The Whole Genome of HeLA cell line - The spark to the ethical challenge revolving around personal genomics

HeLa cells have been vital to making groundbreaking research in science for the past six decades. Many Scientists made million passages from them and shipped them from one place to another but did not put too much thought into where they originally established. Rebecca Skloot gave the cells a life and a history through her book “The immortal Life of Henrietta lacks”. The book dealt not just with the origin of the cells but interwove it with scientific discovery, faith healing and racial issues. This book brought to light many ethical issues that were neglected decades ago. Skloot talks about how the Lackses were kept in the dark about the cells, how important and beneficial they were in moving science forward. This book published a few years ago has gained some more importance this year after the HeLa genome was sequenced.

A little bit of Background…

Early this year, in mid March Lars Steinmetz and his group published the sequence of HeLa genome in G3: Genes, Genomes and Genetics online. The study was comparing the genome of HeLa cells to that of normal tissue. This publication sparked a storm of ethical controversies that forced them withdraw the publication. This is also the first time a genome has been withdrawn from public access. The family stated that the genome sequence is private family information and it should not be published without consent. EMBL describes the genome to be chaotic, complex and fractured representative more of a cancer genome than of the family itself. There seems to be more fire on the grill since consent was not received before establishing the cell line itself.

The ethical conundrum

The argument that Skloot points out in her NYT essay is that since the genome was published long after Henrietta’s time, consent should have been received from her family. While we all agree that patient’s consent is top priority while using samples or data for extending continuing research, having the family consent for them is a whole different ball game. It spurs questions like “Do my unborn children have the right to ban me from making my genome sequence open access?” It is an ethical conundrum indeed. It is easy to argue that one’s genome sequence is one’s own private information and hence the individual’s decision to make it as available as possible but it is difficult to ignore the information the data would provide once a SNP calling or comparative mapping is performed.

The awareness people from a non-scientific background have on human genome sequencing is limited. Having information available online makes it sound like facebook only with 100x more coverage. This is not true. It is important to remember that most of the analysis that comes out of human genome sequencing is a “prediction” with a percentage or a probability number associated with it until it manifests into a phenotype. But it is also important to remember the good that has come out from making sequences publicly available. Publicizing genomes may not be the first aspect that we think about when it comes to our own sequence, but on the flip side when there is an issue for example a rare genetic disease, it opens up more resources and the chance of a remedy when data is available to other researchers.

The can of worms that have been opened because of the HeLa Genome will hopefully help establishing policies regarding sequencing and publishing of human sequences. As we move a step further into personalized medicine, it is important to have this in place but in doing so not forget the direction we want to personal genomics to take or how beneficial it can turn out to be.

A more edited version can be found here

Bird brain - blame it on twitter

I usually wake up super sleepy and the first thing I do is pray or brush my teeth? No I reach out to my  phone and from then on its message alert followed by work email, then news via twitter and then FB. By then I am at the point I am about to take a shower. Yes I understand, none of you want to touch my phone. While I am in the shower its NPR app on my phone or music goes on until I leave the house. Then it’s on my car stereo. The technology is non stop. Then at work, duh obviously. The times when I am actually not hooked on are when I am deciding what to wear and while visiting friends. Well that’s probably it. All our gadgets have coffee stains and god knows what on them. The need to know whats happening is incessant. When the Boston bombing happened I called my cousin who lives there to see if she was ok. She was like “Yeah, why do you ask?” And the wrong news that got retweeted over and over. I was one of them. So excited when something bad happens in the world it’s unbelievable. My husband and I love AT&T though their network sucks big time because you can talk on the phone and still browse the Internet and tweet and facebook. There is a problem right there. The only time we are not hooked on to our gadgets or cable is when we go out to eat and at certain rare occasions at home when we decide quality time over other things. Which is as often as we cook a full meal. Oh and when are running “together” we have our own music or books! That we listen to. There used to be a precious 15minute to an hour when I used to read to sleep. An actual book that’s more than a ten-page article. Now its over take by the “readit later” app.

There was a simple time when my mother would pick up the Hindu paper and skip directly to the obituary section and my father would read aloud everyone’s rasi from the tamil paper whether we like it or not. Last week when they moved, they have to live without Internet for two days. Every time I called my mother the first thing she would say was “internet-e illa de”. And my dad would growl “ that bloody man, what was he thinking, I told him not to unplug it until the last day?” They did not have electricity for few hours a day and got drinking water only for couple of hours a day. Everyone is corrupt.

And news is not news anymore. Just what happened..hmmm. That’s not a good news channel. Everything is an insight. You need to have an opinion Even if you are just a regular person. Anyway the reason for saying all this is that am starting my own Sabbath on Saturday mornings. Just for a couple of hours. Yes and it is going to be after I wake up. I will remember that. Hopefully have less more birdbrain moments from here on! Mazel tov. 

Kick yourself in the butt then go for a run

I will go ahead and say this despite the fear of sounding like a linkedin inspirational!

My mother still fondly remembers the first television they bought together or how they were able to buy a computer without applying for a loan. When you start your career big you lose out on these joys (of course you have other joys like the pleasure of having money). I decided to write about this because of the lack of excitement I had for what I did, especially repetitively.  As a young intern waiting to please you are literally like a sponge absorbing everything and working 200hours a day. But as you grow into what you do achieve a few accolades, you start harboring a pot belly and fail to be the person who kicks themselves in the butt.

A few people who were CEOs or were working into a start up gave some good insights. Crawl before you walk. You will appreciate going through the motions much better. Words like “create your own opportunities” or “self motivation” loses real meaning when you are standing in the job. At least for the lesser beings who do not have a George Church like or Steve jobs like idea every 15 minutes. For the rest of us, we are not ready for the responsibility yet. I kept thinking that som

To my city

·      The city that patronizes gooey butter cake – butteriest of cakes and provel the worst cheese ever.

·      St. Louis is the city where you can find the best draft beer in a couple of minutes but it will take you weeks to make your water drinkable.

·      It’s the city where every next guy you meet will swear on venison and will actually convince you that greens are bad for your health.

·      It’s the city where everything that is not dunked in lard cream cheese or butter is non existential.

·      Where you find the perfect mix of yuppie young libertarians and old staunch republicans. No one talks of socialism.

·      Surprisingly the best music scene ever – home of the blues.

·      The only city in US with old money, dying auto industry, and empty downtown with beautiful history but culture running deep.

·      The city with sky rocketing crime rate that puts Baltimore and Chamba valley to shame.

·      The city where every week there will be a new code for marijuana and you will invariably hear it. Even though you have no intention of buying it.

·      The only city where still your neighbor will offer you an apple pie and volunteer to collect your packages.

·      Where baseball is the only sport that exists.

·      With prettiest of parks and the best of hospitals.

·      With a summer that can put Chennai to shame, with a winter that can drive you nuts but two glorious months of spring and fall.

·      The land where you will be freezing cold in the morning and ready to start a barbecue by night.

·      The only city where tornado is fun and everyone starts “storm chasing” like they are waiting to pack for a vacation.

·      The city that has nothing to offer but still boasts hell rising real estate prices.

·      The city that I was so reluctant to like but managed to make friends and live in with some sense of belonging.

Reality check!

On teaching and learning

It was a lazy Saturday afternoon and after a nice lunch I was reminded on why Coimbatore was so special to me. The mild afternoon breeze, a little bit of sunshine and cotton dust filling your nostrils. Except that I was told that its just regular dust now after the death of cotton industries. We strolled into a deserted school reminiscing everything we loved about school. The trees, the basketball games, lunch under the peepal tree, monkey ladders, choir room, parlor meetings, class masses etc the list was endless except it did not include studying. Being neighbors and going to the same school helped practically live in each other’s heads. We strongly remembered the “pit in the stomach” feeling we used to have right before school reopened. While for a lot of people it may have been what grade or where they stood in class, for us if we were going to get across the failing grade at all. I hated studying to be plain. I hardly had a favorite subject. English maybe but that was only because it wasn’t really a subject. Looking back now studying and learning were two independent things never tied together at school. The ‘want to learn’ was never there or instigated. But now wanting to learn is what keeps us going helps in climbing up the ladder or even live life better. As an educator, it is important to not take that away from a child. As an adult I can see myself being critical and judgmental more often than appreciative. I swore I would never become that. We are ready to criticize, compare and comment but never take the extra minute to engage someone in the subject or thread him or her in to get into our thinking zone. Hardly ever put on the educator cloak. We somehow do a better job of it when we want to sell a product for our company. Several children including me turn out to be bird brained hopping from one subject to the other struggling to stay focus because they are not into it yet. As an adult now, I empathize with the child who doesn’t get good grades or who hates completing a project. She just needs someone to engage her, to make her think with him or her. I agree it takes a lot of effort and time but it maybe worth it.