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.”

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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.

Inside AJHG: A Chat with Jonathan Mill

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 Jonathan Mill to discuss his paper, “Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits.”

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The Mill lab (photo courtesy of Dr. Mill).

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

Jonathan: Our lab studies the genomic basis of complex human diseases, and we’re particularly interested in the mechanisms underpinning transcriptional regulation. The last decade has seen tremendous advances in understanding the role of common genetic variation in health and disease, but genome-wide association studies (GWAS) don’t always identify specific causal genes, and we know that the variants associated with disease are likely to influence gene expression rather than causing changes to the transcribed protein. We have been quantifying genetic and epigenetic variation in large numbers of samples and have been thinking about ways of integrating these datasets to fine-map GWAS regions.

This project built on our previous work using DNA methylation quantitative trait loci (mQTLs) to interpret the functional consequences of common genetic variation associated with neuropsychiatric disease and other human traits. We generated blood mQTL data in the Understanding Society UK Household Longitudinal Study (UKHLS) and used these to refine genetic association data from publicly available GWAS datasets in order to prioritize genes involved in complex traits and diseases. We also sought to identify pleiotropic relationships between DNA methylation and variable gene expression by using publicly available whole-blood gene expression QTL (eQTL) data.

AJHG: What about this paper most excites you? 

Jonathan: First, we have generated an extensive mQTL dataset, using the new Illumina EPIC DNA methylation array to identify over 12 million associations between genetic variants and DNA methylation sites, including a large number not identified by previous DNA methylation-profiling methods. We show that there are many instances of shared genetic signals on neighboring DNA methylation sites and that these associations are structured around both genes and CpG islands. We hope these will be a valuable resource for the genetics community, and our data can be downloaded from our website.

Second, we demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with human traits by using summary-data-based Mendelian randomization (SMR) to identify >1500 pleiotropic associations between complex traits and DNA methylation sites. Finally, we use these data to explore the relationship between DNAm and gene expression by using genetic instruments rather than correlations to infer associations between specific DNA methylation sites and genes.

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

Jonathan: Our results add to an increasing body of evidence showing that genetic influences on DNA methylation are widespread across the genome. We show that integrating these relationships with the results from GWAS of complex traits and genetic studies of gene expression can improve our understanding about the interplay between gene regulation and expression and facilitate the prioritization of candidate genes implicated in disease etiology.

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

Jonathan: Most importantly, pick a subject you are passionate about and make sure your science continues to be fun! The biggest and best-funded labs are not necessarily the best places to train; research is all about teamwork and collaboration, and to me, these are key attributes that trainees and young scientists should look for in selecting a place to study and learn. Don’t be afraid to be wrong, and you should never worry about questioning your supervisor or mentor; I have learned so much from the exceptional postdocs and students in my lab who generally know a lot more than I do! Finally, make sure you keep a good work-life balance; it’s important to switch off and realize there is more to life than grant funding and papers.

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

Jonathan: I live in a small fishing village on the Devon coast just outside Exeter in the UK. When I’m not trying to understand gene regulation in the brain, I spend a lot of time in my allotment attempting to grow enormous vegetables. I also cycle a lot, and last year rode to Paris from the UK along with Eilis Hannon (first author on this paper) to raise money for the amazing Alzheimer’s Society who fund our work into dementia.

Jonathan Mill, PhD, is a Professor of Epigenetics at the University of Exeter and Psychiatric Epigenetics at Kings College London. 

Inside AJHG: A Chat with Sek Kathiresan

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 2018 Curt Stern Award winner Sek Kathiresan (@skathire on Twitter) to discuss his paper ‘Genetic Association of Albuminuria with Cardiometabolic Disease and Blood Pressure’.

Bulfinch Studio; Sekar Kathiresan portrait
Sek Kathiresan, Massachusetts General Hospital/Broad Institute/Harvard Medical School (courtesy Dr. Kathiresan)

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

Sek: In observational studies, many biomarkers including the concentration of protein spilling into urine (albuminuria) are correlated with health outcomes. We wondered if the association of albuminuria with adverse health outcomes reflected a causal relationship or mere correlation. Knowing this is important to determine if decreasing urinary albumin excretion should per se be a target for therapeutic intervention.

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

Sek: In addressing the question above, we identified a bi-directional relationship – genetic predisposition to albuminuria leads to higher blood pressure and genetic predisposition to higher blood pressure leads to more albuminuria. We suspect this reflects a feed-forward loop.

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

Sek: Mendelian randomization is a useful genetics approach for causal inference. The availability of biomarkers, clinical outcomes, and genetic data in a single large study – UK Biobank – is facilitating systematic Mendelian randomization analyses for a range of biomarkers.

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

Sek: Pick an important problem to study – one that not only you care about but also the rest of the world. Figure out the skills and resources you need to address the problem. Then, go out and get the training and resources to attack the problem. Stay focused on the problem and ask yourself, each day, if you are working on the most impactful thing you could be doing.

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

Sek: Life outside the lab is consumed by three children – ages 15, 13, 10. Raising them to be happy, loving, and engaged with the world is a joy.

Sekar Kathiresan, MD, is the Director of the Center for Genomic Medicine at Massachusetts General Hospital (MGH), Ofer and Shelly Nemirovsky MGH Research Scholar, Director of the Cardiovascular Disease Initiative at the Broad institute, and a Professor of Medicine at Harvard Medical School. He has been a member of ASHG since 2004.

Inside AJHG: A Chat with David Kingsley

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 David Kingsley to discuss his paper ‘Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia’.

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Kingsley lab group at Stanford, with co-lead authors Janet Song (standing at left of center), and Craig Lowe (seated at far right). (courtesy Dr. Kingsley)

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

David: We’ve been working on the genomic basis of evolutionary change for many years. We previously found that the deletion of key regulatory sequences can underlie classic evolutionary traits in both stickleback fish and humans. [Co-authors] Craig Lowe and Janet Song decided to look for the reciprocal type of molecular changes: insertion or gain of new regulatory sequences that might contribute to human-specific traits.

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

David: We found a particularly dramatic human insertion in an important calcium channel gene. Where most primates have a single, 30 base pair, non-coding sequence, humans have expanded the 30-mer into a huge tandem array that can be up to 30,000 base pairs long. We found that the expanded human sequence shows enhancer activity in neural cells, suggesting it contributes to increased expression of this calcium channel gene in humans compared to other primates.

We were particularly interested to see that the tandem array is located right between SNP markers that been repeatedly associated with risk of schizophrenia and bipolar disorder in many human genome-wide association studies. We found that different subtypes of the tandem arrays are associated with risk or protective genotypes at the locus, and that the risk-associated arrays have less enhancer activity than other subtypes. We think that this novel structural feature may thus contribute not only to evolutionary differences between humans and other primates, but also to common risk of psychiatric disease within human populations.

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

David: These large tandem arrays don’t appear in the reference human genome, likely because they are unstable when propagated in conventional bacterial vectors, and are impossible to assemble correctly from short sequence reads alone. Conventional SNP genotyping arrays don’t score the repeats, and exome sequencing studies miss the region entirely because the arrays are located in a large intron of a calcium channel gene.

The human-specific arrays are thus a great example of a previously hidden genome feature, that may nonetheless provide a causal basis for functional changes in the gene. The broader lesson is that the human reference genome is still a work in progress, and that lots of important biology may be embedded in the parts of our genomes that are difficult to assemble and still poorly understood.

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

David: Treasure your exceptions, and try to keep an open mind when studying any research problem. The surprises and the things that don’t initially make sense are interesting puzzles that often lead to new discoveries. But you have to embrace results that don’t fit your preconceptions, and then be willing to consider a whole range of new possibilities.

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

David: I love to explore the sky with telescopes at night and have made trips all over the world to enjoy dark skies in both the Northern and Southern hemisphere. Early astronomers slowly groped their way to a better understanding of the larger universe by cataloging individual stars, planets, and nebula with relatively simple equipment. Particular objects can look like stunning “eye-candy” or faint and subtle “mind-candy” in the eyepiece. And as you look at more and more objects, you can gradually build up a larger picture of our place in the solar system, the Milky Way galaxy, and the overall universe.

That actually has lots of parallels to biology. In genetics, we often start with an interest in particular traits or genes. But detailed studies of particular genes can grow into larger studies of chromosomes, whole genomes, variation between individuals, and the molecular basis of evolutionary differences between species. Our glimpses of the whole shebang are still very incomplete. But spend enough fun time looking at stars and genomes, and you end up with a much richer view of humans and where we came from.

David Kingsley, PhD, is an HHMI Investigator and Professor of Developmental Biology at Stanford University. He has been a member of ASHG since 2018.