Professor Henry Louis Gates Jr. joins Dr. Spencer Wells as Headline Speakers for "Family HIstory and DNA: Genetic Genealogy in 2013"

I am so pleased to be able to say that the support for the inaugural independent genetic genealogy conference has exceeded my most ambitious aspirations. My appreciation goes out to Professor Gates, Dr. Wells and all of our wonderful speakers for graciously and enthusiastically accepting my invitation to be part of this groundbreaking event. (You can register here.) The press release announcing the exciting addition of Professor Gates to our schedule follows:

“FAMILY HISTORY AND DNA: GENETIC GENEALOGY IN 2013”

TO FEATURE SPENCER WELLS, PH.D. AND HENRY LOUIS GATES., JR., PH.D.

It’s rare that a new type of event is introduced to the genealogical community. The Southern California Genealogical Society and the International Society of Genetic Genealogy are proud to announce such an event.

“Family History and DNA: Genetic Genealogy in 2013” is a one-day conference designed to fully explore the application of genetic genealogy in researching family history. It will be held Thursday, June 6, 2013, at the Los Angeles Marriott Burbank Airport, Burbank, California. Registrations are open now and an early-bird registration discount is in place through April 30.

“We are so excited that this new conference will break new ground in genetic genealogy gatherings,” said SCGS president Alice Fairhurst, who helped to found the society’s DNA interest group and has been actively applying DNA in her own genealogy research. “Family History and DNA” differs from other DNA events in several ways.

First, speakers are among the most highly respected and knowledgeable professionals in the DNA and genetic genealogy universe.

The opening session will be conducted by Spencer Wells, Ph.D., an Explorer-in-Residence with the National Geographic Society. He leads The Genographic Project, which is collecting and analyzing hundreds of thousands of DNA samples from people around the world. Dr. Wells’ presentation is “The Genographic Project and the Rise of Citizen Science.” 

The luncheon speaker will be Professor Henry Louis Gates., Jr., Ph.D., director of the W.E.B. Du Bois Institute for African and African American Research at Harvard University. Dr. Gates is an American literary critic, educator, scholar, writer and film maker. His programs for PBS, including Finding Your Roots, African American Lives, Faces of America and Oprah’s Roots, explored family histories of a number of individuals through the use of DNA.

Other speakers include Judy G. Russell, JD, CG; Richard Hill; Emily D. Aulicino; Katherine Hope Borges; CeCe Moore; Tim Janzen, MD,; Blaine Bettinger, JD; and Debbie Parker-Wayne, CG. We are grateful for the enthusiastic support shown by all our speakers, especially Dr. Well and Dr. Gates, through their participation in this conference.

Second, “Family History and DNA: Genetic Genealogy in 2013” is produced by independent groups, not for-profit DNA organizations. The Southern California Genealogical Society (SCGS) and the International Society of Genetic Genealogy (ISOGG) have joined forces to offer this inaugural DNA event. While it is independent of financial support by any of the commercial DNA companies, the event will provide equal access to Family Tree DNA, 23andMe, and AncestryDNA.  

CeCe Moore, speaker, conference co-chair and Southern California Regional Coordinator for ISOGG explained, “I've dreamed of a genetic genealogy conference sponsored by ISOGG for a long time, and I am thrilled to be working in cooperation with SCGS on this inaugural event. Holding the conference in conjunction with the Genealogy Jamboree helps us reach many family historians who would otherwise not be able to attend.”

Finally, the event’s three session tracks are organized by the level of experience using genetic genealogy, and not based on the attendee’s knowledge of family history. Sessions include beginner basics, use of DNA in finding adoptee families, famous DNA, autosomal DNA, mitochondrial DNA, analyzing results and other topics. The final hour of the day will be a resource hour, with small-group discussions and supplier assistance.

Complete information about “Family History and DNA: Genetic Genealogy in 2013” and the Southern California Genealogical Society’s 44^th Annual Southern California Genealogy Jamboree can be found on the Jamboree website, http://www.genealogyjamboree.com.

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The Southern California Genealogical Society is located in Burbank, California. It sponsors the annual Southern California Genealogical Jamboree, which will be held June 7 through 9, 2013, at the Los Angeles Marriott Burbank, Burbank, California. The pre-event is the inaugural “Family History and DNA: Genetic Genealogy in 2013” conference.

Upcoming Presentations: Spring 2013

With three presentations last week and a number more coming up in the next few weeks, I am fortunate to have many opportunities to educate genealogists on my favorite subject, DNA. Here is what is coming up on my schedule:

• This weekend, I am presenting at the OCCGS Genealogy BASH in Huntington Beach. This event is a celebration of the 50 year anniversary of the Orange County Genealogy Society held on Saturday, March 2nd from 8:00am - 3:30pm. I am joining seven other favorite Southern California speakers: Barbara Renick, Jean Wilcox Hibben, Norma Keating, Gina Philibert-Ortega, Randy Seaver, Linda Serna, Dawn Thurston and will be giving two talks on genetic genealogy in the afternoon. The event will be held at the Huntington Beach Central Library, 7111 Talbert Avenue, Huntington Beach, CA 92648.

• Next weekend, I will be speaking at Discover Your Roots XI: 11th Annual African American Family History Conference in Los Angeles. This is an all day event on Saturday, March 9th from 9:00am - 4:00pm to be held at the LDS Historical Chapel, 1209 South Manhattan Place, Los Angeles, CA 90019. I am joining 21 speakers at this event and will be giving a beginning genetic genealogy presentation in the afternoon. 

• On March 22nd and 23rd, I will be presenting two sessions at RootTech in Salt Lake City. "The Genographic Project 2.0" will be on Friday and the "Ask the Experts: Genetic Genealogy Panel" will be held on Saturday morning. 

• On March 30th, I will be teaching an all day genetic genealogy workshop for the Chula Vista Genealogical Society.  This is their Spring Seminar and will be held from 9:00am- 3:00pm at the Chula Vista Golf Course, 4475 Bonita Rd, Bonita CA 91902. This workshop will give attendees a good foundation for applying their DNA testing results to their genealogy research. The fee to CVGS members is only $35, $40 to non-members and late registrants after March 22 and includes a catered lunch. You can register here. There will also be copies of Richard Hills' terrific book Finding Family: My Search for Roots and the Secrets in My DNA available for purchase. The Chula Vista La Quinta Inn has a block of rooms reserved for only $80 for the seminar (mention CVGS). Reserve by March 4th to get the discount.

• On April 20th, I will be speaking about beginning genetic genealogy at the Ventura County Genealogy Society at 1:00pm. This will be part of their monthly program series and will be held at the LDS Church, 3501 Loma Vista Rd, Ventura, CA 93003. 

• On May 17th, I will be speaking at the San Diego Chapter of the DAR monthly meeting at 11:00am. The meeting will be held at the Admiral Baker Golf Course, located at 2400 Admiral Baker Rd, San Diego, CA 92120.

• On June 6th,  I will be giving an intermediate level presentation on Autosomal DNA for Genealogy at the Family History and DNA: Genetic Genealogy in 2013 conference. I will be joined by many of the most respected speakers in the field.

• I will be involved in three presentations at the SCGS Genealogy Jamboree on June 7th and 8th, On Friday, I will be participating in the "Genetic Genealogy: Ask the Experts" panel and on Saturday I will be presenting "Using DNA Testing to Discover the Genealogical Roots of Adoptees" and participating in the Blogger Summit panel with Thomas MacEntee. 

Whew...it is going to be a very hectic couple of months! I look forward to meeting many of you while I am busily spreading the news about the fascinating and increasingly exciting world of genetic genealogy!

Family Tree DNA Lowers the Price of the 12-marker Y-DNA Test to $39 in Step Toward Universal Access

A DNA test for only $39 = Universal Access! This is terrific news for anyone who wants to "dip a toe" into the waters of genetic genealogy. It is also a great opportunity to get your relatives' DNA in storage for future use since Family Tree DNA will store it for, at least, 25 years. The press release announcing the news will follow:

HOUSTON, Feb. 20, 2013 /PRNewswire/ -- Family Tree DNA, the genetic genealogy arm of Gene By Gene, Ltd., is dramatically lowering the price of one of its basic Y-DNA tests to $39, making it the lowest-cost DNA test available on the market, in order to take a major step toward universal access by individuals to their personal genetic data. 

By dropping the price of its basic Y-DNA test by 60 percent to $39, Family Tree DNA -- the world's largest processor of Y-DNA and full mitochondrial sequences -- is working to eliminate cost as a barrier to individuals introducing themselves to the insights and knowledge to be gained from personal genetic and genomic research.

Family Tree DNA pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago, and has processed more than 5 million discrete tests for more than 700,000 individuals and organizations since it introduced its Y-DNA test in 2000.

The test investigates specific Y-DNA locations for males that provide individuals with their haplogroup, or the deep ancestral origin of the paternal line.  In addition, it can indicate if different individuals are likely to share a common male line.

Gene By Gene is also working to lower the cost of Family Tree DNA's comparable mtDNA test, which would be applicable to both females and males and provides data on the direct maternal line.  The company expects to unveil new pricing for this test in spring 2013.

As the sponsor DNA Workshop of "Who Do You Think You Are - Live" in London this February, Family Tree DNA expects that the reduced price test will add a great number of individuals to its already large database – the largest of its kind in the world.

"We believe the first step to unearthing your personal and family history is to better understand your DNA," Gene By Gene President Bennett Greenspan said.  "That's why we are continuously investing in new technology and experienced scientists at our Genomics Research Center, enabling us to conduct tests more accurately, efficiently and at lower prices.  Our $39 Y-DNA test is just the latest example of how we are working to help individuals gain access to their genetic data."

Customer Inquiries Individuals interested in Family Tree DNA's $39 Y-DNA test, or any of its ancestral testing products, can visit www.familytreedna.com for more information. 

About Gene By Gene, Ltd. Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests.  DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide.  Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.  

Media Contact: Kate Croft
for Gene By Gene, Ltd.
Casteel Schoenborn
888-609-8351
croft@csirfirm.com

SOURCE Gene By Gene, Ltd.

RELATED LINKS
http://www.genebygene.com

A Visit to Family Tree DNA's State-of-the-Art Lab

The array viewer of FTDNA's Applied Biosystems 3730xl DNA Analyzer - that's DNA!

I have been a bit behind in my postings, but I didn't want to miss the chance to write about the incredible lab tour of Family Tree DNA's awesome facility, which was definitely one of the highlights of the 2012 FTDNA Administrator's Conference for me. I don't know if you all realize it, but Family Tree DNA is the ONLY company in the field that has their very own lab. They process everything from start to finish in their state-of-the-art facility in Houston for the thousands of different DNA tests that they offer. (Thomas Krahn notes that the individual Y-SNP tests alone number over 2900!) Some people might find it comforting to know that when ordering a test through FTDNA, this very trustworthy company is the sole handler of their DNA sample. 

Bennett Greenspan, CEO of FTDNA with stored B-Swab Samples

This lab is even capable of processing exome and whole genome sequences. (These are available through Family Tree DNA's sister division DNA DTC, both a part of Gene by Gene). Max Blankfeld proudly told me that almost immediately after the announcement, they were already receiving orders for both tests. This is really exciting if you think about it. The first company to offer genetic genealogy testing is, according to The Genomics Law Report, also the only company currently offering these advanced tests-of-the-future in a "truly direct-to-consumer manner".  ("Gene By Gene probably does represent, however, the only commercial company currently offering a whole genome sequence in a truly direct-to-consumer (DTC) manner." DNA DTC: The Return of Direct to Consumer Whole Genome Sequencing, Dan Vorhaus, November 29, 2012)

Okay, on to the lab tour! Tim Janzen has kindly shared both his notes and his photos with my readers. I have added to Tim's notes just a bit, but most of what you see below was written by him. (I lost my notes and, although I did use some of them, the photos from my cell phone aren't as nice as Tim's photos from a "real" camera!)

Tim was smiling like this pretty much the entire tour!

On November 12, 2012, Family Tree DNA graciously allowed approximately 30 attendees from the FTDNA conference to take one-hour tours of their laboratory facilities in Houston, Texas. Bennett Greenspan, the president of FTDNA, primarily led the tours and Max Blankfeld led some supplemental tours (for those of us who showed up late!). The tour participants all donned lab jackets for the tour, making us feel very official (I got to be Thomas Krahn). Bennett explained the functions of a number of very important pieces of DNA equipment as he took us through the lab.  (Update - Thomas Krahn has added some very interesting and educational commentary throughout this post. I have added it below or just after what it is referencing. Thanks Thomas!)

"Your Genetic Genealogist" parading as Thomas Krahn
Do you think I fooled anyone?

One of the first pieces of equipment we viewed is used to extract the DNA from samples that are sent to FTDNA. The DNA is extracted through an automated process. Ninety-six samples can be processed at a time. FTDNA can complete 600 extractions per day and has a 98.8% success rate of extracting DNA on the first try.  

Another piece of equipment held primers that are used to test for specific short tandem repeat (STR) tests and single nucleotide polymorphism (SNP) tests. (Note from Thomas Krahn: We're taking the DNA from the DNA tubes and transferring  them to a reaction plate which contains the primers and the rest of the PCR assay. In a previous step the primers were distributed in the correct wells by automatically picking the correct primer pair so that the customer gets the segment sequenced where the marker is located that he's interested in.) This process is also entirely robotized so that multiple tests can be run at a time. The lab must repeatedly change the plastic covers on the pipettes to ensure that DNA from two different samples is never mixed as part of the testing. (Note from Thomas: We use the covers just as a precaution. In case a droplet is released from the pipetting tips during the movement of the robot we want to make sure that the primer assays are not contaminated with human DNA. With lids the primer library is safe. We would easily recognize such a contamination because of mixed basecalls, however primers are expensive and we want to protect the primer library from such a contamination. The chance that DNA samples mix is pretty small because we reduce the speed of the robot drastically while we have the tips over the DNA plate. In any case such a cross contamination could probably not be prevented with a lid method. The pipetting tip is discarded after the DNA from one person is distributed into all the assays that he ordered. Each DNA sample gets a brand new tip so that cross-contamination through the tip itself can be excluded.)

FTDNA's automated equipment that is used to combine DNA with primers

Bennett Greenspan proudly showed off the robotic DNA storage freezer that the company purchased in autumn of 2011. It was designed and manufactured by the engineering company Matrical Bioscience in Spokane, Washington. This piece of equipment took many months to design and build. After it had been built, it was disassembled and shipped to Houston. The installation process in the FTDNA lab took approximately 6 weeks. This chamber stores multiple small trays that hold 96 DNA samples each. The samples are held in small vials about 3/4 inch in height and about 3/8 inch in diameter.  The trays holding the samples are about 4 inches by 7 inches in size. There are thousands of trays stacked on top of each other in a -20 degrees Celsius chamber approximately 5 feet by 8 feet in size. A robot inside this chamber retrieves DNA samples from the approximately 175,000 samples that are stored there in a very strictly regimented and automated fashion. (Note from Thomas: I have just made a query and there are currently 173,012 DNA tubes in the store. However more than 50% of them have been added during the last year. 500,000 is the approximate number when the store is 100% full. We have rigorously sorted out empty and bad tubes from our repository in the past and we run regular compression procedures so that the racks are not half empty.) This robot is wired to a computer station outside the room. At the computer terminal a lab technician can enter a series of kit numbers for DNA samples for which additional testing has been ordered. The technician can then leave the area to do other things while the robot automatically retrieves the samples that were chosen. Ninety-six samples can be retrieved at a time and the retrieval process takes approximately 30 minutes. When the retrieval process has been completed the technician then returns to the storage unit, picks up the tray of samples and takes it to another piece of equipment for the additional testing that the customer has ordered, such as upgraded STR panels or individual SNP tests.

The interior of the MiniStore storage chamber. The robot is retrieving samples.

The functions of other pieces of equipment in the lab were also explained by Bennett. One machine is used for mitochondrial DNA sequencing. There is also another piece of equipment that is used to lyse the cells in each of the DNA samples and prepare them for extraction of the DNA. Additionally, Bennett showed us a room that contains thousands of DNA samples that have not yet been processed. These samples are held in long-term storage at room temperature for eventual use by customers who wish to order additional testing. 

Bennett also took us to a different room where the Geno 2.0 SNP chip tests are being processed. Approximately 154,000 SNPs are tested on a single chip for the Geno 2.0 test. Considering this, the chips are relatively small at approximately 1 inch by 4 inches in size. The actual scanning area is only 5mm by 5mm per assay. (Note from Thomas: On one of those glass slides there are 12 samples processed simultaneously.) At the time we were there, thousands of chips were being processed.  

Bennett holding one of the Geno 2.0 SNP chips

Bennett showed us the new sequencing machines that were recently purchased so that the company can do large-scale complete genome sequencing. The two new Illumina HiSeq 2000 machines can sequence 10 times as much as the Applied Biosystems DNA Analyzers are capable of using 454 sequencing and can sequence a complete genome in three runs. These machines are approximately 2000 times as efficient as using the primers used in Walk Through the Y testing and are 100 times as efficient as the Applied Biosystems 454 sequencer. (Note from Thomas: The HiSeq instruments are producing more sequences so that you get a higher coverage. If the machines are also more "efficient" for finding new mutations by the same scaling factor is still to be demonstrated. Simply scaling the average coverage of 400 KB from the WTY times 2000 would yield 800 MB, however the Y chromosome is only 50 MB long and only 20 MB can be effectively aligned to the reference sequence. To overcome this problem you'll want to enrich for target specific DNA and you'll want to barcode several samples so that they can be pooled together on one instrument run. This again reduces the "efficiency" by quite some significant percentage.) FTDNA has two new Illumina MiSeq DNA sequencers as well. The lab now has the capability to sequence six whole genomes in two weeks and 64 exomes at 80x coverage in one week.

Bennett discussing the two new Illumina HiSeq 2000 high output DNA sequencers

The FTDNA lab tour was an exciting experience. It was very interesting to see all of the technicians at work running the various DNA tests that we as FTDNA customers have ordered. I was incredibly impressed by their vast array of state-of-the-art equipment. Hopefully, Bennett and the rest of his lab staff will continue to allow these tours for attendees at future FTDNA conferences. If you haven't seen it yet, it is well worth your time and I highly recommend it.

The following may be overkill for some of you. If so, I will just say goodbye to you here. However, if you are like me and you just can't get enough or want to gain a better understanding of how this all works from the inside, here is a series of photos from the lab tour.  

FTDNA's Biomek FXP Laboratory Automation Workshop, used for DNA extraction
and primer stamping for pre-arrayed assays (such as FMS or WTY)

FTDNA's automated equipment used to prepare PCR assays

Comment from Thomas: FTDNA's automated equipment that is used to combine genomic DNA with primers to prepare a PCR assay. An in-house developed software controlls the pipetting steps so that the ordered assay is run with the correct DNA.

FTDNA DNA lab technicians at work

FTDNA lab tech pipetting a cheek swab sample to prepare for DNA extraction

Comment from Thomas: This is the only step that still needs to be processed manually because we haven't found a robot that is able to remove the cotton swab from the vial yet.

More FTDNA lab techs at work

Tim checking out FTDNA"s MiniStore re-arraying platform inside the DNA freezer

Comment from Thomas: (This is) where the individual DNA sample tubes are re-arranged to the position where they will be processed in the assay. We try to prevent thaw and freeze cycles wherever possible because they will degrade DNA. So instead of taking out a complete plate (where we may only need a single sample) and thaw it completely, we use this technology of re-arraying tubes in the frozen state so that only the processed samples will be thawed and all other samples will stay frozen. The DNA samples/plates are actually stored in the back compartment and on the left side. Those areas are not clearly visible in the image. 

The interior of the MiniStore storage chamber holds over 500,000 DNA samples
(seen at the back side)

One of the thousands of plastic trays that FTDNA uses to hold DNA samples

Shaking incubation chamber used to lyse cells so that DNA can be extracted

Comment from Thomas: The recipe for the liquid in the sample vials is optimized for long term storage under a large variety of storage conditions. Essentially the high salt concentration will suck out all water from inside the cheek cells (by osmosis) so that the cells form compact clumps and conserve their ingredients. This makes the sample more resistant to mechanical shearing and the high salt concentration also inhibits growth of micro-organisms that could digest the cells. The downside of this is that we need to use harsh mechanical forces when we enzymatically want to open the cells to extract the DNA. Shaking a 2 ml sample tube in an upright position doesn't really move the liquid in the tube a lot. Therefore we turn the tubes horizontally and shake them along the tube axis where the liquid has a longer path to accelerate. This method has been proven to be very effective.

Biomek FXP Laboratory Automation Workstation

Eppendorf Mastercycler thermal cyclers amplify DNA segments

Linda Magellan with 1 of 3 Applied BioSystems 3730xl DNA Analyzers

Bennett with FTDNA's 2 Illumina MiSeq DNA sequencers in the background

FTDNA technician processing Geno 2.0 SNP chip tests

Close-up of tech processing tests, note the SNP chips in the liquid

Stacks of hundreds of Illumina SNP chips that have been completed

Comment from Thomas: Before we dispose the chips to the glass recycling facility, we temporarily store them for a few weeks. During a 48-hour time frame they are still good and since they are barcoded we may have the chance in rare cases to re-scan a chip in case some bad read happened at the scanner.

Bennett holding a box of 100 unprocessed samples being held in long-term storage

FTDNA's storage room where 1000s of unprocessed samples are held...

...Can you see yours?

Water purification system

Comment from Thomas: In order to get ultrapure water for molecular genetic assays (such as PCR) the tap water needs to pass through several steps:
1.) Pre-filter to remove particles such as sand and rust from pipes
2.) Membrane filters to get rid of small particulate material
3.) Ion exchangers to remove Ions and salts
4.) Reverse osmosis to remove organic compounds. At this stage we use the water for general cleaning purpose such as for the lab dishwasher and for rinsing flasks. However to get PCR grade water we continue with:
5.) Another step of ion exchange and reverse osmosis in a laboratory grade water purification system to remove any contamination coming from the plastic tube piping internal of the lab.
6.) Then the water passes a sterile filter before it is bottled in a glass flask to remove bacteria and other micro-organisms.
7.) Finally the bottled water is heat sterilized in an autoclave at a temperature that should degrade all possible DNA chains that may have survived to this point.

We also have a room with two air compressors that supply compressed air for the robots. One of them is a backup system because at an interruption all robots will stand still. They are in a separate room across the hallway because they're quite noisy and produce a lot of heat.

Bennett with Geno 2.0 SNP chips

Illumina MiSeq machine

Bennett demo-ing the Illumina MiSeq machine

Automated pipetting system

Allied BioSystems 3730xl DNA Analyzer, used for sequencing

Comment from Thomas: Each lane represents a sequencing trace where the bases are displayed in 4 different colors. This display format gives the technician a quick overview about the quality of the complete run. The fluorescence intensities are digitized by a analog to digital converter so that it can be saved on a computer, but they still represent analog measurement values. When talking about a digital output the impression could arise that the display shows the scored base-calls which is really processed in a later step.

Max Blankfeld leading the late arrivals

Bennett amuses Lauren (and the rest of us as well)

Did someone ask a question that stumped Bennett?  Nah!

Ever wonder where your customer service calls go?

Jeremy happily assists customers

FTDNA employees preparing DNA test kits

Bye-bye FTDNA! See ya next year.

Thanks to Tim and Rachel Janzen for sharing their photos, Tim for helping to write this and to FTDNA for the spectacular tour.