Genetics and Genomics Digital Forum Nov 2022
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A Two-Day Interactive Event Brought to You by ASHG hosted on November 15 & 16, 2022.
Please review the available agenda.
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This interactive workshop is intended for anyone interested in learning how to impute genotypes and to use the imputed genotypes, highlighting recent reference panels, including the multi-ancestry panel from the TOPMed program and a specialized HLA panel.
Genotype imputation is a key component of modern genetic association studies. The Michigan Imputation Server has thus far helped > 8,500 researchers from around the world to impute > 80M human genomes. This interactive workshop is intended for anyone interested in learning how to impute genotypes and to use the imputed genotypes, highlighting recent reference panels, including the multi-ancestry panel from the TOPMed program and a specialized HLA panel.
A brief overview of imputation and the server will be followed by demonstrations and exercises, including:
1) quality control and preparation of genetic data for use on the MIS with a special focus on diverse ancestries, chromosome X, and the HLA region;
2) tracking runs and use of the application program interface for larger jobs;
3) downloading data from the MIS and preparing data for genetic analysis;
4) performing a GWAS using imputed data and interpreting results, taking into account imputation quality;
5) using the additional features, such as the polygenic risk score calculation.
We encourage participants to ask specific questions about their own projects. Workshop materials, including slides and example data sets, will be made available before the workshop and will remain online at the MIS website. We expect that this workshop will enable participants to generate high-quality imputed data sets and to effectively analyze them.
Christian Fuchsberger
Eurac Research
Sebastian Schönherr
Medical University of Innsbruck
Xueling Sim
National University of Singapore
Lukas Forer
Medical University of Innsbruck
Saori Sakaue
Broad Institute
Albert Smith
University of Michigan
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Contains 1 Component(s) Recorded On: 11/15/2022
This session will feature 3 plenary talks presented at ASHG 2022 plus live Q&A and panel discussion for each
This session will feature 3 plenary talks presented at ASHG 2022. After each 15-minute talk there will be a 20-minute discussion session with additional panelists invited by the speaker, which will include Q&A from the audience.
Moderator: Kiran Musunuru, MD, PhD, MPH, ML
Speakers:
- Hardip Patel, PhD: Australia's National Centre for Indigenous Genomics enabling the inclusion of First Nations peoples in
genomics
- Panelists: Alex Brown, Bastien Llamas
- Rebecca Torene, PhD: Systematic analysis of nonsense-mediated decay escaping protein-truncating variants in
97,728 clinical exomes identifies new Mendelian disease genes
- Panelists: Scott Myers, Kevin Mitchell, Francisca Millan
- Lingyan Chen, PhD: Novel therapeutic target discovery using circulating proteins in up to 42,000 UK Biobank participants
through systematic Mendelian randomization and genetic colocalization
- Panelists: Joanna Howson, Cyrielle Maroteau, Lina Cai
Hardip Patel, PhD
Bioinformatics Lead, National Centre for Indigenous Genomics
The Australian National University
Dr. Hardip Patel is a mid-career bioinformatics and genomics researcher with expertise in large scale genomics and molecular biology research. As the Bioinformatics Lead for the National Centre for Indigenous Genomics (NCIG) and a member of National Indigenous Genomics Network, he is responsible for implementing genomics data infrastructure & analytical platforms to enable precision medicine. His research focuses on developing and using innovative computational biology and bioinformatics techniques to assemble genomes and detect variations using population-scale genomic data. He has co-authored 50 research publications (2500+ citations; 22 h-index).
Rebecca Torene, PhD
Associate Director of Genomics Research
GeneDx-Sema4
Dr. Rebecca Iskow Torene is Associate Director of Genomics Research at GeneDx-Sema4, a diagnostics company specializing in rare diseases. Her research focuses on improving genetics-based diagnostics through innovative bioinformatics and data science strategies. Dr. Torene received her PhD in genetics from Emory University and completed both her postdoctoral research and MMSc in biomedical informatics from the Harvard Medical School. She currently resides in the Washington, DC area.
Lingyan Chen, PhD
Senior Research Scientist at Genetics Centre of Excellence
Novo Nordisk Research Centre Oxford
Dr. Lingyan Chen is a Senior Research Scientist at Human Genetics Centre of Excellence at Novo Nordisk Research Centre Oxford (NNRCO). She obtained her PhD degree from King’s College London and did her PostDoc research in University of Cambridge where she obtained strong skills in Statistical Data Analysis, Population Genetics and Functional Genetics of complex diseases and published high impact research papers. Her primary research interest is to investigate potential causal molecules (i.e. transcriptome, proteome, and metabolome) for CMDs using genomics and other-comics data applying statistical genetic methodologies, such as Mendelian randomization (MR), to inform future therapeutic targets.
- Hardip Patel, PhD: Australia's National Centre for Indigenous Genomics enabling the inclusion of First Nations peoples in
genomics
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Twelve new 5-minute poster talks, not presented at ASHG 2022, including Q&A time for each.
Join this session to see 12 live poster talks, featuring all new content that was not presented at ASHG 2022. Each rapid-fire poster talk will be 5 minutes, followed by a brief Q&A with the presenter.
Moderator: Andrew Marderstein, PhD
Speakers:
- Whole Exome Sequencing revealed spectrum of mutations associated with different myopathy in clinically suspected DMD patients of Bangladesh, presented by Tamannyat Binte Eshaque, M.Sc. Contact this speaker
- ANO7 alters prostate cell mitochondrial gene expression and metabolism, presented by Nasrin Sultana, MS Contact this speaker
- Polygenic scoring and causal inference of posttraumatic stress disorder using electronic health records highlights association with cardiovascular and respiratory traits, presented by Gita Pathak, PhD Contact this speaker
- Multiomic association studies and finemapping prioritises WDR6 and immune pathways to be associated with anorexia nervosa, presented by Danielle Adams, BS/BA Contact this speaker
- The utility of whole exome sequencing in atypical cases of heterogeneous neurological disorders, presented by Zafar Ali, PhD
- A recessive variant in TFAM causes mtDNA depletion associated with primary ovarian insufficiency, seizures, intellectual disability and hearing loss, presented by Farid Ullah, PhD
- Identification of Hypomorphic SEL1L-HRD1 ER-associated Degradation Variants in Infants, presented by Huilun (Helen) Wang, PhD Contact this speaker
- Comprehensive characterization of genetic influences on plasma metabolome in a pediatric cohort, presented by Sek Won Kong, MD Contact this speaker
- 300 Billion Associations - Genetic architecture of 2,071 phenotypes in 658,582 individuals of diverse ancestry in the VA Million Veteran Program, presented by Anurag Verma, PhD Contact this speaker
- CRISPR-Cas9 depletion of high expression genes in human fibroblast samples increases the diagnostic potential for rare disease, presented by Rosario Corona, PhD Contact this speaker
- Deep convolutional and conditional neural networks for large-scale genomic data generation, presented by Burak Yelman, PhD Contact this speaker
- Fundamental limitations on the transferability of polygenic risk scores across human populations, presented by Kaiqian Zhang, MS
Speakers:
- Tamannyat Binte Eshaque, MS
- Nasrin Sultana, MS
- Gita Pathak, PhD
- Danielle Adams, BS/BA
- Zafar Ali, PhD
- Farid Ullah, PhD
- Huilun Wang, PhD
- Sek Won Kong, MD
- Anurag Verma, PhD
- Rosario Corona, PhD
- Burak Yelmen, PhD
- Kaiqian Zhang, MS
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The workshop will provide an interactive, hands-on experience for participants and familiarize the audience with the latest bioinformatics tools that facilitate automation of genetic annotation and pharmacogenomics (PGx) annotation for large-scale, electronic health record-linked health care systems.
Digitalization of patient medical charts in the form of electronic health record (EHR) promotes precision medicine, which promises to be inclusive of a broad view of a person’s care. Disease genetics and pharmacogenomics (PGx) contributes to the success of precision medicine by providing genetic insights from preemptive care and disease diagnosis to drug prescribing recommendation. However, integrating genomics with EHR-linked health care systems is challenging. The ever increasing scale of EHR-linked health care systems ensues an increasing need for automated, computational annotation of genetic information to support fast-paced clinical decision making. This workshop will introduce several bioinformatics tools that facilitate automatic, computable annotation of genetic information. Computable representation of genetic variants is one bottleneck for accurate genetic curation and automatic annotation in analyses following clinical genetic tests.
The first part of the workshop will focus on the Variation Representation Specification (VRS, pronounced “verse”), a recently published standard of the Global Alliance for Genomics and Health for the computable representation of biomolecular variation. VRS allows precise and federatable identification of genetic variants for downstream disease annotations and PGx annotations in EHR-linked health care systems. The associated VRSATILE (“versatile”) framework provides additional tools for representation of variation in computable genomic knowledge exchange. Exemplary applications of VRSATILE include knowledge and evidence retrieval across databases (e.g., functional and clinical databases) and computable representation of PGx variants. The second part of the workshop focuses on automating PGx annotations using PharmCAT (Pharmacogenomics Clinical Annotation Tool). PharmCAT is able to digest genetic information from VCFs, infer PGx named alleles and phenotypes, and generate detailed reports for clinical decision support. The capability of PharmCAT to automate PGx annotation makes it possible to translate clinical genetic test results to clinical decisions and actions at the scale of EHR-linked, large-scale health care systems. The workshop will provide an interactive, hands-on experience for participants and familiarize the audience with the latest bioinformatics tools that facilitate automation of genetic annotation and PGx annotation for large-scale, EHR-linked health care systems.
Michelle Whirl-Carrillo
Dr. Whirl-Carrillo is Co-Principal Investigator and Director of the Pharmacogenomics Knowledge Base (PharmGKB), Co-Director of Informatics for the Clinical Pharmacogenetics Implementation Consortium (CPIC) and Co-Investigator of the Pharmacogenomics Clinical Annotation Tool (PharmCAT). Her research interests include the translation of human genome sequencing data to pharmacogenomic-based therapeutic recommendations. She has 20 years of experience in the field, working collaboratively on many projects and serving on multiple advisory boards. Michelle received her PhD in Biophysics from Stanford University and her SB in Biology from MIT.
Alex Wagner, PhD
Principal Investigator
The Steve and Cindy Rasmussen Institute for Genomic Medicine (IGM) at Nationwide Children’s Hospital
Dr. Wagner is a Principal Investigator at The Steve and Cindy Rasmussen Institute for Genomic Medicine (IGM) at Nationwide Children’s Hospital. He analyzed the content of multiple public knowledgebases of the Variant Interpretation for Cancer Consortium (VICC) and demonstrated the need for data standards and supporting tools for genomic knowledge sharing and reuse. From this work, he took on the development and application of genomic knowledge standards under the auspices of the Global Alliance for Genomics and Health (GA4GH). In 2021, Dr. Wagner was recognized by the National Human Genome Research Institute (NHGRI) as an NHGRI Genomic Innovator for his work in this area. He currently holds leadership and/or invited positions in multiple national and international consortia, including GA4GH, the NIH Bridge2AI program, the HGVS Variant Nomenclature Committee, and the Variant Interpretation for Cancer Consortium (VICC).
Katrin Sangkuhl
Dr. Katrin Sangkuhl is a senior scientific curator at PharmGKB in the Department of Biomedical Data Science at Stanford University. She contributes to the development, maintenance, and application of the Pharmacogenomics Clinical Annotation Tool (PharmCAT) and is actively involved in the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Pharmacogene Variation (PharmVar) Consortium.
Binglan Li
Postdoctoral Scholar
Dr. Binglan Li is a postdoctoral Scholar in Dr. Teri Klein's lab since late 2020. She is interested in genomic medicine and promoting the implementation of pharmacogenomics in clinical care through the development of tools, such as PharmCAT (Pharmacogenomics Clinical Annotation Tool). Her doctoral projects focused on understanding the genetic architecture of complex human traits and translational biomedical research using ‘omics data integrative methods and electronic health records. Binglan obtained a BS from Fudan University, China, and a PhD from the University of Pennsylvania.
Teri Klein
Dr. Teri Klein is the Principal Investigator for the PharmGKB and Professor of Biomedical Data Science and Medicine at Stanford University. Dr. Klein is also the Co-Principal Investigator for CPIC (Clinical Pharmacogenetics Implementation Consortium) and PharmCAT. She was recruited from the University of California, San Francisco faculty and was the Director of the PharmGKB since it began in April 2000 until September 2019. Teri received her PhD in medical information sciences from the University of California, San Francisco and a BA in biology/chemistry from the University of California, Santa Cruz. Prior to becoming the director of the PharmGKB in 2000, Dr. Klein was an Associate Adjunct Professor at UCSF.
Marylyn Ritchie
Dr. Marylyn Ritchie is a Professor of Genetics, Director of the Institute for Biomedical Informatics, Director of the Center for Translational Bioinformatics Institute for Biomedical Informatics, and Associate Director of the Center for Precision Medicine at the University of Pennsylvania School of Medicine. Dr. Ritchie is a statistical and computational geneticist with a focus on understanding the genetic architecture of complex human diseases. She has expertise in developing novel bioinformatics tools for complex analysis of big data in genetics, genomics, and clinical databases, particularly in the area of Pharmacogenomics. She is the co-PI of PharmCAT.
Mark Woon
Mark Woon is the co-technical lead at PharmGKB and PharmCAT and has been with PharmGKB since 2001. He received his BSE in computer science from Princeton University. Prior to working on the PharmGKB project, Mark worked for Sun Microsystems and Netscape Communications.
Wesley Goar
Dr. Wesley Goar is a Senior Bioinformatics Scientist in the Wagner Lab at Nationwide Children’s Hospital in Columbus, Ohio. He obtained his undergraduate degree in Molecular Biology from Brigham Young University and his doctorate degree in Computational Genomics from the University of Iowa. During his graduate training he performed bioinformatics analyses of rare inherited eye diseases using genome, exome, panel, and RNA-sequencing technologies. After graduating, he managed the bioinformatics team for Immortagen Inc, performing cancer diagnostic reports for patients in China. He currently works on the standardization of variant data and the automation of variant assessment.
Kori Kuzma
Kori Kuzma graduated from The Ohio State University with a bachelor’s degree in Computer Science and Engineering. At the Institute for Genomic Medicine, she develops and deploys web applications for the analysis and interpretation of genomic variants.
Katie Stahl
Katie Stahl does full-stack development for the Wagner lab at Nationwide Children’s Hospital, working with research staff to develop open-source bioinformatics applications for efficient data analysis and visualization. Katie received her degree in Computer Science with a minor in Mathematics from Capital University.
James Stevenson
James Stevenson is a software developer in the Wagner Lab at Nationwide Children’s Hospital. He holds a bachelor’s degree in Political Science and Philosophy from the University of Puget Sound and is completing a master’s degree in Computer Science from the Georgia Institute of Technology. His research interests include applications of machine learning techniques in clinical medicine.
Karl Keat
Karl Keat is a PhD candidate in Genomics and Computational Biology at the University of Pennsylvania, where he works in the labs of Dr. Marylyn RItchie and Dr. Dokyoon Kim. His research focuses on pharmacogenomics and mutli-omics data integration for improving drug response prediction.
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Current guidelines from the American College of Medical Genetics and Genomics and Association of Molecular Pathology (ACMG/AMP) are primarily designed for interpretation of genetic variants that impact protein-coding regions of the genome. We formed an expert panel to design recommendations for how to adapt the ACMG/AMP guidelines for variants in other genomic contexts (Ellingford et al. 2021)
Background: Current guidelines from the American College of Medical Genetics and Genomics and Association of Molecular Pathology (ACMG/AMP) are primarily designed for interpretation of genetic variants that impact protein-coding regions of the genome. We formed an expert panel to design recommendations for how to adapt the ACMG/AMP guidelines for variants in other genomic contexts (Ellingford et al. 2021).
Aim of the workshop: The aim of this interactive workshop is to outline key aspects of the recommendations and detail practical steps towards using the guidance in clinical settings. Users will utilize case examples to develop hands-on working knowledge of the modified guidelines. By the end of the workshop attendees will be able to:
- Understand changes to ACMG/AMP rules. Describe the key adaptations to the ACMG/AMP rules that are needed to effectively curate non-coding region variants and detail the extra considerations applicable when applying individual ACMG/AMP rules.
- Access datasets to define relevant non-coding regions. Understand how to access and interpret the key data and tools required to interpret non-coding region variants. Specifically, you will be familiar with how to access epigenetic data to define non-coding regulatory elements, and will know which in silico tools can be used to predict the pathogenicity of different variant types.
- Perform variant classification for a range of non-coding region variants. Know how to practically approach interpretation of non-coding region variants in your own setting having worked through a series of example curations
Expected prior knowledge / experience: This workshop is aimed at clinical scientists and genetics professionals with an active role in clinical variant interpretation. You will have a working knowledge of the current ACMG/AMP guidelines for small sequence variants.
Format: The workshop will be 90 minutes in length, with approximately 30 minutes spent on each of the three main aims outlined above. The first 30 minutes will be a talk on the background behind and the key aspects of the recommendations. The second 30 minutes will be a demonstration on how to access the tools and resources required to curate non-coding region variants, and the final 30 minutes will be an interactive work-through of example variant curations.
Reference: Ellingford JM et al. medRxiv. Dec 2021. doi:10.1101/2021.12.28.21267792v1
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This session will feature 3 plenary talks presented at ASHG 2022 plus live Q&A and panel discussion for each
This session will feature 3 plenary talks presented at ASHG 2022. After each 15-minute talk there will be a 20-minute discussion session with additional panelists invited by the speaker, which will include answering questions from the audience.
Moderator: Erica Davis, PhD
Speakers:
- Endrina Mjuica, MD: Characterizing 54 type-2 diabetes candidate genes using CRISPR/Cas9, in vivo imaging and deep learning in zebrafish larvae
- Panelists: Marcel den Hoed (Group Leader), Christoph Metzendorf (Researcher), Eugenia Mazzaferro (PhD student)
- Scott Younger, MD, PhD: Rapid and scalable preclinical evaluation of personalized antisense
oligonucleotides using organoids derived from rare disease patients
- Panelists: None
- Yi Ding, MS: Polygenic score performance varies across the continuum of genetic ancestry in all
human populations
- Panelists: Bogdan Pasaniuc
Endrina Mujica, MD
PhD student at Marcel den Hoed's Lab
Uppsala University
Endrina Mujica is a PhD student at Marcel den Hoed’s research lab at Uppsala University, Sweden. She obtained her under graduate medical training from the University of Zulia in her home town of Maracaibo, Venezuela. During her medical training, she performed genetic screens to characterize allelic variants associated to metabolic alterations as part of “The Maracaibo city metabolic syndrome prevalence study”. She was then awarded an Erasmus scholarship to pursue the International Master in Innovative Medicine, an Erasmus Joint Master degree. This included courses at both Uppsala University and University of Groningen. Currently, she is doing her PhD studies at Uppsala University at Marcel den Hoed’s lab. The lab is focused on characterizing candidate genes for metabolic diseases using in vivo imaging and deep learning in zebrafish larvae. They have developed systematic and large-scale screens for the study of diabetes, obesity, cardiovascular, non-alcoholic fatty liver and kidney disease. These efforts aim to improve our understanding of disease etiology and help prioritize genes for further in-depth characterization.
Scott Younger, MD, PhD
Director of Disease Gene Engineering
Children's Mercy Research Institute
Dr. Scott Younger is the Director of Disease Gene Engineering within the Genomic Medicine Center at Children's Mercy Kansas City. He has extensive experience working with high-throughput sequencing-based screening technologies and is leading efforts to dissect the molecular mechanisms through which rare genetic variants identified in patients at Children's Mercy lead to disease. Dr. Younger came to Children's Mercy from the Broad Institute of MIT and Harvard where his group worked on the development of CRISPR-based screening methods. He completed his postdoctoral studies at Harvard University as an American Cancer Society Fellow. He holds a Ph.D. in cell and molecular biology from UT Southwestern Medical Center. He also received an M.S. in biotechnology from the University of Texas at San Antonio and a B.S.I. in bioinformatics from Baylor University.
Yi Ding, MS
PhD candidate in Bioinformatics
UCLA
Yi Ding is a fifth-year PhD student in Bioinformatics from UCLA advised by Dr. Bogdan Pasaniuc. She is interested in Bayesian Inference and the probabilistic modeling of complex genetic architecture. Currently, she is working with the UCLA-ATLAS Biobank to investigate the evaluation of individual-level polygenic score performance and the interpretation of polygenic scores across diverse genetic ancestries. Prior to UCLA, she obtained her Master’s degree in Biostatistics from Harvard T.H. Chan School of Public Health and her Bachelor’s degree in Biotechnology from Zhejiang University in China.
- Endrina Mjuica, MD: Characterizing 54 type-2 diabetes candidate genes using CRISPR/Cas9, in vivo imaging and deep learning in zebrafish larvae
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This session features presentations by all 6 Trainee Research Excellence Award winners from ASHG 2022
This session features presentations by all 6 Trainee Research Excellence Award winners (formerly known as the Charles J. Epstein Award) from ASHG 2022. After each presentation there will be an opportunity for live Q&A. After all presentations there will be a 20-minute panel with all the winners.
Moderator: Latrice Landry MS, PhD, MSC
Speakers:
- Frederik Filip Vinggaard Stæger, MS: Genetics and integrated -omics of diabetes and associated metabolic disorders in diverse populations
- Marianne Lemée, MS: Navigating the complex genetic landscape of neurodevelopmental disorders
- Layla Siraj: Massively parallel variant characterization
- Nathan Nakatsuka MD, PhD: Populations evolving: Modeling genetic variation to understand evolutionary processes
- Yosuke Tanigawa, PhD: The methylome and transcriptome of complex traits
- Hai Nguyen, PhD: Let's talk about sex and its contributions to disease risk
Frederik Filip Vinggaard Stæger, MS
PhD Student
University of Copenhagen
Frederik Filip Vinggaard Staeger is a PhD student at the University of Copenhagen (UCPH), Section for Computational Biology. He did his bachelor’s degree in Molecular Biomedicine and master’s degree in Bioinformatics. He contributed to the discovery of a common loss-of-function variant in the Greenlandic population leading to sugar intolerance and associated with an improved metabolic profile. He was awarded the Bio-Elite PhD scholarship and has continued his work with the Greenlandic population under the supervision of Professor Albrechtsen. He was awarded the 2022 Predoc “Charles J. Epstein Trainee Awards for Excellence in Human Genetics Research” for his finding of a novel common diabetes associated HNF1A variant that allows for precision prognostics and (eventually) treatment in the Greenlandic population contributing to a more equitable health care.
Marianne Lemée, MS
PhD Candidate at IGBMC
University of Strasbourg & IMCBio Graduate School
Marianne Lemée is a PhD candidate at the Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Strasbourg, France. She obtained her bachelor’s degree of Science for Health from the University of Reims Champagne-Ardenne, and her Master’s degree specialized in Stem cells and Developmental Biology from the University of Strasbourg with distinction. In 2021, she joined the selective international PhD program of the IMCBio graduate school. In 2019, she joined the laboratory of Dr. Christelle Golzio at IGBMC as an undergraduate student willing to contribute to translational research. Her current research focuses on identifying and elucidating the function of candidate genes involved in neurodevelopmental diseases. Notably, she discovered that dosage imbalance of the chromatin remodeler CHD1L contributes to the 1q21.1 CNV-associated mirrored neurodevelopmental phenotypes.
Layla Siraj
MD-PhD Student in Hilary Finucane and Eric Lander's Labs
Harvard-MIT MD-PhD Program
Layla Siraj is an MD-PhD student at the Harvard-MIT MD-PhD program. After completing her first two years of medical training at the Health Sciences and Technology program between Harvard Medical School and MIT, she began her PhD in the Harvard Biophysics program, where she is advised by Dr. Eric Lander (Broad Institute) and Dr. Hilary Finucane (Analytic and Translational Genetics Unit, Massachusetts General Hospital). Layla’s work focuses on uncovering the architecture of non-coding regulatory regions. Her work has been supported by the NSF-Simons Center for Quantitative Biology. She was awarded the 2022 pre-doctorate Charles J. Epstein Trainee Award for Excellence in Human Genetics Research for her work quantifying the regulatory landscape of >300k variants impacting complex human traits and disease.Nathan Nakatsuka, MD, PhD
Post-doctoral Fellow
The Reich Lab and the New York Genome Center
Dr. Nathan Nakatsuka was born and raised in Honolulu, Hawaiʻi. He graduated from Kamehameha Schools Kapālama High School then attended Harvard College, earning an AB in Chemical and Physical Biology. He then obtained an MPhil in Genetics from University of Cambridge on a Gates Cambridge scholarship, working at the Wellcome Trust Sanger Institute with Inês Barroso. Nathan received his MD at Harvard Medical School in the Harvard-MIT Health, Sciences, and Technology MD track and his PhD from the Systems, Synthetic, and Quantitative Biology PhD program working in the laboratory of David Reich on population genetics of South Asia and the Americas. During his PhD the majority of his work focused on studying ancient DNA to uncover the ancient history of North, Central, and South America. He currently is a postdoctoral fellow at the New York Genome Center in the laboratory of Rahul Satija working on single cell analyses of neuropsychiatric traits.
Yosuke Tanigawa, PhD
Postdoctoral Associate at Computational Biology Lab
MIT
Dr. Yosuke Tanigawa is a Postdoctoral Associate at the Computational Biology Lab (PI: Prof. Manolis Kellis) at MIT Computer Science and Artificial Intelligence Lab. He obtained his BS in Bioinformatics and Systems Biology from the University of Tokyo and his PhD in Biomedical Informatics from Stanford University. He develops statistical and computational methods for disease heterogeneity dissection, polygenic risk modeling, and therapeutic target discovery. Personal website: https://yosuketanigawa.com/.
Hai Nguyen, PhD
California Institute of Regenerative Medicine Postdoctoral Fellow
University of California, San Francisco
Dr. Hai Nguyen is a CIRM (California Institute of Regenerative Medicine) postdoctoral fellow at the University of California, San Francisco. He obtained his undergraduate at Washington State University and his Doctor of Philosophy degree from the University of California, Berkeley. His research focus is on gene regulation, adipose tissue, and obesity.
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The Association to Function Knowledge Portal (A2FKP; a2fkp.org) provides genetic and genomic results for common disease across 11 physiological systems along with interactive tools, with the aim of facilitating broad access to these results. This workshop will familiarize attendees with the A2FKP and outline scientific questions that can be explored using the portal.
Genome-wide association studies (GWAS) have now identified thousands of associated loci for complex diseases and related traits. But despite this success, in only a handful of cases so far have association data been translated to knowledge of causal variants, effector transcripts, biological networks, and potential therapeutic targets. Accelerating progress in this area requires 1) the large-scale integration of genetic association data with detailed, cell type-specific annotation of the epigenome, transcriptome, and proteome, and 2) open-access resources that make these integrated results easily interpretable for research scientists worldwide.
In this workshop we will present one such resource, the Association to Function Knowledge Portal (A2FKP). Supported by NHGRI as a Genomic Community Resource, the A2FKP integrates high quality genetic and genomic datasets, bioinformatic method results, and expert-curated knowledge for multiple classes of disease, including metabolic, cardiovascular, immunological, pulmonary, musculoskeletal, and neurodegenerative disorders. The A2FKP is being developed in collaboration with the research communities in each of these disease areas. Epigenomic and functional results in the A2FKP are aggregated in collaboration with a sister resource, the Common Metabolic Diseases Genome Atlas (CMDGA).
Attendees of this workshop will get an overview of the data underlying the A2FKP, will learn how to query the A2FKP both via the web interface and programmatically, and will practice using its interactive tools to form and test hypotheses about loci and genes of interest. Hands-on exercises will provide instruction in using the A2FKP to answer questions such as:
- Do current genetic and genomic data support the involvement of my favorite gene in a particular disease or trait?
- Which gene in a genetically associated locus is most likely to be causal for the associated trait?
- What is the overall genetic architecture of a particular complex disease?
- For a variant of interest, what is the range of phenotypes with which it is associated? Does it lie within a region that has a potential tissue-specific regulatory role?
- How can I programmatically access the results in the A2FKP?
Attendees are also welcome to bring specific questions from their own research.
Maria Costanzo, PhD
Creative Lead for the Knowledge Portal Network
Broad Institute of MIT and Harvard
Maria Costanzo, Ph.D., is the Creative Lead for the Knowledge Portal Network at the Broad Institute of MIT and Harvard. Costanzo earned her Ph.D. in molecular biology at Harvard University and holds a B.A. degree in microbiology from the University of Pennsylvania. Costanzo’s role on the Portal team is to spread awareness of the resources and to facilitate use of the Knowledge Portals, by writing clear documentation and participating in tool and interface development. Prior to joining the Broad Institute in 2015, Costanzo was a biocuration scientist with the Saccharomyces, Candida, and Aspergillus Genome Databases at Stanford University. She was also employed by Proteome, Inc. and Incyte Genomics, and performed basic research on the genetics and molecular biology of the model organism Saccharomyces cerevisiae (brewer’s/baker’s yeast) at Cornell University.
Noël Burtt
Director of Operations and Development of the Diabetes Research & Knowledge Portals
Medical and Population Genetics Program and Metabolism Program at the Broad Institute of MIT and Harvard
Noël Burtt is the director of operations and development of the Diabetes Research & Knowledge Portals in the Medical and Population Genetics Program and Metabolism Program at the Broad Institute of MIT and Harvard. Burtt received her B.S. from the University of New Hampshire in molecular biology and human genetics. Burtt’s work centers on the operational and organizational leadership of large-scale, international genetics consortia and public/private partnerships for human genetics studies, with a focus on type 2 diabetes and cardiometabolic diseases. Prior to her work at the Broad, Burtt joined the Whitehead Center for Genome Research in 1999 to help develop and scale technologies for genotyping and sequencing, tools that were used in some of the first genome-wide association studies (GWAS). Burtt has also managed two public-private partnerships with Novartis and Pfizer as part of the effort to use human genetics to develop better therapies for diabetes. She has contributed to more than 126 publications of genomic studies of diabetes, obesity, cancer, cardiovascular disease, and other disorders.
Jason Flannick
Assistant Professor of Pediatrics
Harvard Medical School and the Division of Genetics and Genomics at Boston Children’s Hospital
Jason Flannick is an assistant professor of pediatrics at Harvard Medical School and the Division of Genetics and Genomics at Boston Children’s Hospital, and an associate member of the Broad Institute of MIT and Harvard. Flannick received his B.A. in computer science, mathematics, and physics from Cornell University. Flannick later earned his M.S. and Ph.D. in computer science from Stanford University, writing his thesis on approaches to compare protein interaction networks across different species. He spent four years as a postdoctoral fellow in statistical and computational genetics in David Altshuler’s laboratory at Massachusetts General Hospital and the Broad Institute. The Flannick Lab develops computational approaches to use human genetic and broader genomic data to understand or better treat human diseases, with a current focus on diabetes.
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View the Presidential Symposium and Presidential Address from ASHG 2022
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View plenary talks from ASHG 2022 available on-demand