of University of Arizona presented “Ancient European DNA.” Dr. Hammer started with a basic overview of the types of DNA and their inheritance patterns. Family Tree DNA uses DNA microarray technology. To conveniently analyze the massive amount of data, there are various tools including admixture plots, dendrograms or population trees, and principal components analysis (PCA) plots. Dr. Hammer reviewed the African origin and global diaspora of anatomically modern humans. Around 10,000 years ago food production conferred an enormous advantage to farmers over hunter-gatherers.

mike-hammer

Dr. Hammer talked about the overlay of farmer genes over hunter-gatherer genes. The traditional view has been that European genetic variation reflects both of these processes. Genome-wide data supports Europe as a mixture of the two populations. The R1b clade is the most common paternal lineage in western Europe. It is carried by >110 million European men and increases in frequency from east to west. It was traditionally believed to be of Paleolithic (hunter-gatherer) origin. In 2010 and 2012 studies challenged that traditional view. In 2010 Balaresque concluded that Mesolithic hunter-gatherer Y chromosomes were nearly replaced by those of incoming farmers. Busby concluded that haplogroup R-M269 expanded after farming. These ideas were not in agreement but could not be resolved with evidence from living people. Ancient DNA material provides more insight in order to compare across different time frames. They are able to infer whether contemporary people descend from long-term in habitants of a region, or from people who arrived from elsewhere – replacing or admixing with previous inhabitants.”

In 2013 there were 32 ancient Y chromosome samples from France, Spain, Germany, and the Alps. At this layer, none of the samples had R1b. Most of them had haplogroup G. This showed that R1b was probably not Paleolithic.  In 2014 we had the first complete genomes from nine ancient Europeans. These were from Motala, Loschbour, and Stuttgart. This showed three European ancestral components: Western European Hunter-Gatherer (WHG), Early European Farmer (EEF), and Ancient North Eurasian (ANE). Dr. Hammer shared a graph showing the three ancestral components in contemporary Europeans.

3-ancestral-components

This leads to a new view for a three-source migration model. The first R1b is identified in the Metal Ages in Europe.

ancient-nry-haplogroup-frequencies

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To address the question about who were the ANE and how did they make such a large contribution there were two laboratories who published. Each of the two studies had a different focus.

reich-slide

Neolithic Europeans are composed of HG and farmer mixture. The Bronze Age Europeans have added ‘Pastoralist’ component suggested to derive from Yamnay culture from the Pontic-Caspian steppe. Neolithic farmer component is absent in the Yamnaya.

Reichs team did a similar analysis and supports the steppe as a source for genes now found in Europe, with massive migration ~4,500 years ago.
Combined evidence supports the distribution of R1b as a results of major population movements during the Metal Ages. The Bronze Age was the first time metal was used specifically to create weapons. The Iron Age was the first true mass-production of weapons. This has sparked an interest in the cultural and technological innovations.

Expansions of Metal Age genes are shown in populations that preserve the genes. The Kalash do not share much ancestry with any of their neighbors. The culture is unique and there are only about 3,000 members. Their language is Dardic family of the Indo-Aryan branch. Their ancient rites include making of distilled spirits, smoking marijuana, and animal sacrifices. They appear to be descendants of the original Metal Age people from the Steppe.

Dr. Hammer announced that Family Tree DNA is launching a test where one can discover their ancient percentages. Megan from FTDNA showed how to login in to ancientOrigins. It appears on your main page next to MyOrigins.

Questions:
Are the Kalash an isolated population? Yes, and there are studies about them.

Why did the Yamnaya R1b migrate? If there’s a new technology that gives you advantage and your population increases, they represent different dependence on agriculture. If you have a chariot and a horse, why not migrate?

Are there unique isolated populations that do not have roots in Africa? Not that we know of. No population is purely in an archaic form. We all have primarily origins in Africa.

If my metal age invade percentage is 14%, does that imply 14% R1b? His guess is that it will not correlate because there will be a much greater frequency of R1b than your genome wide data will indicate. He thinks there was a sex biased spread because males were more successful at spreading their genes. This indicates a violent takeover. Time will tell if this is the case.

Slides will be available.

Can you determine from which parent your chromosome ethnicity came from? If you have parents from two different regions, you would be a blend of those percentages, I think.

Will there be maps for non-European populations? Yes, they will expand this.

What does other mean? Everywhere else that you don’t see those three layers? (Africans, East Asians, and others who should not have these three components)

Max introduced Bill Griffith of CNBC’s The Closing Bell. Bill was interested in genealogy since 2003. One of his cousins asked him for information on the Griffith family and he had a single handwritten page. She later sent back an email file with the family history and he was immediately fascinated. He noticed an ancestor who had been executed in 1692 during the Salem witch trials and Bill was hooked. He and his wife visited many ancestral locations. He wrote a book called By Faith Alone. In August 2012 Family Tree DNA was having a sale and his cousin convinced him to test. In September, his cousin said they had a weird result and asked them to retest. On October 4 he had an email on his Blackberry from Cousin Doug telling him that he was not an R1 but an I1. He went through the phases of grief. The book is about his journey after his DNA results came back.

Bill is ok with it now. It is the truth. If you are going to begin to research, you must accept that genealogy is the search for truth. If you do it, you must be willing to accept whatever truth you uncover.

Bill went to another company, National Geographic, but he had no idea it was processed in the same lab. When Bill’s brother’s test came back, he was an R1 just like the cousins. Although his 94-year-old mother was the last person he wanted to talk to, he had to talk to her. Unfortunately, she was living far away but he was visiting for her birthday. He showed her his DNA test results and she confessed. Bill was out of sorts for a while and his wife started the research to find out about his biological family.

Bill has learned a couple of things. He is not unusual. His story is not unusual. Almost immediately after the book came out, he began hearing stories from people. One man discovered a daughter by doing a test he got for Christmas. There was one who matched a whole bunch of people including his biological father. This was news to both him and the guy who thought he was his father. Another man found out that he was adopted and that his biological parents were brother and sister. He heard many of these stories and writing about them on his blog.

Bill has realized that he was born a Griffith and raised a Griffith and now realizes that love is thicker than blood. The man he missed out on may have given him genes but the man who raised him gave him love and that accounts for a lot. He will always be a Griffith.

He has learned that people are complex. People sometimes do things they are not proud of. He had put his mother on a pedestal and that did not allow her to be a human being. She was the person who could do no wrong. Now he realizes it was wrong to put her on that pedestal and he needed to let her be a human being. We all do things we are not proud of. He is glad he knows she is a human being. She knows about the book. He was nervous about telling her about it but when he told her, she was ok with it. They don’t talk about this issue any more even though they talk every week. She respects his need to tell the story and he respects that she is from a different generation and does not want to talk about it.
bill-griffiths

Questions:

Have you made contact with any of your relatives? No, because his biological father is gone. His children and grandchildren are on Facebook. He knows enough about them but his fear is that he will show up and they will say, “Not another one!” They don’t deserve that disruption in their lives.

Did your mother know about DNA tests and worry about you finding out? She claims that she wasn’t sure who his father really was. She had convinced herself that Charles Griffith was the father. When she woke up and they gave her the baby, she commented on his red hair. In hindsight, she was probably freaking out.

If you were on the other side of the coin, would you have told your cousin? Yes, absolutely! Bill deals in truth – he is a journalist. Genealogy has taught him the pursuit of truth. Whatever the truth is, you need to reveal it even if it makes you uncomfortable.

Recommendations on how to approach someone with this test result? He told a woman to give a copy of the book first as an ice breaker.

What do you think about adoptees having access to their original birth certificates? I am in favor but that is a nuanced situation and perhaps case by case.

Have you told or given your son the option to name their children your biological name? He was named for both of his grandfathers. Bill has thought about changing his middle name but he doesn’t want his son to use the biological name.

Do you think it should be illegal to obscure or suppress information about biological parentage? He needs to give some thought. He believes that everyone should know the truth but legislation… I don’t know.

Does an adoptee have the right to medical history? That’s the reason he would want to reach out to his biological family. Realistically, half of his medical history is blank. His biological father lived to be 88 and his father’s sister lived to 104.

How did you choose your publisher? His publisher chose him.

Did you have any relatives that denied the results? No, only himself. He was concerned about one relative in California but she took it well.

How did your kids react to the result? They really didn’t. It didn’t bother them at all. They were surprised but there was no angst at all. He thinks it may be because his father passed away before they knew them.

Janine Cloud, FTDNA Group Projects Manager, presented Personal Privacy in Public Projects. Janine said, “DNA has opened a lot of doors. A lot of those doors were closets.”

The pendulum swings between sharing everything and sharing nothing but is there a happy medium? For group projects to be successful, you have to find that happy medium. It needs to be useful yet protect the privacy of individual testers. Ways to do this include having a robust, dynamic, privacy policy. We need to have informed, dedicated group administrators and we need to have respect.

The privacy and confidentiality statement is linked at the bottom of most pages of the website and linked at the point of purchase. There is a project application linked on the projects page. There are GAP guidelines located in the Learning Center and linked in GAP under Resources. It is also on the release form.

We don’t want to show the entire name with results and identifying information such as email. Sometimes MDKA can be a concern as well as the family tree, raw data, and other details.

The key is Express Written Condition.

Basic principles

  • Never share the FULL name of the tester without express written permission.
  • Never share the tester/kit manager’s email or physical address without express written permission.
  • Do not download raw data without express written permission.
  • Do not upload anyone’s raw data to a third party without express written permission
  • Do not place upgrade or add-on orders on project members’ kits without express written permission.

The privacy settings can be found at https://www.familytreedna.com/privacy-policy.aspx.

There is a section of the privacy policy that includes Group Participation. If someone changes their settings and doesn’t see it immediately, it may be a cached delay.

Where are the privacy settings? In the corner where your kit number is, click the dropdown and then click on Privacy Settings. On the Privacy & Sharing page, you can select privacy settings. There is a section on who can see you on the group list and who can view your DNA results.

The Project Application requires administrators to maintain the privacy of project members. Administrators may help members select the privacy settings.

It is important to respect the wishes and rights of the tester. The sample ALWAYS belongs to the tester. If you want to order an upgrade or add-on, and they say no that is their right. Testers and kit managers have the right to change their minds. Just because you can, doesn’t mean you should!

It is really important to name a beneficiary. There is a printable form that can be downloaded and notarized.

If you’re not sure about something, ask before you do it. The groups staff at FTDNA is happy to help.

Questions:

Bennett expressed that the things we have discussed come from experiences.

Is an email acceptable as express written permission? Yes.

If someone provides a pedigree for posting in an email is that permission to post? Max thinks it is express for what they are sending. If it is for something explicit, use it only for that purpose.

When a test owner dies and their children want to take over their parents kit but that parent did not provide a beneficiary, is there anything you can do? Send their conversation with you to groups@ftdna.com and they will explore it. There are issues of estate and litigation that need to be considered on a case by case basis.

Can admins have clear instructions on how to help testers change their privacy settings? There is a section in the learning center on that. They can work on a template for that if administrators prefer that.

What about ordering for dead members with no named beneficiary? The first thing you need to check is if there is an email that was changed in the record. Someone in the family may not be in charge of it. According to the privacy policy, ownerless samples return to FTDNA.

Why do we need beneficiaries since dead people have no rights including no right to privacy especially if they joined the project when they were alive? This is a tough one. Bennett said there are answers here that we can’t give. The last thing you ever want to do is be in a room with an attorney who says, “You just decided to upgrade this dead person?” Make everyone in your project understand that you want to do upgrades. Best is to have the person order their own upgrades.

Can beneficiaries assign beneficiaries after their own death? They would have to replace their name in the field with their own name. This makes FTDNA see the other person as their beneficiary. They would need to create another field for the beneficiary to name their beneficiary. This would be something they can look into.

Is there a way you can grant full access without sharing login information? They have heard this. IT can kick around the feasibility.

What do we do when a member is dead and we had their verbal permission but not express written permission. Can we still order the test? Janine is not a lawyer but she would suggest asking the family.

What do you do when a family member said the testee has died and the family has no further interest in the deceased’s kit? Not an easy answer.

If we have to get express written permission for upgrades, don’t you need express permission to change primers and reagents in the lab? For every test, there is an SOP and it’s written into a book that details all of them. When they change primers, they update the SOP book.

What constitutes written permission? If it is responded on Facebook and you capture that screenshot, then yes, that would be express written permission?

Can FTDNA add two levels of access – full access and view access only? Bennett doesn’t think this may establish what we’re looking for.

What about sharing info with related haplogroup administrators? Max says no. If the admin thinks it’s of interest to another project, then email the individual and let them know that there are other benefits by joining the other project and that is the way for the other project administrator to know about the person’s results.

Are there any plans for developing a platform for testers and administrators to contact one another without exposing actual email addresses? The easiest way to accomplish that would be to send emails through their server and then you would have to log in to get your emails. Bennett hates the idea and the room applauded to support this. Sites that require it don’t have the kind of activity that this platform enables. They don’t want to do anything that would slow down that process. The room clearly wants them to leave it.

We have a sample from a deceased cousin but don’t have the kit number. What do we do? Please contact the team and they will take care of it.

After lunch, there were six breakout sessions about the privacy policy.

During the afternoon session, there were three breakout sessions offered – beginner, intermediate, and advanced. I attended the advanced session “Genographic Project Database: How Genetic Genealogists and Academics are working together” by Dr. Miguel Vilar of the National Geographic Society.

miguel-vilar

Dr. Vilar reviewed that the Genographic Project is an ongoing global study launched by Dr. Spencer Wells in 2005 that aims to map human migration patterns by analyzing DNA samples from thousands of people from across the world. Recently they surpassed 800,000. Current statistics are about 730,000 public participants, 80,000 indigenous samples from field research, and $2.1M granted during the Genographic Legacy Fund.

Geno 2.0 Next Generation ties directly to Family Finder. The results transfer very easily to Family Tree DNA. Geno 2.0 provides three different kinds of useful data. Deep Ancestry includes thousbands of Y-SNPs for nearly every known haplogroup and hundreds of mtDNA SNPs, most comprehensive look, and is just short of a complete mtDNA genome. Regional Ancestry is calculated from 18 biogeographical regions, soon to be 26. There are 60 comparative populations. Hominim Ancestry is included as Neanderthal estimates based on the latest analyses.

Miguel wants to continue to decode the human story hidden in our DNA and now in their database. They want to continue to employ the best genotyping platform available specifically for anthropological genetics, by analyzing a comprehensive set of Y-chromosome, mtDNA, and autosomal DNA AIMs. They want to grow the citizen science component.

They have a collection of more than 15,000 SNPs, and many are still being placed on the tree. They reflect the new origin (A00) and new bifurcations. There are thousands of mitochondrial DNA SNPs and more than 95% in the coding region. Haplogroup calls are based on Phylotree Build 16 and are moving to Build 17 this year. Results are provided as biogeographical regions. They are interactive and grow with the database. MtDNA and Y-DNA results are provided in geographic, historical context for scientists and genealogists.

Geno 2.0 allows you to share a story but not presently to have any communication. The shape of the network diagram also tells you about your haplogroup. The Genographic Project Database, or DNA, is the result of 11 years of work. Currently there are 429,777 consumer participants in Geno 1.0, ~215,000 with Geno 2.0 results, and ~35,000 with Geno 2.0 Next Generation. 65% of these participants opted-in to science.

There is a Genographic Database (DAR) Search tool. You can search by mtDNA haplogroup, Y haplogroup, Y-SNP, mtDNA position (SNP), Place of birth, current zip code, maternal or paternal POB, maternal or oparental ethnicaity and language and the same from grandmaternal and grandpaternal.

Genealogists can also use it to research their own group: Origin, dispersal, and history. We can research by ethnicity and place of birth and migration, zip code if you’re interested in seeing where a certain group lives today, and research by SNP. We can help discover new branches of the Y and mtDNA tree. There are some ongoing projects. For more information, contact mvilar@ngs.org.

In 2015, they published six papers and this year they have published five so far. These may be of interest to genetic genealogists.

Dr. Vilar has been working on ongoing projects around the world. He shared photos of their field work in Chilean Patagonia in 2015. They have 48 Ancient DNA samples with rare and new lineages and 70 modern samples. They had great success with a project in the Dominican Republic.

INSERT PHOTO FROM CAMERA HOW CAN THE TWO WORLDS WORK TOGETHER

If you are working with data in the database and find something, contact Miguel and National Geographic may be able to put you in touch with another researcher. You can jointly apply for NatGeo grant to sample/analyze a new population group and perhaps even publish.

Dr. Vilar is working with six universities and a few high schools. More than 200 educators buy kits every year and they are looking to grow that. The teachers are interested in using it in the classroom as part of the curriculum.

Where is Genographic going in 2017?

Objectives

  • Grow the product to compete in current market
  • Broaden reach internationally (Latin America) and Bring in new audiences
  • Continue to drive engagement and consumer interest in the human story
  • Increase kit sales to support scientific research and cultural legacy
  • Build a Genographic community of Academics and Genealogists
  • Build a larger Education component

There is some renewed interest by the Media division of National Geographic. There will be more DNA articles in 2017 issues. The book Peoples of the World came out in Fall 2016. There are also joint projects with NG Television. These include The Great Human Journey (Spring 2016), The Human Family Tree revisited (December 2016) and they are in talks for more in 2017.

Long range goals are to empower and educate communities by demystifying genetics and bringing science to the field. To demystify the lab, they can use the portable sequencers in the future. Gorwing our knowledge of prehistory, deep ancestry, and human migration through new grants in Ancient DNA and collaborate to sequence 100 million people. They can reach uncontacted groups.

FTDNA Lab Manager Connie Bormans presented “What’s taking so long?!?!?! The Life Cycle of a DNA sample.” There are three main sections. These are Preanalytic, which includes sample collection and accessioning, which is the check-in process. One vial is put in the lab and one is put in storage. Once it goes to the lab, it goes to the Analytic process. This includes the DNA extraction, processing of the test, and quality control. Once the samples are processed, it goes into Postanalytic, which includes data analysis, quality control, and troubleshooting.

Stage 1 Preanalytic can have some sample accessioning issues. On occasion barcodes are written over, no swab is in the tube, two swabs are in one tube, little or no buffer is in the tube due to buffer leakage or spillage during collection, and some other known issues. One person sent in a kit for mtDNA testing. This was the fourth vial because three had failed. The technician noticed that it smelled like ethanol. It was not one of their kits but it was a spit kit that the person sent them. They ultimately figured it out and got it to work but if they had known about it, they could have processed it on the first try instead of the fourth try.

Stage 2 Analytic has more recently implemented controls to predict whether the sample is going to work in the lab. They take several measurements for DNA content and purity. If it doesn’t pass, they discard it and don’t process it. They will request the second swab from storage or send out a new kit. There are sometimes issues with DNA storage and retrieval. They only have one active DNA sample per customer at all times. Multiple tests may compete for the samples. They’ve done work with the time needed to retrieve samples from storage. The machine runs all night overnight so that there is a stack of plates available every morning. Another factor is the test processing. Different tests run at different speeds. There are different times for sample prep, time on the machine, and analysis. NGS tests have an additional quality control step before they go on the HiSeq or MiSeq machines. It’s an expensive test to run and they test the samples in advance to make sure the concentrations are highest.

Stage 3 Postanalytic is where there is a lot more quality control and they review the data. The analysis time varies for test type and depends on the number of samples and the analysis method. Potential issues include dropouts, which are missing STRs or SNPs, and the sample has to be requed. For failed reactions, it means the sample is run and they get no usable data. They reque the sample once and about 95% of the data is good. If there is a second failure, they stop work on that sample and send a new kit to the customer. Sometimes there is data that is ok but it is poor quality. The sample is requeued once. The majority of samples will pass on the second time but if it doesn’t, they discard the sample and start from the beginning. There are several analysis steps involved in Family Finder. The call rate must be >97% and samples below that prompt a new extraction. Generally, the samples have a call rate of >99%.

There are additional Postanalytic quality control measures. For all upgrades, new results are compared to previous results for YSTR, mtDNA, BigY, and SNP packs. Any difference requires review before the data is released. For NGS tests, coverage must meet the minimum required thresholds and low coverage samples are requeued. For family finder, predicted gender based on data must match the gender provided by the customer.

If you do not put the correct gender, they must stop and look at it. They will look at customer data and the release form or sometimes they have to contact the customer. This holds up the whole plate so please do them correctly!

Postanalytic troubleshooting is sometimes necessary. If a sample passes all QC but fails repeatedly, checks are performed to determine the best course of action. They confirm DNA integrity because degraded DNA will affect quality of results. They have to confirm that there is no genetic basis for failure and make sure there are no chromosomal deletions or anomalies or medical procedures. They also have to confirm that the sample is the correct gender. These are mostly YSTR failures for females trying to order Y-DNA tests. Based on the outcome, the appropriate course of action is determined.

The processing of samples is like a marathon. Everyone starts at the same time but everyone crosses the finish line for various reasons. Their goal is to remove or diminish the effect of each factor by predicting the likelihood of success or failure initially, reducing the number of dropouts and reruns, and by increasing the number of samples that can be processed in the same amount of time in the lab.

Questions:

What happens when someone dies but their beneficiary had ordered them a Family Finder and it comes out below your 97 but not much below. Are they out of luck? In special circumstances where no new sample is available, they will review the data and look at the SNPs that have data. Under special circumstances, they will post the data.

What about all the gender issues today? Gender issues today are a psychological issue and they can determine whether the person is male or female.

What do you recommend we do to make sure there is enough material for future testing in an elderly person? Get a spare vial and do a test and save it. Pre-extraction, they have samples from the same vial for 10 years and it’s very stable. Their experience is that if a sample has been extracted, they can reliably run it on anything they offer up to about two years. If it’s still in the buffer, then they have a very good chance of being able to extract it and run it even after 10 years. For unextracted, Bennett says it is almost infinite.

How many tests can be run from one DNA vial? All of their tests can be run from one single vial.

An older gentleman has run several tests. Can we ask him to send DNA for future storage? Yes. If you have an 89 year old mother and you want to test her again, tell customer service and they will check if there is an unextracted vial in stock. If there is nothing in stock, it would be appropriate to ask for a secondary collection kit.

If we order a test for one gender and then change, is there a way to change it? Call customer service before you send in the sample.

What are the benefits of the swab test over the spits kits? Connie says that it’s awful to do the spit kits. It smells terrible, it’s messy, and it’s not easy to automate. They can now extract 1800 samples per day and if they need to, 7 days per week.  Bennett added that the competition never offers public testing because there aren’t enough places to discretely spit.

Can these be used if someone has died? Yes

In the postanalytical stage and a sample passes 3 out of the 4 and is rerun and then run 4 of 4, they compare the two. Always.

What percent of samples that pass all QC fail repeatedly? They are generating data on this now. It’s less than two percent.

The current storage system has been in the lab since 2011. They are exploring options for replacing it. They are talking to several companies and evaluating the pros and cons of each.

When you order an STR upgrade and a SNP at the same time, do you wait for completion of one to start the enxt? No, they withdraw a subset and start one test then put them back within a day or two and they are available for the next test.

Do you test tissues stored in paraffin blocks? No, low success.

Do you have any plans to offer testing of non-standard samples such as hair, teeth, envelopes, and the like? Bennett said the results were almost universally poor when they tried it. They extract plates of 96 by 6, 12, or 18 plates at a time. The likelihood of success is so small and it has to be done on a one off basis so a technician has to spend most of their day working on a single sample. From an economic sample is doesn’t make a lot of sense. If they had a high success rate, he would be willing to disregard those other issues. This is not a good media to count on. There are contamination issues with these kinds of samples, too. They would prefer not to engage in it. Connie also talked about permissions and the problem about surreptitious DNA testing. The litigation risks are high.

Michael Sager had applied for a job a couple of years ago in the lab and there were none available so he started in Customer Service. He is currently a Data Analyst with them. His Master’s degree was with African Dwarf Crocodiles but he has been able to transition. He interfaces with all of the SNP packs.

Michael said that they are getting their tree back up to speed. They have designed some tools that allow him to look at BAM files instantaneously. Implementing tree updates quickly is something he is really happy about.

In May 2015 they had 6,556 SNPs on their tree and as of now here are 23,767 SNPs on the tree and after Monday it will be over 24,000. They have 6,728 unique haplogroup labels and 3,192 total “terminal” nodes. In the end, the best trees are going to come from the admins. Each subject matter expert will have the best tree.

Michael gave some haplotree update guidelines.

  1. SNP Name*, position (h919), mutation
  2. Proposed phylogency/SNP positioning
  3. Provide kit proofs
  4. Avoid heavy recurrent, STR embedded, and other unreliable SNPs
  5. Must be FTDNA generated data
  6. No private SNPs (2+ required)

Michael’s email is michaels@genebygene.com and he is happy to hear from any project admins.

Michael talked about SNP packs. They are carefully designed panels of SNPs that are specific and encompassing to a particular group. (m343, L21, etc.) It is a cost efficient method to move a tester down the tree instead of purchasing a Big Y and instead of just trying to test one SNP at a time and trying to get it right. One of the caveats is that you cannot discover but you can match existing things. You can, however, break equivalent blocks.

Currently there are 77 active panels with about 35 more in various stages of design. They are expanding 8 haplogroups (E, G, I, J, N, Q, R, T) and that number will be up to 9 soon when they release a haplogroup L panel.

The SNP pack process starts with project administrattors who submit panel proposals (140 max). It then goes to computational QC with Dr. Nossa. Then they do a phylogenetic analysis and tree building, validation, content finalization, and released to the advanced orders page. There are a couple of lab techs who process and score every SNP pack order and then they go to Michael for a check and then released to the customer.

Questions:

Can I buy just one SNP used to be no but as of today, every SNP can be purchased individually. They added over 4,000 SNPs to the Advanced Order page. Connie put in a lot of work on that.

Can FTDNA give a table that provides information for the SNPs for Big Y? They will be updating but for right now, he can email you anything that you need to know. There is nothing on the website right now.

Where can we find a list of the packs? On the Advanced Orders page.

How is a SNP deprivatized? Currently a private SNP is something where there is only one case. If someone else comes along positive for the same mutation, it is no longer considered private.

Plans for an I-M253 SNP pack? They are going to make it more like R1b.

Why is the tree not downloadable? They need to kick that around.

How far up the tree can two people match Big Y and get a notification? It seems too far removed? Bennett will work on getting that answered for tomorrow if the person gives him more info tonight.

Do you list all of the names of a single SNP? Michael thinks it means synonyms and no, they do not. For instance, they do not list the alternate S name for L21. What they try to do is use the name that is the most widely accepted.

Will SNP packs be updated automatically as the FTDNA tree expands or as admins request them? When he is scoring these packs, Michael knows if there are unique results. If they are unique and not reflected on the tree, he will update it right then and there.

What is the possible explanation for a positive result in a SNP pack and a later Big Y Bam file that shows negative? There could be a calling error in either one but more times than not, the presumed negative answer is because there was a hole in the Big Y dataset where there wasn’t enough data to make a call at that particular location. Tomorrow there will be a technical explanation to address that.

I ordered a DF21 SNP pack then a modified SNP pack came out right after. Which will be run? If it hasn’t been run yet, see Michael and he can sort out which one to run with you.

There are 6 men in my project who are R-M269 and tested 37 markers. They have matches with Z-156 and U-106. Which one to take? Probably better to take U-106 rather than come up negative on Z-156.

Is it worth it to take a Big Y a second time? Michael would advise against it.

How does Big Y compare to Y Elite? Michael doesn’t deal with anything from FGC so he is not sure.

Do you discard vials that have no readable or usable DNA left? Yes, we will toss it. We always err on the side of having fresh and robust DNA to run successfully and completely the first time.

Is one DNA test always done before another? Connie said they are not always performed in the same order. It’s based on numbers. The products that has the most tests available get pulled first and that varies daily.

I have some extra vials stored in my freezer. Max says they do not need to be stored in the freezer. These vials were used by University of Arizona for anthropological work and it doesn’t matter how you store them. Just this week Max worked with a sample that’s been stored for 13 years. Family Finder may encounter issues with old vials.

Can a SNP pack test for indels? Yes, they do have the ability but they have to be small indels with 1 or 2.

What is the future of Ysearch or any alternative? They have a partnership with MyHeritage and they added DNA tests and the ability for you to embed your Y-DNA results into the trees they have at Geni.com. This will eventually be a much better replacement for YSearch. This week they launched the test under their brand and FTDNA is performing the tests for that.

A group of recent Big Y tests were recently posted then withdrawn then reposted. Should there be a concern? That day one of the file repositories got really full. They were not able to find out whether the matching algorithm had completed successfully for everyone so they removed all the data, made more space, and restarted the process.

What do you do with people with 3 sex genes? In the case of Family Finder, they post the results. There are no anomalies. In the case of Y, Connie does not recall testing anyone. If it’s YXX and they’ve ordered Y, they will post the Y as normal.

Do you have any blank kits available here? Yes, see Janine. Bennett also has a dozen kits in his car because he never leaves home without them.

Do you anticipate the SNP mutation frequency to be the same in all haplogroups? Errors in your DNA do not care what you are. With a larger sample size, Michael expects it to be the same and with Big Y SNPs, that is one every 3-4 generations.

Please share a couple of wow moments you had over the last dozen years? Seeing us is a wow moment for Bennett. Bennett says it started in the proof of concept when the two cousins didn’t match each other. When someone scraped their dog and they tried to get that sample, that was a wow moment. Max added that they used to offer 3 vials. People started making jokes about the third cheek so they discontinued them.

Is the processing log of a failed test available to an administrator? Different tests have different logs. They can tell you the call rate on FF. That’s the only case where they would not post the result from a sample.

I have four men with Big Ys who have a tree to the most recent ancestor in 1380. If you collect these dates it should help you to date these SNPs.? Send info to Michael.

When making a distance from private to SNP on the tree, do you look at the closeness of the relationship? No, they do not look at the closeness of the two testers. He’s not doing tree updates himself. A lot of this is coming from project administrators. He sees no issue with getting as many SNPs that follow guidelines onto the tree as possible.

Max announced the ISOGG get together at the Lonestar Room at 7:30. Non ISOGG members are welcome. Jewish Project Administrators will have dinner in the restaurant at 6:00 PM.

I was told a particular kit was not good for FF in 2004. Is it better now? No, it still requires the same input of quality and quantity. Bennett added that if you tested in the first couple of FF, it didn’t work on that platform but it did work on the Illumina.

How often is the Big Y match updated to reflect the current tree? Matches are dynamic. There is no automatically drawn tree from Big Y data.

How about imposing some reciprocity on people who want to have extreme privacy? If they don’t want to share MDKA ancestor, then don’t let them see others. No freedloading. Bennett said even he understands that.

Are you having a sale after this conference? Bennett and Max will talk about it today and tell us tomorrow what they decide.

Where can we find the SNPs associated within STRs or the HG19 positions? Michael can get them for us and he thinks they are mostly available on Y Browse.

What ancient DNA labs would be able to analyze samples for genetic genealogy? Mike Hammer does not know of any commercial labs

When we discover a novel SNP with two people how do we get that SNP named without a third-party service? Keeping and storing primers associated with the SNPs in a library for something they may run once or twice may get overwhelming. If you think it will be ordered by multiple people, they are willing to entertain it. If you simply want something named, tell Michael.

My project members who are I1 do not have suggestions for SNP packs? If project members have STR results and no haplogroup label, they should have run a backbone if they could not predict them. Anyone in I should have a clear idea of what SNP pack to order but Michael can help with that.

A member is R1a but they match too many men who are R1b at 37 perfect match? Mike Hammer thinks that strange and no one else in the room has seen this. Provide the kit number and they will look at it.

SNP packs – version 1 doesn’t include as many SNPs as version 2 and they can’t get an answer if people who took first can upgrade to second at a reduced price? Bennett wants to finish the 35 SNP packs that has been requested and then go back to the SNP packs and include new discoveries. They will need 1-20 new SNPs and sometimes it will entail starting the panel from scratch. They will probably err on the side of offering a reasonable discount for those who already purchased one a year ago. To help alleviate that, they have also made thousands of individual SNPs available. They will probably make a decision on that in the first quarter.

5:04pm central

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