The following recently published paper goes above and beyond that of a typical Nature Genetics GWAS:
Agarwala, V., Flannick, J., Sunyaev, S., and Altshuler, D. (2013). Evaluating empirical bounds on complex disease genetic architecture. Nat. Genet., 1–12.
The paper is split into three stages, any one of which would constitute their own smaller paper: modeling demography, determining the number of loci impacting disease based on coupling with natural selection and mutational target size, and generating both empirical and simulated results for Type II Diabetes.
The paper starts by comparing demographic models in three previous papers (Gravel et al, Kryukov et al, and Schaffner et al). The authors assess the site frequency spectra, strength of selection, minor allele count for nonsynonymous vs synonymous sites, and linkage disequilibrium patterns. In the end, they adjust the parameters of the three models to generate their own hybrid model to best fit their data. Europeans are the population of interest in this paper because the T2D study participants are all of European descent, and Agarwala choose the following parameters to best fit the data:
NA (ancestral population size) = 8,100
NB (bottleneck population size) = 2,000
t (duration of exponential growth in generations) = 370
r (rate of exponential growth) = 1.29%
NE (modern effective population size) = 227,650
μ (mutation rate per bp per generation) = 2.0e-08
As a population geneticist, this aspect of the paper is the most exciting. Understanding ancestry is a critical part of identifying true associations, rather than simply identifying sites that are informative of ancestry substructure (As an aside, see this interesting recent cautionary tale. Another point that arises from their simulations is that >90% of deleterious NS variants are rare (MAF < 0.1%), but fewer than 45% of all rare NS variants are deleterious. Additionally, most rare variants are recently derived and neutral/weakly deleterious, which are consistent with PolyPhen results.
Of course, there are limitations to their model that could be expanded in the future. Only purifying selection and exome capture regions are considered. Pulses of migration would likely also affect their model. The authors acknowledge these points, and suggest that if their model is consistent with the data, the results are at least reasonable.
Another very interesting aspect of the paper is their model of coupling between purifying selection and the likelihood of disease, accounted for by the variable τ. If τ = 1, variants with large effects on fitness have large effects on the disease, whereas if τ = 0, there is no relationship between selection coefficients of causal mutations and their impact on disease. With simply two parameters (τ and T, the mutational target size), a full range of genetic architecture for complex disease is possible. The authors find that for T2D, the higher the coupling term, τ, the smaller the target size for mutation and the fewer causal loci are expected. Conversely, the lower the coupling term, the larger the target size for mutation and the more causal loci are expected. The authors consider two models that are consistent with the data and have widely varying τ and T values and find widely varying results from their GWAS with large cohort sizes (N=10,000 and N=85,000).
The last portion of their paper looks forward to future T2D studies and estimates the variance explained by varying cohort sizes and genetic ascertainment. At the scale of 250,000 full genomes sequenced (20k cases and 230k controls, matching the prevalence of the disease), they expect that 75% of the genetic variance should be explained. Someday we will surely reach this level, and it will be interesting to see how physicians integrate lab tests for environmental impacts (i.e. how many cheeseburgers you eat a week) and genetic risk. I am curious to see how transferable these genetic risks will be to other populations, given that the vast majority of rare variants are private to populations. I also look forward to seeing how functional genomics is integrated to aid clinical recommendations.
Week 1 = Vacation in Cape Town
Week 2/3 = Meet with collaborators at Stellenbosch University and go to field site where Khoisan samples have been collected
Week 3 = Travel to Namibia and go to Himba field site
Day 1: 30 hour travel from SFO to Cape Town airport
Flights… zomg. Too many flights. We were very lucky starting out and got Business First (zomg) flights from SFO to Frankfurt, Germany, which was amazeballs. We took off flying backwards, which was surprisingly reasonable. Of the 10 hr flight, I probably slept ~5-6 hours on red eye #1. Konrad had I were in 2 middle seats (business seats were 2-4-2 on this particular flight). He was on one side and therefore had a different flight attendant than I did. His was much cheerier than my austere German flight attendant, but both ladies were very nice. After ending up very dazed from the first mid night wake up PST in Frankfurt, I took a ~2 hr nap in the Lufthansa lounge, which felt sooo good. I charged my laptop and we boarded the Johannesburg flight on South African, which has tiiiny seats. Maybe I’m spoiled, but I (5’0″) was a little short on room). When we landed at Jo’berg, we had to re-check our bags and figure out where our gate was. It’s a huge and fairly intimidating airport, and there are “Porters” everywhere. Porters are basically people that pose as friendly airport guides but are really just trying to gouge money out of you by rolling your luggage across the terminal. After being minimally helpful, our porter asked us for a tip, and when Konrad told him he had no rand, asked for anything. When Konrad gave him $3, he acted fairly insulted and asked for Euro and more. At the tired state (20 hrs flying + 6 hour layover) we were in, we basically told him to piss off. We got to our gate, had little time, and boarded our flight to Cape Town. After arriving we were greeted with a super friendly Taxi driver in the airport. After our Jo’berg Porter experience, we didn’t think we could trust him, but he insisted after we were outside the airport by the taxi stands, and in the end we gave in. He gave us the rundown on Cape Town and gave us lots of suggestions for good tourist sites to see and how to travel cheaply. Overall he was great!
Day 2: Delicious french restaurant and fun night out with locals
I’m not even sure when this day really began. We took a several hour nap, talked to the travel desk at the Westin, and decided to go to a French restaurant called Aubergine that we though would be relatively easy on our unsettled stomachs. We ordered our appetizers. Konrad got the Aubergine Souffle, which he though was relish. I got the special, which I had forgotten was ostrich tare tare. Ostrich is a bit like beef but less bloody. Tare tare is, as expected, a bit of a scary dish to have in a 3rd world country, but digestively fine. Later we ordered entrees, which were (ZOMG) amazing. Konrad got the Angelfish, which was ~1/2 fried broccoli and ~1/2 fried angelfish. Both were delish. I got the quail coq au vin, which was def the best coq au vin I’ve ever had (and maybe that exists). Later we ventured to the Waterfront after hearing there was live music and were pleasantly surprised with the fun atmosphere. We heard a band playing (in a not great way, but playing memorable and fun songs), and decided to stop in for a beer. We decided to try some South African beers after hearing the cabbie rave about them. I ordered a Milk & Honey Ale. It was pretty good, but tasted a little more like a lager. Konrad ordered a Ferryman’s Ale. It was our favorite of the two. Later we ordered beers that we both knew we would like (Me: Wittbier, Konrad: Kilkenny), and were both pretty happy. While we were sipping our beers and watching the performance, we noticed a group of people next to us drinking small dark shot-sized drinks. Curiosity killed me, and I asked them what they were. The guy named his drink (lolz) and bought us a round. Then we bought them a round, they bought us a round, and we chatted the night away. Around comes 2-3 AM.
Day 3: Cape Point Tour, Ostriches, and PENGUINS!!!
ZOMG wtf did we do last night and why were we so dehydrated? We arrived in the lobby around 8:30 after choking down some last minute take away pastries from breakfast for our Cape Point Tour. On the way down the coast right outside Cape Town, we saw zebra, springbach, and crocodile pelts, and our driver indulged us with a stop. The next place we came across was Camps Bay, which was amazingly beautiful. It was a little reminiscent of Santa Barbara, but a lot prettier. Apparently the cheapest houses there go for about R20,000,000 (~$2M). We continued on our journey down the coast over Chapman’s Peak. Our driver, Ben, told us that when sailors first arrived, the forgot a gentleman named Chapman on the beach. They arrived after 4 days of leaving him there and were pleasantly surprised to find him still in one piece! (I.e. not eaten by a leopard.) We got to Hout Bay, where we stopped and took a quick boat ride around and saw a ton of seals and some gorgeous views. We saw a sculpture garden outdoor store and looked around. There were more sculptures than I could ever have imagined in one place, and they were very pretty. We hopped back in the van and next arrived at the Cape Point ostrich farm, which was pretty high on the list of awesome things during the tour. We grabbed a bag of pellets and trembled while feeding some terrifyingly large birds. They are apparently the closest living relatives to dinosaurs, which you can see in their hilarious feet (camel toes?). We were told that when they attack, the start from the top with their one giant sharp claw and work their way down, ripping whatever they’re attacking apart. We made sure to keep our distance. We finally arrived at the Cape of Good Hope, which is the south-westernmost point in Africa. We walked out on the beach and enjoyed the view. Next was Cape Point, which was pretty but not too spectacular. It jutted out of the coastline a bit and there was a lighthouse at the end. Next, we finally made it to Simonstown. At this point we were starving and had a pretty good lunch of fish & chips. My fish was Kingklip, which was raved about by all. It was pretty good. We next went to see the African penguins, which we were most excited about and was definitely the most awesome! They are pretty small (maybe a little over a foot tall), and generally adorable. We got to see them coming ashore and awkwardly waddling along the beach. We took a few pictures with our traveling penguin near real live penguins! It was awesome. After spending quite a while watching them from an awesome vantage point, we piled back in the van and drove up the coast (sleeping most of the way after a tiring day + jet lag). We got back to the hotel and napped, then went to dinner at a mediocre restaurant called Sevruga that was recommended to us. Their take on sushi involved cooked tuna, which was a little weird, and the texture was really bland. We later realized at the hotel’s breakfast that they can actually make pretty good sushi, so we think the restaurant just sucked.
Day 4: Table Mountain & 3 bays helicopter tour
The day’s weather was absolutely gorgeous and sunny. After the previous day’s tiring events and the jet lag, we decided to sleep in and take our time with breakfast, then take a hike up Table Mountain. The cable car was down, so we knew there was no quick and easy way up or down. After breakfast (no traditional American foods… more seafood, breads, dry meats, and fruits), we inquired about a helicopter tour around Cape Town since things are pretty cheap in South Africa. We learned around 11:30 that there was a tour at 4 PM, so we decided to hustle up and down Table Mountain, knowing that we would get gorgeous views on the clear day from both activities. We were told by people that the hike took anywhere from 2 – 5 hours to get up and another 1-2 hours to get down. We got up to the base of the hike by noon. We hiked up in 1.5 hours (i.e. we were pushing ourselves and sweating our butts off) and got to the top around 1:30. The views were incredible all the way. Cape Town is a gorgeous city unlike any other, and I’m so happy we got to see it after the tiring hike up. We could see far in all directions, including all the way to Cape Point, which we had seen the day before. We rushed down and caught a cab back to the hotel in time to shower before leaving for the helicopter ride. We saw the city and its surrounding areas from an amazing vantage point, and our pilot, Charlie, gave us some aerial perspectives. Many of the houses on the back side of the table were gigantic, and they all had pools. After we came back, we were starving from our hike. We went to a restaurant called Baia on the waterfront, which had amazing seafood. We were super content with our meal. We wandered around the waterfront mall a little bit. Afterwards, we caught a cab back to our hotel and tried to get some sleep before the next day’s 4:45 wake up, but jet lag got the better of us. I have no idea how 3 days in we were still so jet lagged, but I’m really glad we had some freedom to adjust.
Day 5: Great white shark cage diving
We caught the shuttle from our hotel that left at 5:15 in the morning. What had we gotten ourselves into? We very sleepily drove from Cape Town to Gansbaai, which is the nearest place that tour guides are allow to operate close enough to the shore to see Great White sharks (even though there are a plenty near Cape Town… I guess they don’t want them to become too accustomed to humans, but our guide told us the same shark only stays in the bay for 2-3 days). We got out to the info room and our guide, Viad (I think), gave us a rundown of the day’s rules and expectations. We ate a simple breakfast of pastries, and took the boat ride out for ~15 minutes. Apparently the mornings are usually a little better for the lack of swells, but the sharks are equally active during the morning and afternoon. All I can say is OMG I am so happy we took the early boat out. The sharks are attracted to the boat because the crew throw “chum” in the water, which is basically ground up smelly fish. The boat rocked like crazy, and I stood port side next to the chum waiting to lose my breakfast for ~5 minutes before hitting the upper deck from a nap. I was very happy to have held it all in, but I felt fairly awful (and was definitely not the only one) until I got in the water. The first group went and were in the water for ~30 minutes. They saw a shark roughly twice from the cage, where the guides yell “down, down, down” when the sharks get close so you can see them underwater. The visibility was rather poor, and it was really hard to see them until they were right next to the cage. After the first group went in, we took our turn, hoping that being in the water would help settle my stomach. That was definitely an understatement. The water was ~60-62 degrees F, and we thought no big deal since the Pacific is much colder, but we were so wrong. We totally froze. Chattering teeth and a freezing cold wet suit made the experience a bit miserable until we saw the sharks. The first one we saw only above water because the water was too murky to see below. The second time I caught a glimpse of its tail ~5-10 ft from the cage. There was a bit of a break, and Viad told us to make like seals. Willing to try anything to get through the freezing cold, we did. A few times there were breaks in the clouds, and the sun warmed us amazingly (though not beyond chattering teeth). Towards the end of the probably 20 minutes we were in the cage, shark after shark started coming by, and we saw it lots under water. The last time I saw it, its swam right past me, and it rattled the cage a few times. That totally made it worth it. For the rest of the time, we didn’t feel sick at all, and we could see the sharks through the water very clearly from the upper deck. The last shark that we saw jumped a bit at the bait and caught it before the crew could pull it away, eating one of the tuna heads. The sharks we saw ranged from ~2.5-3.5 meters. They were huge! We made our way back to land and grabbed some more lunch before driving the 2 hours back to Cape Town, during which everyone except our driver fell asleep. We finished the day off with some time in the spa’s jacuzzi and pizza at the waterfront.
Day 6: Aquila Big 5 Game Reserve
We got a glorious ~9 hours of sleep after a relatively tiring previous day and left at ~6:45 in the morning. The views on the way there with the sunshine through the clouds on the mountains were rather beautiful. On our way into Aquila, we saw a baboon walking down the road looking like he was hitchhiking. It was pretty adorable. When we got to the lodge we were warmed in the beautiful lodge and had a very full and delicious breakfast with some champagne to start the day. We got in the back of the safari vehicle and took the back seat in order to get some good pictures out the pack. One of the first animals we saw were hippopotamuses. We were unsure whether they were rocks. We also saw elephants, which walked directly past the truck. We also saw some springbachs (alive, not their hides this time), zebras, and wildebeests all standing together in the sun. We saw a water buffalo lying in the grass, and our guide told us that it was the most dangerous of the big 5 (even moreso than the leopard). We also saw a giraffe roaming around with an eland, and we figured they were oddly paired up because they were lonely. Our guide let us walk around, but we seemed to scare them away. Apparently they are somewhat shy animals. We also got to see lions in an enclosed area (presumably so they wouldn’t eat the other animals), as well as crocodiles, lions, and leopards at the rescue center. For dinner, we wandered down Long Street and happened upon a tapas place, which had amazing foods. Additionally, our waiter, Jason, was from Durban but had worked in Stellenbosch for ~4 years before Cape Town at a winehouse, and gave us tons of recommendations for tastings.
Day 7: Work day
It was pouring pretty much all day today, so we stayed inside and caught up on work. At the end of the day, we rewarded ourselves with a couples’ massage (so relaxing!) followed by dinner, where the hostess judged my shoes pretty sternly. I ordered steak, which was a little too rare for my likings. In other words, I hadn’t intended to order 8 – 10 ounces of steak tartare. The dessert was a cheesecake served with crystalized carmel and sorbet, which we liked.
Day 8: Wine tasting
We experienced South Africa’s wine valley in style–chauffeured by a driver named Rush. Based on our waiter’s recommendations and his own ideas of what to experience, he took us to lots of amazing places. The whole day is a bit of a blur, but my favorite winery was definitely the 3rd place we visited (Warwick). Our server was awesome and told us a cute story about Kunigunde and a wedding cup, which she had us drink from. It was pretty cute. We also got to pet a cheetah. Unexpected, but totally awesome! We ate lunch at Fairview, which also had amazing wines and cheeses that we kept running back and forth to try. Our driver suggested we visit Ernie Els, which wasn’t our favorite and our waitress was incredibly slow, but the views were gorgeous and the winery was very pretty. The first place we stopped at had a well behaved dog who led us to the wine, which was probably the best part about the whole enclosed place. The wine was rather drinkable, and I’m blanking on the name of the estate. I’m not sure how the day got away from us, but we stopped at one last vineyard before 5 where she gave us double pours for each tasting and hurried everything along. We finally ended up in Franschoek, which had a cutesy store (Indaba) where we bought some souvenirs and was right next to Die Wijnhaus, which was where we ate and had bought some wines. We drove back and then ate dinner at Gold Restaurant, which had a 14 course African menu (my waist hurts just thinking about this day), and we enjoyed the live dancing and interactive dinner entertainment. We walked both to and from the restaurant, which is what I’m considering to have saved our livers that night.
Day 9: Goodbye to Konrad and hello to Brenna
In the morning we packed, ate some breakfast, and went to the waterfront to get a new camera since Konrad left his charger behind, got caught in the rain and also bought an umbrella. I got a relaxing facial, and we left for our respective destinations (Konrad back to the east coast, and me to near the Stellenbosch medical campus). Brenna and I ventured into a small town and got some groceries, a phone, and ate dinner at a cutesy and tasty bistro called Arugula. The food was very good, and our hostesses were very awesome to drive us around a bit. We had a relatively early night after her very long, jet lag-inducing flight.
Day 10: Museum in Cape Town and dinner at Eileen’s
We ate breakfast early (~7:30) and I took a shower. As I was getting ready, the power went out. It came back on after ~20 minutes. When it came back on, Brenna took a shower, but it went out again after ~5 minutes. Fortunately it was only out the 2nd time for ~2 minutes, but Brenna still ended up with a cold shower. We walked outside to try to find a taxi and realized that the guy who runs the B&B had arrived (his wife, daughter, and “the help” were looking after us the previous day), but he was locked out of his house. After he found his way in, he drove us to Cape Town to the Iziku South African museum since it was pretty rainy and chilly. Walking around with Brenna at the museum was very interesting. She knows a lot about South African history and the treatment of the Khoisan through her field work, and she had some interesting comments about the representation of the people versus the actions taken by the government. When we first walked in, we saw bone awls, which she mentioned are one of the first archeological finds to indicate modern human behavior. We also saw scratch patterns in ochre, which she expressed skepticism about being a manifestation of modern human “art” since it was used as a tool to pound stakes, and in everyday use, so she suggested that it was hard to tell whether the scratch patterns were actually intentional. We spent a lot of time walking around the anthropology section, which had mostly rock art from the Khoisan. One exhibit we stopped by really struck Brenna because an elderly Khoisan lady who had died recently that she has sampled was featured next to rock art in Kan. We wandered upstairs to the section on Karoo, which had a lot of impressive fossils from dinosaurs ~250-254 Mya. As we were leaving the museum, we happened upon some ancient human skulls in some tucked away corner of the museum, including Australopithecus sediba. They also had a partial skeleton of an ancient hominid, which was surprisingly small. After our day in Cape Town, we returned for a bit and then headed to dinner at Eileen’s and Paul’s (collaborators at Stellenbosch) house with Marlo and her husband, Daniel. They were super nice, and conversation was lively. Eileen and Paul both know quite a bit about native plants and animals, and Marlo joked that they are honorary rangers. We returned to our guest house rather late.
Day 11: Work Day and dinner with Marlo + her husband
As a result of returning late, we overslept breakfast a bit, and our host was rather annoyed that we weren’t at there in time. He expected us at 8, but we didn’t arrive until 9. When we got there, we again had an enormous English breakfast. Then I worked on a manuscript all day, and Brenna and I took a peaceful walk around the gold course near our B&B. For lunch, we went to a little farmhouse and ate in a restaurant near a bistro that didn’t have room, but they had the same menu. We shared a pizza and salad. The pizza was good, but the salad seemed to have had sand or something in it. We walked back to the B&B and resumed working. Later Marlo picked us up and we had dinner at her and Daniel’s house. Their house was rather enormous and gorgeous. She said it was ~25 years old, which is apparently on the old side for Cape Town, but had been added on and renovated 5 years ago. There was an indoor grill where they made a delicious sausage (braai?) and chicken skewers. They also made salad, garlic bread, and dessert, which was a very tasty cake with pudding. Apparently they are very into their pudding. We also had a cabernet sauvignon/merlot blend. I think the merlots from South Africa taste better generally than the Napa Valley merlots. Afterwards, Daniel brought out Witblits, which is apparently like moonshine and is made out of grapes. This was supposedly a “nice” Witblits. To me, it burned and tasted like a very harsh vodka/whiskey. Michelle and her husband Mark told us stories from when they lived in India for ~6 months. They said they had a lot of intentions to travel while they were there, but didn’t feel comfortable since they didn’t speak the language and the rickshaw drivers drove like madmen and always tried to charge them more than they should have, so they mostly stayed at home while they were there. Mark works at Amazon with AWS, and we talked a little bit about the cloud. According to him, it was started in South Africa. At the end of the night, they drove us back to our B&B. We had told our host, Bach, that we would not be taking breakfast Monday, Tuesday, or Wednesday, and he had seemed a little offended.
Day 12: Talks & work
I had prepared a very short presentation about working with exome sequencing data and presented it in the morning to Eileen’s lab. No one had worked with next generation sequencing data, so there were few questions about the sequencing itself, but a few more questions about details of the samples. Afterwards, I transferred the data and my slides to Marlo. Later, Brenna gave a talk to the department, which was rather crowded. She talked largely about David Poznik’s recent Y chromosome paper in Science and a bit about deleterious mutation work that she and Jeff had worked on with the genome data. At the end, she briefly mentioned Julie’s and my work on height and pigmentation. She had a ton of people talking to her afterwards about her work, with lots of interest in human origins in South Africa. We went to lunch with Eileen’s lab afterwards, which was interesting. The cafe originally said 2 orders the lady brought out, which were not what we ordered. Later she came back with the exact same dishes (one with a little avocado added), and said they were what we had originally ordered. We spent the rest of the day talking with people and getting some work done, then went to the mall to get a water purifying system since we weren’t sure what we would have in Namibia while we are camping. It turned out to be more of an ordeal than I expected, and we ended up going to 3 different stores, each which had their own favorite story about what worked. In the end, we got some tablets and one purifying water bottle. Later that evening, we went to dinner again with Marlo and Daniel and a place with traditional South African cuisine. I ordered Malay chicken, which was basically a hearty home cooked meal with lentils and strange spices.
Day 13: Eileen’s lab, Day 2
We went to Eileen’s lab and talked about some projects for Caitlin, a student who is wrapping up her Honors. In South Africa, the Bachelor’s degree is 3 years, and an additional year gives people an Honors degree. Next year, she will be working on her Master’s, and she is very interested in population genetics. She will likely therefore be working with Brenna next year. Eileen, Brenna, Marlo, and I were throwing out ideas for projects relating to population genetics and tuberculosis. Afterwards we met with Michelle about reviews she had gotten back from her AIMs paper that she had submitted to PLoS One. For the rest of the day, I worked on a manuscript and used the internet for the last time in ~1.5 weeks.
Day 14: Leaving for Upington
We had to leave for the airport by ~8 am and we still hadn’t gotten ahold of host to pay, so Brenna tracked him down, and it turned into a bit of a fiasco. The window in the very front had large stickers that said Visa, Maestro, Mastercard, etc. However, he told us that he wouldn’t take cash. So we had no warning, and he also charged us far more than what we expected. Since it was a B&B, we expected the breakfast to be included. Instead, he charged us R90 per breakfast. To give you an idea of the cost, we stopped at lunch today and the most expensive lunch on the menu was ~R50, and all the portions were huge and the food was very good. In addition, when he first got there we were on our way to Cape Town to go to a museum, and he told us a taxi would be very expensive so he was happy to drive us. Note that he first kept us waiting for ~20 minutes while he broke into his house since he couldn’t find his key, and his truck did not have 3 seats, so he put a pillow in the middle and basically said you’re small, make do. Since we assumed he was doing us a kindness, we were like sure whatever. We took a taxi back, which was R245. We got the bill, and he had charged us R200 for that transport. Lastly, Brenna had put down a 50% deposit via wire transfer, and had written the transfer in rand. He said that R125 less than she had written had come through, which I strongly doubt. Anyways, the place was very nice, but Bach was a bit weird, greedy, and deceitful, so I definitely would not stay there again. Brenna and I didn’t have enough cash, but fortunately Marlo had enough to supplement ours to pay the bill when she came to pick us up for the airport. Bach was very friendly when we left, but I told him he should take down the credit card signs since it was very deceiving. He said very few people use credit cards anymore and that it was expensive. Ya right. We were happy to be on our way to the airport and out of that place. Unfortunately when we got to the airport, the lady at checkin seemed to have it out for us. Four of us had bags, and I had 2 large ones with one full of camping and sampling gear. She said one of mine was overweight, but hadn’t systematically split weight between the 4 of us. I’m not really convinced that that was actually a problem. In addition, I told her I was a star gold member, and that I should get more baggage allowance, but she said that didn’t matter. She wrote 6 kg on Marlo’s boarding pass and told me to go pay for it. I asked if I could have my passport and she said no. She was being extremely short with us and I completely lost patience and walked off. The other lady that I talked to explained that South African Express was operated by Air Link, which was not part of the star alliance. OK, fine. She asked for my ID and I gave her my driver’s license, since the other lady seemed to be holding my passport hostage. Fortunately the other lady that I paid for excess luggage was very nice and accommodating, or I probably would have completely lost it. In the end, it was ~R170, which is much cheaper than in the US. We got on our plane, had a quick and easy flight, and arrived in Upington. We first got some groceries and then had lunch at a cafe in town, which was very good and had enormous portions. Then we went to see Grace, who heads up the South African San Institute (SASI). We talked with Lyana, who seems to be leading the community center with Collin. Brenna had not met them before and explained that the San Council turns over every 2 or 3 years with charges of corruption. Right now, there is no San leader because after the last leader died, ~8 families each came up with their own leader and the government also started controlling a little bit of the money. We next drove the ~2 hours to Andriesvale. It was a desert road with not too much happening. We got in to our little lodge at Kalahari Trails, and then went to to Molopo Lodge for a glass of wine and to then have dinner with the German film crew. There were 3 of them: Niel, Felix, and Sebastian. Sebastian is the student who is in charge of the project (and perhaps the most sane one), and the other two are working. They showed us some of their pictures from the trip, told us how they had asked the person sitting next to them on the plane in San Francisco if they could stay with them, and gotten stuck in the mud on a “shortcut” in the Kalahari. It was all pretty entertaining.
Day 15: Sampling begins!
Today we tried mostly to recontact people for whom we had run out of DNA. We met up with our translator at SASI around 9 and drove around the different peoples’ houses in the sand. We also saw the new medicinal plant plant facility that had been built, which was very nice. Most of the people we talked with were outside their houses. We returned community results to people, letting them know what 2 published studies had said. We also gave them preliminary results about ongoing studies. I learned that it’s very important not to give individual results because knowing the amount of San ancestry each person has can upset the political balance in the community. After we gave results, we said the we had run out of DNA or had very little and wanted to collect more if they still wanted to participate. People that agreed were re-consented, Brenna performed an ethnographic interview to make sure she had the same person as before, they spit ~2 mL in a tube, and were given a gift for participation. Marlo was a key player in the sampling because she speaks Afrikaans fluently and read the consent forms and explained results much more quickly to them than we would have been able to with a translator. We also collected some new samples. In addition to explaining the current results, reading the consent, performing the ethnographic interviews, having them fill the spit kits, and giving a gift, we also measured height and pigmentation. Marlo was in charge of explaining the results, she and our translator explained the consent forms, Brenna performed the interviews and recorded measurements, Caitlin measured height and collected the spit, and I collected pigmentation measurements and gave the gifts (t-shirts). Each new sample collection took ~20-30 minutes, which was longer than I had realized. Most places we stopped, we talked to one or two people. We broke for lunch at our translator’s house so he could eat with his family, while we ate sandwiches we had packed by the car. The last place we stopped for the day, we took collected 5 peoples’ samples and collected phenotypes for all of them. I was really surprised by the last individual, who had basically hung around for the > hour while we collected the 4 other individuals’ samples repeating over and over that he wanted a t-shirt (the gift we were giving for participating). Brenna kept repeating that the t-shirts were for participating in the study, and he kept then telling us that he wanted to participate. We thought he was a little strange, and our translator seemed a bit weary of him. In the end, his persistence led us to sample him and give him a t-shirt. One of the questions Brenna asks during the ethnographic interviews is what languages you and each of your family members speaks. He gave a list of about 5-8 languages per person, and we got the impression that he was lying. Our translator also said he was lying. He was also difficult to follow. One of the languages he said he spoke was English, but it was pretty incomprehensible. After the last 5 sample collections and especially the last one, we were all pretty tired, so we went to get a drink. When we got there, the German film crew was there and met up with us. After drinks, they took us to a family’s house that had dressed up in traditional attire (not what they actually wear now), including animal skin loin cloths and hats. They were planning to have a dinner where they sang and danced, and the film crew wanted to film when the sun went down. In the meantime, they filmed us going through the process of collecting a typical sample. We started around 4:30 and were fortunately limited in time by the amount of sun left. A 10 minute sample collection took them about 2 hours to film between all of the retakes, and the camera man was perfectionist. After he filmed the sampling, it was time for the film crew to film the Khoisan singing and dancing around the file while they cooked. I told Brenna I was going to get my jacket from the car, and Marlo, Caitlin, and I were bringing stuff down while the crew took their last shots of Brenna. She asked if I could get her jacket while they took their last few shots of her since the desert gets very cold very suddenly when the sun goes down. When we were all by the car, a man pulled us aside. He was speaking Afrikaans, so I understood very little of what he said, but by Marlo’s reaction it seemed like he was interested in the community results. We talked with him for quite a while, and our translator had walked off. Brenna joined us later, and the man asked us to sit with him in a space away from the fire. The talking went on for what seemed like forever, and I really had no idea what was happening. At one point he tried to get our names, but and he had to go around the circle ~3 times to remember them all. At one point Marlo translated that he wanted us to give him R100 for the information he gave us (which he hadn’t asked for beforehand… beginning to sound a bit like Bach from the Greens Guest Houses :P). Brenna said that we were not allowed to give anyone money and that the information helped all of the KhoeSan, not just him. At the end of the ~30-45 minute conversation, Marlo nodded and said “I’m uncomfortable. I think we should go.” I was a little surprised, and she later mentioned that he was very threatening and had basically told us to leave two girls with him while the other two went and fetched money. Marlo later told me that he said I was worth R250 (~$25)… good to know my value. 😛 He kept saying that the films come and go but they never pay him anything. Again, we said we had nothing to do with the filmmakers and that they had already paid the community to film there. We talked to our translator, and he said that he was disappointed that the man had made the decision for the entire community. We asked him what we should do and he thought we should all go, so we told the filmmakers that we were leaving. Caitlin later said she smelled alcohol on the man’s breath. I talked with Brenna about alcohol and its influence on the community. She was very disappointed about the liquor store and said that alcohol had caused a lot of problems in the community, because every time a family got a small amount of money it was immediately spent on alcohol. Additionally, the people don’t seem like they process alcohol very well. We encountered two men who were drunk that day and had ~an hour long interaction with each of them. Both times we never saw them drinking, and yet they remained drunk the whole time. We talked later with the professor that runs the Kalahari Trails, and she said that the man we talked to had been in four alcohol-related car accidents and was very violent. We were very glad we left.
Day 16 (9/6/13): Sampling continues!
We began the day visiting the medical clinic in Askam, the nearest town to Andriesvale. Marlo is in Eileen’s lab and is interested in tuberculosis, and we were wondering if the impoverished conditions and the cold winter led to a higher prevalence of TB in among the KhoeSan. We were very impressed with the organization and utility of the clinic. They gave us a book that had documented the number of patients seen by the clinic each month, number of individuals tested for TB, number of individuals that were positive, and number of individuals on treatment. There were only a handful of cases each month, ~10% of what individuals they tested which were in the 2-4 dozens. Afterwards we walked over to a little coffee shop that neighbored the clinic while we waited for our translator to get some results. We had a very nice stop, getting muffins, scones, coffee, juice, etc. There was a very adorable dog there playing fetch. It was already noon and Brenna wanted to get moving, saying that she didn’t normally allow such slow-moving days. We went to a new home where our translator mentioned that there were people who had expressed interest in the study. At first we went to a 80+ year old woman’s house. The houses were much sturdier than the typical places we had been previously, but they were not particularly well maintained. After we collected the little old lady’s sample, we went across the way to where the community leader was. We collected 5 new samples. It felt like one thing after another, and we were all a bit tired afterwards. It was already ~3, and we were running low on kits, so we went to meet up with the filmmakers. They filmed me being “healed” from stomach pains. The KhoeSan healer told us his name in Nama, which was something like !Kohop, meaning porcupine. He didn’t want to show all of the healing traditions because some of them were sacred, so he used devil’s cloak instead. I wasn’t really sure when to respond to him since I obviously don’t speak Nama, but we made due. He joked around with us and made some very lewd but funny comments. The filmmakers took some more shots of Brenna, and we called it an early day.
Day 17 (9/7/13): Last day of sampling
We only started the day with 3 kits left, so we sampled 3 new individuals that were interested in taking part in the study and gave out shirts. Poor Caitlin… one of the guys came and grabbed her and told her he had lost a tooth in the last few days, so the tube was a bit bloody… gross. We tried to also recontact a few individuals who had participated in the study and told them about the results. We had recontacted everyone we could and given out all the shirts by noon, so we called it an early day and grabbed lunch at the cutesy coffeehouse in Askam. We also stopped at another place to buy crafts. Afterwards, we dropped off our translator early and paid him for his work, then went back to our guest house before meeting up with the film crew for the last time. We had ~an hour break, and we mostly relaxed and read. Then we drove out to meet them. We had some issues while getting the car stuck in the sand and had to be pushed. The film crew interviewed Brenna and me about our work and took a few transition shots. Afterwards we met up at the Molopo Lodge for drinks and a small dinner. The Germans were very entertaining and we learned a bit more about their work. We called it a night and went back to the lodge, and I talked with some interested elderly travelers about our work.
Day 18 (9/8/13): Off to Namibia
In the morning, Brenna and I took a walking tour with our guide Andrei and other people at the lodge where he told us what kinds of animals the tracks in the sand corresponded with. We packed up, dropped some extra food off for SASI, and drove to the Upington airport.
Characterizing the Role of Prdm9 in Genome-wide Hotspot Recombination
A few people have requested my qualifying exam while looking for references about recombination or preparing for their own quals. Because they were off-topic when I took them, it is unrelated to my research. For your viewing pleasure (and to attempt to fool my psyche into believing that an off-topic qual was a valid use of time), I give you my quals proposal and my quals presentation.
For fonder memories of the elation that occurred just over an hour after I shakily entered the room, I will have you note the date of the exam: October 31, 2011–Halloween. I wore a Minnie Mouse costume, during which I proposed mouse studies. One specific experiment involved dissecting mouse testes for ChIP-seq. I think I may have been the first (and only so far… here’s looking at you future second years) Stanford PhD student to take quals in costume. I nervously entered the room the day of my quals. My first committee member to enter, Gavin Sherlock, sat down and said with British sarcasm, “I see you’re taking this very seriously.”
Note to future quals takers: A pass is a pass and that’s all that matters.
I am a graduate student in the Department of Genetics at Stanford University working toward my PhD in Carlos Bustamante’s lab. My interests are in the demographic history of humans at the level of genomic and gene expression diversity, particularly as humans migrated out of Africa and underwent various bottlenecks.
To learn more, please click the relevant links.