
Counsyl is Pioneering A New Bioinformatics Wave - daslee
http://techcrunch.com/2013/04/23/counsyl/
======
_ihaque
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.)

------
tikhonj
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.

------
chime
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.

~~~
coherentpony
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.

------
geuis
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.

~~~
zmitri
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.

~~~
geuis
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.

~~~
zmitri
I suppose I can show the emails:

> 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.

------
troymc
There's something I'm not understanding here:

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?

~~~
cycrutchfield
There are a couple of steps that a carrier couple could take in that
situation:

* IVF-PGD (like the couple in the article): [http://en.wikipedia.org/wiki/Preimplantation_genetic_diagnos...](http://en.wikipedia.org/wiki/Preimplantation_genetic_diagnosis)

* Use a donor egg or sperm

* Adoption

* 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.

------
argumentum
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_.

~~~
buss
> 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.

~~~
argumentum
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.

~~~
buss
> 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.

~~~
argumentum
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!

------
doublescythe
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.

What is Counsyl valued at?

------
lvs
What's revolutionary about 400 SNPs for $599? There's absolutely no chance to
compete with that kind of product and pricing.

~~~
rcthompson
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?

~~~
buss
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.

------
jacoblyles
I'm looking forward to Balaji's Coursera class:
<https://www.coursera.org/course/startup>

------
drakaal
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.

~~~
_ihaque
Insurers have been barred by law from discriminating based on genetic
information since 2008:
[http://en.wikipedia.org/wiki/Genetic_Information_Nondiscrimi...](http://en.wikipedia.org/wiki/Genetic_Information_Nondiscrimination_Act).

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.

*edit to add the last paragraph

~~~
drakaal
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.

~~~
cdjk
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.

------
minikomi
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.

------
jonchang
How is this different, from, say, 23andme? Does it do whole genome sequencing
in addition to SNP chips?

~~~
daslee
The 23andme founder talks about this here on quora: [http://www.quora.com/How-
do-the-tests-conducted-by-Counsyl-d...](http://www.quora.com/How-do-the-tests-
conducted-by-Counsyl-differ-from-those-conducted-by-23andMe)

The Counsyl CTO gives the tl;dr response: 23andMe is recreational genomics,
Counsyl is clinical genomics.

------
gforst
Totally agree this will be huge. Marketing it will be interesting but I am
guessing OBGYN's maybe the doorway for this. Congrats.

------
siculars
So it costs $99 if your insurance pays for it.

So the insurance company gets the genetic report.

And your child happens to be born with a disease that was noted with a 25%
chance of occurrence.

Will your insurance balk at paying your child's health bills? Oh, who knows...

~~~
_ihaque
The report goes to your doctor. We don't issue reports to insurance companies.

~~~
shawn-butler
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.

[0]: <http://thomas.loc.gov/cgi-bin/bdquery/z?d110:HR00493>:

