About a month ago I put up my first post on this weblog. I argued that South Asians have been genetically undersampled, which is rather alarming considering that Indians, Pakistanis, Bangladeshis, Nepalis, Sri Lankans, etc., are 1/6th of humanity. The alarming part is that understanding population genetic structure is considered a prior condition of much medical genetic research. Without taking into account genetic relatedness one can not usefully establish correlations between particular variants and particular diseases or traits. For example, it is well known that South Asians have a high risk for diabetes, but the possible risk variation within this genetically diverse group has barely been addressed (there is some data which indicate that Bengalis and South Indians are at more risk than Punjabis). Continue reading →

The 2009 paper Reconstructing Indian population history was a watershed in understanding the genomics of South Asians. Before this point the studies had been with unrepresentative samples, fewer markers, or, South Asians were only a sidelight. This paper put the focus on South Asians to elucidate the group’s population history (it still undersampled eastern South Asians, though this seems part of the plan because of their focus on two, not three, ancestral Indian components). If you want to know more about the paper, here is the ungated version. But in this post I want focus on an issue which you can find only in the supplements to the paper.

The HapMap project, which surveys genetic variation in world populations, has a set of Gujaratis, from Houston, Texas. This is currently the primary population of Indian origin you have to work with in the public data sets. There are other South Asian populations in the public domain, but their number of markers is far lower. So the Gujarati sample is very useful right now. But one thing that immediately jumps out at you is that there are in fact two Gujarati clusters. In the PCA plot I’ve extracted from the supplements you see the two largest components of genetic variation. PC 1, the x axis, separates whites from South Asians, and PC 2, separates one group of Gujaratis from everyone else. What’s going on here?

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Two issues compel this post. One is practical. The other is more, shall I say, spiritual (or at least fun!). In regards to the first, a few weeks ago I reviewed a paper which reported that the efficacy of response to a particular leukemia treatment regime was dependent on the amount of Native American ancestry an individual had. One has to be specific here, because many people who are white or black American have significant Native American ancestry (Brett Favre’s paternal grandfather was Choctaw), and many people who identify as Native American may not have as much Native American ancestry as others. But for the purposes of this blog post, I want to bring to your attention the figure above, which I extracted from the paper. Its implications may pose a major problem in the future for South Asian biomedical research in the United States. Continue reading →

Wired has a totally charming story of one man’s quest to understand and beat the confounding scratch-off lottery ticket:

Mohan Srivastava, a geological statistician living in Toronto, was working in his office in June 2003, waiting for some files to download onto his computer, when he discovered a couple of old lottery tickets buried under some paper on his desk. The tickets were cheap scratchers–a gag gift from his squash partner–and Srivastava found himself wondering if any of them were winners. He fished a coin out of a drawer and began scratching off the latex coating. “The first was a loser, and I felt pretty smug,” Srivastava says. “I thought, ‘This is exactly why I never play these dumb games.'”

The second ticket was a tic-tac-toe game. Its design was straightforward: On the right were eight tic-tac-toe boards, dense with different numbers. On the left was a box headlined “Your Numbers,” covered with a scratchable latex coating. The goal was to scrape off the latex and compare the numbers under it to the digits on the boards. If three of “Your Numbers” appeared on a board in a straight line, you’d won. Srivastava matched up each of his numbers with the digits on the boards, and much to his surprise, the ticket had a tic-tac-toe. Srivastava had won $3. “This is the smallest amount you can win, but I can’t tell you how excited it made me,” he says. “I felt like the king of the world.”

Delighted, he decided to take a lunchtime walk to the gas station to cash in his ticket. “On my way, I start looking at the tic-tac-toe game, and I begin to wonder how they make these things,” Srivastava says. “The tickets are clearly mass-produced, which means there must be some computer program that lays down the numbers. Of course, it would be really nice if the computer could just spit out random digits. But that’s not possible, since the lottery corporation needs to control the number of winning tickets. The game can’t be truly random. Instead, it has to generate the illusion of randomness while actually being carefully determined…”

Srivastava had been hooked by a different sort of lure–that spooky voice, whispering to him about a flaw in the game. At first, he tried to brush it aside. “Like everyone else, I assumed that the lottery was unbreakable,” he says. “There’s no way there could be a flaw, and there’s no way I just happened to discover the flaw on my walk home.”And yet, his inner voice refused to pipe down. “I remember telling myself that the Ontario Lottery is a multibillion-dollar-a- year business,” he says. “They must know what they’re doing, right?” [Link]

This story reiterated in my mind how important it is to have a good understanding of science and mathematics in modern society. Consider how many activities in your day are governed by a mathematical code or logical pattern of some kind. Every minute you spend on Facebook you are helping Facebook perfect and equation to predict what you might buy for example. Nerds are poised to inherit the future.

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Earlier this week, an article in the Journal of Personality and Social Psychology detailed some provocative new findings:

Are you happy? Well don’t try to be happier; you might become less happy. That is the gist of a multi-cultural study published recently in the Journal of Personality and Social Psychology.

The study by University of Virginia psychology professor Shigehiro Oishi and colleagues at three other institutions found that, on average, European-Americans claim to be happy in general – more happy than Asian-Americans or Koreans or Japanese – but are more easily made less happy by negative events, and recover at a slower rate from negative events, than their counterparts in Asia or with an Asian ancestry. On the other hand, Koreans, Japanese, and to a lesser extent, Asian-Americans, are less happy in general, but recover their emotional equilibrium more readily after a setback than European-Americans.

“We found that the more positive events a person has, the more they feel the effects of a negative event,” Oishi said. “People seem to dwell on the negative thing when they have a large number of good events in their life. [Link]

So in a nutshell, what this article is saying is that “Whitey” is happier than me on a day-to-day basis (which is why he’s always whistling), but that I get over a bad day or a negative life event with greater ease than him. Could it be that since Asian families are likely to be newer to America (i.e. fewer generations removed from Asia) we are instilled with a certain sense of fatalism engrained within the family? When a grandparent or relative died in India and our parents couldn’t be there, we watched them deal with it and recover as best they could from afar. As another example, when we are the victims of racism we have to shake it off and keep going. A European American may not have to deal with some of these things. The study (and take it for what its worth) is essentially saying that Asian Americans have built up a greater immunity to bad news than European Americans.

“It is like the person who is used to flying first class and becomes very annoyed if there is a half-hour delay. But the person who flies economy class accepts the delay in stride…” [Link]