Inside AJHG: A Chat with Stephen Kingsmore

Posted By: Sara Cullinan, PhD, Deputy Editor, AJHG

Each month, the editors of The American Journal of Human Genetics interview an author of a recently published paper. This month, we check in with Stephen Kingsmore to discuss his paper “A randomized, controlled trial of the analytic and diagnostic performance of singleton and trio, rapid genome and exome sequencing in ill infants.”

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Stephen Kingsmore, MD, DSc, holding his patient, Maverick Coltrin. The photo was taken in April 2018 at the Frontiers in Pediatric Genomic Medicine Conference.

AJHG: What prompted you to start working on this project? 

Stephen: We’ve been working on implementing rapid whole genome sequencing in infants in intensive care units since 2011. We have two Guinness world records for fastest time to genetic diagnosis (the current benchmark is 19 hours). In the first 35 infants we tested, we saved two lives by changing therapy from that based on the clinical diagnosis to that based on the molecular diagnosis. Ever since then, we’ve been on a mission to understand how to make this reality in every intensive care unit in the world.

AJHG: What about this paper/project most excites you? 

Stephen:  Randomized controlled trials are very exacting. This is just the second randomized controlled trial of clinical genome sequencing! You’re never sure whether a clinical trial will really test the desired hypothesis. I was most excited that we clearly showed that ultra-rapid whole genome sequencing, with fastest time to diagnosis, was best for seriously ill infants in intensive care units (ICUs). As with every previous study, I now know how to redo the current one!

AJHG: Thinking about the bigger picture, what implications do you see from this work for the larger human genetics community?

Stephen: This manuscript is part of a growing body of evidence that demonstrates that infants in ICUs with diseases of unknown etiology benefit from rapid whole genome sequencing by virtue of the consequent implementation of precision medicine. We anticipate that 30,000 infants per year would benefit from this in the U.S. The current study was unique since almost one half of infants in ICUs were eligible for enrollment. As a result, we found that genetic diseases are much more common than previously expected.

AJHG: What advice do you have for trainees/young scientists?

Stephen: Think about a career in genomic medicine – the genomic medicine tsunami is coming and we’ll need every genetic counselor and medical geneticist to deliver this new type of care. For the first time, genomics will save lives day in, day out.

AJHG: And for fun, tell us something about your life outside of the lab.

Stephen: I’m reading the Bible in a year. I’m 2/3 of the way through and it yields specific thoughts for each day, as well as continually adjusting my thinking to the bigger, long-term picture. It started as a chore and now is a vital part of my day.

Stephen Kingsmore, MD, DSc, is the President and CEO of Rady Children’s Institute for Genomic Medicine at Rady Children’s Hospital. He has been a member of ASHG since 2007.

Inside AJHG: A Chat with Alan Beggs

Posted By: Sara Cullinan, PhD, Deputy Editor, AJHG

Each month, the editors of The American Journal of Human Genetics interview an author of a recently published paper. This month we check in with Alan Beggs to discuss his paper ‘Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project’.

Several members of the BabySeq research team
Several members of the BabySeq research team, including (L to R) Katie Dunn, Casie Genetti, Ingrid Holm, Alan Beggs, Robert Green, and Pankaj Agrawal. (courtesy of Dr. Beggs)

AJHG: What prompted you to start working on this project? 

Alan: It is well established that genomic sequencing of individuals with a likely genetic disease has clear and recognized benefits that easily outweigh the risks and costs.  However, we are just beginning to appreciate the potential benefits and costs of prospectively sequencing healthy individuals. There is a lot of hope around the prospects for disease prediction, presymptomatic diagnosis, carrier detection, pharmacogenomics and other potential benefits of genomic sequencing, and an equal amount of concern around the risks of misuse of genetic information, misinterpretation of probabilistic results or negative personal impacts such as anxiety, increased family stress or loss of trust that such information might engender.

The NIH Newborn Sequencing In Genomic medicine and public HealTh (NSIGHT) program was conceived to explore the implications, challenges, and opportunities of genomic sequencing in the newborn period. Together with our colleagues here in Boston, and in Houston, Robert Green and I designed the BabySeq Project to experimentally measure the medical, behavioral, and economic outcomes by prospectively sequencing both healthy and sick newborns and then following the consequences of returning results to them, their physicians and to their medical records.

AJHG: What about this paper/project most excites you? 

Alan: Although thousands of both healthy and sick individuals have undergone genomic sequencing by now, BabySeq represents one of the first prospective, randomized controlled trials of sequencing for which disease detection was not a primary goal. By enrolling newborn participants regardless of their medical status we can achieve one of the less biased comparisons within a human population. Although our sample size is modest, we were surprised to find in the sequencing arm that 9.4% of the infants, including ten of 127 healthy newborns, harbored what we considered to be a monogenic disease risk alleles, in other words, genetic variants that are predicted to cause disease using current best practices for determining disease-gene association and variant interpretation. Such a high rate of predicted genetic morbidity suggests either that we currently underestimate genetic contributions to common disorders such as heart disease or cancer, or that our variant predictions of pathogenicity or assumed disease gene penetrances are over estimated.

I think the randomized controlled aspect of this study is something else that excites me. It is providing an important opportunity for Amy McGuire and her team at Baylor to more rigorously assess the psychological and social implications of having genomic information at an early age. Funding permitting, we aim to follow the BabySeq families in both the sequenced and control arms well beyond the one-year follow-up surveys currently in progress, and I expect that we will be able to provide some hard data to address some of the concerns surrounding potential negative implications of learning genetic information.

AJHG: Thinking about the bigger picture, what implications do you see from this work for the larger human genetics community?

Alan: This is a difficult question to answer!  Of course, just about everyone who has interviewed me has asked whether I think sequencing of newborns will become standard of care. The first point I make is that, for the foreseeable future at least, we absolutely do not view this as a replacement for traditional newborn screening, which targets a carefully chosen group of treatable diseases using tests with well-established and high degrees of sensitivity and specificity.

There is no question in my mind that rapid genomic testing is indicated for newborns with undiagnosed medical conditions that may have a genetic basis, and it is gratifying to see that geneticists and neonatologists are rapidly adopting this, and that third part payers are finally starting to come around and reimburse for this. Although I’m confident the data will eventually show that the risks of newborn sequencing in healthy infants are acceptably low, the benefits will be harder to establish and are likely to be uneven: most newborns will not have immediately actionable findings, but identification of carrier states will occasionally lead to identification of couples at-risk for future pregnancies, and presymptomatic diagnosis of even untreatable conditions such as Duchene muscular dystrophy, will help some families avoid having affected children in the future. Occasionally, and with increasing frequency, an early diagnostic finding will lead to potentially life saving interventions or surveillance, as in the case of the families we identified with variants for hereditary cancer syndromes. As our understanding of disease-gene associations and variant interpretation improves, more and more children will stand to benefit from such information.

The newborn period is a hectic and disruptive time for new families, so I think genomic sequencing for healthy babies is more likely to be eventually offered in late infancy or early childhood, much like many vaccinations are offered today. Before this happens though, it will be up to us, the professional genetics community, to engage with our colleagues, legislators, third party payers, and most importantly the public, in a discussion to determine when the broader societal benefits justify the risk and the costs, and to ensure that genetic information is protected to avoid misuse and discrimination.

AJHG: What advice do you have for trainees/young scientists?

Alan: Follow your heart and pursue the questions that excite you, but be mentally flexible and look for opportunities to work with outstanding scientists who will appreciate and support your efforts. Early in my postdoctoral career, my advisor passed away suddenly and I was faced with a career-altering dilemma. I was fortunate to find an outstanding new mentor in Dr. Lou Kunkel, and my career path shifted abruptly to focus on neuromuscular disease, and eventually genetics and genomics of rare diseases.  Science, and society, are constantly evolving, so put aside your preconceived notions of what “should” or “will” happen, and follow the data and opportunities wherever they lead.

AJHG: And for fun, tell us something about your life outside of the lab.

Alan: I like learning about new things, so I tend to be a generalist with broad interests who enjoys tinkering and trying different things. I’m not an expert in any one area, but I’ve dabbled in woodworking, I like repairing broken things, from dishwashers to lawnmowers (YouTube is great for that!), and I’ve got a killer fish tank at home. I also love to be outdoors, and I’m just as happy raking leaves, cleaning my gutters, or shoveling snow in the middle of the night as I am kayaking or skiing.

A longtime ASHG member, Alan Beggs, PhD, is Director of The Manton Center for Orphan Disease Research at Boston Children’s Hospital and the Sir Edwin and Lady Manton Professor of Pediatrics at Harvard Medical School. 

FDA Takes Steps to Advance Genomics Technology, Encourage NGS-based Test Innovation

Guest Post: Laura M. Koontz, PhD, U.S. Food and Drug Administration 

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Laura M. Koontz, PhD, U.S. Food and Drug Administration (courtesy Dr. Koontz)

Genomics is advancing at an unprecedented pace, a fact that will come as no surprise to members of ASHG who work on the front lines of this exciting field. Over the past few years, the FDA has been working with stakeholders from across the genomics community, including ASHG, with the goal of applying our regulatory authorities to genomics in ways that encourage innovation and ensure that tests provide accurate and meaningful results to patients. Recently, we announced two new FDA Guidances on next generation sequencing (NGS)-based in vitro diagnostics that are intended to encourage further development of these powerful tests and enable more efficient regulatory review by FDA.

The first guidance, “Use of Public Human Genetic Variant Databases to Support Clinical Validity for Genetic and Genomic-Based In Vitro Diagnostics,” describes an approach where test developers may rely on clinical evidence from FDA-recognized public databases to support clinical claims for their tests and provide assurance of the accurate clinical evaluation of genomic test results. Using FDA-recognized databases will provide test developers with an efficient path for marketing clearance or approval of a new test. Further, FDA believes that this guidance will encourage crowdsourcing of NGS evidence generation, curation, and data sharing, advancing the development of high quality precision medicine treatments and diagnostics.

The second guidance, “Considerations for Design, Development, and Analytical Validation of Next Generation Sequencing (NGS)–Based In Vitro Diagnostics (IVDs) Intended to Aid in the Diagnosis of Suspected Germline Diseases,” discusses FDA’s considerations for analytical validation of NGS-based tests intended to help diagnose suspected germline diseases. The Agency believes the analytical validation recommendations laid out in this guidance could spur the creation of consensus standards for NGS-based tests that will be developed by the community and potentially recognized by FDA. Moreover, the guidance articulates FDA’s belief that NGS tests for germline diseases could potentially be classified in class II (moderate risk)  based on conformance to the recommendations in this guidance or to standards that address these recommendations, which would allow FDA to consider exempting them from premarket review.

The Agency believes these guidances will provide test developers with a more efficient path to market, improving FDA’s ability to protect public health by ensuring these tests provide accurate and meaningful results, while at the same time speeding patient access to NGS assays by lowering barriers to innovation. And importantly, the guidances will help to give patients, payers, researchers, and clinicians greater confidence that NGS platforms can reliably be used to inform critical treatment decisions and improve patient outcomes.

To learn more about these two guidances, please join the FDA for a webinar on Thursday, May 24, from 2:00-3:30 p.m. U.S. Eastern Time.

Laura Koontz, PhD, is a member of the Personalized Medicine Staff in the Center for Devices and Radiological Health at the U.S. Food and Drug Administration. She has a PhD in Molecular Biology and Genetics and was the 2012-2013 ASHG-NHGRI Genetics & Public Policy Fellow.

Social Issues Committee Initiates New Duty to Recontact Statement

Posted By: Jillian Galloway, MS, Science Policy Analyst at ASHG

The ASHG Social Issues Committee (SIC) is taking the lead on an important issue affecting genetics and genomics researchers, namely the duty to recontact research participants. At ASHG 2017 in Orlando, the Board of Directors asked the SIC to draft a Society statement offering greater guidance on this topic.

Over the past few years, advances in next-generation sequencing technologies and the volume of genomic information produced have raised thought-provoking questions regarding the ethical, operational, and regulatory considerations of recontacting research participants about new genomic information that is clinically significant (such as a new interpretation of the pathogenicity of a variant harbored by participants). For individual researchers and their associated institutions, questions of whom, when, and how to recontact are daunting. What’s more, for many, the preliminary question of whether researchers have an ethical duty and/or professional obligation to recontact participants is not easily answered.

To involve the ASHG community early in planning the scope and key points of the statement, Yvonne Bombard (SIC chair) and Howard Levy (SIC member) presented this topic at a CoLab session during the Annual Meeting. They described how new IT advances make greater data sharing possible and could facilitate the dissemination of information from researcher to participant. They also outlined emerging questions when considering the duty to recontact, such as 1) What kind of information is relevant and useful for participants? and 2) How does one appropriately and responsibly inform participants and use technology to facilitate contacting and recontacting?

CoLab attendees provided many insightful comments useful for informing the ASHG statement. For example, they noted that research is not an open-ended commitment: funding ends and teams disband, raising questions about researchers’ duty to contact participants with new or updated information after the study ends. Attendees also discussed operational difficulties in recontacting participants or revisiting results. Furthermore, questions were raised about the appropriate method for contacting participants. Such comments highlighted the complexities of the issues and the challenges faced by researchers today.

As the SIC begins drafting the Society statement on this issue, we welcome you to submit your thoughts on the topic to policy@ashg.org. All comments submitted will be shared with the SIC.

Jillian E. Galloway, MS, is a Science Policy Analyst at ASHG. Learn more about ASHG’s activities in Policy & Advocacy.  

Inside AJHG: A Chat with Wouter de Laat

Posted by: Sarah Ratzel, PhD, Science Editor, AJHG

Each month, the editors of The American Journal of Human Genetics interview an author of a recently published paper. This month, we check in with Wouter de Laat, PhD, to discuss his paper, “Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping.”

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Carlo Vermeulen, MSc, first author of the paper (left); and Wouter de Laat, PhD (right) (courtesy Dr. de Laat)

AJHG: How did you begin working on this project? 

Wouter: The realization that our TLA technology is powerful for targeted haplotyping of any genomic locus of interest triggered us to think about clinically relevant applications. Our background in thalassemia research and our close collaborations with the University Medical Centre Utrecht soon made us excited to explore whether TLA haplotyping would enable non-invasive prenatal diagnosis for monogenic diseases.

AJHG: What about this paper most excites you? 

Wouter: Two things. To me, the fact that our knowledge acquired through basic research on the structure and function of our genome led us to develop a novel prenatal diagnostic test emphasizes once more the societal relevance to support fundamental research. I find this important to mention, coming from a country where national policy makers propagate almost exclusively the virtues of translational research. The other very rewarding aspect of this project was our interaction with Dutch, Greek, and Iranian clinicians who work daily with cystic fibrosis and thalassemia families: they made us truly appreciate the clinical impact of this work.

AJHG: Thinking about the bigger picture, what implications do you see from this work for the larger human genetics community?

Wouter: I expect that, now that pre-conception screening programs for severe Mendelian disorders are being implemented in our health care system, non-invasive prenatal diagnosis (NIPD) methods will be very welcome alternatives to the more burdensome invasive tests for giving desired comfort during pregnancy. A genetic test based on a simple blood draw may in the future also provide risk couples opting for embryo selection with an easy means to confirm that the familial disease was not transmitted to the child. And variants of the NIPD method presented here may offer an attractive way to confirm parenthood, for example following in vitro fertilization.

AJHG: What advice do you have for trainees/young scientists?

Wouter: Always, even if you are considering pursuing a tenure track academic position, ask yourself at the end of your PhD and certainly as an early postdoc: am I, and is my CV, in the top among my peers and am I truly passionate about science? If not, realize that there is a world of careers outside of academia that may be equally inspiring and rewarding to you and that this is the moment to start exploring these opportunities.

AJHG: And for fun, tell us something about your life outside of the lab.

Wouter: Scientists are sometimes not very different from other human beings. To recharge the batteries, I love doing sports (soccer, cycling) and love traveling with my wife and three daughters: we just returned from an amazing trip to Sri Lanka.

Wouter de Laat, PhD, is a Professor of Biomedical Genomics at the University Medical Center Utrecht, Professor at Utrecht University, and Founder of Cergentis.

How I Work: Brian Shirts

Posted By: Elisabeth Rosenthal, PhD, Member of the ASHG Communications Committee

We sat down with ASHG member Brian Shirts, MD, PhD, to learn more about his work at the cutting edge of clinical genetic diagnostics, including how his work intersects with his faith.

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Brian Shirts, MD, PhD. (courtesy Dr. Shirts)

ASHG: Tell us about your position and how it fits into your institution and its goals.

Brian: I am Assistant Professor of Laboratory Medicine at the University of Washington. Being in a clinical department means part of my job is doing clinical genetic testing in patients. Since I am at a university, the other part of my job is teaching and doing research. In order to have this position, I did medical school and doctoral training in human genetics. Then I did specialty training to be board certified in Clinical Pathology and Molecular Genetic Pathology. When I started graduate training, I did not know that the position I currently have existed. When I first met a physician who specialized in genetic diagnosis, I quickly realized, “That is what I wanted to do all along!”

Working at a university, I need to be on the cutting edge of clinical genetic diagnostics. I specialize in hereditary cancer testing and understanding the health effects of extremely rare genetic variants. When I say “extremely rare”, I mean genetic variants that I may see for the first time when I look at the results of a patient receiving clinical genetic testing, or a variant that may have only been seen in one or two other people in the world. In cancer risk genes, these variants are usually inherited and clustered in families, so I like to call them family-specific variants.

I am lucky because my research interests and my clinical work go well together. I spend over half of my time doing research and developing translational applications that will allow myself and others to apply my research discoveries to clinical diagnostics.

ASHG: How do you keep up with the latest in genetics science and use this in your work?

Brian: I try to attend the ASHG Annual Meeting and the Association for Molecular Pathology meeting as often as I can, as I think these are the best forums for the latest in genetics science and genetic diagnostics, respectively. I also read several journals and go to journal club presentations as often as I can.

ASHG: What are your favorite genetics websites?

Brian: I have to give a plug for my website on family studies for rare variant classification: findmyvariant.org. Some of my other favorite genetics websites for non-geneticists are: Genetics Home ReferenceLearn.Geneticsmy46, and Genetic Alliance.

ASHG: What are you currently reading/thinking about?

Brian: I am always thinking about how to apply population genetics principles to clinical diagnostics. For something completely different, I like to read the best books that my kids are reading. I am currently reading “Mr. and Mrs. Bunny–Detectives Extraordinaire!” by Polly Horvath.

ASHG: What everyday thing are you better at than everyone else? What’s your superpower?

Brian: When I go to church, others tell me that I have an extraordinary talent for asking appropriate yet thought provoking questions during Sunday School. Being an outspoken scientist in a faith community can be difficult to navigate, but communicating with people from different backgrounds is a really important skill to develop.

Brian Shirts, MD, PhD, is Assistant Professor of Laboratory Medicine at the University of Washington. He has been a member of ASHG since 2004.