Inside AJHG: A Chat with Tychele Turner

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 Tychele Turner to discuss her paper “Sex-based analysis of de novo variants in neurodevelopmental disorders.”

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Tychele Turner, PhD (courtesy Dr. Turner)

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

Tychele: Since my early graduate studies, I have been interested in understanding the etiology of autism, and in particular, I have been intrigued by the observed sex bias in autism. It has been well established that there are more males (~80% of individuals with autism) than females with autism. Over the past ten years, evidence has been accumulating for a “female-protective effect” whereby females with autism more often than males with autism have variants of interest that are rare variants of large effect.

During my postdoctoral work with Dr. Evan Eichler, I received an Autism Science Foundation fellowship to further explore this effect. While many groups had focused on a pooled male and female approach, we chose to look at it in reverse, in the thousands of sequenced parent-child trios with neurodevelopmental disorders that have been published to date and are now in our de novo variant database. The greatest reason we began to work on this project is because sex bias is a common feature of many disorders and we want to help to determine why this occurs so as to inform future studies into the genetic architecture of human disease.

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

Tychele:  One of my favorite aspects of the paper is that we utilized a discovery/replication cohort approach to identify genes with significant excess in neurodevelopmental disorders. While this has been a common approach in genome-wide association studies it has been uncommon in studies of de novo variants. This was very helpful to us in identifying genes of high confidence. Related to this, as a person who enjoys thinking about numbers, I was excited that we were able to study so many sequenced parent-child trios from the literature (~9,000 families and ~27,000 individuals) as a discovery cohort.

This highlights a real benefit of data sharing in our genetics community. In addition, we were beyond grateful to GeneDx for providing us with replication data (~19,000 families and ~57,000 individuals) for the genes we initially identified as significant in our discovery cohort.

Since we were determined to find out if there were differences in gene discovery in males and females and the possible genes that could be sex-biased, we found it was critical to have this two-stage (discovery and replication cohort) analysis. Probably the most striking result in the paper, to me, was that our gene discovery in ~3,000 females was similar to our discovery in ~6,000 males and that the X chromosome genes reaching significance were only found in females.

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

Tychele: There are a few implications of this study for the human genetics community. It provides lessons learned about the sex bias in human disease and also emphasizes why the NIH has generated policy around the inclusion of sex as a biological variable. While our study focuses on neurodevelopmental disorders, we think the findings provide insight into other phenotypes as well. Our study highlights the importance of studying the rarer class (in autism it is females) to identify rare variants of large effect.

First, we find that study of the rarer class enables greater gene discovery and in studies where funding or sample sizes are limiting, it may be beneficial to prioritize the rarer class individuals. Second, we show that there are a few genes that are significant in only one sex and those genes primarily reside on the X chromosome. Third, we find that the genes we discovered converged to one network involved in chromatin biology.

When you look at the gene set, surviving replication, you realize that they could have almost all been identified by only focusing on females. This suggests that useful biological insights can be derived from a study of the rarer class. There is much work that remains in understanding how sex bias occurs in disease, but we think this study provides one way to think about this issue.

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

Tychele: Remember that all scientists struggle from time to time, and that even when you think you know how someone’s career has gone, you often do not know the struggles they have faced. Find a good network of mentors both inside and outside of your department. Most importantly, if there is something you are passionate about scientifically, pursue it. There’s no limit to what you can do, and you never know when or where the next great scientific breakthrough will be!

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

Tychele: One of my favorite things to do outside the lab is to read books from the library. It is fun to take some time to “go on adventures” through literature, and you don’t even have to leave “home”. I also enjoy spending time with my family in Michigan.

Tychele Turner, PhD, is an Assistant Professor in the Department of Genetics at Washington University School of Medicine. She has been a member of ASHG since 2013.

Inside AJHG: A Chat with Stephen Kingsmore

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Genomic Medicine at the Population Level: Your Questions Answered 

Posted By: Alissa Ortman, Associate Director, ASHG Digital Programs

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In September, ASHG and The American Journal of Human Genetics (AJHG) hosted a webinar to discuss large-scale, national studies that have been launched to collect phenotypic and genomic data on large populations. They also discussed how the data from that work should be shared around the world. If you missed it, you canwatch the recording or read this blog that summarizes the event.

This topic generated numerous audience questions, not all of which were able to be answered. Fortunately, the All of Us Research Program communications team was able to answer some of them after the webinar.

Attendee Question: When will All of Us start recruiting from smaller cities across the country? Example: I live in Tallahassee, FL. and am interested in joining.

All of Us: Recruitment is now open nationwide at https://www.joinallofus.org/en. Meanwhile, the program is gradually expanding its reach to collect physical measurements and samples from more participants in different areas across the country and will invite more participants to schedule a visit in time.

Attendee QuestionHas any uninterpreted genomic data (not results) been returned yet to any All of Us participants? If so, how much? If not, when is that anticipated to begin?

All of Us: No, not yet. We have not yet begun genetic analyses, either genotyping or whole genome sequencing. Participants will be able to request access to their raw genetic data in time. Our plans and timeline for the return of information are currently under development and will be subject to review by our Institutional Review Board.

Attendee Question: Do you anticipate expanding the data All of Us will return to participants—specifically, in line with recent FDA guidance around pharmacogenomics?

All of Us: Over time, the program plans to return various types of information. Genetic results will likely include information about ancestry and traits, pharmacogenomics, and findings tied to 59 genes associated with risk of specific diseases for which there are established medical guidelines for treatment or prevention. The specific details about what the program will return and when are under discussion and will be reviewed by our Institutional Review Board.

Attendee QuestionIt is great that genomic data is being used in novel ways for diagnosis of rare, even new diseases. However, what efforts are being made to make novel treatment options available to the individual patients?

All of Us: The mission of the All of Us Research Program is to accelerate health research and medical breakthroughs, enabling individualized prevention, treatment, and care for all of us. We hope novel treatments will be discovered based on the data available through the program and understand that these options then need to get to the folks who need them most. In August 2019, All of Us awarded $4.6 million in initial funding to Color, a health technology company, to establish the program’s nationwide genetic counseling resource. Through this funding, Color’s network of genetic counselors will help participants understand what the genomic testing results mean for their health and their families.

Attendee QuestionWill any training sessions be available for how to use the cloud data of All of Us Project?  

All of Us: Once the Research Hub is made available to all researchers (anticipated for 2020), All of Us will announce plans for upcoming training sessions on how to use the platform.

Thank you to our webinar sponsor, Illumina, whose sequencing and array technologies are fueling advancements in life science research, translational and consumer genomics, and molecular diagnostics. For more information, please visit illumina.com or contact their population genomics team at populationgenomics@illumina.com.

 

Inside AJHG: A Chat with Heidi Rehm

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

Each month, the editors of The American Journal of Human Genetics interview an author of a recently published paper. This month, we check in with Heidi Rehm to discuss her paper, “Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network.”

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Heidi Rehm (photo courtesy of Dr. Rehm).

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

Dr. Rehm: We (Broad Institute and Partners Laboratory for Molecular Medicine) as well as Baylor College of Medicine were funded to provide genomic sequencing and interpretation support for Phase 3 of the eMERGE program.

AJHG: What about this paper most excites you? 

Dr. Rehm: Understanding our genomes will require large scale data sharing, harmonization and analysis across many research and health systems. This paper represents key steps in harmonizing and scaling genomics in the context of real-life healthcare systems.

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

Dr. Rehm: We hope that our work sets the groundwork for more clinical laboratories standardizing the intake of genetic testing orders and output of clinical reports for consumption by electronic health systems which we hope will be embraced as we all try to best integrate genomics into the practice of medicine.

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

Dr. Rehm: Clinical genomics is an exciting field with tremendous growth happening. Come join us!

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

Dr. Rehm: I have two teenagers, so life outside the lab right now is mostly following them around to sports events and college visits. Most weeks I get to play at least one game of ultimate Frisbee in the evening when I’m not traveling. And of course a favorite family activity is watching John Oliver as the only way to survive the current political climate in the U.S.!

Heidi L. Rehm, PhD, FACMG, is Chief Genomics Officer in the Department of Medicine for Massachusetts General Hospital, and Medical Director of the Broad Institute Clinical Research Sequencing Platform. She has been an ASHG member for over 20 years. 

Advancing Research and Privacy: Achievements, Challenges, and Core Principles

Posted By: Les Biesecker, ASHG President

Today, ASHG issued a new Perspective in The American Journal of Human Genetics (AJHG) entitled, “Advancing Research and Privacy: Achievements, Challenges, and Core Principles”. In the Perspective, the ASHG Executive Committee emphasizes the tremendous value of data sharing to advance genetics and genomics research, and the ongoing and unwavering commitment of members of our field to protecting the privacy of research participants. It also articulates core privacy principles that the Society believes should apply to all human genetics and genomics research.

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ASHG’s newest Perspective appeared today in AJHG.

This Perspective is timely given the current global debate on data privacy and the many countries establishing new broad citizen privacy protections, the European General Data Protection Regulation (GDPR) being a notable example. Within these discussions, it is important to emphasize that genetic privacy in publicly funded research is well-regulated and researchers are careful custodians of research participants’ genetic information. It behooves us, both in the U.S. and in other countries, to monitor proposed policies to ensure they balance important consent and privacy protections with the vital health and medical benefits that can come from genetics and genomics research.

The new Perspective notes that, within the U.S., many genetic privacy laws apply only to federally funded research. Increasingly, researchers in our community—both in academia and industry—recognize the potentially useful role of data generated by entities that are not federally funded to pursue shared health goals. We believe these data should be secured using standards equivalent to those for federally-funded entities.

Thus, to enable these data to be collected ethically and benefit all consumers through future improved health and medicine, ASHG believes the core principles described in the Perspective should apply to all genomic research, irrespective of the funding source. The Society was encouraged by recent efforts by a collective group of private companies to develop core privacy principles, and ASHG is eager to foster further dialogue to advance research data privacy policies that advance the shared values of the research community and adhere to informed consent and privacy best practices.

This is the third in the Perspectives series. We look forward to continuing the dialogue on important policy issues at the Annual Meeting, through AJHG, and other venues.

Leslie G. Biesecker, MD, is 2019 President of ASHG. 

Inside AJHG: A Chat with Natalie Telis

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

Each month, the editors of The American Journal of Human Genetics interview an author of a recently published paper. This month, we check in with Natalie Telis to discuss her paper, “Public Discussion Affects Question Asking at Academic Conferences.”

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Natalie Telis, PhD (courtesy Dr. Telis)

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

Dr. Telis: At one of the first conferences I went to, I realized after a day that I was the only woman who’d asked a question. And I remember thinking, “That’s weird, right?”

But then I second guessed it. I said, well, there were maybe 10 questions today. If 1 in 10 people in the audience are women, that participation is actually representative. What information would I need about this conference to discover whether this is representative participation?

Part of being a computational biologist is that you have a skill set that applies to computational problems — not just biology problems. So I started drawing on that skill set to try to learn more about this problem, and things kind of evolved from there!

AJHG: What about this paper most excites you? 

Dr. Telis: I am really excited about the opportunity to explicitly set goals, and then to use these techniques to measure whether our interventions get there. If our goal is to increase proportionate participation, it’s easy to say: “Well, having 50% of people in the room be women will help us get there.” But does that actually come to bear? We can test that question now (and learn that it doesn’t work that way). That can help us build powerful interventions to change culture and reshape access for underrepresented groups in science more broadly.

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

Dr. Telis: The human genetics community is still grappling with questions about representation and participation across the board, not only for women scientists but across intersectional categories. I do hope that raising these questions in a scientific way has contributed to more discussion around inclusion and representation. We definitely still need to ask, what do we want our community to look like, and how do we get there?

This work provides a precedent and hopefully a computational framework for testing that. And that’s a critical infrastructure we need to develop as we attempt to create change.

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

Dr. Telis: Any question is an opportunity to hone your scientific skills. Asking questions about questions didn’t seem like human genetics to me, but the computational techniques I’ve learned were ultimately what I used to solve that problem. Being a scientist is an opportunity to live and work on the edge of what is known — bring that curiosity in the face of uncertainty with you wherever you go!

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

Dr. Telis: I don’t really believe in New Year’s resolutions or setting a goalpost (especially because I always miss them), so instead this year I started trying to numerically track things I want myself to do more of. So I’m surprised and shocked and very proud to say I’ve read 27 books so far this year! Making space for all that fiction reading, not just paper reading, has made me more refreshed, inspired, and creative in my research.

Natalie Telis, PhD, is a Staff Scientist at AncestryDNA. She has been an ASHG member since 2014.

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.”

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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.