Sapana Vora, PhD Candidate

Only July 7th, 2009, I successfully defended my thesis proposal and became a PhD candidate in Cancer Biology at the University of Chicago. The process was both informative and a little nerve wracking, and I'm glad it's over. My committee is smart, thoughtful, and truly engaged with my project and I am grateful to have them all signed on until the bitter end. Unlike at my prelim, I was able to amicably banter with my adviser and another prof and truly felt at ease the whole while, even when they asked me questions I couldn't answer. We did find the gaps in my knowledge and I have vowed to fill them to overflowing before my SRP (student research presentation) next February and certainly before my next committee meeting sometime next summer.

So what's my thesis project? In short, a case-control genome-wide association study of genetic susceptibility for the development of therapy-related acute myeloid leukemia (t-AML). What it basically means is that I'm going to genotype the germline DNA (what you're born with) of patients who are treated (more or less) the same way for the same primary cancer and see what's different between the people who develop t-AML (cases) and those who do not (controls). In terms of genetics, I'm primarily interested in SNPs (single nucleotide polymorphisms) and CNVs (copy number variants) found across the genome (genome-wide). It's the differences we're interested in, because they could potentially serve as markers or beacons representing susceptibilities to developing t-AML, a secondary, treatment-related cancer.

For those not familiar with the whole PhD process, it typically goes something like this:
Year 1: Take classes and rotate through labs (usually 10-weeks apiece).
Interim: Take some preliminary/qualifying exam to test knowledge and confirm student is ready to continue in the program. Join a lab for the thesis project.
Year 2: Take any remaining classes and fulfill TA requirements.
Interim: Assemble thesis committee (adviser+ at least 3 other profs, at least two of which are within one's department). Successfully write + present = defend thesis proposal.
Years 3-?: Conduct thesis research. Fulfill any class/TA requirements remaining. Meet with thesis committee at least once a year. Attend conferences, meetings, etc.
The End: Successfully write + present = defend thesis. Send copies to the five people who will ever read it. Graduate and put "Dr" in front of name. Figure out what to do with rest of life.

I am currently in the second "interim" stage. Now, all I need are my cases, controls, and data before I can move on. You know, small things.

California Dreamin'

[The last time I posted was June 9th. This is rather sad. I vow from here on out to post at least once a week, hopefully on interesting things going on in my life and barring any dearth of such news, at least interesting thoughts going on in my head.]

The past two months have been rather exciting though anxious at times. First the trip to California. On June 11th I flew out to California to celebrate Saket's graduation from Stanford. The flight was horribly delayed and I joined my family hours late, only to arrive exhausted to some terrible news. My Dad's mother's health had taken a turn for the worse and our greatest fears rapidly darted to the front of our minds. We promptly canceled our weekend at Yosemite (quite a shame, since my dad loves Ansel Adams' photography and longed to see the subjects in person) and started searching for the earliest flight to India. Unfortunately, my dad didn't have his passport with him (something I've made a personal point to always have with me when I travel, just in case...) so trip planning was slightly complicated. Our friends and neighbors, the Shahs, were a tremendous help in packing Dad's things and getting him to and from the airport as quickly as possible. We really owe them. He left on the 12th, just a day before Saket graduated.

The graduation ceremony was fun, though the sun was a bit intense (the tan lines have only just fully faded). We got to meet a lot of Saket's friends, tour the gorgeous campus, and enjoy a performance by the (in) famous Stanford band (tree included). Pictures are up on facebook.

The next couple of days were spent in the City. We toured the Marin Headlands with had incredible views of the Bay. We visited the fabled Berkeley campus where Greek architecture is the style of choice and meeting places and cafes just scream *liberal*. Just walk along the streets bordering campus and you'll inhale more than fresh, left-slanting air. We also ate at this great little Thai restaurant and basked in the glory that is Thai iced tea (half tea, half half-and-half, and half sugar).

We also had 2.5 days schedule for Lake Tahoe and it was a splendid trip. We had heard much tell of the lake but never got around to seeing it, despite our many trips to the Great Bear Republic. Though the skies threatened rain the first afternoon, they promptly cleared for the next two days and we were showered with glorious weather. We took a few hikes, took lots of pictures of the lake, visited a Scandinavian castle, ate some of the best pizza I've ever had, found a delightful Thai restaurant with approximately 8,000 vegetarian choices, and in general enjoyed ourselves.

While I was busy having fun, a rather serious deadline was bothering me. My thesis proposal was scheduled for June 26th which mean the written part needed to be done by the 19th at the latest. I "worked" on it on and off but was starting to panic that I wouldn't get it done in time (poor vacation scheduling, eh?). Viewing the highly enjoyable Star Trek reboot with the sibs pushed the deadline further back but not forgotten. Sachi and Mom were scheduled to leave the next day (the 19th) and I was determined to just finish it all in one day. Then I got the email.

The stepmother of one of my committee members had passed away. Tim's, my friend and labmate, thesis proposal was scheduled for the 22nd and had to promptly be rescheduled. We decided it was best that he take my spot (since we share the same committee and the room was already booked) and that I reschedule to a later date. My new date ended up being July 7th, which meant I just received an 11 day extension. While my heart broke for my professor, part of me couldn't help rejoicing at the turn of events. Not quite schadenfreude, but too close for comfort.

With a deadline suddenly lifted, I found myself free to actually enjoy the last couple of days I had with my brother in California. We still worked in a student center for most of the 19th, though more or less relaxed the rest of the time. We played Smash Brothers with Nader until 3 a.m., toured the campus art museum (famous for its Rodin sculptures), attended a lovely BBQ with the people from DripTech (we got cool shirts too), attended an amazing farmer's market, and of course got more froyo (frozen yogurt for the uninitiated). I was sad to leave Cali but am seriously considering finding a post-doc out there someday....