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Thread: Bonnie Schrack's A00/Cameroon project -- what happened?

  1. #11
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    UPDATE #1
    Your patience will be rewarded
    Tonight we saw Matthew appearing on PBS, on the First Peoples TV series, about the evolution and migrations of humankind. Jacqueline Johnson, to whom we owe the discovery of A00 through her research on her Perry ancestors, played a great role, telling her family's story and what it led to. Matthew was shown in Mbetta, his home town, where he brought the film crew from Wall to Wall productions, the creators of the documentary. When they approached us, their project seemed so good that we didn't want to turn down their request to see Matthew in action in Africa, even though we weren't ready to actually begin our field work.

    We would never start the gathering of samples for our study without having passed through the entire ethical review process that's required of all human subjects researchers in our time. This is vital to prevent exploitation or inhumane treatment of the people who donate their DNA for the sake of scientific progress. But it has been an awfully long process for us, mainly because we had no experience, and no advisers to teach us how to write the lengthy and complex documents required. Over time, we did discover the incredible talents and generosity of Blaine Bettinger, attorney and genetic genealogist, who played a crucial role by drawing up our Materials Transfer Agreement, and helping us greatly with the many revisions the ethical review committee required of us.

    All of this was gradually being played out, but the filming could not wait for it to all be completed. So what transpired was that Matthew enacted the sampling just for the film crew (who had brought their own informed consent forms), and the samples from that occasion are not being used in our study. They will not be included among our pool of samples that will be analyzed and studied. This is unfortunate, of course, but not a terrible loss, as there are many more men in the Nkongho-Mbo villages who have not yet been sampled. Most of the A00 originally found among the samples Matthew collected years ago, were from a neighboring village, Njungo, rather than from Mbetta. Since that village hasn't yet been touched, we aren't worried.

    Today, the ethical review committee met for their second, and we hope final review of our Research Protocol, the plans for the study. The word we've heard is that it was a positive review. There is just one final step -- a senior professor has to sign off on the package, giving his seal of approval. We hope very much that this will take place by the end of this week. Keep us in your prayers! I'll update you right away on this major development. Thanks for your support -- this project has not faded away, but is very much alive!
    http://www.pbs.org/first-peoples/home/
    http://www.pbs.org/first-peoples/episodes/africa/

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    Thanks for posting thus update. It's great that Blaine Bettinger came to the rescue.

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    The samples are collected at last and will be tested at YSEQ, screening for A00 individuals.

    Wow! Matthew has told me that they had a wonderful day in Fontem, and got a huge number of samples! In fact, they may have used up all the kits we had! He says the donors came from all over the area. He will have recorded where each of them is from, so this is excellent. I'm waiting to hear from him to confirm that the kits are gone. If so, it will be time to hurry home and ship the samples to YSEQ!

    https://www.facebook.com/A00.Cameroon.Project?fref=nf

    My understanding is the available funds were exhausted for the YSEQ kits the sample collection. More will be needed for eventual Big Y testing. Please, donate for this citizens science project!
    https://experiment.com/projects/whic...haplogroup-a00

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    Some results for A00 are posted on a web site in March 2015 or earlier. While I do not know if they are directly related to or generated by the project discussed in this thread, they might be useful to some people.

    These results can be retrieved from the following link: http://evolbio.ut.ee/chrY/, where file 0_READ_ME.txt says: "The data for Mbo samples belonging to haplogroup A00 are downloadable as bam-files: GRC13292545.chrY.bam and GRC13292546.chrY.bam"

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    UPDATE #2
    We Have Results!

    Bonnie Schrack & Matthew Fomine Forka Bonnie Schrack & Matthew Fomine Forka posted September 26, 2015

    Dear friends and supporters,

    There's lots of happy news I'd like to share with you now, and with it, I hope you may forgive me for having neglected to share our progress for a while.

    After we received our approval from the ethical review board at last, Matthew quickly set out on our first field trip to gather samples. And he was successful! He visited a total of nine villages, with a large majority of the samples from Mbetta, Lebock, Njungo, Nveh, Njentse, and Azi. He collected a total of 204 samples, and would have brought back more if he hadn't run out of kits. For each sample, we have a signed consent form, and a data sheet full of detailed information on the DNA donor and his family history. Matthew has scanned all of those 408 sheets, and sent me the electronic copies.

    These samples were all then shipped to YSEQ in Berlin, where the DNA is being extracted and tested as quickly as Thomas and Astrid can manage, given the other demands of their business. As anyone who has experience with YSEQ knows, that's pretty fast! They have already run 17-marker STR tests (their Alpha panel) on 116 of the samples. The results of those tests clearly show the highly distinctive A00 haplotype in no less than twenty of the samples tested so far! That means seventeen percent of the 116. I'd been hoping the amount of A00 might, in the best of cases, reach ten percent!

    There are some striking patterns in the results already. 85% of the A00 so far are from the Bangwa (Nweh) people, and 15% from the Nkongho-Mbo. This is despite the fact that nearly 57% of the samples collected were from Mbo, and only 37% were from Bangwa. Once all the results have been fully tabulated, we can provide more complete statistics. It will take a while to transcribe all the rich data from those handwritten sheets into electronic spreadsheets.

    So at the moment, we have 88 more samples yet to be tested in the coming days, and this is speaking only of the STR tests. These samples are from places where we expect the rate of A00 to be at least as high, if not higher than some of those already tested.

    Some SNP testing has already begun. The first six A00 that we found have been tested for two SNPs. One was FGC25576, found in a Perry family sample; it's one of the SNPs defining our proposed A00a haplogroup. The other was A4985, found in a Mbo sample (before this project), one of the SNPs that define our proposed A00b. Here are the results:

    FGC25576.jpg

    We're excited to see that sample #3086 is negative for both SNPs, though his haplotype has only one difference, 14-31 at DYS389I & DYS389II, as the Mbo have, instead of 13-30 like the rest of the Bangwa. His line may have branched off at least a little before the split between those two other groups. Obviously, we'll want to do more in-depth SNP testing, which will start soon.

    The pattern seen above also tends to confirm the hypothesis I've mentioned in the past, that the Perry family are more closely related to the Bangwa than to the Mbo.

    All the other A00 we find will also be tested for those same two SNPs, and then we'll evaluate our options for further testing of those samples.

    What's next? Matthew would like to head back to the field quite soon, in the second half of October, when the school where he teaches has a break. Our current plan is for him to visit the region of the Bamileke people. Matthew, an ethno-historian, has said "The similarity in names, language, dancing style and all other aspects of life suggest that the Bangwa are 90 percent Bamileke." By testing a good number of Bamileke, we'll be able to see whether the heritage they share includes A00, or not. It is possible that the A00 among the Bangwa comes from the indigenous people who originally inhabited the hills, before they arrived several centuries ago, or it could also have been present among the Bamileke earlier. Our results should give strong evidence to answer that question.

    The next field trips should be even more exciting. One of our goals is to collect the most diverse samples of A00 possible, to uncover its internal structure. By sequencing the Y-DNA of A00 lines that have diverged and settled in different parts of Cameroon, we should be able to get a good idea of when those different lineages had a common ancestor, and understand better how the peoples among whom it's found are related.

    One trip will take Matthew westward into the lowland regions close to Nigeria, where the Banyangi and Ejagham peoples live, toward the Cross River, home of the endangered Cross River Gorilla. These villages are also on the roads that led to the old Nigerian port of Calabar, where captives from Cameroon's highlands, including some Bangwa, were sold into slavery in the past. He has never before sampled in the western regions, and only 16 Banyangi have been tested in his past research, but there are versions of Bangwa history which say that these peoples make up a significant element of their founders. Members of the A0 haplogroup have been found in Nigeria, but we have no idea yet whether A00 are also found in that direction. The famed Iwo Eleru cave is in southern Nigeria, where a skull with archaic features has been found that dates to only 13,000 years ago, suggesting long survival of diverse humans in that region.

    In his other trip, he'll seek to sample members of several of the different Pygmy communities of Cameroon, who live to the South and East. Among the Pygmy peoples, Matthew collected 53 samples in 2006, and two of them belonged to A00! These communities are far from the highlands where the Bangwa and Mbo live, so we can expect that their A00 will be quite distinct. This should be extremely interesting!

    In order to make those trips possible, we'll be needing to undertake a new fundraiser, as almost two years have passed since our first ones. It will also be needed to allow us to test the Bamileke samples. The funds that currently remain to us will cover only the fieldwork with the Bamileke, but not the lab work. Thomas and Astrid will gladly keep the samples for us until we have the funds. We hope our friends will share our satisfaction with the results we're obtaining so far, and will want us to finish what we've set out to do.

    In the meantime, I hope you'll all follow our updates, and see some photos from the field trip, on Facebook, at http://www.facebook.com/A00.Cameroon.Project.


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    Hi guys, a new round of fundraising is on for the A00 project. They need to reach $10480. which is not going very well for now.
    https://experiment.com/projects/go-w...stern-cameroon


    Our first field trip was a big success! Matthew collected 204 Bangwa and Mbo samples, and we found that 35 of them belonged to A00! Our second field trip yielded 206 more samples, still to be tested.
    We'll now look for A00 samples among the Banyang and Ejagham, further West, on the way to Nigeria.
    Why? Many are curious whether there could be a connection between A00 and the archaic admixture in a human skull from Iwo Eleru, Nigeria. And histories of the Bangwa say that some of their ancestors may been Banyang. Will we be able to find any A00 among them?

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    Smile How Far We've Come: the 3rd Lab Note from our project

    Hi all! I'll try to check in with you more directly from now on. Since you are interested enough to read our entire Lab Notes, I'll first post the 3rd one here:

    Our friends who've been with us since 2013 know what a long journey it's been. Now I'd like to bring you up to date on our project's progress.

    After the long and arduous process of winning approval from the ethical review board finally succeeded on July 6, 2015, Matthew immediately launched our first field trip in late July, which lasted through most of August. On this trip, as I mentioned in the last Lab Note, he collected a total of 204 samples. I want to tell you about the full results we now have from these samples.

    Out of the 204, we had technical issues with a fair number of samples, due to Matthew working in a humid, African forest environment, and this meant that we ended up with results from 176 samples. We've now made changes in his work flow so that the samples have a better chance to dry, and we expect to have considerably better results in the next round of testing.

    The results from those 176, samples, though, were great! This chart shows how they break down:

    Results-First-Trip.png

    As you can see, these are very successful results, considering there were so few known A00 samples in the world previously!

    The 11 Mbo samples mentioned in our 2013 paper with Mendez and Hammer, were only a few of the ones Matthew had collected in 2001-2006. But they were picked out of the Center for Genetic Anthropology database because they were the largest number of A00 from any one ethnic group. What that reflected is the relative ease with which Matthew can obtain large numbers of samples from his own people, the Nkongho-Mbo.

    But it doesn't reflect at all where the highest concentration of A00 is found. We can now clearly see that with 40% A00, the Bangwa represent the epicenter of A00 in this region, and very possibly in the world.

    As I shared in the last Lab Note, we found that so far there are two main subgroups of A00, defined by different Y-SNP mutations, which, naturally, divide along ethnic lines: A00a among the Bangwa, and A00b among the Mbo. We also found the one Bangwa sample which didn't belong to either subgroup. We're very much looking forward to seeing his full Y chromosome sequence, to see what kind of a branch he belongs to!

    In October, Matthew went on another field trip, this time to sample some of the Bamileke, neighbors who are closely related to the Bangwa, but have been separated by the division between the English and French-speaking parts of Cameroon. In his earlier work, Matthew hadn't found any A00 among the Bamileke he sampled, but "Bamileke" is a very broad umbrella term, including diverse people from a wide area. Those he previously sampled were migrants living in entirely different areas of the country, and Matthew believes it may be a different story when we sample those living very near to the Bangwa, who believe they have Bamileke origins. This time he collected 43 samples in Fongo-Tongo, 36 in Bafou, and 15 in Bameka.

    Matthew also visited some different Bangwa villages in October that he hadn't been able to get to in his first trip, and made a return visit to Njentse. He sampled 27 men in Essoh-Attah, a southeastern Bangwa village, 50 in Ndungated, to the north, and 35 in Njentse, where he'd previously only been able to collect 10. This will give us an even richer sample set of A00 to study, hopefully revealing some variance.

    Matthew found that some of these towns had a diverse population made up of many ethnic groups. This was particularly notable in Ndungated, where the samples included 39 from a variety of non-Bangwa people, and Fongo-Tongo, where there were 25 non-Bamileke. A total of 60 samples were collected on this trip from people other than Bamileke or Bangwa. Since we have good data on their places of origin and languages, as well as that of their parents and grandparents, we should be able to use them to get some insights about the populations of other parts of Cameroon.

    All of the 206 samples collected in October have now been shipped to Berlin and are now being extracted and stored in YSEQ's lab, awaiting their chance to be tested. We're in need of some very substantial funding now, as it will cost us over $4500 just to get started on those. YSEQ is very reasonable, but with so many samples, lab costs really add up!

    The next trip is planned for January, to the regions directly West from the Bangwa and Mbo. Matthew will be sampling in Tinto and Besongabang, both Banyang towns, and Eyumojock, of the Ejagham people. There has been migration back and forth between these western peoples and the Mbo and Bangwa, and we want to see whether A00 is found at all among them. In his earlier sampling, Matthew only collected one Ejagham and seventeen Banyang samples, and we think it will give a better picture of Cameroon's diversity to find out what the Y-DNA of this area looks like.

    Our funding will also have to cover all the usual expenses for this trip, as well as those of shipping kits and samples back and forth, to and from YSEQ. And then we'll want to test those new samples! We can't even hope to cover that future lab expense in the current fundraiser, so another one will be needed down the road.

    It will also be needed for the most exciting trip, to the Southeastern region, where people short and tall live side by side, the smaller being known as "Pygmies" (a term which we should try to avoid, as it's often considered derogatory.) Matthew found several A00 in that region in his earlier work, among people of both statures, and it should be extremely interesting to see if we can find some this time around. Their A00 should be as divergent from that of the Bangwa as we could hope to find. So stay with us as the project advances, there's so much still to see!

    Please join us in our scientific adventure, which we hope will contribute to revealing our human origins. If you possibly can, we need your financial support, whether you can afford $5 or $1000.

    Here's the link where you can donate to our current fundraiser: http://Experiment.com/Go-West.

    We also need your help to spread the word to wider circles of people. If you like using Facebook, please invite your friends to our event page, by posting this link: https://www.facebook.com/events/420996664765025/. Our main Facebook page is https://www.facebook.com/A00.Cameroon.Project/. Hope to see you there!

    P.S. We're putting a newsletter together for everyone interested in the project. If you'd like to receive it, please sign up at http://goo.gl/forms/vRKtLFsdDK. We'll never use your email address for spam or share it with 3rd parties, and you can unsubscribe at any time

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    Exclamation

    Donations have ground to a halt, guys. Without some support from members of the community, we won't be able to test those 200 samples that are waiting, or look for A00 in other regions, much less discover new branches of the Y-tree. C'mon, your donations are needed now, if this fundraiser isn't to fail! We *can* do it, if everyone chips in and spreads the word.
    Experiment.com/A00west

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    Here are some new pictures that Matthew took in the Bamileke town of Fongo-Tongo, where he collected 43 samples.
    Overview-FongoTongo-2walking2.jpgDSCN1107.jpgNurse-4.jpg
    Last edited by Bonnie; 12-11-2015 at 10:19 PM.

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    Wish I could, but I'm still unemployed and surviving on pogy, and the bureaucrats are now giving veiled threats to cut me off prematurely.

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