Inside AJHG: A Chat with Lluis Quintana-Murci

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 Lluis Quintana-Murci (@quintanamurci) to discuss his paper “Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation.”

Lluis Quintana-Murci
Lluis Quintana-Murci (far right) with the members of his lab, including Martin Silvert and Maxime Rotival (courtesy Dr. Quintana-Murci)

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

Lluis: My laboratory is interested in the evolution of human populations and their long-standing relationship with infectious agents; half of the lab thus works on population genetics questions and the other half focuses more on population/systems immunology. In the context of this project, it all started back in 2016, when we found that Neanderthal introgression has affected innate immunity genes as a whole, and that some innate immunity genes (e.g., the TLR1/6/10 cluster) display extremely high levels of Neanderthal ancestry (Deschamps et al. Am J Hum Genet, 2016).

Later that year, we also found that Neanderthal introgression has been pervasive among regulatory variants (eQTLs), in particular those involved in responses to viral stimuli including influenza (Quach et al. Cell, 2016). The next natural question was then to explore how Neanderthal-introgressed variants in the genomes of non-Africans have affected more generally transcriptional and post-transcriptional regulation, focusing on promoters, enhances and miRNA-mediated regulation, in different tissues and cell types.

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

Lluis: Several things. First, although Neanderthal introgression has had relatively little effect on miRNA-mediated regulation, a mechanism that in general tolerates little variation and is highly evolutionary constrained, a few Neanderthal variants in a few miRNAs can exert a massive impact on downstream transcriptional programs. In general, I am fascinated by the fine-tuned “smart” way miRNAs function.

Second, I am excited about our results of enhancers, in particular the enrichment in Neanderthal ancestry we find in enhancers that are active in T cells (yes, sorry, I have a biased interest in all immune-related processes). What is even more interesting is that the excess of Neanderthal ancestry we observe in T cell enhancers is not due to increased Neanderthal introgression. Instead, it results from a higher human-Neanderthal divergence at these elements. This may reflect past adaptation in the Neanderthal lineage for this type of enhancers.

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

Lluis: This work highlights once more the potential benefits of admixture between our ancestors and other human forms, such as Neanderthals or Denisovans. The latter were adapted to their environments, whereas our ancestors entering Europe or Asia were less adapted. In this context, acquiring advantageous variation through archaic admixture is a fascinating topic, with obvious consequences for the larger human genetics community. Indeed, such archaic admixture increasingly is being shown to affect molecular phenotypes such as gene expression or mechanisms of gene regulation (e.g., this study) and more generally, organismal phenotypes such as traits and diseases (e.g., skin pigmentation, sleeping patterns, allergies) in present-day human populations.

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

Lluis: Be open while doing research, be curious, be rigorous, exchange a lot with other trainees and PIs, read a lot, and MAINLY, have fun and be passionate! Meaning both in your working and non-working life. Enjoy the work, do not suffer from it! For me, this is rule number one. If you follow this rule, great findings will follow…and, yes, a bit of luck also helps.

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

Lluis: I like to garden (actually, I can spend hours gardening), to bike, and, increasingly, to run. These three things really empty my mind and recharge my batteries. Also, I do need to go at least once per year to Mallorca (where I was born). Having lived there until I was 20 gave me a handicap for life: my need for sun and sea (and I live in Paris…). There’s nothing that relaxes me more than getting into the turquoise Mediterranean water and swimming!

I also love art exhibitions, almost exclusively modern art, and pop if possible! I spent last summer in NYC on a mini-sabbatical at Rockefeller University, and I really enjoyed the exhibitions there!

I also like to read. I can compulsively read historical biographies. When I enjoy somebody’s life, I can read 30 books about them even if most of them say the same thing. A recent example is the life of Princess Marie Bonaparte – a psychoanalyst and close friend of Sigmund Freud, whom she helped escape from Nazi Germany. I also love reading about contemporary politics: one of my preferred topics is the so-called “Spanish transition,” the period starting 1975-1980 when Spain transitioned from being under Franco’s non-democratic regime to being the modern, open-minded country that is today. Obviously, I like books about evolution, but then, that is more work-related again…

Lluis Quintana-Murci, PhD, heads the Unit of Human Evolutionary Genetics in the Department of Genomes and Genetics at the Institute Pasteur. He is a first year member of ASHG.

Inside AJHG: A Chat with Susan Slaugenhaupt

Posted By: Sarah Ratzel, PhD, Science Editor, 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 Sue Slaugenhaupt to discuss her paper, “ELP1 Splicing Correction Reverses Proprioceptive Sensory Loss in Familial Dysautonomia”.

Slaugenhaupt Lab (photo courtesy of Dr. Slaugenhaupt)

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

Sue: When I arrived at Massachusetts General Hospital as a postdoctoral fellow in 1991, one of the projects in Jim Gusella’s lab was focused on mapping the gene for familial dysautonomia (FD). Given my background in gene mapping, I became involved in the project and once we mapped the gene, I took over the project aimed at identifying the mutation. Once we cloned the gene and discovered that it was a mRNA splicing defect, I became fascinated by the idea of modifying splicing as a route to therapy, and my lab has worked on this ever since. I have known many FD patients and their families for over 25 years, and our work is driven by the desire to develop a disease modifying therapy for this devastating disease.

AJHG: What about this paper most excites you? 

Sue: Developing a mouse model for FD was a huge challenge since the disease is caused by a tissue-specific reduction of ELP1 protein. In 2016, we succeeded in generating a phenotypic mouse model and this paper describes the first trial of a potential therapy in our mouse. I am very excited that our treatment was able to increase the amount of ELP1 protein in the peripheral nervous system and, most importantly, rescue two of the most debilitating aspects of the disease, gait ataxia and kyphosis.

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

Sue: There are many efforts underway to generate therapies that target mRNA splicing, including small molecules, antisense oligonucleotides, and exon-specific U1 snRNAs. A significant fraction of human genetic disease mutations impact mRNA splicing, so this is an exciting time. These therapies are targeted at the molecular mechanism of disease, not at symptoms, and we are likely to see new treatments for many previously untreatable genetic diseases over the next several years.

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

Sue: Find a good mentor. One who cares more about your future and your career than their own. Look outside your own lab, and fight against the tide that keeps you locked in an unproductive situation too long.

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

Sue: I’m moving to a condo overlooking the beach next month and I can’t wait!

Susan Slaugenhaupt, PhD, is Scientific Director, Center for Genomic Medicine at Mass General Hospital Research Institute and Professor of Neurology at Harvard Medical School. She is a member of ASHG’s Board of Directors.


Defining the Responsibility to Recontact Research Participants

Posted By: Staff

This week, ASHG and eight partner organizations issued a position statement outlining whether, and to what extent, there is a responsibility to recontact genetics and genomics research participants when new findings emerge that suggest their genetic information should be interpreted differently.

Today, ASHG and partner organizations issues a statement in AJHG addressing the responsibility to recontact research participants.

Variants of uncertain significance get reclassified at a relatively high rate – up to half of such variants have been reclassified in the past decade. One paper found that 12% of these reclassifications had the potential to alter clinical management.

We sat down with Yvonne Bombard, PhD; and Howard Levy, MD, PhD, lead authors on the statement, to get their take on the issue.

ASHG: Why did the Social Issues Committee tackle this topic?

Yvonne: Genetics and genomics researchers are at the forefront in collecting and analyzing data related to sequence variant interpretations, which is continuously evolving. This means that a variant’s clinical significance might be reinterpreted over time as new evidence emerges regarding its pathogenicity or lack thereof. This raises ethical, legal, and financial issues as to whether there is a responsibility to recontact research participants to provide updates on reinterpretations of variants after the initial analysis.

While clinical recommendations on the responsibility to recontact research participants with such reinterpretations have begun to emerge, the Social Issues Committee decided to tackle this topic because there is a lack of guidance on the responsibility for researchers. We were fortunate to have collaborative partners on our Workgroup from clinical, research, and laboratory settings across various countries and jurisdictions. The statement reflects their synergistic efforts and the care these members took to carefully craft a comprehensive set of recommendations.

Howard: Perhaps the most obvious but most important concept in this position statement is the recognition that recontacting individuals to keep them abreast of new knowledge is a desirable and laudable goal. The problem is that we live in a world of limited resources, and the cost of achieving this goal can be onerous.

As Yvonne points out, there is only limited guidance on recontact in the clinical arena, and none in the research arena. ASHG and our partner organizations are fortunate to count among our memberships expert clinicians, researchers, laboratorians, educators, counselors, social scientists, bioethicists, lawyers, and patient advocates from around the world. We are uniquely suited to address this topic with the broadest possible representation and perspective.

There is a long history of thinking about clinical care and research as independent, non-overlapping contexts. But in recent years we’ve been recognizing and grappling with the reality that the lines between the two are blurry and sometimes not well-defined. In genetics, many of us serve in both roles concurrently, which can create real or perceived conflicts of interest. It is incumbent on all of us to work as hard as we can to be aware of these potential conflicts and respond appropriately. Having principled and evidence-based guidelines upon which to rely is an invaluable resource in helping us to evaluate these situations and determine the right course of action.

ASHG: What are the key differences between the research and clinical contexts?

Howard: While the intent of biomedical research is ultimately to improve or maintain health and avoid, treat, or cure disease, the proximal goal is to generate knowledge that forms the foundation of that ultimate benefit to society. Direct benefit to individual research participants is wonderful when it occurs, but is not the primary purpose of the research. Conversely, clinical care puts the benefit of the patient front and center as the primary goal.

Thus, in the clinical context, recontact can be argued as furthering the goal of maintaining information and informed consent, so that individual benefits can be maximized and individual harms minimized. But in the research context, the ethical desirability of recontact is not as strong, because the main goal is generation of new knowledge, not individual benefit. In fact, recontact in the research context can be argued as ethically undesirable if the recontact consumes so much resource that the research itself can’t be completed. In addition, while there are mechanisms available to seek at least partial financial compensation for clinical recontact on a case-by-case basis, there is no such funding mechanism in the research context.

Yvonne: The workgroup carefully considered differences between the research and clinical contexts to determine a reasonable set of floor/ceiling recommendations, balancing these imperatives across research and laboratory settings. We also developed a decision tree, which walks a researcher through whether and how to implement these recommendations within their particular research context.

ASHG: What factors affect the strength of the responsibility to recontact?

Yvonne: The workgroup considered a variety of factors that would affect the strength of the responsibility to recontact, and recommended that this responsibility is stronger when:

  • The research is active, ongoing, has funding, and participant contact details are up-to-date
  • The informed consent process set an expectation of potential contact or recontact
  • There is high certainty about the new interpretation of the genetic variant
  • The reinterpretation would be relevant to the condition being investigated

If the interpretation of a given variant is related to the condition under study or reasonably expected to affect participants’ medical management, the Workgroup recommended that there is a strong responsibility for researchers to attempt to recontact participants to offer updated results. If the reinterpretation is not expected to affect medical management, recontact is advised rather than strongly recommended.

Conversely, the statement recommends that there is no responsibility for researchers to hunt or scan the genomic literature for changes in variant interpretation, and that any responsibility to recontact should be limited to the duration of research funding. Additional recommendations address the practicalities of informed consent, involvement of institutional review boards, timeliness and protocol of recontact, and structuring of future research studies.

Howard: Clinical utility to the participant is prioritized higher than personal utility or benefit to family members. And issues of practicality have to be considered, too. Some of these judgments may be subject to bias, and we therefore encourage consultation with and input from IRBs, ethics boards, and clinical consultants.

ASHG: How might advances in IT address practical challenges in fulfilling this responsibility?

Yvonne: Advances in IT will likely reduce the opportunity costs of recontact and open up new avenues of keeping patients and research participants informed. Most electronic medical record systems and many clinical laboratories now offer portals through which patients might see their data, interact with clinical, laboratory, and support staff, and access educational material. As our IT resources and our databases continue to evolve, it is plausible that much of the effort of recontact could become automated. When a variant is reclassified, an automated notification could be sent to all patients and research participants known to harbor that variant, alerting them of the revised interpretation and prompting them to log into the portal to view the new information and associated material.

Howard:  As the volume of identified and re-interpreted variants continues to increase, IT solutions will be critical to handling these immensely large numbers at scale, at much lower cost, and more rapidly than doing so manually.

IT solutions can also reduce the risk of biased or uneven approaches to attempting recontact. Humans may consciously or subconsciously vary their method of communicating information, and sometimes make mistakes in adhering to informed consent, research protocols, and other policies governing the recontact process. An automated, algorithmic approach is still subject to human bias and error in creating and implementing the rules that drive the process, and is obviously not as personal as direct human communication, but is by definition consistent from case to case.

ASHG: What infrastructure would be needed to maximize the impact of such IT advances?

Yvonne: This future vision depends upon well-developed and interoperable databases, including both the interpretations of the variants and the lists of who has each variant. Potentially difficult questions about identity and privacy will need to be answered. There are also significant concerns about the “digital divide” and economic disparities; increasing reliance on IT solutions has the potential to create disparities among people who are unable to or choose not to utilize such resources. There will always be situations that require more nuance and explanation than an automated algorithm can achieve. But there is hope that IT enhancements can significantly lower the costs and barriers to recontacting research participants when it is considered desirable to do so.

Howard: Perhaps more challenging than creating the infrastructure of standardized and interoperable databases will be establishing societal and cultural expectations surrounding privacy, security and sharing of the data, and developing the necessary IT tools to collect, maintain, revise, and respect individuals’ preferences regarding such data sharing. With all of that in place, patient-facing portals built into IT systems and yet-to-be-developed apps can deliver timely and relevant information to consumers who choose to receive it, and pair that information with additional education and support modules to help them make the most of that information.

Yvonne Bombard, PhD, is an Assistant Professor at the University of Toronto Institute of Health Policy, Management and Evaluation; Director of the St. Michael’s Hospital Genomics Health Services Research Program; and Scientist at the St. Michael’s Li Ka Shing Knowledge Institute. Howard P. Levy, MD, PhD, is an Associate Professor in the Division of General Internal Medicine & McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. 

Inside AJHG: A Chat with Nancy Cox

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 Nancy Cox to discuss her paper “GRIK5 Genetically Regulated Expression Associated with Eye and Vascular Phenomes: Discovery through Iteration among Biobanks, Electronic Health Records, and Zebrafish.”

Nancy Cox, PhD (photo courtesy Dr. Cox)

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

Nancy: I presented some of the preliminary studies from this work at a work-in-progress meeting at Vanderbilt, and Ela Knapik, who directs the zebrafish core here, saw the presentation and asked the question at the end, “Why don’t you knock out GRIK5 in zebrafish?” And so we talked afterward and agreed to collaborate on this project. I expected it to take forever — I was totally unprepared for how rapid CRISPR can be. But it has been a fantastic collaboration and we are working together on several additional really fun projects now.

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

Nancy: Trying to understand how polygenic contributions to disease work is challenging because the effect sizes for any individual variant are quite small. This was a different kind of discovery because we had used a gene-based method and found associations to a pattern of phenotypes, not just a single diagnosis. I think that helped to us to focus the follow-up to the zebrafish studies more broadly and think about how we might test for a relationship between vascular development and eye disease.

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

Nancy: I hope that people will begin to think more seriously about using very large-scale phenome information from electronic health records as an adjunct to genetic studies, which we can afford to do in only smaller numbers of individuals. The biobank at Vanderbilt is big — 250,000 subjects, but there are many more (millions) with quality phenome information but no DNA. Finding ways to use both should stretch our ability to make and extend discoveries.

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

Nancy: One of my mentors used to remind me on a regular basis that there is no shortage of interesting things to do in science — things that are so interesting they are hard to resist. But only a subset of those things are also important with respect to bigger picture questions or implications for other parts of biology. You have to continually ask yourself whether what you are doing is both interesting and important to insure that you are able to continue, and be funded, to do research that you find irresistible.

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

Nancy: I really love the music scene in Nashville! It is amazingly diverse, and we take advantage of the opportunities to hear great music every chance we get.

Nancy Cox, PhD, is Director, Vanderbilt Genetics Institute; Professor of Medicine, Division of Genetic Medicine; Director, Division of Genetic Medicine; and Mary Phillips Edmonds Gray Professor of Genetics at Vanderbilt University. She was the  ASHG President in 2017

Inside AJHG: A Chat with Elizabeth Wright

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 Elizabeth Wright to discuss her paper ‘Practical and ethical considerations of using the results of personalized DNA ancestry tests with middle-school-aged learners’.

Elizabeth Wright, PhD
Elizabeth Wright (photo courtesy Dr. Wright)

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

Elizabeth: I could give you a long answer about being a former middle school science teacher and what drove me to get a PhD in Science Education, but simply put, I am committed to finding ways for each and every student to see themselves connected to science and each other, and supporting teachers in that work.

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

Elizabeth: I am equally thrilled and cautious about having adolescents use their own personal DNA to explore who they are genetically, genealogically/socioculturally, and intentionally. We are not all of one thing and none of another. We can use what we know about pieces of ourselves to imagine something new and amazing. We can reveal these pieces of ourselves to our families and friends and see how we are connected to each other and the grander tree of life.

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

Elizabeth: In the previous question I mentioned a bit about what thrills me. I am cautious because the privacy issues surrounding over-the-counter, direct-to-consumer DNA testing are monumental, and ever-shifting. It is both exciting and nerve-wrecking to ask, and watch, young scholars to embark on this intellectual journey. The engagement and electricity in the classroom when young scientists encounter themselves in new and unique ways keeps me going.

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

Elizabeth: I think the most important thing I would say is: you belong here. You belong in science. Your voice, your experiences, your viewpoint are all incredibly important. If you feel left out or unwelcome, create your own community and persevere because you are going to change things.

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

Elizabeth: I’m a Red Sox season ticket holder and I love the game of baseball. I’ve been to baseball games in 27 different MLB parks, and 3 AAA baseball parks. Also, I love Orangetheory Fitness! Base-Push-All Out, that’s good advice.

Elizabeth Wright, PhD, is a postdoctoral fellow in the Jablonski laboratory at Pennsylvania State University.

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. 

Inside AJHG: A Chat with Vijay Sankaran

Posted By: Sarah Ratzel, PhD, Science Editor, 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 Vijay Sankaran to discuss his paper, “The Genetic Landscape of Diamond-Blackfan Anemia.”

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

Vijay Sankaran, MD, PhD
Vijay Sankaran (photo courtesy Dr. Sankaran)

Vijay: When exome sequencing was starting to be done routinely around 2009, we reasoned that Diamond-Blackfan anemia would be an ideal disease to study using this approach. At the time, only a few ribosomal protein mutations had been described in this disease and we thought that such sequencing approaches could help us better define the pathogenesis of this disorder. We did identify some non-ribosomal protein mutations through focused efforts (e.g. GATA1), but we kept sequencing more individuals to more comprehensively define the genetic landscape of this blood disorder. This paper describes the comprehensive analysis of the full cohort of individuals we studied.

AJHG: What about this paper most excites you?

Vijay: There are three things that excite me most about this work. First, this paper is really the culmination of several years of incredibly hard work by a number of talented trainees in our group, as well as fabulous colleagues. It is great to see their work put together and presented so nicely. Second, I think this analysis can serve as a model for other systematic studies in cohorts of individuals with a range of rare diseases. It provides a framework for thinking about how to perform comprehensive analyses in rare disease cohorts, while also illustrating major challenges in trying to define genetic etiologies. Third, I think the work nicely outlines the future directions we hope to take to better define the genetic causes for the remaining ~20% of cases and understand the basis for the variable penetrance observed.

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

Vijay: We have examined a rather large cohort of ~470 individuals with a rare disease that occurs in ~1 in 200,000 live births. This cohort took many years to put together and required extensive international collaborations. Despite the considerable size of this cohort (for a rare disease), we still could not define the potential genetic etiology for a number of individuals in the cohort. Our burden analyses nicely show how we are sufficiently powered to detect mutations in the exome that explain > 5% of cases in the cohort. Given all of this, our findings emphasize the need for larger analyses of such rare diseases. This can only happen through collaboration. Different investigators need to be willing to come together to maximize our ability to identify additional genetic causes for rare diseases. While many in the human genetics community appreciate the importance of such efforts, I still find that many colleagues in my clinical field and others are hesitant to share data. As a physician, I realize that doing so is critical for all patients and individuals affected by rare diseases.

AJHGWhat advice do you have for trainees/young scientists?

Vijay: Probably the most useful advice I can offer is that any trainee should pursue problems and work in environment where they can most enjoy their work. I have been incredibly fortunate to work in environments, both as a trainee and faculty member, where I have been given the freedom to pursue problems I am passionate about. As a result, I have also tried to create an environment in the lab that can enable trainees to do the same, which I believe is very important.

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

Vijay: One of the things I enjoy outside of lab is exploring the fantastic restaurants in Boston and listening to jazz music (particularly when it is live).

Vijay Sankaran, MD, PhD, Assistant Professor of Pediatrics at Harvard Medical School and an Attending Physician in Hematology/Oncology at Boston Children’s Hospital and the Dana-Farber Cancer Institute. He has been an ASHG member since 2016.