Monday, February 17, 2014

Why we didn't sequence HeLa

Recently, another paper about HeLa's genome sequence was published in Nature. Along with that came an article explaining how the ethical ramifications of publishing the sequence of HeLa were handled before this recent paper's release.

My friend Dr. Cuiping Pan asked about why, when we were deciding on a cell line to whole genome sequence and publish back in 2008, we chose U87MG rather than HeLa. Here is my response:

At the time, we had a big argument about whether to do HeLa. We all knew it would be higher profile to do HeLa, but even in 2007/8 we were aware that the cell line had been derived without Henrietta Lacks' informed consent. Meanwhile, obviously HeLa is the most commonly used cell line, so we knew it would be more useful generally than U87MG, which we identified as the most commonly used glioma cell line but also only around the twelfth most commonly used cell line generally. [A quick Pubmed search finds 1,110 papers with the term "U87MG" in them, compared with 78,343 for HeLa!]

So it came down to an ethical choice versus a utilitarian choice, and it happened that the ethical choice would also be less "rewarded" with references, high impact journals, et cetera. In fact, we spoke with Nature and were basically told it would be harder to publish U87MG than HeLa there (but it's a moot point because we also wanted to support open access and Plos, which is why we went for Plos Genetics at the time).

Anyway, looking back I think we made the right choice. Back then, Francis Collins was not head of NIH and the book on Henrietta Lacks had not been released yet. The [European] group who subsequently sequenced HeLa got in a lot of hot water.

As for U87MG, we looked into its history. It was an anonymously donated sample that had been consented as far as we could tell in Germany. [Note: This is all off the top of my head, so don't use that as a primary reference, please.] The particular individual it was derived from was not publicly known that we could see, though his identity is still likely in the medical records of the hospital where he was treated. We did not try to find out who he was, because keeping him anonymous and deidentified was the ethical choice.

Also, on a practical level, doing a male genome seemed interesting since it would get us Y chromosome, but that was a minor and not very compelling reason.
I am of the opinion that as geneticists and genomic scientists, we must do things above the board and be very careful about informed consent and protecting people's identities. There is literally nothing as identifying as the genome, so we must be cautious and considerate in all cases. This is why, before ever considering sequencing something, we always need to consider the ethical implications.

HeLa, the cell line, is something we simply cannot give up on now. It is too late, and it has done too much good and it has too much future potential to do good in the future for all of us. But even with that in mind, I still feel using it and even sequencing it is questionable. It's a hard feeling to shake and it's sourced at the fact that the person who the cell is derived from never consented. I think, over the past few years, the dialogue between health science and the Lacks family has been a very good change, and I'm very happy the Lacks have basically consented to use of HeLa generally.

Really, it goes to show why it is so important for us to do as much as possible to behave ethically from the start. To avoid these types of situations in the future.

Monday, January 21, 2013

Where have I been?

I was never someone who blogged a great deal. But once or twice a month, I would put hand to keyboard and come up with something to talk about that is relevant to my favorite field of study: Genetics.

I have every intention to continue doing that. But last April I started working for a small start-up company, and I've been very busy. And I do mean busy. I thought I was busy before in graduate school and my post-doc, but with the exception of grant time or paper writing, I can honestly say I have never been as busy as I have been the past nine months.

That's right, I've been working in industry for nine months. I'm not sure if I mentioned that before. Admittedly, I'm working at a start-up, so it's not quite like joining Massive Dynamic and getting lost in the army of scientists doing this or that. It's much more fun than that. I would say it isn't quite at the level of the Internet start-up era in the late 90s/early 00s, but it's interesting.

The genomics field is really heating up. It's great to see how rapidly it is advancing. And the competition is fierce. Every little company competing in this space is exceptional with exceptional people, exceptional goals, and (hopefully) exceptional funding.

There was a time where I was gung ho about staying in academia. I still love academia and research. But I began to see the writing on the wall about two years ago, when I realized that, frankly, the way academia has handled genomics has resulted in a few massive centers for genomics and sequencing and then a lot of little centers that amount to core facilities servicing their attached universities. I took note of what opportunities there were, and there seemed to be a lack in academia. Perhaps it's because of the funding situation with the NIH and the way it has funded massive centers over smaller sequencing projects.

Meanwhile, at the same time, I saw a number of start-ups in this space popping up. Places that had money and drive to advance the science of genomic analysis--which is exactly what I had wanted to do in my academic career.

I tried writing a grant once where I had planned out ten years of work with the goal of advancing genomic analysis and after reading it through a few times I realized I would have had far better chances securing VC funding with that grant than obtaining an R01 from the NIH. That's the moment it struck me that perhaps the most rapid and impressive advancement in this area will take place in industry for the time being.

I basically feel validated when I see the Biobase mark on the ANNOVAR website, or the Appistry logo on the GATK website.

That's not to say that I would never return to academia. I would love to, and if there's a shift in the wind and it pushes me back in that direction, I would go there. But for now, I would just say that I am having a very good time in the industry, learning new skills but also flexing my strengths.

Anyway, that's where I've been. I'm still around. I'm just working longer hours.

Tuesday, November 6, 2012


Beating #Election2012 on Election Day in the US. Human genetics has made it, people. Step aside, Charlie Sheen.

Monday, November 5, 2012

Save the Square Watermelons

Also, I just realized I've had over 25,000 hits on this blog. Thanks for reading! I hope it's been useful and interesting!

Thursday, November 1, 2012

"Why I Don’t Want to Know My Genome Sequence"

"Why I Don't Want to Know My Genome Sequence"

Kind of interesting to read this as someone who at least has his own exome sequenced and has learned a lot from it. It's kind of interesting to read it in contrast to my own post explaining why I wanted to sequence myself.

It ends with a funny statement:
An osteoarthritis mutation manifested itself as an inability to play an F chord at age 33. A p53 mutation and then another that bloomed in response to years of orthodontia X-rays gave me thyroid cancer a few years after I gave up the guitar. And I don’t need a genetic test to know I didn’t inherit my father and grandfather’s psychotic depression. 
Ron Crystal, even though he’s among the sequenced, has the right idea: don’t smoke, exercise, eat a healthy diet, and don’t worry about DNA sequences. That’s good enough for me – at least for now.
This is one of those statements used to make one's self feel better about not doing something he or she wants to do. That's my feeling, at least.

To be more specific, let's use myself.

Sure, I could have lived my life thinking my borderline migranes were from caffeine withdrawel and my mother and not bothered to find out the exact mutations likely to cause it and therefore which drugs may actually have a beneficial effect on me. I could have. But I didn't.

I could have lived my life thinking my intestinal issues were due to a bad diet or food allergies. Because clearly copious amounts of salad, low fat, low carb, low salt is a bad diet, right? And clearly my wife who eats the same things and has zero gastrointestinal issues is just lucky. Oh no, it must be food allergies. It couldn't possibly be that I inherited two mutations, one from each parent, that damage a particular gene already known to be causative for gastrointestinal problems (among a number of other things that I happen to have that most general practitioners wouldn't link together).

I could have survived without knowing I have asthma. Maybe.

I mean, go ahead and live in ignorance if that's your thing. If you're not interested in your own genetics, then fair enough. You're not alone. But it was damn reassuring to me, personally, to figure out exactly what genes are mutated and how those are causing conditions that negatively effect me.

And I would say not only am I healthier, but I'm also more aware of my health. And that's a good thing.

And that genetic information isn't going to expire.

Anyway, let's not devalue our genetics this way. The fact that we don't know everything yet doesn't make the data itself less valuable. Yes, it will take effort to understand but then again, so does nearly everything about your health and life.

I see it as a great thing.

Wednesday, October 31, 2012

ASGH2012 Fail

Monday, October 22, 2012

Misunderstood: Genetic tests and the people who don't understand them

On Friday, I was made aware of a story about a boy in my town (Palo Alto, California) who was being transferred from his school to another school against his and his parents wishes. He didn’t do anything wrong and he didn’t want to leave. Instead, the administrators at his school made this decision based on genetic information they were given by the parents. Genetic information that they apparently did not understand fully.

The Story

The original story made a bit of a splash, with articles on major news sources. Here are a few links explaining the fiasco:
The original article that exposed what happened.
An official response from the superintendent of the school district.
An SFGate article that exposes important facts about this case.
The article I first heard about the story in.

The basic story goes like this:

A boy named Colman Chadam is being forced to transfer out of his current school in the middle of the school year because he carries mutations that cause cystic fibrosis (CF). CF is a relatively common yet fairly severe genetic condition.  Kids with CF should not be in close proximity to one another because they can easily infect each other with respiratory infections. In other words, a school would not want two kids with CF in the same class, and would probably be justified in keeping them separated for their own health (though it’s unclear if forcing them to go to separate schools is even necessary).

CF can be predicted genetically—we are aware of major CF mutations (in the CFTR gene) in the population and a standard genetic tests can identify them. But CF is typically diagnosed through a non-genetic test called a sweat test, and is otherwise a rather self-evident disorder because it is a serious condition. It affects one in twenty-five Caucasians. Moreover, the genetic tests are necessarily conclusive—one could carry mutations for the disease yet not have it.

The thing is, Colman was apparently never diagnosed with CF. He has never displayed any symptoms of the disorder. Instead, according to the SFGate article, Colman was found to have mutations in CFTR that could potentially cause CF. But they haven’t for him.

For whatever reason Colman had a genetic test including CFTR eleven years ago. It’s unclear in the articles I’ve found, but I’ve been told he’s likely to have tested positive for a sign of CF at birth and then had the genetic testing to confirm, but the disease never manifested later. So despite not having cystic fibrosis, his parents are aware that he carries mutations in the CFTR gene.

And, probably without thinking that there could be serious ramifications for Colman, his parents told the school that he carries mutations for CFTR when they were asked to report any pertinent genetic information.

The SFGate article discusses the progression from an innocuous bit of irrelevant “medical” information to Colman being transferred out of his school:

“A few weeks into the school year at Jordan Middle School, school officials took note of Colman's medical history, information that eventually was shared with another Jordan parent whose two children have classic cystic fibrosis and are predisposed to chronic lung infections.”

Can anyone else see some major problems with this little statement? First off, school officials were looking into this child’s medical history why, exactly? He does not have cystic fibrosis, so why was it being followed up so heavily by the administration? Second, his information should never have been shared with the other parent who has two kids with CF.

Moreover, with one in twenty-five Caucasians carrying mutations for CF, there’s likely to be numerous children at the same school carrying CF mutations who are not being transferred because they never had any symptoms and they never had a genetic test. That’s one of the things that makes this action by the school so unreasonable.

So I tried to think about how this could have happened.

I think what probably occurred was that Colman’s parents reported his CFTR mutations just in the interest of being fully compliant with school rules that say, “Tell us everything (or else),” which most parents are probably familiar with.

Then a nurse or administrator or someone (who hopefully had permission to see Colman’s records) who was familiar with cystic fibrosis (at least at the level of understanding that two kids with CF shouldn’t be in the same class) noted that Colman had CF mutations and misunderstood that to mean he has cystic fibrosis.

I’m not sure whether the other parents were really informed or not (at least one article suggests they were—if they were, they shouldn’t have been). But what I can imagine is that in the interest of avoiding any potential problems (imagined or otherwise), they decided to transfer Colman out without really understanding that he does not have cystic fibrosis.

There’s some pretty strong evidence of this in a letter from the superintendant that was posted on PaloAltoPatch. I’m pasting it below for posterity:

“The Palo Alto Unified School District strives to meet the needs of all students and to ensure that a safe and welcoming learning environment is provided for all our students and staff. To be clear, this commitment includes caring for our students with medical needs.
“At this time, our District serves students who are diagnosed with Cystic Fibrosis (CF), a serious medical condition that creates a need for our staff to observe strict protocols on cleanliness in order to help protect these students' fragile condition. I am proud that our staff energetically and compassionately works to observe the necessary protocols for these students. Further, I am proud that our staff thoughtfully embraces these, and all, students.
"A recent story that appeared in the San Francisco Chronicle addresses the distance -- the literal physical distance -- that must be constantly maintained between children with CF in order to avoid bacterial cross contamination. I want to stress that medical authorities clarify that CF is not a health threat to the general public (a theme that was touched on in the story), but it is a topic of concern for non-sibling children with CF.
“As background, at the beginning of this school year, we became aware that students (not related) with CF were on the same middle school campus. Based on the advice of medical experts, who stress the need for non-sibling CF patients to constantly maintain a specific distance from each other, we thought it best to place the students at different campuses. Again, based on the advice of medical experts, this is the zero risk option, and most certainly helps our District deliver on its commitment to provide safe learning environments.
“We asked the family of the student who is new to our District if they would consider moving their child to Terman Middle School. We asked because Board policy gives priority site choice to students who are established at a site, and the other students have been with our District for years. Sadly, it was this request that caused the controversy, and the media coverage.
“I want to stress a few critical points.
“First, at both of these schools the dedicated staff are stepping up and working to provide these students with excellent learning environments. We are grateful for their professionalism and compassion.
“Second, we are education professionals, not medical experts. I assure you that we will take action based on recommendations from medical authorities. Expert advice will be balanced by the PAUSD Board policy that strictly instructs our District to ensure we provide a safe learning environment for all students. To be clear, our Board of Education places the highest priority on student safety, in all situations and in protecting the privacy interests of all students.
"Finally, we must be honest about the fact that we are talking about public schools, not medical facilities. We will strive to implement all health and safety protocols to help protect the health of these children; however, the harsh reality of a busy middle school campus, where students ranging in ages from 12 to 15 share a cafeteria, restrooms, the gym and locker room, a library and other settings, is that it might be virtually impossible to maintain a specified separation and sanitation protocols at all times. This reality is what made us gravitate to the separate campus option. CF is a life-threatening condition, and in this context, based on the information provided to us at the time by all parties, we believed that zero risk was the best course of action. We hoped that these families would agree.
“This topic is understandably emotional for the families involved, and we will work with them to meet the needs of their children. However, I must again stress that we will follow the advice of medical experts, who we trust will help us understand the option that eliminates, if possible, all risks.”
Charles F. Young, Ed.D.
Associate Superintendent Education Services
Palo Alto Unified School District

I feel that this letter clearly shows that at the very least, Dr. Young here was under the impression that Colman has cystic fibrosis. But he apparently does not. He carries mutations in CFTR, but he doesn’t have CF. Here’s another piece of evidence that Dr. Young and the other administrators are misinformed, thinking that carrying CFTR mutations is equivalent to having CF:

“The administrators sought medical advice, Silverman said Thursday, which resulted in a recommendation from Dr. Carlos Milla, of Lucile Packard Children's Hospital, saying that, ideally, children with cystic fibrosis would attend separate schools.
The recommendation was not based on knowledge of Colman's specific medical history, his parents and their attorney said prior to Friday's court appearance.”

Why else would they seek medical advice about whether children with cystic fibrosis should attend the same school unless they thought that Colman actually has cystic fibrosis? Rather than speaking with a medical doctor, they should have consulted with a board certified genetic counselor (which Stanford, where they received consult on this issue, has a number of). At the very least they should have spoken with a medical geneticist or even just a geneticist like yours truly. They didn’t even know that, though, because they collectively did not even realize genetics makes a huge difference here.

The Lesson

I honestly do think this is all a big misunderstanding. I hope that the administration is willing to admit a mistake was made and rescind their decision to transfer this kid over a misunderstanding about how cystic fibrosis works.

But to me, it’s also a troubling sign. I’ve sequenced my own exome. I know genetic facts about myself, and if Colman’s case is any indication, I would have no immediate recourse if that information were to be used against me in a legal way. What’s happening to Colman has yet to be ruled on, but regardless, his life is still being thrown to the wind while these decisions get made based on misunderstanding and ignorance about how genetics and disease work.

Moreover, what of my own future children? Or my current relatives? Information comes out about me and that information is shared by my relatives, at least in part. Could it be used against them by people in positions of power who don’t understand genetics?

These are major reasons I’ve yet to share my genetic information with others openly. I would absolutely love to make my data public, to reap the benefits of the community at large studying my genome. I had plans to do just that, but I have yet to enact them for these reasons. Because the current protections do not consider all possible problems—like this issue with Colman Chadam.


Currently, I can’t stress with people enough that they have to protect themselves. I love the idea of living in a perfect world where we can share our genetic data and not be subject to prejudice (intentional or unintentional) as a result. But we honestly don’t live in that world yet, so those of us who have been sequenced should seriously consider whether sharing our data is in our best interest.

That includes not sharing genetic information with, for example, your kid’s school district. Of course we think it’s pertinent information they might need, but they do not need to know that your child carries CFTR mutations (only whether or not the child actually has CF).

As for Colman and his family, I think they need to push this. At the personal level, what’s happened to Colman is certainly unjust and possibly illegal. And for the PAUSD and its administrators, they need to learn a lesson here—that they need to fully comprehend what’s going on with students medically before making blunt-ended decisions about what to do with them. That if they are confronted with genetic information, they need to see a genetic specialist to interpret it correctly.

On a more general level, it needs to be recognized that genetic information cannot be used to discriminate against people even in the most innocent-seeming way, even when it feels like the right thing is being done. Until then, we who have genetic information about ourselves need to be careful with it and how we share it.

This issue is starting to spring up as genetic testing becomes more common. Imagine if a young person has genetic predisposition to asthma, but has yet to have an asthma attack. Do you stop that child from playing soccer or do you give her an inhaler just in case? The first one is, in my opinion, genetic discrimination. The second one is just common sense (or at least it should be).