Encouraging Screening Before Pregnancy: My JScreen Story

12 Dec

JScreen’s creation involved multiple people in different circumstances, times, and places all experiencing some event or spark of intuition and creativity that grew into the will to do “something” to prevent Jewish genetic diseases.  “Something” grew into JScreen. For me, inspiration first struck when I was giving a talk to a group of other faculty members at Emory University in Atlanta about Jewish genetic screening in 2007.  The idea that we should use a combination of online education and saliva screening to make it easier for people to be screened struck me so suddenly, that I stopped my talk and just stood still for what was probably seconds, but felt like minutes. 

I had been wrestling with the dilemma of how best to encourage screening for years.  Trained as a genetic counselor, I had witnessed couple after couple bringing their infants into our clinic, only to be told that their child was suffering from a devastating condition.  The parents inevitably cried out “but no one in our family has this!”  They were right, of course, but that didn’t help their baby.  These types of diseases often come out of nowhere.  Sadly, many of these parents hadn’t been offered screening by their physicians, or if they had, the issue wasn’t raised until the pregnancy was well underway. As it stands today, genetic carrier screening is typically offered, if at all, when a couple is already pregnant.  This timing is understandable, because they may not show up in a clinic before conceiving.  Pregnancy, though, is not the optimal time for screening to be offered.

Professional groups, such as the American College of Obstetrics & Gynecology[1] and the American College of Medical Genetics[2], support the belief that preconception screening should be encouraged.  Studies bear out the reasons why.  Sparbel et al. published an article in 2009[3] eloquently describing the difficulties that prenatal screening raises for women who can’t help but view their options through the “prism” of their pregnancies.  Prior to conception, a couple who discovers that their children are at risk for a genetic disease can carefully review their reproductive options, which can range from using an egg or a sperm donor to adoption to preparing for the possibility of having an affected child by marshalling resources for early treatment.  Outside of the pressures of pregnancy, couples can take their time to learn about the condition, talk with parents of children who are affected, and make the best decisions for themselves.  Many of the ethical concerns surrounding carrier screening evaporate outside of the context of pregnancy.

To be clear, I do not mean to imply that prenatal screening is not helpful.  Many couples find the information they learn from prenatal diagnosis to be invaluable for providing peace of mind, deciding whether to continue a pregnancy, or planning for the birth of an affected child.  For example, a couple who learns that their child will have a condition might decide to move closer to relatives who can help with the care of a child with special health care needs.  Prenatal diagnosis is an important tool.   If the goal, though, is to prevent disease, many options are simply not available by the time prenatal screening is being considered.

Also, while newborn screening programs exist to identify children with some genetic conditions, only a few conditions are included, leaving parents in the dark about their child’s need for early intervention.  While newborn screening is designed to find babies before they become sick and begin treatment early, affected babies are still sometimes identified too late. Knowing that a baby is at risk or is affected early can be lifesaving in these situations.

As a Southerner, perhaps I feel the painful preconception/prenatal screening dilemma more acutely than do some of my colleagues.  Interest in prenatal testing is considerably lower where I practice in Georgia due to the politically conservative or religious values that are prevalent.  I feel a grave sense of urgency to figure out a way for screening to become common place BEFORE pregnancy.  I know that if we don’t find a way to make this a reality, screening won’t be an option for many of the people I work with, and they and their children will continue to suffer from preventable conditions.

So, why doesn’t preconception screening readily occur?  One reason is that ordering the testing is logistically difficult in many cases.  One of my past roles at Emory was to work with the Newborn Screening (NBS) Program, as their genetic counselor.  As such, I received calls from parents and other relatives of babies diagnosed through NBS wanting to arrange for carrier screening.  They had seen firsthand the impact of a condition on their family, and wanted to learn if their children would be at risk.    Few of these people who contacted me lived anywhere near a genetic counselor.  In one case, the uncle of a child diagnosed through NBS wanted screening, but he lived in rural Colorado.  I spent upwards of 5 hours on the phone with his physician’s office helping them identify the best place to send a sample, determine how much it would cost, and explain the results when they were finally available. In another case, a woman whose daughter was found to be a carrier of cystic fibrosis through NBS didn’t have a physician who could order the screen at all.  As a result, she was never able to have screening.  I couldn’t help but believe that it just shouldn’t be this hard!  For these reasons, when the idea for JScreen struck me, I couldn’t help but answer the call.

JScreen is a public health initiative whose goal is to overcome many of the barriers to preconception screening by taking advantage of the fact that we can now test saliva.   By combining online education with access to certified genetic counselors, our program aims to make screening easily accessible, affordable, and on a very pragmatic level useful in a way that prenatal screening just can’t be.

JScreen opened its virtual doors in September of this year.  It would be simplistic to believe that this program is the singular answer to preventing Jewish genetic diseases; people smarter than I have wrestled with this problem for decades.  The barriers to screening are complex, and will continue to be so.   I do believe, though, that JScreen is a step in the right direction; we are a piece of the puzzle that can ultimately lead to widespread preconception screening.  It’s an audacious goal.  For now, though, I can’t help but smile when a JScreen test is requested by someone who has checked the box “non-pregnant.”  I can’t help but pray for many, many more.

T_Page_2012_crop

 Tricia Page is the Senior Director for the JScreen program at Emory University in Atlanta, GA.  After receiving her B.S.  in Genetics from the University of Georgia, she received her Master’s degree in Genetic Counseling from the University  of Texas Health Science Center at Houston in 1996 and h er certification from the American Board of Medical Genetics  in 1999. At Emory, Tricia worked as the Director of Genetic Counseling Services, Program Manager for Newborn  Screening, and the Assistant Director of the Genomics and Public Health Program prior to taking her current roles.  In  her current position, Tricia focuses on delivery of genetic services from both a clinical and public health perspective.  She is interested in non-traditional service delivery models, especially those capitalizing on advances in genetic testing and health education.  Tricia is a fourth generation Georgian who enjoys spending time with her family, gardening, and training for triathlons.

1. Genetics ACo: ACOG Committee Opinion No. 442: Preconception and prenatal carrier screening for genetic diseases in individuals of Eastern European Jewish descent.Obstetrics and Gynecology 2009, 114(4):950-953.

2. Grody WW, Cutting GR, Klinger KW, Richards CS, Watson MS, Desnick RJ: Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Genet Med 2001, 3(2):149-154.

3. Sparbel KJH, Williams JK: Pregnancy as Foreground in Cystic Fibrosis Carrier Testing Decisions in Primary Care. GENETIC TESTING AND MOLECULAR BIOMARKERS 2009, 13(1):133-142.

One Step Closer to Genetic Literacy

11 Nov

At Counsyl, we are starting a free series of educational webinars to promote genetic literacy. Clinical genetics is evolving quickly, and genetic counselors are a limited resource. Physicians and nurses often tell us that it’s hard to keep up. Even as a genetic counselor, I find it challenging to stay current with all of the new clinical applications of genetics, like non-invasive prenatal screening, whole exome sequencing, inherited cancer panels, and personalized genomics. There is plenty of data showing that physicians and nurses are not very comfortable with genetics. Depending on the specialty, some may have only had one course of genetics in school.  At a time when genetics is becoming an integral part of all facets of medicine, this is surely a problem.

Our goal is simple: engage medical professionals through simple and practical tools for education. We’re all about making things accessible at Counsyl. So, mark your calendars and spread the word. Our first webinar is scheduled for January 23, 2014 and the speakers include Caroline Lieber, Dr. John Marshall, and Dr. Bryce Mendelsohn.  The topic is “Understanding Expanded Carrier Screening & Its Benefits to Your Patients.” You can sign up at www.counsyl.com/webinar. Future topics will expand beyond Counsyl to include a broad range of “hot topics.”

For a glimpse of what to expect from our first webinar, check out the bios of our awesome speakers:

Dr. John Marshall

Dr. John Marshall

 

Dr. Marshall has served as Clinical Professor of Obstetrics and Gynecology at UCLA, Chairman of Obstetrics and  Gynecology at Harbor/UCLA Medical Center,  and Clinical Professor of Biomedical Sciences and Medical Education at Mercer University School of Medicine Savannah Campus.  He authored over 100 scientific publications and currently works for Counsyl.

Caroline Lieber

Caroline Lieber

 

Caroline Lieber is the former Director of the Joan Marks Graduate Program in Human Genetics at Sarah Lawrence College. She is actively involved in professional education and recently traveled to Guatemala to assess the provision of genetic counseling services abroad. Caroline is a genetic counseling consultant for Counsyl.

 

Dr. Bryce Mendelsohn

Dr. Bryce Mendelsohn

          

Bryce Mendelsohn received his MD/PhD in Molecular Genetics and Genomics from Washington University in St. Louis. Since that time, he completed a clinical residency in Pediatrics. He studies metabolic disorders and has tremendous interest in the pediatric application of genome-era technologies.

 

For suggestions on future webinars or a chance to speak on a hot topic, submit ideas to Kenny Wong, Director of Genetic Services at Counsyl, by filling out this form: http://csyl.us/qzfPO

A Fun Friday Post

25 Oct

We were so amused by this rap video on the discovery of DNA, we just had to share. Enjoy!

Efficient Django QuerySet Use

23 Oct

Jayson Falkner gave a talk at a recent Django Meetup in San Francisco on the advanced use of Django’s QuerySet API based on lessons learned at Counsyl.

Below are the slides and audio.


Continue reading

True Facts About Time Zones

27 Sep

Here at Counsyl we use Python, Django and Postgres as key components of our software technology stack. As part of modeling and tracking a complex business process we often need to answer the question so often and so eloquently asked by the philosopher Morris Day: What Time Is It? And also, what time was it? When did that happen? When does this need to happen?

The three software packages mentioned above provide tools for tracking time accurately, but there are some traps you can fall into if you are not careful. I recently investigated a time-related anomaly in a subsystem I maintain and discovered some interesting facts about Django time settings. The results of that investigation are now available as a simple Django application in the Counsyl GitHub repository.

This particular problem revolves around time zones. A time zone is a set of rules for determining a clock reading, say 11:00 am on July 24, 2011, given a fixed point in time. Or, given a clock reading, determining the fixed point in time it refers to. Just knowing the clock reading isn’t enough because that clock reading occurred multiple times around the world.

Let’s call any representation of a fixed point in time a timestamp, even if part of the representation is implicit (maybe we just happen to know that some clock reading is for Pacific Standard Time). As a timestamp makes its way from a Python application using Django to Postgres and back again it passes through the application code, the Django ORM, the Python database adaptor and finally Postgres before returning back again in the reverse trip.

So that gives us three timestamps we might care about:

  1. The timestamp we started with.
  2. The timestamp we stored in Postgres.
  3. The timestamp we loaded from Postgres.

Of course, for a particular timestamp in step 1 we’d want the other two to be equivalent, i.e., to refer to the same fixed point in time even if they might use different representations. But, if you are not careful, all three could be different from each other.

The README file in the Django application has the full explanation and the application itself has the details, but here is a high-level summary.

Python represents timestamps with datetime objects which come in two flavors, respectively called aware and naive, but which could also be called ‘explicit time zone’ and ‘implicit time zone’. An aware datetime in Python is a clock reading and a particular time zone representation. Such a datetime is an unambiguous representation of some fixed point in time. A naive datetime has no explicit time zone reference, we just happen to know (hopefully) what time zone it happens to be in.

The trouble comes in with naive datetimes and daylight savings time. If you are using an implicit time zone that has daylight savings time, then there are naive datetimes that can mean two different fixed points in time. That’s because when you have a daylight savings “fall back” event, where for example the clocks might go from 2:00am to 1:00am, then the same set of clock readings repeat themselves on the same day one hour apart. If the time zone is implicit, you cannot distinguish between datetimes in the first hour and datetimes in the second.

There is a related but subtler trap when it comes to daylight savings “fall forward” events where the clocks might go from 1:00am to 3:00am and skip all the 2:00am times. For the full explanation see the example Django application above. That application stores and then loads two such troublesome timestamps using different methods and then checks to see that the timestamps we stored and loaded matched the ones we saved. The application has all the details, but here are the results:

Screen Shot 2013-09-27 at 12.10.10 PM

In either case the solution, and the moral of the story, comes straight from the Zen of Python: explicit is better than implicit.

Dave PeticolasDave Peticolas is a software engineer at Counsyl. Prior to that he was a software engineer at Lucasfilm for ten years. He has contributed to numerous open source projects including GnuCash and Twisted, and is the author of a popular introduction to Twisted and asynchronous programming at http://krondo.com. He’ll be giving a talk  “Django, Postgres, Timezones, and You” at the Django Meetup in San Francisco on 10/9/13.

Our Forever Baby

16 Sep

Img194

I’m no expert in genetics, but one thing I know for sure; genetic testing has changed the course of my life.

My husband Ryan and I met on a college cross-cultural trip to England. Less than a year later, we were dating and three years later, we were married. He pursued me with all his might, and I gave in – I thank God for my weakness every day. His gentle heart, sensitivity, goofiness, and ability to run faster than anyone I know won me over. Ryan is the textbook definition of a well-rounded man, and I like to think I’m his perfect counterpart.  Where he lacks patience, I can wait forever. Where I lack tolerance, he accepts without hesitation.

He proposed where we went on our first official date – Hershey Park. It was amongst the loud thunder of a roller coaster and screaming kids that he got down on one knee and asked me to be his – forever. The ring was upside down and I wasn’t sure whether to laugh or cry. Of course, I said “yes!” Our wedding day was the most perfect, sunny day ever. Naturally, we got married inside. I’d never risk rain, I’m a big planner (read, “control freak”),  and it was really a perfect day. I remember several weeks later, a friend said, “Erin, I don’t know anyone who looked as happy as you on their wedding day. You looked truly happy.” I’ve been known to wear my emotions on my sleeve and this time it paid off – to have my family and friends see the joy I felt was a true blessing.

And so that’s when the love story of “us” got started. We knew that we were quite the pair right from the start, but it wasn’t until we started trying to have kids that our destiny began to unfold before our eyes.  Simply “getting pregnant” wasn’t working.  I intuitively felt like something was wrong, and after 6 months of Clomid {to initiate ovulation}, 1 month additional hormones, 1 failed IUI, and 2 failed IVF cycles, I knew something was wrong. We actually attempted 3 IVF cycles, but one was switched to an IUI because of the lack of viable eggs. I was on the highest dosage of medication and still….only 2 eggs. Our fertility specialist suggested I get tested for Fragile X syndrome, which could cause premature ovarian failure – this might provide an answer to our problem. It just made sense to get tested for Fragile X, as well as, 100+ genetic diseases in a Counsyl test.

We felt assured that it would be a $100 test to give us some comfort in knowing nothing was wrong and we could continue with hope and trust that my supplements would boost my eggs and get us the healthy embryos we needed to transfer! I remember the call we got from our nurse like it was yesterday. She said “we just got your Counsyl results and it’s….interesting” (insert crickets and my rapid heartbeat here). After what felt like forever she asked me if I had a piece of paper and would like to “write some things down.”

Ummm…okay.

When you don’t say “Hereditary Thymine-Uraciluria” every day it’s kind of hard to get out in one breath – it took her several + a spelling. After I hung up the phone, I knew that the direction of our lives had changed. I knew my plans were certainly not my own and nothing was going to continue as planned. Ryan and I both were on the same page here and thought aloud: “seriously?” Was there really one more thing?

Our parents had the same reaction to the news. We were all kind of in disbelief. None of us knew anything about Hereditary Thymine Uraciluria – nothing. All we knew was that our child would be at 25% risk for a genetic disease that could cause serious mental and physical disabilities.

I always knew Ryan and I were a special pair, but the risk for both of us to be carriers was 1/10,000. If that’s not special, I’m not sure what is. So we did what we’ve been doing throughout our entire journey; researched our options, talked with genetic counselors, and prayed that God’s perfect plan would continue to reveal itself to us. And it has. The Counsyl test was what one might call “the straw that broke the camel’s back.” With no transfer-worthy embryos, old acting ovaries, and a really random genetic disease mutation, we felt God was trying to tell us something – “stop trying to do it yourselves!”

I felt immediate relief in knowing what we were going to do, and then I was hit by what it really meant. We both feel that God was directing us to stop, but WOW was it hard to accept. Making the decision to adopt is one thing, but accepting it is something completely different. The desire for us to have children has never wavered throughout our journey. I don’t have words to express the joy and excitement I feel for what’s ahead for us. I know, with certainty, that God continues to work in our lives and the baby He blesses us with will be a gift.

Our families couldn’t be more excited. We wasted no time initiating the adoption process and we’re officially waiting to hear from the agency. This means that any day now, we could get a call saying “you’re parents!” I imagine that will be another life changing moment. Although this process has felt impossible at times, I thank God for bringing us through it…although that might sound crazy! I’ve discovered strength that I didn’t know I had and have felt peace that only arrives after the hardest of storms.

Screen Shot 2013-09-16 at 8.54.59 AM

I’d encourage anyone going through the throngs of infertility to remain hopeful, stay informed on all that’s happening and don’t be afraid to steer away from the plans you create for yourself. We’ve decided that no matter how long we have to wait for our “forever baby” we’re starting our “happily ever after” right now. The desire of our hearts will be fulfilled, and I cannot begin to imagine how special and unique that will be for us.

Erin and her husband Ryan live minutes from “The Sweetest Place on Earth,” Hershey, Pennsylvania. Erin loves to stay active, spend time with her dog Phinley, and update her personal blog.  Erin currently works as an elementary school computer teacher and is looking forward to her dream job as “mom.”

No better time in history

4 Sep

My wife has a fatal, dominant genetic disease, and in spite of this, I count us among the luckiest people to have ever lived. 

Mostly this is because we have each other.  But also because we have careers we love, a cause we’re passionate about, and a fiery hope that animates our every day.  All of which is new, and inextricably tied to the era in which we live.

When we found out in December 2011 that she had inherited from her late mother the mutation that causes fatal familial insomnia, we had no background in science.  I had studied city planning and she had studied law, and we had careers we felt okay about and no particular cause other than living a good life.  But we weren’t willing to take bad news sitting down, and because it was the 21st century, we didn’t have to.

I see now that I had never shown proper gratitude for the Internet until that time in our lives.  We embarked on a heretofore-impossible binge of Wikipedia and Open Access papers, learning everything we could about fatal familial insomnia.  It’s a genetic prion disease, meaning the mutation creates a deformed version of the otherwise-innocuous prion protein (PrP), causing it to form infectious protein particles called prions, which can spread across the brain. 

To record and organize our thoughts we created a WordPress blog, CureFFI.org.  After some night classes, Sonia swapped her old job for a position working with induced pluripotent stem cells and I swapped mine for a position in bioinformatics – surely two of the world’s newer job titles – in a Huntington’s disease lab.  The blog continued to be a repository for all we learned, and eventually it became half of my brain.  Writing posts is how I check that I understand a new concept.  Searching for them is how I find that one citation I need or grab that version of the Python code that I know for sure worked.  When our site went down for a few days in Fall 2012, my productivity dropped by half.

Something else remarkable happened.  From the beginning we’d been cold-emailing prion researchers we’d heard about or read about to try to talk to them and hear what they were working on, with about a 20% reply rate at best.  As the months went by and posts piled up, our blog began to hit top 5 in the Google rankings for the incredibly specific terms that only people in the field would ever search for: PrP alpha cleavage, conformation-dependent immunoassay, doxycycline CJD.  Soon I started getting messages through the Contact Us form from names I only knew as authors on papers, saying they liked the blog and would I like to Skype sometime.

A few months ago, I got one such contact from Dr. Armin Giese, a researcher who had read my review of the new anti-prion drug candidate he had just published: anle138b.  He turned out to have ambitious plans to push the molecule towards clinical trials and he told me everything he was working on.   I wanted to know if this compound would work against genetic prion diseases, and he didn’t have any data on this.  So last week our non-profit, Prion Alliance, launched a crowdfunding campaign on Microryza to fund a study of this drug in a model of GSS, a genetic prion disease not unlike fatal familial insomnia.  Our friends and family donated first, but within a week, more than half of the donor list was names we’d never seen before: friends of friends who had seen retweets, reshares, news feed updates.  People there was simply no way we could have reached before the social media era.  (Shameless plug: the campaign runs through 9/27 – check it out!)

But despite my soaring gratitude for living in the day of Wikipedia, WordPress, Twitter and Microryza, by far the most indispensable technology for this whole enterprise is: genetic testing.  The mean age of onset for fatal familial insomnia is 49.  Sonia is 29.  When in history has anyone had twenty whole years to dodge a bullet?  As the pace of technology accelerates, the scythe of death seems to move slower in comparison.

The kind of genetic testing we did – sending a blood sample in for Sanger sequencing – isn’t actually as new as the other technologies I mention.  It’s been available to patients pretty much since the mutations that cause most genetic diseases started to be discovered a couple of decades ago – 1992 in the case of fatal familial insomnia.  But it’s on the rise – perhaps due to greater awareness, generational change, anti-discrimination legislation, who knows why else.  In any case, it’s just beginning to achieve its transformative potential. 

Here’s one example of why.  Prion diseases are rare, but they seem even rarer than they are because they’re so rapidly fatal.  These illnesses claim about 250 lives per year in the U.S. but the average time from first symptom to death for the most common forms of the disease is just a few months, meaning that probably only 100 or 200 Americans are sick with a prion disease at any given time.  This is a matter of incidence versus prevalence.  The latest estimates for Huntington’s disease would give it an incidence of about 1100 new cases per year in the U.S., making it a bit more than four times as deadly as prion diseases, but with a median disease duration around 20 years its prevalence is more like 100 times that of prion diseases.  And it shows: the number of Huntington’s disease advocates doing everything from blogging to organizing fundraising walks is enormous.  By contrast I find that when I search Twitter for #prion, a significant percentage of Tweets are my own.

This is why when Dr. Giese first contacted me about anle138b, he said I’d changed his thinking on prion diseases.  He had always assumed that the low prevalence of prion diseases put a fundamental limit on how significant a patient advocacy contingent could exist to push research forward.  Unlike in Huntington’s disease, which is 100% genetic, most prion disease cases are sporadic – we have no earthly idea why they happen – and to make matters worse, they’re hard to diagnose.  Most patients don’t get a correct diagnosis until 2/3 of the disease has already passed.  By the time the family hears the words “Creutzfelt-Jakob disease” their loved one is inches from death.  They are devastated, but by this point there is nothing they can do for their loved one.  A soulful and devoted few do choose to get involved in research or advocacy – these are incredible people whom I admire and respect deeply – but most just pick up the pieces of their lives and move on.

But here, Dr. Giese said, was a new animal: someone armed with genetic information, with 20 years to devote their life to a cure.  Obviously, Sonia and I are far from the first – we’ve now met tens of other genetic prion disease carriers on Facebook, the blogosphere, and at the CJD Foundation conference – though we might be the first to become scientists.  But collectively we, all of us, are a new animal.

30,000-odd Americans die in traffic accidents each year.  Safety is improving year by year, but I submit to you that if the 300,000 people who will die this way in the next decade knew who they were today and could vote and advocate and fundraise to forestall their own fate, it would be improving a whole lot faster.  But until an accident happens, its hypothetical victim is no one in particular, it’s just a Schroedinger’s cat, .0001 of each of us.

For genetic diseases it doesn’t have to be this way: testing can give us decades of advance notice to take action.  Of course, for genetic results that are immediately actionable, such as Angelina Jolie’s BRCA mutation, the benefits to the individual are clear (though that isn’t the end of debate on the matter).  For diseases with no treatment or cure today, whether to get tested is a deeply personal decision.  We think there are lots of good reasons to do it, but that doesn’t mean it’s right for everyone.  However, at an aggregate, societal level, the benefits of genetic testing are undeniable.  We finally have the power in our hands to analyze enormous datasets, and that means we need enormous numbers of people – every one of the thousands of datapoints in my Huntington’s disease datasets is a single brave person who made a personal decision to enroll in a clinical study and share their genetic information.  And we need more.  So too with every private dollar that’s fundraised, every NIH dollar that’s allocated, and every discovery made by researchers who became scientists after learning their own genetic status – and by researchers inspired by a personal connection to patients they care about.

One of the arguments I’ve heard for not getting tested is the fear of determinism; that knowing one’s fate might taint every day in between.  I submit there is no such thing as genetic determinism.  None of us know our fates.  We only know that the future is what we make it.

Eric Minikel is a Computational Scientist at the Center for Human Genetic Research at Massachusetts General Hospital and a co-founder of Prion Alliance, a non-profit research foundation devoted to finding a treatment or cure for human prion diseases.  He and Sonia Vallabh changed careers and started Prion Alliance in 2012 after learning that Sonia had inherited the genetic mutation that causes fatal familial insomnia.  The views expressed here are Eric’s own.

 

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