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.”

Angelina’s fans worry cancer screening is out of reach

24 Apr
Angelina Jolie credits BRCA screening for helping save her life.

Angelina Jolie credits BRCA screening for helping save her life.

The enthusiastic response to Angelina Jolie’s New York Times account of how she’s dealing with a mutation in the BRCA1 gene illustrates the power of an authentic story. (And okay, it also says something about the power of Angelina.)  But among the hundreds of comments she received thanking her for sharing her story and highlighting the importance of breast cancer screening, another theme emerged: The concern that Angelina received good health care because she is, well, Angelina.

Jen D, from NJ, was among those who wrote she couldn’t identify with the star’s experience: I appreciate Ms. Jolie’s essays about her health decisions. I do wish she would acknowledge — bluntly — that women’s “choices” are not always as robust as hers apparently are. Lack of health care, lack of sufficient health care, family finances, work situation, etc. can constrain these choices considerably. Sarah Strohmeyer, from Vermont, called on Angelina to make ready access to good healthcare her next cause: I only wish 99% of women WITH cancer, much less pre cancer, had the advantages you had. Could you please make this your next cause? I’m sure no one in Congress would look away were you to appear and testify.

There’s no question Angelina’s willingness to share her story improves screening awareness, says Kaylene Ready, Counsyl’s product lead on the Inherited Cancer Screen. After announcing in May 2013 that she was at high risk for cancer, the rate of BRCA screening jumped 40% in the week afterward and stayed elevated throughout the rest of the year, according to an AARP study. “But it’s clear we have a long way to go in letting people know that screening isn’t just for people with her means,” says Kaylene. “When I saw those comments I felt sad that people feel they don’t have access and a sense of urgency about getting the word out about Counsyl.”

“We’re doing everything we can to make taking a screen easy”

Counsyl is rolling out a campaign for an expanded version of the Inherited Cancer Screen in the next couple of months. Front and center is its affordability and the high touch benefit of having a genetic counseling session included with every screen. Getting out that message will rely in part on stories like Angelina’s, told by women and men who have taken the screen and can share why it mattered.

Making it possible for more people to get screened is a big part of what excites Kaylene about working at Counsyl. She’s also motivated by former patients who didn’t have that advantage, including a mother in her early 30s who lived near her in a small town in Texas. She was diagnosed with triple negative breast cancer, the most aggressive form, and died soon after, leaving behind three children. “She’s the person I always think of when Angelina talks,” says Kaylene. “If only she’d been able to get tested earlier she might be alive.” At Counsyl, the goal is to make sure more people like her have that chance.

“I want people to know,” says Kaylene, “that we are doing everything we can to make taking a cancer screen as affordable and easy to take as possible.”

MDs get a “shared language” for discussions on carrier screening

18 Mar

When an oncologist assigns Stage One status to a tumor he’s letting his patient know they’re catching the problem early. It’s the kind of shorthand that’s missing in most clinical conversations about expanded carrier screening. Basically, there’s been no easy way for a doctor to indicate how serious a particular genetic disease is. Gabriel Lazarin, who works closely with physicians in his job as Director of Genetic Counselors on Counsyl’s clinical sales team, decided to see if he could change that.

Gabriel Lazarin at Counsyl headquarters.

Gabriel Lazarin at Counsyl headquarters.

“I wanted to give physicians and patients a shared language,” says Lazarin, who joined Counsyl five years ago as its first genetic counselor. “A way to talk about the impact of a disease in a way that’s more objective than saying “it’s not that bad,” or “it is bad.” Two years ago he helped organize a study to establish a scale for rating genetic diseases and in December the Severity Index was published in Plos One Journal.

The result is that a physician can now easily guide patients interested in carrier screening to a customized outcome. There are patients who find it alarming that they’re carriers for early hearing loss, for instance, while others don’t really mind. Patients can choose to be tested for every disease on the panel, including GJB2-related hearing loss, rated 2, or moderate. Or maybe they only want to be evaluated for conditions that have been rated 4, or profound, such as Canavan disease and Smith-Lemli-Opitz Syndrome. The beauty of the Severity Index is that it’s up to patients to decide on their level of tolerance. Says Lazarin, “I hope this starts us down a path of making it easier for physicians to discuss screening with their patients.”

Internship with a genetic counselor sparks a career

Lazarin has always loved science and as an undergrad at Stanford was naturally drawn to genetics. News about the genome was exploding in the early 2000s and when an advisor noticed his interest he suggested Lazarin consider genetic counseling. Intrigued, he shadowed a genetic counselor and discovered he loved it. He spent a couple of years after graduation working in the Stanford admissions office but couldn’t shake the connection he’d felt so he applied to the masters program at the University of Texas Health Science Center at Houston.

IMG_2205Lazarin arrived at Counsyl after a stint working in a high-risk pregnancy clinic in Phoenix doing prenatal genetic counseling. His chance to be a Counsyl client came a couple of years ago when he and his wife, a family physician who lives with him in New York City, decided to have a baby. “I knew to not expect anything bad but I also know from clinical experience that the unexpected happens,” he says. So it was a relief, he says, to find their children weren’t at significant risk. In December, he and his wife welcomed a healthy baby girl.

Lazarin, who recently explained his study approach in a guest post on the DNA Exchange, says he’d love to do more research. “I think we’re helping advance the field of genetic counseling by taking something complicated and turning it into something predictable,” he says. “I’m happy to be working with an organization that’s so willing to share information that benefits everyone.”

 

Statement issued by medical experts recognizes growing popularity of expanded carrier screening

4 Mar

Explaining the value of expanded carrier screening just got a whole lot easier. Five professional organizations, including ACOG, ACMG, SMFM, NSGC, and the Perinatal Quality Foundation, recently issued a joint statement in the March issue of Journal of Obstetrics & Gynecology (1) that helps clarify for physicians how to use expanded carrier screening and, even more important, who can benefit from it. By doing so the group clears up misconceptions that have prevented many men and women from getting screened. It also validates Counsyl’s commitment to reaching a broader population and offering genetic counseling support.

This is the first instance in which a coalition of medical organizations has issued a statement on expanded carrier screening, and it was time. Thanks in part to the drive by Counsyl, among others, to make screening more affordable, expanded carrier screening has become a much more common practice. “One impetus for doing this was the recognition that many practitioners were already offering it and it was time to provide some guidance,” says Dr. Jim Goldberg, Counsyl’s Chief Medical Officer and a reproductive genetics expert who was one of the authors of the Joint Statement prior to joining Counsyl.

Misconceptions about who’s eligible for ECS hurts families

Another even more important reason for issuing the statement on carrier screening is that outdated thinking means many growing families are missing out on its benefits. Carrier screening, the group says, is no longer just for people with a family history of a disease or a parblog image journalticular ethnic background. “Ethnic-based panels miss couples at risk for an offspring with a significant disorder,” says Dr. Goldberg. In acknowledging the importance of making carrier screening a routine part of preparing for a baby, the joint statement “basically supports everything we’ve been saying about the utility of screening more people for more diseases,” says Shivani Nazareth, Counsyl’s Director of Women’s Health.

There’s still no consensus on the severity of diseases a screening should include but that may be next. Says Nazareth, “I think this is an acknowledgment that we’re moving in the direction of having a standard of panel of diseases that we screen for prior to pregnancy, no matter what your background or ethnicity.”

Highlights of the joint statement:

Carrier screening is useful and gives patients critical information and options. “Carrier identification allows for preconception planning as well as the option of prenatal diagnosis for the couple at risk. Early identification of affected pregnancies allows condition-specific counseling and care.”

Carrier screening is an important part of preconception and prenatal care. While the statement does not replace individual society medical guidelines, it offers direction to doctors who wish to offer carrier screening to patients. In other words, it validates that this practice is here to stay.“Carrier screening for inherited genetic conditions is an important component of preconception and prenatal care.” They go on to state“Whether the practitioner follows current professional society recommendations or uses expanded carrier screening, the goal of preconception and prenatal carrier screening is to provide couples with information to optimize pregnancy outcomes based on their personal values and preferences.”

Carrier screening should not be limited by ethnicity. The authors acknowledge that relying on ethnicity and/or ancestry to determine what diseases to screen for has limitations, especially in our “increasingly multiethnic society.” The authors indicate that carrier screening should offer the same set of diseases to all patients, regardless of race or ethnicity.
“All individuals, regardless of race or ethnicity, are offered screening for the same set of conditions” due to “inaccurate knowledge of ancestry in our increasingly multiethnic society” and “recognition that genetic conditions do not occur solely in specific ethnic groups.”

Candidates for carrier screening include: a) women of reproductive age before conception; b) egg and sperm donors; and c) pregnant couples. Preconception screening can be offered sequentially or in tandem (both partners at the same time) but for pregnant couples it makes more sense to screen mom and dad at the same time.

Genetic counseling for at-risk couples is an important part of the expanded carrier screening process. The authors agree that it is not practical or necessary for doctors to explain each condition to patients before testing. But while pre-test genetic counseling for each disease is not required, at-risk couples need genetic counseling to understand what it means to be a carrier.“Health care providers who use expanded carrier screening should have a plan to provide accurate information to patients identified as carriers of a condition.” This is further evidence that Counsyl, which offers post-test genetic counseling with every screen, is doing it right.

1. Edwards JG, Feldman G, Goldberg J, et al. Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the american college of medical genetics and genomics, american college of obstetricians and gynecologists, national society of genetic counselors, perinatal quality foundation, and society for maternal-fetal medicine. Obstet Gynecol. 2015 Mar;125(3):653-62

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