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.

Inside AJHG: A Chat with Levi Teitz and David Page

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

Each month, the editors of The American Journal of Human Genetics interview the author(s) of a recently published paper. This month, we check in with Levi Teitz and David Page to discuss their paper “Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages.”

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Levi Teitz, PhD, and David Page, MD (photo courtesy Dr. Page)

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

Levi: Our lab has a long history of studying the Y chromosome, but the ampliconic regions were always a bit of a mystery because of how difficult they are to study, due to their complex architecture and high sequence identity between copies. With the advent of high-throughput sequencing technologies and large, publicly available datasets, it seemed like a good time to revisit questions about amplicon variation and evolution with those new tools at our disposal.

David: The Y chromosome has been an enigma to geneticists for the last century, largely because it doesn’t play by the usual rules of being transmitted from both mother and father, and recombining with a homolog along its length, in meiosis. Despite being a sex chromosome, the Y chromosome is transmitted clonally – asexually – from father to son to son; it stands apart from all other nuclear chromosomes in this respect. This has led to all manner of unfounded insults regarding the Y chromosome’s character, medical relevance, and future prospects. My colleagues and I have spent decades defending the honor of the chromosome in the face of these insults.

AJHG: What about this paper most excites you? 

Levi: The new evolutionary questions it raises. The amplicons are extraordinarily divergent between species – so much so that it’s essentially impossible to reconstruct the steps that evolution took to get from the ancestral mammalian or primate amplicons to modern-day Y chromosomes. When we began this project, we expected that we could observe these evolutionary steps by looking within only humans. Instead, we found that the amplicon variation within human populations is an evolutionary dead end, and that the ancestral amplicon structure has been preserved for hundreds of thousands of years! This is a bit of a paradox: why is amplicon structure maintained in humans but so divergent between species? This is a hard problem, but solving it should provide incredible insight into amplicon evolution and function.

David: Learning something unanticipated about a subject you love is exciting. Massive palindromes and amplicons carrying spermatogenesis genes were known to dot the genomic landscape of the human Y chromosome, and they are frequently subject to deletion or rearrangement through non-allelic homologous recombination. The excitement for me here arises from both a computational advance and a biological insight. First, graduate student Levi Teitz, with guidance from Helen Skaletsky, mastered the computational challenge of robustly and accurately discerning the copy numbers of many different Y amplicons from whole-genome shotgun sequence data. Second, Levi applied these computational tools to the 1000 Genomes males, thereby characterizing Y amplicon copy number variation (CNV) around the globe. While the existence of such Y-amplicon CNV was unsurprising, the predominance of consistent patterns of Y-amplicon copy numbers around the globe (actually, across Y chromosome haplotypes) surprised me, and indicated that natural selection had optimized and consistently favored specific copy numbers for a host of Y amplicons. Natural selection, whose ability to maintain genes on the clonally transmitted Y had often been impugned, has evidently been effective at policing Y-amplicon copy numbers. Natural selection is alive and well on the human Y chromosome, even the parts where we might least expect it!

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

Levi: Beyond improving our understanding of the Y chromosome, our work highlights the fact that the genome can change in unexpected ways. Much genomic research today focuses exclusively on the parts of the genome that are easiest to study: single-copy coding sequence. This paper demonstrates that not only does the rest of the genome have profound evolutionary and phenotypic effects, it also varies in ways that are exquisitely dependent on its repetitive structure. In fact, it would be impossible to understand the phenotypic and evolutionary stories without first understanding the underlying complex structure of these genomic regions. There are still parts of the human genome where complex structures are unresolved; who knows what we will discover when those parts are properly sequenced?

David: Genetically inclined students of human biology, medicine, and evolution tend to focus their efforts on the parts of the genome that are most readily analyzed – the civilized, single-copy parts that approach most closely our Mendelian expectations. But there is so much to be learned in the relatively understudied and untamed parts of the genome where palindromes, amplicons, and segmental duplications bend the rules, demanding special attention to technical and analytic matters but offering rich rewards to the curious and persistent.

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

Levi: I’m a trainee and a young scientist myself, so I don’t have much career experience to draw upon, but my advice would be to never forget the human factor when choosing what to work on and who to work with. If you are surrounded by good people and you enjoy working with them, your science will be better for it.

David: Work with people whom you like, respect, and admire, on questions that you personally find to be compelling. Nothing is more satisfying than finding value and meaning where others think not to look.

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

Levi: I’m an amateur baker and have recently started accumulating kitchen gadgets, including a doughnut filling injector, a rotating cake stand, and a frying pan just for blintzes.

David: I love to explore the outdoors, and especially mountains and lakes, with family and friends, in all seasons. I would point out that some of our oldest and most acclaimed National Parks – Yellowstone and Yosemite – begin with the letter Y.

A longtime member of ASHG, David Page, MD, is Director of the Whitehead Institute, Professor of Biology at the Massachusetts Institute of Technology and Howard Hughes Medical Institute Investigator.

Inside AJHG: A Chat with Amy O’Connell

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 Amy O’Connell, first author of ‘Neonatal-Onset Chronic Diarrhea Caused by Homozygous Nonsense WNT2B Mutations.’

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Amy O’Connell (front row, left) and her lab. (courtesy Dr. O’Connell)

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

Amy: My work in Dr. Agrawal’s genetics lab focuses on confirming the functional consequences of novel mutations identified by whole exome sequencing. We identified individuals from two families who harbor homozygous nonsense WNT2B mutations and display similar severe congenital diarrhea phenotypes, suggesting this is an important gene for gut physiology. It seemed important to try and get to the bottom of it, especially since what we observed differed from what mouse studies concluded, where knocking out Wnt2b revealed no gut phenotype.

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

Amy: I am an immunologist by training, so I am excited about the potential connections between inflammatory triggers and Wnt2b. Our paper begins to explore this relationship by showing that TLR4 expression is altered in the absence of Wnt2b, but I think there is more to this story and I’m continuing to work on it.

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

Amy: To me, this project underscores the importance of personalized medicine and genomics approaches. Wnts are a very important family of molecules, and WNT2B is highly expressed in the intestine, but until now it has been somewhat neglected, viewed as being non-essential, and thought to be fully redundant with other Wnt pathway molecules. That patients with loss of Wnt2b are so severely affected clearly suggests otherwise. Taking what we’ve learned from three patients will have implications for our entire understanding of the regulation of intestinal stem cells, a good reminder that translational science works in both directions.

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

Amy: First of all, be wary of free advice. It’s not usually about the advisee. Given that, one of the best lessons I’ve learned is that it is okay to change your plans if you find that what excites you in science is not what you started off trying to do or become.

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

Amy: I have a 2-year old and two miniature schnauzers, so I get to do a lot of playing when I’m not at work. Yesterday I got to be a ballerina, ride to the “pizza store” on a “horse”, and build a doggy castle. It’s terrific exercise for the imagination!

Amy O’Connell, MD, PhD is a Neonatologist at Boston Children’s Hospital, and an instructor at Harvard Medical School. She has been an ASHG member since 2018. You can find her on Twitter at @PostCallScience.

Inside AJHG: A Chat with Garry Cutting

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

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Garry R. Cutting, MD (courtesy Dr. Cutting)

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 Garry Cutting, to discuss ‘Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity.’

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

Garry: This project is part of an ongoing effort to interpret the molecular consequences of all variants in the CFTR gene. The variants selected for this study are associated with a wide-range of disease severity, allowing us to determine the utility of functional assays for variants that associate with moderate to mild forms of disease.

AJHG: What about this paper project most excites you?

Garry: We were surprised to find that a number of the putative disease-causing missense variants had minimal effect on protein function and that predictive algorithms have difficulty interpreting these “minimal effect” variants. Conversely, it was reassuring to find that incorporation of functional data improves annotation using expert and ACMG/AMP criteria.

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

Garry: Missense variants are challenging to interpret and many are labeled as variants of unknown significance. Our study indicates that classifying missense variants, especially those associated with intermediate severity of disease, will require functional testing in the appropriate context. Our work also shows that current predictive algorithms should be used with caution as they tend to overcall missense variants as deleterious.

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

Garry: The explosion of DNA variant information provides a wonderful opportunity to investigate their effect upon RNA transcription, RNA splicing, protein stability, and protein function. Individuals who become facile with these techniques will be highly valued as we move from DNA sequencing to variant annotation and elucidation of disease mechanism.

AJHG: Tell us something about your life outside the lab.

Garry: I really enjoy working with my hands to repair something broken or build something new. Unlike the long time frames that we experience in science, fixing something can produce results in a much shorter time frame. Sometimes things go wrong, but you always seem to learn something new when you undertake projects that are out of your established area of expertise. Consequently, I fully agree that circuit breakers and water supply values should be turned off before undertaking home projects.

Garry Cutting, MD, is an Aetna/U.S. Healthcare Professor of Medical Genetics at John Hopkins. He has been a member of ASHG since 1997.