A scientist studies how fragile X syndrome affects one family – her own

27 Aug
Alex and her fiance, Donny.

Alex and her fiance, Donny.

We didn’t know fragile X syndrome runs in our family until my nephew was born. My sister, Desiree, had her son two and a half years ago and almost from the start he didn’t seem like most other babies. He was born with large protruding ears and had low muscle tone. He also wasn’t feeding correctly, which eventually led to a diagnosis of failure to thrive. And he screamed. A lot. Much more than your typical fussy baby.

My sister was concerned and had him tested for a number of different problems. Everything came back negative. Then my mom remembered something my dad’s cousin had told her once, maybe 26 years ago. He’d said something like, ‘We had children with fragile X and you might want to think about that when it comes time for you to have kids.’

That was the clue we needed. What came next has made a big difference to my family. It even changed the way I’m thinking about my career.

“My sister was matter of fact about the results. She’s science-y like me.” 

Desiree had Roan tested for fragile X syndrome, a genetic condition linked to intellectual disabilities, which can be profound in some cases. We learned that the gene responsible for fragile X syndrome is called FMR1, which is on the X chromosome. The FMR1 gene shows up in four forms and is characterized by the number of repeats of a pattern of DNA called CGG repeats. The greater the number of CGG repeats, the more severe the condition.

Roan has more than 200 CGG repeats. Above 200 the FMR1 gene shuts down, or methylates, which means it can’t produce a specific protein. The lack of this protein is what causes fragile X syndrome. Roan has a full-blown case of it.

My sister was matter-of-fact about the results. She’s science-y like me, with a masters that involved tracking salamanders in North Carolina. I’m getting a masters in cancer research. The news gives her a chance to find ways to support Roan. He’s doing okay but still too young for us to know for sure how severe his case will be.

“Usually people are horrified. I just find the whole thing really interesting.”

After finding out about Roan my sister and I became students of fragile X syndrome. We’ve learned that we – along with my Dad – are all premutation carriers, which means we have 55 to 200 CGG repeats. I have 101 repeats, slightly higher than my sister who has 85. Premutation carriers have an unstable mutation of the gene and symptoms can develop over time. My Dad, for instance, is now experiencing some memory loss and tremors. Other symptoms include being especially susceptible to anxiety and depression, especially if you’re a woman. And early menopause.

Usually people are horrified on getting news like this. But, like my sister, I did not freak out. If anything I just find the whole thing really interesting. I’m also relieved. I pretty much knew I was a carrier and had been frustrated by not being able to get my repeat number. Finding out that it’s higher than 100 means I have a 50 percent chance of having affected sons.

This will definitely change how I have a family. I have the option of going through IVF with sorting to make sure the embryo is healthy. But IVF is expensive. Whether I can afford to do that kind of depends on how my career plays out. I might just go ahead and get pregnant and see how it goes. If we do have biological kids we’ll probably just have one.

“The Counsyl experience was so great I’m thinking about switching careers.” 

We may also decide to adopt. I’m engaged to Donny who’s awesome. He’s half Native-American and we’ve talked about adopting a Native-American baby, which I think would be cool. Finding out that I’m a carrier hasn’t changed the way Donny feels about me. He’s a calm person and doesn’t let things bother him. We have a nice life together. He manages a bar. We have a couple of cats. We’ll have kids however we’ll have kids. Since I’m only 25 we have time to think about it.

Taking the test with Counsyl was such a positive experience. From the moment I ordered the test to the time I got the results things went smoothly. What really stood out for me was my meeting with the genetic counselor.

It was so great I’m thinking about switching from a career in cancer research to genetic counseling. Right now I’m a lab rat and do bench work. I don’t mind it. But I don’t like not interacting with people. I like what genetic counselors get to do – sit with people and explain the science of genetics and how it affects them. I think I’d be good at that.

-Alex Moffitt

Doing my research led to a love affair

20 Aug


I’m the kind of person who does my research before making an important decision. As the only child of a single mom who worked as an electrical engineer at NASA, my scientific approach to life may be something I inherited. I really loved growing up on the sunny space coast and being a ‘NASA brat.’

Lacey and Sejin are expecting a girl.

Lacey and Sejin are expecting a girl.

When I learned that my fiance, Sejin, and I were going to have a baby I immediately started looking into the safety of ultrasounds and other types of prenatal testing. I had a lot of questions for my OB, who suggested I take the Informed Pregnancy Screen and gave me a pamphlet. That started my love affair with Counsyl. I love everything about Counsyl.

I love how non-invasive the test is. I love the box the test comes in and the enclosed card with my number on it that lets me track the results online – a very cool part of the user experience. I emailed employees whenever I had a question and every person I’ve spoken with has been so nice, friendly, and on top of their game. Since I’m just finishing up school and money has been tight Counsyl also helped us with financial aid. Another highlight was having my results explained by a genetic counselor.

“Here’s what I also loved: Finding out we’re having a girl!”

My results! Here’s what I also loved: Finding out we’re having a girl! I really wanted a girl! I’m my grandmother’s only grandchild so all we know in this family are girls. Sejin wasn’t quite as happy – I think he wanted a boy. But he’s also hoping a girl is calmer than he was as a toddler. We also learned that her chances of having any kind of chromosomal abnormality are really low.

“Getting answers – one way or the other – is a huge relief”

There’s a lot going on right now in our lives. Sejin and I are engaged to be married and our baby is due this fall. He just got a new job in sales and I’ve gotten a part-time job developing an interactive curriculum on statistics. I’m happy because it’s a great job for a new mom. (I still won’t make as much money as I did when working my way through college as a cocktail waitress on a gambling boat in Florida!)

yAUS22Z_vaMFJQAs5w7Ar6mymjcpHpUggKzhr0ln-epVd5JqWwSYBQpf8pDQiRsJq1Nz0h_lH91W61HeqFsR63GJATSyYxE2TmnW-k3zokh6Djb2BKWub0XQaZ3su_r5AnfRdrMZMTEbaVCITPek5DUx-8z7RaRb5oUzTV1F1DF9FjPLjHVxo2AONfwaaOYA1gZPj3i4BG1dgtRiQ91VkJXsnNMezRpNBeing pregnant is really stressful because you want to make sure you’re doing everything right for your baby. Taking the Informed Pregnancy Screen has helped me sleep better because getting answers – one way or the other – is a huge relief. I truly believe this type of non-invasive, personalized science is the bright future of medicine. Now I can focus on the fun things, like the baby registry and picking out a name.

-Lacey O.

A daughter decides to find out her cancer risk

7 Aug
Victoria Reynolds and a photo of her younger self with her mother shortly before she died.

Victoria with a photo of her mother taken a few years before she died.

The strongest memory I have of my mom was making jam with her in our big Victorian house. I was very young and she was very sick. At age 41 she was diagnosed with stage 4 breast cancer after using hormone treatments to become pregnant with my sister Elizabeth. Five years later she died. I was only nine years old and so used to having a sick mom that I remember wondering how other mothers found the time and energy to cook dinner.

I’ve grstories--ics-2@2xown to look like my mother and as I got older I worried I might have inherited the bad part of her along with the good. My family is pretty forthcoming about the fact that cancer runs in the family. My mother had four sisters and one passed away when I was seven of colon cancer. My aunts have been tested and one of them has the genetic mutation.

My fears changed the way I live. I’ve read lots of articles and don’t use microwaves, drink from plastic bottles, or use birth control pills. I eat lots of pomegranates and stay very active.

I also went to college and became an English major. I made friends and found a boyfriend.

I didn’t think about my cancer risk every day but it was often enough that I realized it was inhibiting my happiness and making it hard to plan a future. I knew I wanted to find out whether I’d inherited the genetic mutation so I could do what I could to combat it. But I also wanted to find the right time.

“My heart was pounding as I logged in. My results lit up the screen.”

Then I developed an ovarian cyst. Part of the treatment was going on the pill and when I told my doctor why I didn’t want to do that she recommended I take the Counsyl screen to find out once and for all whether I’d inherited my mother’s cancer. It was my senior year of college. By February I had decided to order the screen.

My results arrived one very cold day when I was in theater rehearsal. I ran out of rehearsal without telling the director and asked only my best friend to come with me. We got to the library and sat down in front of a computer. My heart was pounding as I logged in.

My results lit up the screen. Negative.

I turned to my friend who was looking at me and sobbing with joy. As we hugged I told myself I wouldn’t have to worry anymore. I wouldn’t have to go through what my mother did. I could live my life the way I want to.

Victoria and her sister Elizabeth.

Victoria and her sister Elizabeth.

Finding out has been liberating. My two-year-old relationship has become much more loving now that I don’t have to worry that it might work out and any children we’d have would be punished with my genes. I’ve always wanted to teach English but I held off on applying to Masters programs. Now I know I’ll go to graduate school but before I do I’m going to do something else I love – go west and go skiing for a year. Hey – I have time!

My family was ecstatic though my 17-year-old sister asked if that means she’ll have the genetic mutation. I said no, that’s not how it works. After I told everyone in my family the good news their first reaction was pure joy. The second was that now we have to get Elizabeth tested.

-Victoria Reynolds

Finding out you’re one in a million can be life-changing

30 Jul
Kerri and Logan, who just turned one.

Kerri and Logan, who just turned one.

Stanley was our first baby. He’s the bulldog my husband, DJ, and I adopted after we moved in together. We named him after the sports bar in Chicago where we met right after DJ graduated from Northwestern. I was in my junior year. We didn’t get together immediately – at the time we were dating other people. But it wasn’t long before we decided we wanted to be together.

DJ was the first to want to get married. It took living together for a year before I knew I was ready, too. And it was the same way with kids. He was ready. I wanted to wait. When I turned 30 the timing suddenly felt right.

I made an appointment to see my doctor who suggested I get a complete screening after she learned my Mother is Jewish and my Dad Irish Catholic. She also recommended we use Counsyl and told me that until recently getting a test like that would have cost thousands. Now it’s much cheaper.

“The chances he was also a carrier were very small. I wasn’t worried.”

20150628_LW_0786I took the test and two weeks later discovered I’m a carrier for only one disease – glycosylation type 1a, a metabolic disorder. The doctor reassured me the chances DJ was also a carrier were extremely small – like close to one in a million – so I wasn’t worried. I asked DJ to take the Family Prep Screen just in case.

The doctor called me right away with the results. Unbelievably we were both carriers for the same very rare genetic condition. The doctor told us that many children with this condition die even before they’re born and those who are born generally don’t make it to their first year. If they do survive they typically spend their lives in a wheelchair and can’t communicate.

I remember thinking, “What the heck?!” It was so different from what we’d been expecting to hear.

We spoke with Jessica, a genetics counselor at Counsyl, and had a chance to ask ourselves what genetic conditions we could handle as a family. Prior to getting our DNA tested it had never occurred to us that anything could be wrong with our children.

“No mistake about it – we were a one in a million couple.”

Given how very low the odds were we also decided to take the test again. DJ is Puerto Rican and his family came from Spain. We really thought a mistake had been made. Counsyl offered to let us take the test again, this time for free.

No mistake about it – we were a one in a million couple.

We decided we needed more time to think about what to do next so we put our baby project on hold. About five months later I ended up getting pregnant anyway.

We were happy and freaking out at the same time. We also decided not to tell anyone. When I was about three months along we went ahead and had diagnostic testing done at Cedar Sinai Hospital in LA. Because the condition is so rare we could find only one lab that could evaluate the sample and it was all the way across the country at Emory University Hospital in Atlanta. Right around that time there was a huge crazy snowstorm and the lab was forced to shut down. It took forever to get the results.

“This experience changed the way we’re having a family.”

This story ends well. We have a healthy baby girl, Logan. Like her parents, she’s a carrier of glycosylation type 1a, which means she’s just fine. Everyone who meets her says she is the happiest little girl they’ve ever seen. We are beyond blessed. Still, we don’t think we can go through again what we did to have her – it’s just too emotional. When we’re ready for our second child we’ll pursue IVF in a way that allows us to test an embryo for this genetic condition.20150628_LW_0983

We share information about Counsyl with our friends all the time. It’s so important to plan for your future and DNA testing makes it easier. There’s a 25 percent chance we’d have had an affected child and without the screening we’d never have known.

Now we do know and it has changed the way we’re having a family. The Family Prep Screen is easy, it’s so affordable, and it gives you information that’s really important to the future of your family. I’m not sure why everyone who wants a child isn’t having it done.

For the love of Pete: Challenging what it means to live with SMA

16 Jul
Allyson and Tim Henkel with Lucy, Ian, Chris, and Pete at Expo 2015 in Milan.

Allyson and Tim Henkel with Lucy, Ian, Chris, and Pete at Expo 2015 in Milan.

Pete and his twin sister, Lucy, were born 11 years ago into our very busy family. We already had two boys, Ian and Chris, and had learned to expect kids to develop in a certain way. But by the time Pete was a few months old he moved really slowly, just his upper body, and looked really uncomfortable.

At first I was curious and just kind of Hmmmm. But when he was six months old I decided to bring it up with his pediatrician. The doctor kind of waved me away, wrote a prescription for physical therapy, and told me he was fine.

Pete wasn’t fine and neither was I. It’s miserable to suspect something is wrong with your child and not know what it is. You can’t rally around the problem, you can’t fundraise, you can’t embrace anything.

“We reacted differently. My husband lay on the floor. I called people.”

Pete lost his ability to roll over a few months later and the physical therapist recommended we see a neurologist. The doctor tested our son, who was nine months old by then, and asked us to come to her office.

I wish I could tell you otherwise, she told us. But it’s most likely spinal muscular atrophy. These babies don’t usually live past their second birthday.

Spinal muscular atrophy, or SMA, is a genetic disease that affects the motor nerve cells in the spinal cord and eventually takes away the ability to walk, eat, and breathe. It’s the number one genetic cause of death for babies.

My husband, Tim, and I reacted to the news very differently. He lay down on the floor and couldn’t move. I immediately started calling people.

“He’ll be fine. As long as he can play he’ll be happy.”

All these years later I still remember how people reacted – or maybe I only remember the comments that were helpful.

We’ll put stickers on his wheelchair, my neighbor told me.
I know a child with SMA who is nine years old, another friend said.
He’s going to be fine. As long as he can play he’ll be happy.

It was such a relief to hear that last response, which came from the genetic counselor we met with. What she said has shaped the way we’ve raised Pete.

We’ve put stickers on his wheelchair and taken him parasailing, skiing, and snorkeling. He’s traveled to Costa Rica and Bonaire and this year we went to Italy. He’s about to enter sixth grade and has his own group of friends. He and his sister, Lucy, regularly go to the neighborhood pizzeria on their own, without me. Pete gets to enjoy many of the same privileges of being a kid as his sister and brothers do.

Recently it’s become harder for him to keep up. Pete’s having more trouble using the joystick on his power wheelchair and to bring him to Italy we had to carry an oxygen concentrator, which helps him breathe more easily, along with a ramp.

Coming up with accommodations is sometimes a headache. But we want him to live while he’s here. I hope he has a good long life but you don’t know.

“People feel good when they embrace a kid like Pete.”

I’m involved with the Philadelphia chapter of Cure SMA and we encourage anyone who’s planning to have a child to get carrier screening so they can make the right choice for their family. I know there are people who will decide not to have a child. But getting the information early also gives you time to do the research and prepare to live with a child with SMA. When I talk to people who have just gotten a diagnosis I try to give them as much hope as possible.

Having a child like Peter is humbling but I’ve learned more from being his mom than from anything else in my 46 years. So many people have contributed to his happiness. And he has given back. People feel good when they embrace a kid like Pete so his story is a happy one. Even if Pete’s life is short it has served a huge purpose.

– Allyson Henkel

Allyson Henkel lives in Philadelphia with Tim, a real estate developer with a focus on affordable housing, and their four children, who range in age from 11 to 16. She just left her job as a Spanish teacher and plans to focus next on working with the children of Latin American immigrants. She’s very active in her local chapter of Cure SMA, which hosts Walk-n-Roll and Muscles for McKenna. Counsyl helped sponsor this year’s fundraising event. Allyson’s story is part of the Counsyl Storytelling Project, which highlights the role of DNA testing in people’s lives.

Sharing data is part of Counsyl’s DNA

10 Jun
Team Genomic: Matthew Leggett, Chris Beaumont, Matthew Rassmussen, and David Tran

Team Genomic: Matthew Leggett, Chris Beaumont, Matthew Rassmussen, and David Tran

Every year a group of engineers and scientists at Counsyl take the genetic variants they’ve teased out after many long fluorescent-lit hours of sequencing – and share the data. The beneficiary of this hard-won information? Everyone. Or rather anyone who uses ClinVar, an open data archive set up by the National Institutes on Health to advance our understanding of the role of genetic variants in health. The more thoroughly these gene variations are known, the higher the quality of the information available to patients who want to manage their health risks.

“There’s a gestalt of sharing here at Counsyl that we’ve made a priority,” says engineer Chris Beaumont, a member of the team that most recently submitted data to ClinVar, noting the information is not patient-specific and complies with HIPAA regulations. “Here, access doesn’t just mean affordable screening for all; it also means access to information.”

“There’s a gestalt of sharing here that we’ve made a priority”

That spirit of sharing has helped define the company from its start. When Counsyl released its first DNA screen in 2009 it was customary for genetic testing companies to treat sequencing breakthroughs as proprietary information. Counsyl made a different call. It has always made its data public, including sharing findings on more than 23,000 patients screened for carrier states in Genetics in Medicine (2013). Counsyl was an early contributor to ClinVar and it participates in the Global Alliance for Genomics and Health, which aims to promote genomic medicine by standardizing information sharing.

Counsyl’s willingness to share has attracted the attention of free-the-data activists, including filmmaker Joanna Rudnick, who lobbied hard for improving access to screening after being diagnosed with a mutation in BRCA1 when she was 27 and discovering the prohibitive cost of screening. In a recent talk at Counsyl she shared the difference that publishing rather than patenting genetic information has made to people like her. “We hoped one day the test would be under $1,000,” she said. “It’s nice to be realizing that eventuality.”

“It’s troubling that the information is out there but you don’t know it”

The genomics team, which includes Matt Rasmussen, Matthew Leggett, and David Tran, is working on making its submissions more automated and frequent. The work can be tedious but the payoff is huge. For every instance that scientists have to collect information that’s not in ClinVar, several more hours of labor must be spent researching alleles. “The more we can do to get the data out there the more we can do to scale this effort so we’re not spending several hours per variant,” says Chris, who helped develop an infrastructure for data sharing while working in Harvard’s Astronomy department.

There are still companies that don’t share data on ClinVar, which explains why Joanna Rudnick and others continue to work as free the data activists. (Counsyl is featured in the Free the Data Hall of Fame.) It also means that some companies know more about the health risks associated with mutations in a given gene than others, which means some patients may not have access to this vital information. “It’s troubling that this information is out there but you as a consumer don’t know it,” says Chris. “Our goal is to identify every mutation as either benign or deleterious.” And then share it.

Submissions to ClinVar by organization

The data that Counsyl shares with ClinVar is particularly rich. Each point on the plot above shows a particular organization's contribution to ClinVar. The horizontal axis shows the total number of mutations reported to the database. The vertical axis shows how many literature references have been associated with these mutations. Compared to other organizations with a similar number of total classifications, Counsyl has recorded a larger number of literature references. Counsyl's contribution to ClinVar is both

The data that Counsyl shares with ClinVar is particularly rich. Each point on the plot above shows a particular organization’s contribution to ClinVar. The horizontal axis shows the total number of mutations reported to the database. The vertical axis shows how many literature references have been associated with these mutations. Compared to other organizations with a similar number of total classifications, Counsyl has recorded a larger number of literature references. Counsyl’s contribution to ClinVar is both “wide” and “deep” — it has classified many mutations, each of which is associated with a rich set of literature references.

Startup veterans talk Silicon Valley mystique and advice for new graduates

20 May

Stanford hosted a 50th anniversary event recently in honor of its computer science department and more than 600 people showed up to celebrate, including Counsyl CEO Ramji Srinivasan (Stanford ‘03). He spoke on the Startup panel with three other accomplished Stanford graduates – Sam Altman (‘07), president of Y Combinator, Clara Shih (‘05), CEO of Hearsay Social, and Jerry Yang (‘90), formerly of Yahoo and now founding partner at AME Cloud Ventures. Moderated by Kara Swisher, the Executive Editor of Re/code, the hour-long talk ranged from an examination of Silicon Valley mystique to what you’d do differently if you were graduating today.

All four panelists noted how much friendlier the startup environment has become for Stanford graduates since they left the school. They also agreed that Silicon Valley, with its high density of talent, is still a good place to launch a business.

For Ramji, Paul Graham’s book, Hackers & Painters: Big Ideas from the Computer Age, was an early inspiration and part of the reason he gave up his post-Stanford job at Morgan Stanley, where he’d covered the Internet industry as a research analyst. “It got me excited about the idea of returning to Silicon Valley and doing something more important,” he says.

His advice for new graduates? Consider healthcare. “Healthcare is insanely backward,” he told the audience, “which makes it a huge opportunity for new graduates. Information-driven technology that helps patients make decisions needs good people.”

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