Biology of Genomes 2018: The Past and Future of Genomics

Posted By: Emily C. Glassberg, PhD Candidate, ASHG Communications Committee

A few weeks ago, I attended the 31st annual Biology of Genomes (BoG) meeting at Cold Spring Harbor. In addition to highlighting the amazing research that comprises the current state of genomics, this meeting highlighted the storied past and bright future of the field. The enthusiastic participation of attendees, both at the meeting and on Twitter, shows incredible energy and momentum as we try to understand the genome’s role in biology, evolution, and disease.

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Attendees network at Biology of Genomes 2018 (Credit: Constance Brukin; copyright CSHL)

Genomics Present

The seven scientific sessions covered functional genomics, medical genomics, computational genomics, and evolutionary genomics, as well as genome engineering. Seeing this varied body of work at a single meeting clearly demonstrates that theory, experiment, high-throughput screening, and countless forms of new technology and data analysis all play central roles in shaping our current understanding of the human genome.

And, while the human genome was the primary subject of study, non-human genomes got coverage as well. Highlighted research included the genomes of near relatives, like Neanderthals; to those of best friends, like dogs; to those of model organisms, like yeast. Crowd favorites included Jaemin Kim’s and Elaine Ostrander’s talks using dogs as a system to learn about the genetic basis of complex traits (for the science as well as the adorable pictures).

The scientific programming also included two keynote speakers, Wendy Bickmore and David Page. Bickmore discussed her group’s work on how 3D chromatin structure relates to the mechanism by which enhancers – particularly long-range enhancers – interact with promoters to regulate gene expression.

Bickmore’s emphasis on the need to assay enhancer function in vivo was echoed elsewhere at the meeting. In particular, Emma Farley spoke about high-throughput measurements of enhancer function in the model chordate Ciona. In combination, these talks sparked a conversation about whether current computational models are looking in the wrong places when it comes to predicting enhancer activity and specificity.

Page presented his group’s work on the evolution of sex chromosomes with an eye to understanding sex differences in health and disease. Page’s question of whether and how males and females “read their genomes differently” connected to broader questions that recurred throughout this year’s meeting –  how do we understand the genome dynamically? When and how does the same genome lead to different outcomes?

The ways in which the genome and its downstream effects change over time and space is a big open question, and this year’s BoG showcased many approaches to tackling it:

  • Ben Strober and Jonathan Griffiths both used time-course gene expression data to track how gene regulation changes throughout cellular differentiation and development.
  • Jake Yeung shared an example of dynamic chromatin interactions and rhythmic promoter-enhancer contacts that are connected to circadian rhythm.
  • Christina Leslie presented work on how the chromatin state of tumor specific T-cells changes during cancer progression and how that influences disease treatability.

And that’s just a sample of the exciting work in this space! While we don’t yet have clear answers to these questions, the research discussed at BoG reveals a landscape that is complex, nuanced, and fascinating. What a great time to be in genomics!

Genomics Past

In addition to discussions spanning the range of the current field of genomics, BoG included a brief talk in memoriam of molecular and developmental geneticist John Sulston, who passed away on March 6, 2018. Dr. Sulston was well known for his seminal work in the now-model organism C. elegans, as well as his role in the Human Genome Project. Eric Lander also toasted Jim Watson for his role in the Human Genome Project, and to celebrate his 90th birthday. Lander and other BoG organizers later apologized for the toast, as it was seen by many in the community as minimizing Watson’s history of racist and sexist commentary.

Genomics Future

And, finally, no meeting would be complete without a vision for the future of the field.

A panel on the Ethical, Legal, and Social Implications of genomics research included four perspectives on the promises and pitfalls of germline genome editing. While there is considerable excitement around using CRISPR to cure genetic disease, many issues remain regarding proof of safety as well as ensuring equal access to the technology. Following a lively discussion during the question-and-answer, the consensus seemed to be that germline genome editing is a distant future. In the meantime, we can focus on the application of currently available options, like genetic screening and assisted reproductive technologies.

The National Human Genome Research Institute (NHGRI) also engaged researchers in its current strategic planning initiative, which began in February 2018 and will be completed in 2020. NHGRI is collecting input on priority areas to help the institute live up to its mantra, The Forefront of Genomics.

Of course, the scientific discourse at Biology of Genomes isn’t limited to the talks. The three lively poster sessions were great opportunities to exchange ideas. And many spirited discussions took place during the coffee breaks, over the traditional Cold Spring Harbor banquet, and down at Blackford bar. All told, there’s a lot to look forward in genomics!

Emily C. Glassberg is a PhD Candidate in the Department of Biology at Stanford University. She serves on ASHG’s Communications Committee and has been an ASHG member since 2014.

Happy 10th Birthday, GINA!

Posted By: Derek Scholes, ASHG Senior Director of Policy & Advocacy

Ten years ago today, President George W. Bush signed into U.S. law the Genetic Information Nondiscrimination Act, better known as GINA. The enactment of GINA in 2008 was the culmination of a determined 13-year campaign by congressional champions and advocacy groups, including ASHG, to establish nationwide legal protections against genetic discrimination in the workplace or through one’s health insurance. Today, in recognition of the anniversary and the enduring importance of the law, ASHG is launching a short video to help spread the word about the law.

 

One reason why ASHG has always been a strong supporter of GINA is because it helps reassure the public that they can volunteer for genetics research, or take a genetic test at the doctor’s, without worrying that this will affect their job, their health insurance, or their privacy. It was for this reason that leaders of the Human Genome Project were calling for the establishment of protections against genetic discrimination in the mid-1990s. At the time of its passage, Jo Boughman, PhD, ASHG’s then-Executive Vice President, wrote, “Americans can feel more confident that their personal genetic information cannot be used against them, and encouraged to participate in scientific research studies that require the collection and storage of genetic data.”

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Former President George W. Bush signs the Genetic Information Nondiscrimination Act on May 21, 2008, in the Oval Office.

But GINA is only effective in reassuring the public to the extent that people know about the law. Since its passage in 2008, however, studies have repeatedly shown that most individuals are not aware of GINA or its protections. A 2011 study found that only 16% of Americans knew of any law protecting their genetic privacy. Similarly, a 2015 survey of U.S. residents found that 79% were unfamiliar with GINA. This lack of awareness is found within health care too, with research finding most physicians and nurse practitioners do not know about the law. Together, these studies suggest an ongoing need to raise awareness about GINA if it is to be effective as originally envisioned.

ASHG is playing its part. As well as watching the video, please check out ASHG’s statement about the 10th anniversary; today’s Research!America blog post by ASHG President David Nelson; and a blog post from former ASHG/NHGRI Genetics and & Public Policy Fellow Daryl Pritchard, reflecting on his time working in Congress on GINA.

GINA is designed to prohibit genetic discrimination within health insurance. Since GINA’s passage, there has been ongoing discussion in the genetics community regarding whether there should be similar legal protections in the U.S. against genetic discrimination for ‘the other insurances’ – life, disability and long-term care, protections that go beyond the current patchwork of state laws. Two issues commonly discussed are (a) whether there is a strong, evidence-based case for establishing such protections and, if so, (b) how one would craft such a federal law, or series of state laws, to establish such protections. Let us know your thoughts below, or write to us at policy@ashg.org.

For more information on ASHG programs in policy and advocacy, visit the Policy & Advocacy page.

GINA Turns 10: A Look Back at its Passage

Posted By: Jillian Galloway, Science Policy Analyst, ASHG

As the Genetic Information Nondiscrimination Act (GINA) turns ten, ASHG caught up with Daryl Pritchard, former ASHG/NHGRI Genetics and Public Policy Fellow, to discuss his time in Rep. Louise Slaughter’s office working on the passage of GINA and her legacy as the woman who championed genetic information protections in Congress.

ASHG: Trained as a geneticist, how were you able to work in Rep. Slaughter’s office?

Daryl: The opportunity came through the ASHG/NHGRI Genetics & Public Policy fellowship. The fellowship really opened doors for me. It was how I got to see all of the passion Rep. Slaughter had for genetics and science.

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Congresswoman Louise Slaughter and Daryl Pritchard, 2003 (courtesy Dr. Pritchard)

ASHG: What was your role in Rep. Slaughter’s office?

Daryl: I was the first fellow and needed to find an assignment on Capitol Hill, and was drawn to Slaughter’s office because of the GINA legislation. GINA was a personal priority for me and something Congresswoman Slaughter was deeply passionate about. I took on the role of Health Legislative Assistant that year. As a geneticist, I could contribute to public understanding of the bill, translating the law’s benefits into layman’s terms. Beyond GINA, I would handle any scientific or health policy issue. GINA was the primary reason I was there, but other important health issues were also on the docket.

ASHG: What was your involvement with GINA while working in Rep. Slaughter’s office?

Daryl: It was pretty intense. The bill had first been introduced in 1995 and I was there in 2003. She needed to gain her colleagues’ support for the legislation and educate other members of staff and the public about its importance. So I drafted talking points for public communications and ‘Dear Colleague’ letters to drum up support from her fellow members of Congress. I would represent Louise at various visits and would promote her vision of protections for the American public against genetic discrimination.

ASHG: Why do you think the passage of GINA was so important to her? 

Daryl: She often talked about being the only microbiologist in Congress and being a scientist early in her career. She recognized the importance of scientific research for health and realized that without adequate protections for patients and research subjects, there would be a lingering fear or reluctance on the part of the public to get testing. This, in turn, would stifle the advance of health discovery and the incorporation of genetic information into care.

She had a second motivation as a patient. A clear influence was the death of her sister from pneumonia despite being in doctors’ care. Louise knew genetics was key to improving health, but that if genetic information were used by employers or health insurers, there was a possibility for that information to qualify or disqualify one from coverage or benefits, hiring or firing.

ASHG: What can you tell us about Slaughter’s reaction to the passage of GINA?

Daryl: Louise was really pleased. A lot of hard work, dedication, and time had gone into its passage. To finally get GINA approved as a bicameral and bipartisan piece of legislation reflected her tireless efforts to advance the bill. Referred to as the first civil rights legislation of the new century, it was so necessary for the American public. She believed it was a no-brainer that it should be passed. She congratulated then-President Bush and her colleagues for bringing it to fruition.

ASHG: Ten years after its passage, how can the genetics community help ensure that GINA is implemented as intended?

Daryl: GINA is a great victory for patients and scientists, and you can expect that employers and insurers will continue to challenge it. The genetics community should look at challenges as they arrive and defend the law for its original intent. A key thing to keep in mind is that GINA prohibits even the collection of information by health insurers and employers. Lingering fears about genetic discrimination do not come from a fear of employers’ or insurers’ good intentions, but rather from a concern that genetic data could be exploited or misused. The genetics community should continue to oppose collection of genetic information by employers and health insurers.

ASHG: How is the passage of GINA an example of the impact that the ASHG/NHGRI fellowship has on advocacy?

Daryl: The fellowship promotes the advancement of research and the importance of genetics and genomics. Its impact is far-reaching, and GINA is just one example. Many bills before Congress have a need for genetics and genomics expertise. It is essential that the science is accurately represented in those conversations.

The ASHG/NHGRI fellowship brings the voice of genetics and genomics to legislation and needs to continue to do that by having a presence in different congressional offices. We need to be there. I appreciate the opportunity to have been the first fellow. The experience has been influential in advancing my career.

Daryl Pritchard, PhD, is Senior Vice President of Science Policy at the Personalized Medicine Coalition. He worked in Rep. Slaughter’s office in 2003 through the ASHG/NHGRI Genetics & Public Policy Fellowship.

Following the Path of ASHG’s Statement on Pediatric Genetic Testing

Posted By: Cara Cavanaugh, MSc, Cell Press

What happens to a paper once it is published? After the research is over, the proofs are reviewed, and the paper is out in the world, how is it used and by whom?

To answer these questions, we traced the post-publication trajectory of ASHG’s position statement, “Points to Consider: Ethical, Legal, and Psychosocial Implications of Genetic Testing in Children and Adolescents.” The statement was published in The American Journal of Human Genetics (AJHG) in 2015 and was an update from two decades earlier. Following the history of the paper since its publication shows us the reach that an ASHG position statement can have over three years.

About the Position Statement

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Published in 2015, the statement has been cited by a variety of sources, including academic, legal, and public discourse.

The position statement gives recommendations for when and why families should decide to perform genetic tests on children and adolescents. “We felt that it was timely to update the statement across a range of issues,” says first author Jeffrey Botkin, MD, MPH, a professor and chief of the Division of Medical Ethics and Humanities at the University of Utah. “Our primary focus was genetically testing children for adult-onset conditions when there is no intervention during childhood. There hasn’t been a lot of research on the impact of such testing because folks felt that it was unethical under any context. We wanted to soften the perceived stance that such testing should never be conducted and have the position of the society be a little more flexible. We recognize that there may be circumstances when such testing might be appropriate for the child and family. We also wanted to encourage more research on these issues.”

Academic Citations and Public Conversation

Since its publication, the position statement is one of the top downloaded papers in AJHG’s history, with over 5,000 downloads as of 2018. After publication, to make the content more accessible to readers, ASHG created infographics that explain the issues and intricacy around childhood genetic testing. The paper has been cited by Genetics in Medicine, Pediatrics, Blood, Nature Reviews Genetics, and more than 80 other academic titles.

The statement has also been cited outside of the scientific research context. For example, it has impacted legal academic discourse. In one 2016 paper, Sénécal et al. discuss the legal approaches to healthcare decisions for minors in the European Journal of Human Genetics to the ASHG position statement as a “more nuanced approach” to how genetic testing should be pursued. They praise the statement for advising that physicians should inform families of all genetic testing options, even if the family has decided not to pursue any tests. Another paper by Otero in the European Journal of Health Law uses the position statement in a narrower context, specifically to analyze European and Spanish legal frameworks. These papers are just two of several examples of how one position statement from scientists can contribute to legal analysis internationally.

In addition to the academic studies discussed above, the position paper was also featured in the mainstream media. It gained coverage in NPR, VICE, and Pacific Standard. Exposure in these news sources helped engender public conversations online about the ethics of genetic testing in children.

What’s Next?

This paper shows the broad reach the ASHG community has in important societal and cultural issues of our time. As genetic testing appears more frequently in the news and becomes increasingly controversial, especially with products like direct-to-consumer genetic testing kits, it is imperative that we fully debate and consider how this could affect children and adolescents. ASHG policy statements, like the one published in 2015, provide us with long-lasting resources for continuing those discussions.

Cara Cavanaugh, MSc, is a Marketing Contractor at Cell Press. She earned a BA in History of Science from Princeton University and a MSc in Science Communication from Dublin City University while on a Fulbright Award.

Inside AJHG: A Chat with Barbara Evans

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

Each month, the editors of The American Journal of Human Genetics interview an author(s) of a recently published paper. This month, we check in with Barbara Evans of the University of Houston, to discuss her Commentary, “HIPAA’s individual right of access to genomic data: reconciling safety and civil rights.”

Through such Commentaries, AJHG encourages individuals in the genetics community to share their personal views on a policy issue. Distinct from journal editorials and official ASHG statements, it is our hope that these commentaries will help spur discussion within the field.

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Barbara Evans, University of Houston (Credit: S. Chandler)

AJHG: How did you become interested in this topic?

Barbara: Last summer, I was getting a lot of calls from research participants who were having trouble exercising their HIPAA right of access to their own genomic data. The HIPAA Privacy Rule is a U.S. federal privacy law. It grants people a right to obtain copies of data about themselves that is stored at HIPAA-regulated facilities. Since 2013, the Privacy Rule protects genetic data and, since 2014, its access right extends to data stored at HIPAA-regulated labs. People heard that they have a right to see their data, so naturally they wanted to see it. Many were being told “no.” Law professors play an informal role as society’s help line for questions about the laws we write about. I write about HIPAA, so I’m like the canary in the coal mine if a new HIPAA problem is emerging: my phone starts to ring. I checked around, and other HIPAA lawyers were getting those same calls from frustrated research participants. “Strange…why now?” we wondered. It seemed worth looking into—which, for a Law Prof, means you write an article. This is the article.

AJHG: What about this topic most interests/concerns you?  

Barbara: Regulatory lawyers are like primary-care docs: when someone shows up with a regulatory problem, you order a battery of diagnostic tests. The first test you run is to trace back in legal history till you find the statute (the Act of Congress) that gave rise to the regulation. Like most people, I always assumed that HIPAA’s access right must flow from the HIPAA statute. That’s true, but with a fascinating twist. As it relates to genetic information, HIPAA’s access right flows from a mandate Congress laid down in the Genetic Information Nondiscrimination Act of 2008. It’s a civil right! That fact has impacts that my commentary explores.

What concerns me most? Under the U.S. system of law, one of the worst ways things can go wrong in a democracy is if government agencies, which are supposed to protect people, take actions that deprive people of their civil rights. Your right under HIPAA to see your own genetic information is a federally protected civil right. That limits the range of actions regulators like the U.S. Food and Drug Administration and the Centers for Medicare and Medicaid Services, which regulates clinical labs, can take to block people’s access to their own genomic data. My commentary hopes to spark a dialogue about ways to address valid safety concerns about individual data access, without violating people’s civil rights.

AJHG: Tell us a bit more about the bigger picture—for scientists and the general public.

Barbara: Using people’s genomic data in research offers huge benefits to society, but it exposes people to privacy risks and other threats to their civil rights. Dating back to the dawn of the information age in the early 1970s, Congress has approved policies that let researchers use people’s data to advance public health and research. The quid pro quo is that Congress has consistently stood by the idea that if researchers have broad access to your data, then you should have broad access, too. Doesn’t that seem fair?

People who want to block individuals’ access to data need to appreciate that, over the past 50 years, Congress gave this matter a lot of thought and commissioned multiple ethical analyses. What they found is that if you want to take people’s access away, you can do so. But in return for taking people’s access away, you would then need to severely curtail researchers’ access to people’s data as an alternative way to protect people’s civil rights. So which world do you want? In World 1, researchers and people both have broad access to the people’s data. In World 2, neither group has access. Those are the two ethical options. It’s just not ethically defensible to have a World in which researchers have broad access to people’s data, but the people do not.

AJHG: What advice do you have for trainees?

Barbara: If your job doesn’t excite you and make you feel useful most of the time, get another job. Risks work out more often than we are led to believe. Take them. You hold your talents in trust, and you have a fiduciary duty to shepherd your talents to a green pasture where they can thrive.

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

Barbara: It’s generally tranquil, but last year was anything but with Hurricane Harvey, 52 inches of rain, fences down, and administering a portfolio of family interests across Texas. The saving grace is the lack of speed limits on rural Texas highways and discovering—in the fullness of middle age—the joy of really fast cars.

Barbara Evans, PhD, JD, LLM, is an Alumnae College Professor of Law and a Professor of Electrical and Computer Engineering at the University of Houston.

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.