Full disclosure: I work for Counsyl. (In fact, if you watch the video at the bottom of the article, I'm the second speaker.)
The cool thing (well, one of many) about Counsyl is that there are a lot more things going on than pure biology and bioinformatics. Making genomics truly accessible is a software challenge that goes way beyond bioinformatics. There's obviously statistics, machine learning, and robotics running the lab; however, even more problems are pure engineering tasks. For example:
- How do you design the UI/UX around presenting data on 100 genes which can cause severe illness, but which most doctors (let alone patients) have never heard of?
- How do you efficiently accept orders from clinics across the nation, using a mix of web, paper, and EMR (electronic medical records) systems? (For bonus credit: deal with EMRs shipping fresh today on Windows 3.1. For double bonus credit: figure out how to bypass that ancient cruft and bring clinics into the 21st century.)
- How do you bill insurance companies when it can be opaque to even find out which insurance company pays for a given patient's procedures?
- How can you share data with the scientific community in as open a way as possible, without compromising patient privacy?
There's a huge amount of work to be done, so if you're interested in helping out, give us a look: https://www.counsyl.com/jobs/.
(It looks like this article is getting multiply posted, so please accept my apologies for hitting this one too.)
The coolest thing about Counsyl is that it's taking the tech startup philosophy and ideas and applying them to biology. Software is eating the world, and Counsyl is bringing that to a new--and very important--arena.
An added benefit is that much of what Counsyl does does not depend on the actual biology behind it. I attended one of their infosessions at Berkeley, and I remember a whole bunch of jobs like managing supplies and billing that are simultaneously nontrivial and unrelated to the actual domain. I've never much liked biology personally, so that's very promising.
If you want to work on something meaningful but don't really like genetics or medicine, Counsyl still seems like a great option.
I had a great experience of going through Counsyl's early-stage recruitment/interview process. They actually found me through a single post I made here on HN! The problems they gave me were very interesting and I got to Skype with the key engineering team members for a full day. I wish I could've moved to CA to take up on their offer but due to personal circumstances, I could only do remote. I don't get to say this often enough - I have the utmost respect for their founders, their vision, and the brilliant team they have gathered. If you are reading this and qualify for one of their job openings, I highly recommend you apply.
I applied and went through a very enjoyable three interviews with the CEO and two others. They seemed really interested in me and yet they never got back to me.
I had a lovely 2-3 month contract with Counsyl last year to help them build some internal systems. I have to say that they really have their stuff together and working with the team was a lot of fun. I've mostly had to stay silent the last year about what they're doing due to NDA and such, and won't say much here, but I HIGHLY recommend anyone looking to have kids consider going through Counsyl's program.
Also, if you are an engineer and are approached to join the team, give it every consideration. Those guys are so smart it's scary. Learning how microfluidic assays work was one of the coolest things I'd seen in a long time.
Their recruitment is quite annoying. I never sent in anything and they sent me emails saying thanks for applying and to fill in a slot on the calendar for when I could meet. Their approach to the process immediately turned me off.
Perhaps I'm not understanding correctly. You didn't send a resume yet you were scheduled for an interview anyway? That doesn't make a terrible amount of sense.
> Hi Dmitri,
>
> Thanks for applying to Counsyl back in August. At the time we didn't
> have any openings in engineering but now we do.
>
> We'd like to schedule you for an initial phone interview with Rishi
> Kacker, VP of Engineering, to learn more about your interests and how
> you may fit in at Counsyl.
>
> Please book an appointment here: http://bit.ly/Rishi_appointments
>
> Enter in your full name in the "What" section and the best number to
> reach you in the "Where" section of the appointment slot.
>
> Email me once you've finished booking your appointment so that I can
> confirm that it went through.
I responded saying -- hey this is spamming me and is kind of disrespectful/underhanded approach to recruiting and they said:
Hi Dmitri,
This is definitely an error on our part. I'm sorry for the annoyance.
It looks like your name was pulled up as an exceptional candidate back
in August (likely from a HackerNews thread). You should have only
been contacted to check for interest, but unfortunately, you were sent
a stock email (as if you had previously applied).
See the attached linkedin profile PDF from August.
I'm sorry again for this clerical error. I'll look further into the
root cause and hopefully we can prevent this type of error in the
future. I'd be happy to take a call if you have further concerns.
EDIT: On the linkedin profile they mentioned and sent via screen shot, it explicitly says no recruiters.
If my spouse and I do the tests and find out there's a 25% chance our child will have a particular health problem, what are we supposed to do about it? Adopt? Roll the dice anyhow?
In the article, there's a couple that did the test then decided to do in vitro fertilization (IVF), but I don't see how that helps. It seems to me that any offspring that arise from IVF are going to have the same probability of having the health problem. What am I missing?
* For certain diseases like phenylketonuria, which are not life-threatening if certain dietary restrictions are followed, the pregnancy can proceed as normal but the baby can't be fed anything with phenylalanine in it.
Far be it for me to rain on this parade, as the founders seem great (and probably somehow related to me given their last name), but if I were to bet on a startup capitalizing on the moore's law change in genomics, it would not be this one (or any other existing company).
Why? From what I can tell, Counsyl is doing genotyping as opposed to sequencing. The latter is what is undergoing "moore's law" price declines.
Second, from the comments by employees on this thread, and the CEO's statement from the article, they are spreading themselves too thin by aiming to be the so-called "Apple" of genomics. Apple didn't start by trying to control the "full-stack", and it wouldn't be Apple if it did.
Third, any company that has Steven Pinker and Henry Louis Gates as advisors, at this stage, seems to be aiming at the wrong things: media exposure and political/legal maneuvering (Our test requires a doctor's prescription) as opposed to making something people want.
> Second, from the comments by employees on this thread, and the CEO's statement from the article, they are spreading themselves too thin by aiming to be the so-called "Apple" of genomics. Apple didn't start by trying to control the "full-stack", and it wouldn't be Apple if it did.
Counsyl started out using a third party lab to process the samples. The founders had a vision of being a pure software company. It turned out that the outside labs they tried all had terrible quality control and we had to re-test samples more often than not. That's totally unacceptable for the stakes of a pre-pregnancy genetic test. So they decided to run a lab in-house and it has been one of the best decisions made in the history of Counsyl. We have an amazing statistical process control team making sure that everything performs as expected. Control plates are constantly moving through our pipeline to catch any mishaps, and we are automating as much as we can in the lab, both to scale and to eliminate human error. We have no known false positives or false negatives, and we've found errors in the 1000 genome project's data (expect a publication about that sometime in the future).
> Third, any company that has Steven Pinker and Henry Louis Gates as advisors, at this stage, seems to be aiming at the wrong things: media exposure and political/legal maneuvering (Our test requires a doctor's prescription) as opposed to making something people want.
Pinker has been an advisor for many years, long before we left stealth mode. (I believe this to be the case with most of our advisors, but I only know for sure about Pinker because I'm a fan.) We have been operating silently since 2010 and have only just now lifted the veil. The test requires a prescription because of the state of health regulation in the US. We give medically actionable information so we're required to get a prescription.
I don't doubt that you all are good engineers/scientists, and that whatever processes you seek to optimize, you will.
But these things will happen anyway, whether at Counsyl or at another well-funded company with high-quality people.
Whether Counsyl has happened upon some key insight or technology which will make it a revolutionary company is another question. I don't see enough in the article or amongst the comments by employees here to indicate as such.
The points about Pinker etc are not that these aren't impressive people, but rather what do they have to do with the technology or business of Counsyl other than snob appeal?
What disturbs me is the seemingly coordinated release of the article, with the overwhelmingly positive comments by employees here, and rapid defense of any criticism. The challenges to Counsyl, for the most part, seem rigged to disseminate more information about the company.
Yes, you are proud of your company and what its doing, but (again) it seems like you guys are focused on the wrong things.
> The points about Pinker etc are not that these aren't impressive people, but rather what do they have to do with the technology or business of Counsyl other than snob appeal?
Ah, I see your concern. That's an understandable critique coming from outside of this industry. I had similar thoughts before I got more familiar with why we have the advisors that we do. Our industry (that is, genetic testing) is a minefield. Lots of people have strong opinions about it and there are many unanswered ethical questions. We need ethicists as advisors to help us make the right decisions. I can't tell you the number of times I've heard the question "So you're like GATTACA?" (For the record: No!) When your customer base is primed for strong negative reactions you need great minds to help inform both the public and your own decisions.
> What disturbs me is the seemingly coordinated release of the article, with the overwhelmingly positive comments by employees here, and rapid defense of any criticism.
Heh, I promise nothing suspicious is afoot here. TechCrunch came by a few weeks ago in preparation of writing a story. We've all been eagerly awaiting its release and as soon as it was up it got announced on our internal "chatter" email list. As you can imagine, when your startup gets profiled on TC it causes a bunch of excitement and we all immediately went to HN to upvote and comment (incidentally, I think we set off the voting ring detector on one of the submissions since we were all voting from the same IP). We love this place and all believe in what we're doing. Nobody was instructed to say nice things or defend the company.
disclosure: I'm a software developer at Counsyl. The above are just my opinions, I am not speaking on behalf of Counsyl, &c. &c.
Ok, points taken. I understand the optimism .. its usually a great thing, and I could be being overly paranoid. All the same TC is so 00's, just launch yourself on HN.
Regardless of my criticisms, I do hope that every startup working in good faith to change the world does so, so good luck!
The second iteration of Counsyl's test is a sequencing test. It's already been launched. It was referenced in the article. Expect a third iteration to include additional diseases in the near future.
2.5% of all births last year? So 100,000 people tested? I'm surprised it's not higher. Shouldn't everyone thinking of having children be taking this test?
Impressive how much data these guys are managing.
My only question is, when is Google buying Counsyl? David Drummond is an investor right? This seems like a no-brainer acq for goog to move into health care data.
To pose the same question in another way: what does Counsyl give you for $599 that companies like 23andMe don't already give you for $99? I couldn't find anything on the counsyl website that addresses this.
Edit: Actually, I think the difference might be that Counsyl is marketing to a clinical market, as opposed to 23andMe which is direct-to-consumer. Since I've read that 10x price overhead for clinical stuff is typical (from a link on HN a while ago), maybe $599 isn't too bad a price in that market for something that is $99 direct-to-consumer. Who knows?
The primary difference is that we're performing a clinical grade test that gives our patients actionable information. We only test for autosomal recessive disorders that will affect the health of your children. Unless you've been tested before, you don't know if you're a carrier. If both parents test positive for the same mutation then your child has a 25% chance of being born with the disease. This information allows you to make an informed decision about how to bring a healthy child into the world. (You have a few options once you have our test results -- in-vitro, adoption, or a normal pregnancy if the disease is manageable).
23andMe gives you SNP mutation results for many more genes that may or may not be associated with the disease that they report. They do a pretty good job of curation, but their SNPs do not guarantee your future disease status. Knowing that I have 2.3% higher odds of getting diabetes later in life is not going to meaningfully impact my day-to-day life, I already knew diabetes runs in my family, after all.
23andMe is great, don't get me wrong (many of us at Counsyl are 23andMe members, including myself), but they provide a different service for a different market.
Our test requires a doctor's prescription and we include a free genetic counseling session (from our own licensed genetic counselors) for all patients. Finding out that you and your partner are carriers for a serious disease can be a big surprise and cause a lot of confusion and stress. We have great GCs to explain the effects of each disease and how they could manage it in a child, if they choose to have a normal pregnancy. We're more than just a SNP testing lab, we want to give you all of the information you need to have a healthy pregnancy.
disclosure: I am a software developer at Counsyl, currently working on insurance automation and internal tools for our support staff.
Counsyl's test is at most $99 if you do not have insurance. Most major insurance companies now cover the test, so you're usually just making a $20 co-pay. You're looking at the insurance billing rate - compare $599 to tens of thousands of dollars that Lab Corp or Quest charge to screen just a few diseases. Counsyl screens for over 150+.
I like things like this for diagnosis. The problem is in how insurance, employers, parents, and prospective mates will view it. GATTACA jumps to mind.
Just because you can mine the email on Gmail to find everyone who secretly likes Justin Bieber and market to them doesn't mean you should. My genetics are much the same. Until I can mine them in the privacy of my own home with my own equipment and control what data is shared I won't do it.
I don't know if HIPAA governs the privacy of Counsyl, but even at that level of medical privacy I'm not sure I would want it. being disqualified from insurance, or military or being an astronaut because I got a swab of my cheek is not worth it.
[edit] fixed Gattaca spelling as mentioned by others.
Counsyl definitely falls under the scope of HIPAA; we do tests at the request of physicians, so we're like any other lab as far as privacy is concerned. Your employer, parents, or prospective mate would only know about the results if you decide to tell them.
It's also important to note exactly what Counsyl is testing: we're look at severe single-gene disorders, things that in most cases cause severe disability or early death. Importantly, if you only have one defective copy of a gene for which we test, you won't show symptoms of the disease. This is not the kind of thing that should affect your employer or insurer. And, if you're a carrier, it's probably something you should discuss with your prospective mate: if he or she is also a carrier for the same disease, there's a 1/4 chance of your child having that severe condition.
Legally if you fail to disclose that you knew you are a carrier for a severe disease to a prospective spouse prior to marriage it could be grounds for annulment, or a fault divorce. Sorry I don't have the case law at the moment, but I am aware that there was such a case involving Huntington's disease.
Huntington's disease is autosomal dominant, so essentially you're going to get it or not. I don't believe counsyl tests for Huntington's, and probably only tests for recessive traits where you can be a carrier like cystic fibrosis.
I can kind of understand that logic with Huntington's but I'd be surprised if it applied to recessive traits as well.
GINA is Only for predisposition. Anything that is diagnosed through genetics is fair game. If you use genes to detect that I have something like Fabry Disease which you either have or you do not based on the genes you can be asymptomatic and still have the disease and you will develop it eventually.
Your statement about privacy is already suspect since your opening comment talks about sharing that data. The two are mutually exclusive. As soon as your system is sharing, rather than me sharing I have no privacy.
It depends on the level of 'sharing.' If it's just statistics (e.g. 10% of people that use our service have discovered X disease), then I don't know how much of your privacy is pierced.
10% of people who used service discovered they have BrandonWirtz's Disease.
Requirements:
Male.
Primarily Caucasion as primarily limited to Arian Descent.
Symptoms onset at 55.
Not symptomatic for those with BMI under 22.
With this information I can take the 100% and cut the list to 50% that are male. 50% that are caucasion. (25%) Would have already know if they were over 55 so we cut another 25% Strip last names for ones that would not be of the right heritage. Suddenly the eligible candidates are only 12% of the total. I know that 80% of those are the people on that list.
That's how mining works.
You can't share data anonymously becuase each facet of data allows me more information to piece things together.
Sharing has to be opt in. But if it is opt in then it is no longer statiscitally relevant. Because just as an example. People are going to be less apt to share data if they have a disease associated with a stigma. Which will skew the results.
[Brandon Wirtz's Disease is an imaginary disease used for demonstration only. I don't have any genes shared with other humans as I am from another planet.]
I'm currently taking a class in data privacy, which is about assessing privacy risks using a mathematically rigorous formalization (differential privacy, see http://en.wikipedia.org/wiki/Differential_privacy ) and developing algorithms to allow for minimal risk release of private databases and avoid attacks like yours above. Your post makes it seem like you might enjoy reading more about the field; you should check out this survey of the field: http://www.cs.ucdavis.edu/~franklin/ecs289/2010/dwork_2008.p...
Those formula's assume the creator knows all the variables. I have data on things like Probablity a First name is of which race. When names started to appear for determining maximum Age. Search data for identifying people who were worried they had a disease.
Often a single piece of data will cause the intersection of two traits to be 80% accurate. You can't mathmatically predict these things because you don't know how many factors I have.
There are zip codes where only 1 in 100 people are of a given race. There are diseases that only 1 in 100k people have done a search for and only 1 in 500k people have. These kinds of things you can't formulaize.
This is not true at all. Differential privacy works to counteract EXACTLY these types of attacks. There are some very basic proofs that the privacy guarantees of a differential private release mechanism is not at all weakened by external data, such as what you've listed. Differential privacy attempts to minimize the risk of being a row in a database given that the attacker knows the values of every other row (and has whatever external data he wants).
Maybe I'm missing something. How does "10% of our customers have X disease" allow you to get down to a specific person?
| With this information I can take the 100% and cut the list
| to 50% that are male. 50% that are caucasion. (25%) Would
| have already know if they were over 55 so we cut another
| 25% Strip last names for ones that would not be of the right
| heritage. Suddenly the eligible candidates are only 12% of
| the total.
| I know that 80% of those are the people on that
| list.
What list? Are you somehow taking a list of names from outside and correlating them based just on 'X%'?
Things like cookie inspection allow a data miner to get a list of known customers of a company. I can tell you every RackSpace Customer, Every Amazon Shopper, Every FaceBook User.
If you have seen those ads on FB that are for something you just searched on Amazon, or that want to sell you hosting for a place you already have hosting with you know what I mean.
If you have enough data about the factors that are common of people with a disease, and then compare that with percentage of people known to have that disease from a set.
If 10% of Company's American clients have Disease X, and Disease X requires you live in a cold climate to be diagnosed ( Raynaud's for example ) then you can exclude the people who live in a warm climate.
Now if you want to target people with Raynauds and you know 80% of the clients live in California,Texas, And Nevada. You know that 50% of the remaining clients have Raynaud's.
This is of course a contrived example, and uses much less data than would be used by a Data Miner.
For the people saying "no there are formula's we can prevent this from happening" yeah you know who made those formula's? The People who make money selling data. And thos formulas are to keep you from thinking it is dangerous.
I think you meant GATTACA, the movie? To anyone who hasn't seen it, fantastic movie. Highly recommended.
Re: your other points. I think your concerns are well placed, however this isn't something that's specific to Counsyl; 23andme presumably also carries the same risks. At any rate, I do believe they hold your genetic information to the same standards as required in HIPAA.
There is growing evidence that genetic testing to the extend it is used in GATTACA is impossible. For example you can't predict a baby's future height. Sure, you can tell a normal distribution from genetics which is narrower than the distribution of the general population, but it's not as predictive as people might assume.
Genetic data has proven to yield a lot less information than was expected. That might change in the future, but I don't believe health insurance companies could make a business case for genetic discrimination even if they were allowed too.
I agree with you completely. I was merely pointing out that it was a great sci-fi movie worth watching. Not as some sort of foreshadowing of future societal outcome. Plus, what's portrayed in the movie (i.e. discrimination based on genetics) is disallowed by law, at least in California.
As someone who studied biotech (with an agricultural focus though), who now works in software, this is a very exciting development. Ah, to live in California! I do love Tokyo though.
And what is the ethical burden on the physician at this point?
Isn't there an obligation to provide all medically relevant information to the insurance company?
I am confused by your answer.
As to the parent question, the Genetic Information Nondiscrimination Act of 2008 [0] bars employers and health insurers from using genetic information to deny coverage, charge higher premiums, or discriminate in hiring.
It however doesn't affect other providers such as life insurance, disability insurance or long-term-care insurance which would obviously be needed over the lifetime of any infant suffering from any serious malady. These providers are free to use genetic predisposition information to discriminate under federal law. A few individual states bar this activity as well.
Kind of a giant loophole that I have no idea why Congress didn't anticipate.
The cool thing (well, one of many) about Counsyl is that there are a lot more things going on than pure biology and bioinformatics. Making genomics truly accessible is a software challenge that goes way beyond bioinformatics. There's obviously statistics, machine learning, and robotics running the lab; however, even more problems are pure engineering tasks. For example:
- How do you design the UI/UX around presenting data on 100 genes which can cause severe illness, but which most doctors (let alone patients) have never heard of?
- How do you efficiently accept orders from clinics across the nation, using a mix of web, paper, and EMR (electronic medical records) systems? (For bonus credit: deal with EMRs shipping fresh today on Windows 3.1. For double bonus credit: figure out how to bypass that ancient cruft and bring clinics into the 21st century.)
- How do you bill insurance companies when it can be opaque to even find out which insurance company pays for a given patient's procedures?
- How can you share data with the scientific community in as open a way as possible, without compromising patient privacy?
There's a huge amount of work to be done, so if you're interested in helping out, give us a look: https://www.counsyl.com/jobs/.
(It looks like this article is getting multiply posted, so please accept my apologies for hitting this one too.)