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March 12-15th, 2018

Human Genome Meeting 2018

PACIFICO, Yokohama, Japan

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Scientific Programme

Note: The programme below is accurate as of February 2018 and is subject to change.

RIKEN Trainee session will be held at RIKEN YOKOHAMA CAMPUS
For the venue, please click HERE
Time Monday, March 12, 2018
9:30 - 10:30

What are the Critical Factors to Publish Well?
Meet the Editors from Science, Nature Genetics, Nature Communications, and Human Genomics
Chair: Karen Avraham, Tel Aviv University, Israel

10:30-10:40 Opening remarks (Piero Carninci)
10:40-11:10 Talk by Dr. Jürgen Reichardt (HUGO Council member)
11:10-11:40 Talk by Dr. Edison Liu (HUGO Council member)
11:40-13:00 Lunch & optional RIKEN Lab tour 1, 2
13:00-13:30 Talk by Prof. Karen B. Avraham (HUGO council member)
13:30-15:00 Trainee oral session 1
(15 minutes) Joachim Felix Luginbuhl
"Inferring transcriptional regulatory networks controlling direct conversion of induced neurons using Convert-seq"
(15 minutes) Werna TC Uniken Venema
"Single cell RNA sequencing of T cells in Crohn’s disease identifies tissue specific drug targets"
(15 minutes) Quan H Nguyen
"Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution"
(15 minutes) Hidetaka Uryu
"Accurate prediction of chromatin conformation status using deep neural network model"
(15 minutes) Raissa Relator
"Finding statistically significant marker combinations from genomic data for survival analysis"
(15 minutes) Maciej Trzaskowski
"GENOME-WIDE ASSOCIATION ANALYSES IDENTIFY 44 RISK VARIANTS AND REFINE THE GENETIC ARCHITECTURE OF MAJOR DEPRESSIVE DISORDER"
15:00-15:30 Break
15:30-17:00 Trainee oral session 2
(15 minutes) Saumya Agrawal
"Identifying long noncoding RNAs associates in human cells"
(15 minutes) Robert Young
"The consequences of promoter birth and death for human genetic and phenotypic variation"
(15 minutes) Nehir Kurtas
"Chromothripsis: evolution of de novo small supernumerary marker chromosomes from trisomies"
(15 minutes) Michal Andrzej Pawlak
"Identification of epigenomic regulatory networks of heart development"
(15 minutes) Yun Rose Li
"Rare Copy Number Variants in Over 100,000 Subjects Reveal Novel Disease Associations in Cancer and Autoimmunity"
(15 minutes) Margherita Francescatto
"omicsCNN: a general deep learning framework for omics data modeling and classification"
17:00-18:30 Break & Meet the experts (HUGO Council members and invitees)
18:30-18:40 Awards & Closing
Time Tuesday, 13 March 2018
9:00 - 9:15 Opening
9:15 - 10:45

Symposium 1 - Cancer Genomics
Chair: Yasushi Okazaki, Japan

Symposium 2 - Integration of Large Datasets
This session is sponsored by RIKEN"

Chair: Michael Snyder, USA

(30 min)

Tatsuhiro Shibata, NCC, Japan
"Epigenetic landscape influences the liver cancer genome architecture"

Ajay Royyuru, IBM, US 
"Data + AI = Insights in Biology & Medicine"

(30 min)

Yutaka Suzuki, U of Tokyo, Japan  
"Multi-omics analysis of cancer cells"

John Mattick, Garvan Institute, Australia  
"The transformation of medical research and healthcare by genomics and big data"

(30 min)

Scientific talk by

1) ThermoFisher Scientific - Alex Teoh
"Comprehensive Genomic Profiling, a tool for Precision Medicine in Clinical Practice"

2) PacBio

[SCIENTIFIC TALK by Thermofisher Scientific] in Symposium 1 “Cancer Genomics”
Speaker

Alex Teoh, Ocology Product Specialist and Support (OPIS)

Talk Title:

Comprehensive Genomic Profiling, a tool for Precision Medicine in Clinical Practice

Abstract:

In the recent year, tumor molecular profiling using NGS is emerging as part of precision medicine initiative. The ability to characterize tumor by genetic subtypes and oncogenic drivers have led to improve in cancer patient treatment selection, drug development processes and more precisely targeted trial design. Molecular typing is not something new in the field and in fact it is a routine practice in standard molecular medicine or pathology laboratory using convention method such as PCR, qPCR, Sanger, FISH, and IHC. However, conventional method screening is laborious, time consuming, limited molecular target and biopsy tissue. Thus, using a small amount of sample couples with AmpliseqTM technology together with OncomineTM informatics, it streamlines the conventional screening processes using NGS in characterizing tumor molecular profiling with the ultimate goal of achieving better patient outcomes

Masayuki Yamamoto, Tohoku Medical Megabank Organization, Japan  
"Tohoku Medical Megabank Project- A National Challenge to Realize Personalized Medicine"

10:45 - 11:15 Coffee Break & Exhibition
11:15 - 12:00

Plenary 1: Nancy Cox, Vanderbilt University, US
"Using the Medical Phenome to Extend Discovery in Biobank Research"
Chair: Charles Lee, USA

12:00 - 13:00

Luncheon Session by ThermoFisher Scientific

[Luncheon Session 1] by Thermofisher Scientific
Speaker

Andrew Hutchison, Global Product Manager

Chair

Michelle Hwang, Regional Market Development Manager

Talk Title:

Innovations on Ion Torrent Technology, now in HD

Luncheon Session by Tommy Digital Bio (PacBio)

[Luncheon Session 2] by Tommy Digital, PacBio
Speaker

Jonas Korlach, Chief Scientific Officer

Pacific Biosciences, 1305 O’Brien Dr., Menlo Park, California 94025

Talk Title:

Accessing the full size-spectrum of human genetic variation using PacBio long-read SMRT sequencing on the Sequel System

Abstract:

Structural variation accounts for most of the base pairs that differ between two human genomes, and causes many genetic disorders. The ability to study structural variants, in addition to smaller single nucleotide variants and indels, is critical to understanding how genetic variation impacts health and disease in the era of Precision Medicine.

New PacBio sequencing methods including; low-fold long-read WGS, targeted long-read sequencing, and structural variant calling and visualization tools, have made it feasible and efficient to access and study the full size-spectrum of human genetic variants in-phase, across individual human genomes, with an economical study-design.

By applying these new PacBio long-read sequencing methods to Precision Medicine and Human Population studies, human genetic research scientists have recently reported discovery of novel causative genetic variants in disease studies, demonstrating the value of a long-read approach for novel disease gene discovery.

Speaker

Tetsuo Ashizawa

Houston Methodist Research Institute, Houston, TX

Talk Title:

Internal sequences of large pentanucleotide repeat expansion alleles in SCA10

Abstract:

SCA10 is an autosomal dominant cerebellar ataxia caused by a large (up to 21kb) expansion of an intronic pentanucleotide repeat in ATXN10. Conventional sequencing technologies were unsuitable to generate contiguous sequences of the large size of SCA10 expansion alleles.

Using the Single Molecule Real Time (SMRT) sequencing technology, we have obtained long sequence reads of PCR-amplified expanded SCA10 alleles. We also used CRISPR-Cas9 to attach an adapter sequence that allows for enriching restriction fragments containing SCA10 repeats and obtained SMRT sequences of expanded repeats. The sequence results were compared with Sanger sequences of shotgun-cloned sheared DNA containing expanded SCA10 repeats and with results of repeat-primed PCR patterns analyzed by conventional and pulse-field capillary electrophoresis.

These studies showed that internal sequences of expanded SCA10 repeats are interrupted by a long stretch of repeats consisting of variable repeat units. There are three major patterns of expansion, which we designate types A, B and C. In all three types of expanded SCA10 repeats, the 5’ end starts with >30 tandemly repeated ATTCT units. Type A expansion alleles consist of mostly pure ATTCTs for the entire length. Type B alleles contain (ATTCT)n with an insertion of (ATTCC)n at the 3’ end of the repeat whereas type C alleles show the (ATTCT)n(ATCCT)n(ATCCC)n configuration, where each n varies. Although this suggests instability of the expanded repeat, transitions between types of the expansion allele are rare.

The repeat expansion type could serve as a biomarker that predicts phenotypic variants in SCA10 patients, including the disease severity. An increasing body of evidence suggests that the pathogenic mechanism of SCA10 is a gain of toxic function of the mutant RNA containing corresponding repeat expansions. We found that the different repeat tracts within the expanded SCA10 alleles interact with RNA binding proteins (RBPs) with different affinity. Transgenic mice expressing different types of SCA10 repeat expansions showed disparate phenotypes that correlate with clinical manifestations of patients with SCA10. Together, we hypothesize that the internal sequences of large microsatellite repeat expansions are critically important in the pathogenic mechanism of SCA10.

12:00 - 13:30 Lunch
13:30 - 15:00

Symposium 3 - DNA Damage and Replication
Chair: Karen Avraham, Israel / Ingrid Winship, Australia

Symposium 4 - Data Sharing for Personalized Medicine
Chair: John Mattick, Australia / Momoko Horikoshi, Japan

(30 min)

Inna Kuperstein, Institut Curie, France
"Signalling network map of innate immune response in cancer reveals signatures of cell heterogeneity and polarization in tumor microenvironment"
Kwong Wai Choy, The Chinese University of Hong Kong, Hong Kong
"Identification of balanced chromosomal rearrangements among participants in the 1000 Genomes Project by low-pass whole genome sequencing"

Ewan Birney, EMBL, UK  
"Big Data in Biology and Medicine"

(30 min)

Hidetaka Uryu, National Research Institute for Child Health and Development, Japan
"Accurate prediction of chromatin conformation status using deep neural network model"
Yun Rose Li, Children's Hospital of Philadelphia, USA
"Rare Copy Number Variants in Over 100,000 Subjects Reveal Novel Disease Associations in Cancer and Autoimmunity"
Vanessa Sancho-Shimizu, Imperial College London, UK
"The genetic basis of invasive meningococcal disease revealed thorough whole exome sequencing"

Sir John Burn, Newcastle University, UK  
"Variant interpretation: a global challenge"

(30 min)

Scientific talk by BGI - Shida Zhu
"NGS based panel solution of detecting BRCA mutations and homozygous recombination deficiency"

[SCIENTIFIC TALK by BGI] in Symposium 3 “DNA Damage and Replication”
Speaker

Shida Zhu, BGI-Research

Talk Title:

NGS based panel solution of detecting BRCA mutations and homozygous recombination deficiency

Abstract:

BRCA plays essential roles in DNA double-strand breaks repair through homozygous recombination by interacting with multiple DNA damage responsive proteins and regulating expression of genes in related pathways. Loss of BRCA function leads to accumulation of chromosome damage, instability of genome and predisposes to tumorigenesis. Thus, BRCA mutation testing has been proved effective and necessary as companion test to PARP inhibitors.

Here we report a systematic solution to detect BRCA mutations based on next generation sequencing in a high-resolution manner. Combining optimized panel design and analysis results from high accurate sequencing data, we have established the largest Chinese cohort dataset towards BRCA genes, including pathogenic mutations, VUS and benign mutations. Furtherly we developed a comprehensive HRD (homozygous recombination deficiency) tool which could enable extensive exploration of potential functional defects driven by BRCA and other related genes to evaluate PARP inhibitor response.

Scientific talk by Fabric Genomics - Martin Reese
"Accurate and Rapid WGS Interpretation with Fabric Genomics in clinical care"

[SCIENTIFIC TALK by Fabric Genomics] in Symposium 4 “Data Sharing for personalized Medicine”
Speaker

Martin Reese, Ph.D.- Co-Founder, President, and Chief Scientific Officer- Fabric Genomics (formerly Omicia)

Talk Title:

Accurate and Rapid WGS Interpretation with Fabric Genomics in clinical care

Abstract:

Laboratories, healthcare systems, and country projects all share a need for an intelligent, modular and powerful compute infrastructure in order to manage large-scale genomic interpretation, analysis, and clinical reporting. These projects typically include research, data mining, and clinical healthcare reporting components that require a broad array of tools and supporting resources. Additionally, there is a need for the preservation of patient genetic data for future re-interpretation and clinical outcome studies.

At the core of a precision medicine project is genome interpretation, which has to demonstrate both accuracy and clinical utility to improve patient care. In this talk, we will discuss Fabric Genomics’ Opal Clinical software platform, a scalable software-as-a-service (SaaS) solution for interpreting vast amounts of NGS data from panels, exomes, and genomes. We will highlight examples of genomic testing that are transforming medical care, such as the 100,000 Genomes Project in England and Rady Children's Institute for Genomic Medicine (Rady Children’s). The 100,000 Genomes Project, spearheaded by Genomics England (GeL), is a country study aimed at identifying disease-causing genetic variants in patients and families with rare genetic diseases and cancer using WGS. Opal Clinical has provided GeL with potential causative candidates in 44.7% of cases. At the core of Opal Clinical are Fabric Genomics’ leading algorithms VAAST and Phevor, which are gene ranking methods developed and published in collaboration with the University of Utah. Another example that we will present will be from Dr. Stephen Kingsmore’s clinical group in pediatrics at Rady Children's Hospital. That group has a goal of rapid genome sequencing and analysis, with a 24-hour turnaround time from blood sample to result for critically-ill pediatric patients. Fabric Genomics' Opal STAT version of Opal prioritizes extremely urgent pediatric cases, and guarantees the delivery of comprehensive annotations on whole genomic data in less than 1 hour. We will present scientific results from these examples, as well as infrastructure features that address many concerns of scaling large scale genome projects, including data storage, scalability, data access, integrations, and regulatory requirements.

Scientific talk by BGI - Yonggang (Jason) Zhao
"BGISEQ Based Tech Services Highlight & Featured Applications"

[SCIENTIFIC TALK by BGI] in Symposium 4 “Data Sharing for personalized Medicine”
Speaker

Yonggang (Jason) Zhao, Int'I Tech Services Business Unit Director

Talk Title:

BGISEQ Based Tech Services Highlight & Featured Applications

Abstract:

BGISEQ platform is an industry leading high-throughput sequencing solution, developed by BGI’s Complete Genomics subsidiary in Silicon Valley. The system is powered by combinatorial Probe-Anchor Synthesis (cPAS), Pattern Array technology and DNA Nanoballs (DNB™) technology, followed by high-resolution digital imaging. The combination of linear amplification and DNB technology reduces the error rate while enhancing the signal.

At this point in time, Whole Genome Sequencing (WGS) provides the maximum possible information about the human genome. WGS interpretation also provides fundamental guidance for precision medicine. However, the sequencing cost is one of the important determinants for the widespread use of WGS. Technology enhancements have enabled lower sequencing costs. Gobally, BGI is the most cost effective provider of high quality WGS with only hundreds dollar. This presentation will give an introduction to the various applications of BGISEQ based WGS solutions.

15:00 - 16:30 Coffee Break & Poster Walk Session & Exhibition
16:30 - 18:00

Symposium 5 - Single Cell Biology
Chair: Sumio Sugano, Japan

Symposium 6 - Human Development
Chair: Walter Bodmer, UK / Shoji Tsuji, Japan

(30 min)

Yasushi Okada, RIKEN, Japan  
"Live cell imaging technologies for single-cell analysis – How can imaging meets genomics?"

Jennifer Mitchell, University of Toronto, Canada  
"Enhancer switching regulates Sox2 during the transition from embryonic to neural stem cells"

(30 min)

Sten Linnarsson, Karolinska Institute, Sweden
  "A molecular atlas of the mouse nervous system by single-cell RNA-seq"

Amalio Telenti, Human Longevity, US  
"Analysis of 150,000 human genomes"

(30 min)

Stephen Quake, Stanford University, US
"Physiology and Aging Probed with Single Cell Genomics"

Scientific talk by BGI - Radoje (Rade) Drmanac
"stLFR: a novel bead based method for highly accurate whole genome sequencing, haplotyping, and scaffolding"

[SCIENTIFIC TALK by BGI] in Symposium 6 “Human Development”
Speaker

Radoje (Rade) Drmanac, Ph.D.
Chief Scientific Officer
Complete Genomics, Inc.

Talk Title:

stLFR: a novel bead based method for highly accurate whole genome sequencing, haplotyping, and scaffolding

Abstract:

Whole genome sequencing (WGS) technology has improved enormously since the completion of the human genome project. BGI have launched $600 WGS on BGISEQ-500RS in 2017, with the new sequencers MGISEQ-2000 and MGISEQ-200 the cost will be lower and widely used for both research and clinical test. However, there are still many aspects of WGS that require improvement before we can achieve perfect genome sequencing. Here we describe and provide a full protocol for a novel technology, single tube long fragment read (stLFR), that enables WGS, haplotyping, and contig scaffolding. Like the original LFR, stLFR is based on the concept of co-barcoding long DNA fragments. However, unlike the original version that used the compartments of a 384-well plate, stLFR uses the surface of beads to create millions of individual compartments in a single tube. Using a combinatorial process over 1.8 billion unique barcodes have been generated enabling almost no overlap of barcode sequences between beads in a typical reaction. Using stLFR we demonstrate near perfect variant calling and phasing of the genome of NA12878 in contigs with an N50 of >12 Mb. We also demonstrate that complex structure variants can be detected and properly ordered using stLFR data. This was all possible with a single stLFR library, we did not require a separate library to generate high quality variant calls. We also performed scaffolding of contigs generated from SMRT reads and show that stLFR can improve the genome assembly. We believe stLFR represents a potential single library solution that will enable WGS, phasing, SV detection, scaffolding, and ultimately dipoid de novo assembly. Importantly, stLFR does not significantly add to the cost of library preparation and it is easily automatable in 96-well plate format.

18:00 - 18:30 Travel to Welcome Reception venue
18:30 - 20:30 Welcome Reception
Tuesday, 13 March 2018
Plenary Speaker
Vanderbilt University, US

Dr. Cox worked for many years on the analysis of sequence data in the context of the T2DGENES project, and also collaborating in generating content for portal serving results and analyses for sequencing and other genome studies in type 2 diabetes. A major focus of current research is in conducting research in BioVU, the biobank at Vanderbilt University, in which we have DNA samples on more than 230,000 subjects linked to electronic health records going back average of ~10 years, and up to 20 years.

Dr. Cox and her team develops methods for analyzing genetic and genomic data and then applies those methods to the analysis of genome data on common diseases and translational phenotypes, such as pharmacogenomics traits. They have a particular focus now on the integration of information on genome function with methods for the analysis of genome data on disease and complex traits. Her most recent methods development has focused on the development of genome predictors of expression of genes across all GTEx tissues. Using GTEx as a reference panel for predicting gene expression phenotypes is analogous to the way 1000 Genomes Project data have been used as a reference panel for imputation of SNP data.

Symposium Speaker
National Cancer Center, Japan

Dr. Shibata received his MD/PhD in pathology from the University of Tokyo. He then did his post-doctral research in the University of California, Irvine. He has been Chief of Cancer Genomics Division at the National Cancer Center, Tokyo since 2010, and concurrently been professor in the Laboratory of Molecular Medicine, University of Tokyo since 2014. His research interest includes cancer genomics, tumor pathology and bioinformatics. He is also a PI of the Japanese research group in the International Cancer Genome Consortium, and has been working on liver, biliary tract and gastric cancers.

University of Tokyo, Japan

My lab employ versatile applications of next generation sequencing technologies, such as Whole Genome/Exome Seq, RNA Seq, ChIP Seq and Bisulfite Seq to understand the biological meaning of the identified genomic mutations. Advent of the next generation sequencing technologies has enabled us to analyze thousands of human genomes. Consequently, a rapidly increasing number of mutations have been identified and associated with various diseases, such as cancers. However, it still remains elusive how these mutations invoke changes in epigenome, transcriptome, or proteome functions. For the diseases as exemplified below, we are conducting an integrative analysis of multi-omics data, namely DNA methylation, histone modifications, biding patterns of transcriptional regulatory factors and gene expression patterns. Furthermore, to complement currently undetectable layers of transcriptome regulations, we are developing novel methods, based on the latest genomic technologies, such as next generation sequencing, single cell analysis and single molecule sequencing technologies. Also, as a one of the representative sequencing centers in Japan, we are distributing the next sequencing platforms and the related technologies widely to the research community.

IBM, US

Ajay Royyuru leads Healthcare & Life Sciences research at IBM. His team is actively pursuing high quality science, developing novel technologies and achieving translational insights across this industry, including areas of cancer, cardiac, neurological, mental health, immune system, and infectious diseases. Scientific interests and active projects include genomics, protein science, systems biology, computational neuroscience, health informatics, miniaturizing for medical devices, and nano-biotechnology.

Working with institutions around the world, he is engaged in research that will advance personalized, information-based medicine. Ajay previously led the life sciences research portfolio through the Computational Biology Center and led the IBM Research team with National Geographic Society on the Genographic Project. Ajay has authored numerous research publications and several patents in structural and computational biology. His work has featured in The New York Times, The Washington Post, BBC, Forbes, Scientific American, Nature Medicine, and Nature news articles.

After his undergraduate and masters education in human biology and biophysics from All India Institute of Medical Sciences, New Delhi, Ajay obtained his Ph. D. in molecular biology from Tata Institute of Fundamental Research, Mumbai. He had postdoctoral training at Memorial Sloan-Kettering Cancer Center, New York and a brief stint at scientific software development before joining IBM Research.

In 2016 Ajay was named an IBM Fellow, the company's pre-eminent technical distinction. Ajay is a member of International Society for Computational Biology, IBM Academy of Technology, and IBM Industry Academy.

Garvan Institute, Australia

John Mattick is the Executive Director of the Garvan Institute of Medical Research. He spent much of his career at the University of Queensland, where he was Foundation Director of the Institute for Molecular Bioscience and the Australian Genome Research Facility. He was recently named by NHMRC as the one of the all-time high achievers in Australian health and medical research, and by Thomson Reuters as one of the world’s most influential scientific minds. His honours and awards include the inaugural Gutenberg Professorship of the University of Strasbourg, the Order of Australia and Australian Government Centenary Medal, Fellowship of the Australian Academy of Science and the Australian Academy of Health & Medical Sciences, Honorary Fellowship of the Royal College of Pathologists of Australasia, the International Union of Biochemistry & Molecular Biology Medal, the Human Genome Organisation Chen Award for Distinguished Achievement in Human Genetic & Genomic Research, and the MD Anderson Cancer Center Bertner Memorial Award for Distinguished Contributions to Cancer Research. He has overseen the development of a number of startup enterprises, including most recently one of the world’s first clinical genomics companies.

Tohoku Medical Megabank Organization, Japan

Since our initial discovery of the GATA transcription factor family, we have been investigating the molecular mechanisms of transcriptional regulation in physiologically essential processes, especially hematopoietic differentiation and homeostasis. To conduct those researches, we have utilized an integrative approach, that includes: 1) transgenic and mutant mouse studies, 2) numerous in vitro molecular biology and biochemical techniques, and 3) high-throughput biology paired with computational bioinformatics. Current our projects focus on: 1) regulatory interactions between GATA1 and GATA2, 2) GATA2 function in hematopoietic stem cells, and 3) leukemogenesis caused by disruptions in GATA1 function.

Also, we have discovered that a novel molecular pathway, the Nrf2-Keap1 system, can respond to oxidative stress by inducing detoxification enzymes. We aim to elucidate in greater detail the molecular basis of this “Environmental response”. The transcription factor Nrf2 is a critical mediator in this system that comprehensively regulates expression of numerous stress responsive enzymes and detoxification enzymes. Conversely, Keap1 constitutively suppresses Nrf2 activity through rapid Nrf2 degradation. Thus Nrf2 activation equates with liberation from Keap1 suppression. Furthermore, Keap1 functions as a sensor of oxidative and electrophilic stresses. Thus our laboratory has made pioneering contributions to the understanding of the cellular and molecular basis of the oxidative stress response.

Yasushi Okada graduated from the University of Tokyo, Faculty of Medicine in 1993 and obtained a medical license. After JSPS research fellow at the Graduate School of Medicine, the University of Tokyo, he became a research associate at the same university. He moved to RIKEN in 2011 as a Team Leader in Quantitative Biology Center. In 2016, he was invited to the current professor position at the Department of Physics, the University of Tokyo with a cross-appointment with RIKEN. He has been studying the working mechanisms and the physiological functions of a molecular motor, kinesin by the combination of wide variety of imaging techniques such as single molecule imaging, cryo-EM, X-ray crystallography, and fluorescent live cell imaging. Recently, he is extending these imaging technologies for the applications in single cell analyses.

Karolinska Institute, Sweden

Sten Linnarsson took his PhD in 2001, studying neurotrophic factors regulating neuronal survival, growth and plasticity. Instead of a postdoc, he founded a company to develop methods for gene expression analysis and single-molecule DNA sequencing. In 2007, he was appointed assistant professor and in 2015 Professor of Molecular Systems Biology at Karolinska Institute. He was awarded the 2015 Erik K. Fernström Prize for his work in single-cell biology.

Linnarsson’s aim is to discover the complete lineage tree of the developing human nervous system. To achieve this goal, he uses single-cell RNA sequencing, RNA single-molecule FISH, and advanced computational methods. Ultimately, he hopes to discover general principles of how cells acquire and maintain their molecular identities.

The European Molecular Biology Laboratory, UK

Ewan Birney is Director of EMBL-EBI with Dr Rolf Apweiler, and runs a small research group. He played a vital role in annotating the genome sequences of human, mouse, chicken and several other organisms; this work has had a profound impact on our understanding of genomic biology. He led the analysis group for the ENCODE project, which is defining functional elements in the human genome. Ewan’s main areas of research include functional genomics, assembly algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences) and compression of sequence information.

Ewan completed his PhD at the Wellcome Trust Sanger Institute with Richard Durbin, and worked in the laboratories of leading scientists Adrian Krainer, Toby Gibson and Iain Campbell. He has received a number of prestigious awards including the 2003 Francis Crick Award from the Royal Society, the 2005 Overton Prize from the International Society for Computational Biology and the 2005 Benjamin Franklin Award for contributions in Open Source Bioinformatics. Ewan was elected a Fellow of the Royal Society in 2014 and a Fellow of the Academy of Medical Sciences in 2015.

Ewan is a non-executive Director of Genomics England, and is a consultant and advisor to a number of companies, including Oxford Nanopore Technologies and GSK.

Newcastle University, UK

Professor Sir John Burn obtained an MD with distinction, a first class honours degree in human genetics from Newcastle University, where he has been Professor of Clinical Genetics since 1991 and a consultant specialist since 1984. He led the regional NHS Genetics Service for 20 years and helped to create the Centre for Life which houses an education and science centre alongside the Institute of Genetic Medicine and Northgene Ltd, the identity testing company he launched in 1995. He chairs DNA device company QuantuMDx. He was knighted in 2010, chosen as one of the first 20 ‘local heroes’ to have a brass plaque on Newcastle Quayside in 2014. He received the Living North award in 2015 for services to the North East 2000 – 2015. He is also a non-Executive Director of NHS England.

University of Toronto, Canada

Our research investigates how the genome is folded and organised in the nucleus and how this organisation influences regulation of gene expression. We often think about transcription as occurring on a particular gene in a linear manner whereas the nucleus is a three dimension organelle into which the genome is folded and organised. Recent work has shown that all transcription occurs at discreet compartments within the nucleus, termed transcription factories, with genes moving in and out of these compartments as they are expressed and silenced. Furthermore, distal enhancers have been shown to physically contact the genes they regulate forming tissue-specific chromatin loops. Our lab uses a combination of Molecular Biology and Cellular Imaging Techniques combined with genome-wide approaches and bioinformatics analysis to investigate the mechanisms that underlie tissue-specific regulation of gene expression and genome folding.

Human Longevity Inc., US

Amalio Telenti joined Human Longevity Inc. in 2014. As CSO, he directs advanced analytics in genomics and research initiatives at HLI. He led the analysis of the first 10,000 deep sequenced human genomes, as well as the definition of a map of conservation and organization of the regulatory structures in the human genome. He also is a member of the faculty of The Skaggs School of Pharmacy and of the Department of Medicine at UCSD. Prior to joining Human Longevity Inc., Amalio Telenti served as Professor and Director of the Institute of Microbiology of the University of Lausanne, Switzerland where he actively developed a program of host-pathogen genomics. He is member of the Scientific Advisory Board of PosNoGap \ Swiss Platform for Advanced Scientific Computing, of the Center for Integrative Genomics, U. of Lausanne, of the Institute Pasteur – Chinese Academy of Sciences, Shanghai, and was member of the Scientific Executive Board of the Swiss National Program for Systems Biology. Amalio Telenti is American Board certified in Internal Medicine. He carried out medical training at the Mayo Clinic in Rochester, MN. Amalio Telenti is a member of the Swiss Academy of Medical Sciences.

Time Wednesday, 14 March 2018
9:00 - 10:00

Special Session - HUGO Past Presidents Session

Sir Walter Bodmer, Thomas Caskey, Gert-Jan van Ommen,
Yoshiyuki Sakaki, Edison Liu, Stylianos Antonarakis

10:00 - 10:30 Coffee Break & Exhibition
10:30 - 12:00

Symposium 7 - OECD Session (Microbiome)
Chair: Dr. Richard Johnson, USA

Symposium 8 - HVP Session
Chair: Ada Hamosh, USA

(20 min)

Dr. Young-Do Nam, Head/Senior Researcher, Research Group of Gut Microbiome, Korea Food Research Institute, Republic of Korea; Dr. Hiroshi Ohno, Laboratory for Intestinal Ecosystem, RIKEN, Japan

Johan T den Dunnen , Leiden University, Netherlands
"Standards and sharing: essential for optimal DNA-based diagnostics"

(20 min)

Dr. Takaaki Abe, Division of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Japan; Dr. Ingrid S Surono, Food Technology Department, Faculty of Engineering, BINA NUSANTARA University, Indonesia

Gunnar Rätsch, ETH Zurich, Switzerland
"BRCA Exchange: Sharing Global Knowledge about BRCA1/2"
(20 min)

Mr. Hiroki Kurokawa, Johnson & Johnson, Japan; Mr. Ye Yin, CEO, BGI Genomics Co., Ltd, Shenzhen, People’s Republic of China

Ingrid Winship, U of Melbourne, Australia
"The equitable use of genomics in clinic practice"
(20 min) Dr. Mark Bale, Deputy Director, Science Research and Evidence Directorate, Department of Health, UK; Dr. Hermann Garden, Policy Analyst, OECD, France Carsten Lederer, The Cyprus Institute of Neurology and Genetics, Cyprus
"The HVP Global Globin 2020 Challenge and the ITHANET Portal: pioneering global epidemiological data collection and removing the diagnostic divide"
(10 min)

Q&A

Q&A

12:00 - 13:30 Lunch
12:00 - 13:30 Lunch (President Invited Lunch with Press - By Invitation)
12:00 - 13:00

Luncheon Seminar by Agilent Technologies

[Luncheon Session 3] by Agilent Technologies
Speaker

Osamu Ohara

Department of Technology Development, Kazusa DNA Research Institute

Talk Title:

Tales of Times Now Past in Human Genomics

Abstract:

Thirty years have passed since I came into the research field of human genomics. It started off as an encounter of DNA sequencing technology in my case. While the DNA sequencing technology I encountered 30 years ago went in and out of fashion in history of molecular biology, it was a nice gateway for me to enter the field of genomics from biophysics. However, thirty-years is a long time for a researcher’s life and thus I have witnessed that many topics/technologies have come and gone during this period. An important lesson learned is that we might easily miss core and essential concepts in genomics if we get caught in technological trends at superficial level too much. What is the best way to keep our research mind healthy and vital, particularly for young researcher? Taking the lessons from the past is obviously an approach to take to address this concern.

Because my research mind is still in biophysics, I might be an appropriate person as a storyteller of what is the happening of human genomics in an equitable manner. In this luncheon seminar, I would thus like to talk about some tales of “Times Now Past” in human genomics. Topics will be as follows; dawn of high-throughput DNA sequencing, Exploration and characterization of unknown human transcripts, integration of multi-layer omics data for getting a comprehensive understanding of the biological system, and real-world applications of omics technologies in medical sciences. In the last of the seminar, I hope future perspectives will be also discussed.

Speaker

Charmian Cher

Director, Clinical Strategy (Asia Pacific), Diagnostics and Genomics Group, Agilent Technologies K.K.

Talk Title:

INNOVATIONS THAT ADVANCE HUMAN HEALTH

Luncheon Seminar by Illumina

[Luncheon Session 4] by Illumina
Speaker

Dr. Mandy Ballinger

Group Leader, Genetic Cancer Risk, Program Manager, Genomic Cancer Medicine Program, Garvan Institute of Medical Research

Talk Title:

Heritable cancer risk in the genomic era

Abstract:

Premature death from cancer is a significant health and economic issue costing the Australian economy more than $4 billion annually. Health care expenditure on cancer is highest in the last 6 months of life so risk-stratified early detection and intervention are critical to cost-effectively reducing the impact of cancer on the community. Cancer is a genetic disease. Traditional clinic-based identification of heritable predisposition is giving way to genomic technologies applied to well annotated clinical cohorts, yielding a richer, more complex landscape of the hereditary basis of cancer. The International Sarcoma Kindred Study (ISKS) is a clinic based cohort formed to investigate hereditary predisposition in a previously understudied population with connective tissue cancers. Using a 72 cancer gene panel and a rare variant burden analysis (RVBA) we not only identified monogenic drivers but also polygenic contributions to sarcoma. Sarcoma patients with an excess burden of heritable deleterious genetic variants had a younger age at diagnosis and family histories atypical of hereditary cancer syndromes. Heritable risk correlates with early age at diagnosis. The Genetic Cancer Risk in the Young Study (RisC) and the Lions Kids Cancer Project (LKCP) is a combined cohort of 1400 young (0-40yrs) cancer patients. Using whole genome sequencing we aim to investigate further the heritable drivers of disease. Key to this is the Medical Genome Reference Bank (MGRB), a control cohort of whole genome data from 4000 well elderly Australians. The MGRB is being used in a RVBA of all early onset disease cohorts. Translation of genetic insights into better management of risk is pivotal to the value proposition for genomics, most likely through early cancer detection. Organ specific surveillance has been implemented in some hereditary cancer syndromes, but no surveillance has been available for multi-organ or non-specific cancer risk. Li-Fraumeni syndrome (LFS) is the paradigm case with a lifetime multi-organ cancer risk approaching 100%. There are no international consensus guidelines that take into account the multi-organ nature of the risk. In 2012 we began a surveillance study utilising whole body MRI in LFS. There are currently 40 participants and we have detected 7 new primary malignancies that have been treated with curative intent. We recently led a meta-analysis (n=578) and showed that new primary asymptomatic malignancies were detected in 7% of participants by whole body MRI at baseline across all age ranges. We are extending our study to include all individuals with multi-organ or non-specific cancer risk identified by genotype. We aim to inform identification of those at greatest heritable risk and influence clinical risk management in the genomic era of personalised medicine impacting on public health investment and lessening the burden of cancer on society.

13:30 - 15:00

Symposium 9 - Genome Editing
Chair: Gert-Jan van Ommen, Netherlands

Symposium 10 (RIKEN session) - Anatomy of the Human Genome
Chair: Piero Carninci, Japan

(30 min) Andrea Crisanti, Imperial College London, UK
"Editing population genetics for vector control"

David Hume, U of Edinburgh, Scotland
"Guilt by Association. Insights into innate immunity, cellular processes, transcriptional networks and complex trait genetics from the FANTOM5 data"

(30 min)

Karen Avraham, Tel Aviv University, Israel
"CRISPR/Cas9 genome editing to create mouse models for human deafness"

Stefania Giacomello, SciLifeLab, Sweden
"New insights into the human heart development using a combined spatial and single-cell transcriptomics approach"

Alistair Forrest, U of Western Australia, Australia
"An atlas of human functional long non-coding RNAs "

(30 min)

Scientific talk sponsored by EDITAS
- Ben Kleinstiver, Massachusetts General Hospital / Harvard Medical School
"Enhancing the safety and versatility of CRISPR genome editing"

[SCIENTIFIC TALK sponsored by EDITAS] in Symposium 9 “Genome Editing”
Speaker

Ben Kleinstiver
Massachusetts General Hospital / Harvard Medical School

Talk Title:

Enhancing the safety and versatility of CRISPR genome editing

Scientific talk sponsored by TWIST BIOSCIENC
- Emily Leproust, CEO, Twist Bioscience
"RAISING THE BAR: MAXIMIZED SCREENING EFFICIENCY AND TARGET SPECIFICITY WITH HIGH UNIFORMITY PRECISION GRNA SYNTHESIS"

[SCIENTIFIC TALK sponsored by TWIST BIOSCIENCE] in Symposium 9 “Genome Editing”
Speaker

Emily Leproust

CEO, Twist Bioscience

Talk Title:

RAISING THE BAR: MAXIMIZED SCREENING EFFICIENCY AND TARGET SPECIFICITY WITH HIGH UNIFORMITY PRECISION GRNA SYNTHESIS

Abstract:

Genome editing is a rapidly evolving field that touches various applications. The discovery of the CRISPR system and its ability to deliver precision editing of a single locus or thousands of loci simultaneously has transformed molecular biology and fueled synthetic biology. This highly parallel approach to genome editing enables significant reduction on time and cost for identifying variants that impact protein form or function. However, to fully realize the power of this system in providing screening efficiency, accuracy and uniformity of oligo synthesis is critical to ensure target specificity and complete guide representation. Traditional DNA synthesis is limited in its ability to deliver reliably on these requirements. With its innovative silicon-based DNA writing technology, Twist Bioscience’s platform, which has the lowest error rate in the industry, addresses these limitations, delivering high quality sgRNA template libraries at scale, enabling precision targeting of few and up to thousands of loci simultaneously and ultimately maximizing screening efficiency.

Jay Shin, RIKEN, Japan 
"FANTOM6: From Discovery to Functional Understanding of Long Non-Coding RNA"
15:00 - 16:30

Coffee Break & Poster Walk Session & Exhibition

16:30 - 18:00

Oral Presentation Sessions
Chair: Thomas Caskey, USA

Trainee Award Presentation
Chair: Yoichiro Kamatani, RIKEN / Kyoto University, Japan

(15 min)

Danielle Posthuma, VU University Amsterdam, Netherlands
"GWAS meta-analysis (N=279,930) identifies new genes and functional links to general cognitive ability"

Joachim Felix Luginbuhl
"Inferring transcriptional regulatory networks controlling direct conversion of induced neurons using Convert-seq"

(15 min)

Quan Nguyen, The University of Queensland, Australia
"Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution"

Werna TC Uniken Venema
"Single cell RNA sequencing of T cells in Crohn’s disease identifies tissue specific drug targets"

(15 min)

Saumya Agrawal, RIKEN, Japan
"Identifying long noncoding RNAs associates in human cells"

Maciej Trzaskowski
"GENOME-WIDE ASSOCIATION ANALYSES IDENTIFY 44 RISK VARIANTS AND REFINE THE GENETIC ARCHITECTURE OF MAJOR DEPRESSIVE DISORDER"

(15 min)

Päivi Pajukanta, UCLA, USA
"Variants at the enhancer-promoter interactions of human primary adipocytes drive adipose gene expression"

Robert Young "The consequences of promoter birth and death for human genetic and phenotypic variation"

(15 min)

Alessandra Breschi, Centre for Genomic Regulation, Spain
"The molecular basis of the cellular taxonomy of the human body"

Margherita Francescatto
"omicsCNN: a general deep learning framework for omics data modeling and classification"

(15 min)

Tamra Lysaught, University of Singapore, Singapore
"Building Trustworthy Governance for Sharing Genome Data: The case of Singapore"

Yun Rose Li
"A multi-omic approach to the "shared" biology of pediatric autoimmunity"

18:00 - 18:30 Travel to Conference Dinner venue
18:30 - 20:30 Conference Dinner (Ticketed Event)
Wednesday, 14 March 2018
Special Session Speaker

Walter Bodmer was born in 1936 in Frankfurt am Main, Germany, came to England at a very young age and went to Manchester Grammar School and Cambridge University where he studied mathematics. Having become fascinated with genetics, taught by R A Fishers as part of the mathematics course, in Cambridge, he did his PhD with Fisher in population genetics. He then went as a Post Doctoral fellow in 1961 to work with Joshua Lederberg at Stanford University and to learn molecular biology. While there, eventually as a member of the Faculty for eight years, he initiated the work with his wife, Julia Bodmer, and with Rose Payne, which contributed to the discovery of the HLA system, and also his long standing involvement with somatic cell genetics.

In 1970 Walter Bodmer returned to the UK to take up the chair of genetics at Oxford. In 1979 he left Oxford to become Director of Research at the Imperial Cancer Research Fund Laboratories in London and was appointed the first Director-General of the Fund in 1991. On retirement from the ICRF in 1996, he returned to Oxford University as Principal of Hertford college, and as head of the ICRF, now CRUK, Cancer and Immunogenetics laboratory at the Weatherall Institute of Molecular medicine.

Walter Bodmer was one of the first to suggest the idea of the Human Genome Project and was first a Vice- President, and then the second President of HUGO. He has made major contributions to human population genetics, somatic cell genetics, the development of the HLA system and more recently to cancer genetics, especially as applied to colorectal cancer.Walter Bodmer was elected FRS in 1974, Knighted in 1986 for his contributions to science, is a Foreign Associate of the US National Academy of sciences and is the recipient of more than 30 honorary degrees and memberships and fellowships of scientific and medical societies.

Baylor College of Medicine, US

Dr. Caskey was the CEO of The Brown Foundation Institute of Molecular Medicine at UTHSC-Houston. Dr. Caskey served as Senior VP, Human Genetics and Vaccines Discovery at Merck Research Laboratories, West Point, and as President of the Merck Genome Research Institute.

Dr. Caskey is Board Certified in Internal Medicine, Medical Genetics, and Molecular Genetics with 25 years of patient care experience. Member of: National Academy of Sciences, Institute of Medicine (Chair, Board on Health Sciences Policy), Royal Society of Canada, past President: American Society of Human Genetics & Human Genome Organization, and Texas Academy of Medicine, Engineering and Science. He is an editor of the Annual Reviews of Medicine.

Dr. Caskey received numerous academic and industry honors. His genetic research identified genetic basis of 25 major inheritable diseases and clarified the understanding of “anticipation” in triplet repeat diseases (Fragile X, myotonic dystrophy and over 25 others). His personal identification patent is the basis of worldwide application for forensic science and he is also a consultant to the FBI in forensic science.

Dr. Caskey is currently directing a program of Precision Medicine with Young Presidents Organization (YPO) co-sponsored by The Cullen Foundation for Higher Education. The program won the YPO International Award for most innovative education program. He is a Consultant to Human Longevity, Inc. and a member of the Board of Metabolon, Inc., both, leaders in precision medicine technology. Recent publications address the utility of genome wide sequencing to preventive adult onset diseases. His current research focuses on the application of whole genome sequence and metabolomics of individuals toward the objective of disease risk and its prevention.

Gert-Jan van Ommen, PhD, is former head of the Department of Human Genetics of Leiden University Medical Center (1991-2012), founder of the Leiden Genome Technology Center, director of the Center for Medical Systems Biology and board member of BBMRI-NL, ASHG and P3G. He is a founding member of BBMRI-ERIC, BBMRI-NL and co-coordinator of projects BBMRI-LPC and NeurOmics. Van Ommen is Editor-in-chief of the European Journal of Human Genetics, past president of HUGO and of the European and Dutch Societies of Human Genetics and past and current member of several committees in the fields of genetics, innovative health care, genomics, bioinformatics, biobanking, ethics and IP issues.

Van Ommen is specialized in neuromuscular diseases and biobanking. His main aim is to help improving diagnosis, therapy and prevention of rare and common diseases, including the societal aspects of genetic advances. His group has pioneered the diagnosis of genetic disease: performing the first prenatal diagnosis using DNA markers of DMD, developing many innovative gene mapping and mutation detection techniques, generating the first megabase map of a human gene (DMD). As of 1998, his group has been pioneering the exon-skipping approach as a therapy for DMD, in close collaboration with Leiden biotech company Prosensa since 2003, in 2015 acquired by Biomarin (San Francisco, USA). In this same year their first antisense-based DMD therapeutic product, Drisapersen, was submitted for approval to FDA and EMA.

Dr. Yoshiyuki Sakaki was born in 1942 at Nagoya, Japan. He is the Professor of University of Tokyo, Institute of Medical Science, Human Genome Center and also the Project Director of Genomic Sciences Center at RIKEN. He has been heavily involved in the Human Genome Project and acted the Vice-President of HUGO, the Representative of "Genome Science" Project, and a five-year Human Genome Project of Monbusho, Japan. He has been the President of HUGO since April, 2002. His major interest is molecular biology of Down Syndrome and other neurological disorders. He recently completed the sequencing of chromosome 21 and is now particularly working for molecular pathogenesis of Down Syndrome. In addition, he identified a responsible gene for familial amyloidotic polyneuropathy (FAP) in 1984, and human biological clock gene "period" in 1997. Also his group demonstrated for the first time that human LINE-1 is a retro-transposon in 1986. He was awarded to "Chevalier" from France Government in August 2001, in recognition of his contribution to the scientific co-operation between France and Japan.

The Jackson Laboratory, USA

Dr. Edison Liu is the president and CEO of The Jackson Laboratory. Dr. Liu joins the Laboratory from the Genome Institute of Singapore. As founding executive director, Dr. Liu built the GIS from a staff of three into a major research institute of 27 laboratory groups and a staff of 270, with faculty in functional genomics, computational biology, population genetics and genome-to systems biology. Before moving to Singapore in 2001, he was the scientific director of the National Cancer Institute's Division of Clinical Sciences in Bethesda, Md.

Born in Hong Kong in 1952, Edison Liu obtained his B.S. in chemistry and psychology, as well as his M.D., at Stanford University. He served his internship and residency at Washington University's Barnes Hospital in St. Louis, followed by an oncology fellowship at Stanford. From 1982 to 1987 he was at the University of California, San Francisco, first in a haematology fellowship at Moffitt Hospital and then as a postdoctoral fellow in the laboratory of Nobel laureate J. Michael Bishop. From 1987 to 1996 he was at the University of North Carolina at Chapel Hill, where he rose to director of the UNC Lineberger Comprehensive Cancer Centre's Specialized Program of Research Excellence in Breast Cancer, the director of the Laboratory of Molecular Epidemiology at UNC's School of Public Health, chief of medical genetics, and chair of the Correlative Science Committee of the national cooperative clinical trials group, CALGB.

University of Geneva Medical School, Switzerland

Stylianos E. Antonarakis is currently Professor and Chairman of Genetic Medicine at the University of Geneva Medical School, and the founding director of iGE3 (institute of Genetics and Genomics of Geneva). He received his MD (1975) and DSc (1982) from the University of Athens Medical School, and after a specialization in Pediatrics in the University Hospital, Athens Greece, moved to Baltimore, Maryland to the program of Medical Genetics at the Johns Hopkins University School of Medicine with Haig H. Kazazian and Victor McKusick (1980-1983). He joined the faculty of the Johns Hopkins University in 1983 and rose to full professor of Pediatric Genetics, Biology and Medicine in 1990.

In 1992, he moved to Geneva, Switzerland to chair Genetic Medicine in the University of Geneva. His research work includes the molecular bases of monogenic disorders and complex genetic disorders including the beta-thalassemias, hemophilias, and trisomy 21. His laboratory participated in the human genome sequence and functional analysis, particularly on chromosome 21. He has published extensively (more than 620 well-cited papers) in the scientific literature, and is co-editor of the current edition of the classic textbook “Genetics in Medicine”; he is listed as one of the highly cited scientists by the ISI institute (more than 40,000 citations; h-index 99). He was the President of the European Society of Human Genetics (2001-2002), member of the HUGO Council and President Elect of HUGO for 2013-2016, foreign member of the Academy of Athens (2003), member of EMBO (2006). He was awarded the Society of Pediatric Research Young Investigator Award (1984), International Jerome Lejeune Prize (2004), the European Society of Human Genetics Award (2005), and was elected to the Society of Scholars of the Johns Hopkins University (2006), and the American Academy of Physicians (2010). He was awarded the Commander of the Order of Phoenix medal from the Hellenic Democracy (2007).

His current interests and research projects are the functional analysis of the genome, effect of human genetic variation to phenotypic variation, the molecular pathogenesis of trisomy 21 and polygenic phenotypes, the functional characterization of the conserved fraction of the genome, diagnostics and prevention of genetic disorders, and the societal implications of genetics and genome research.

Symposium Speaker
Leiden University, Netherlands

Johan T. den Dunnen (PhD) is professor Medical Genomics, working in the depts. of Human Genetics and Clinical Genetics at the Leiden University Medical Center (Leiden, Nederland). He is a trained biologist, specialized in molecular biology/molecular genetics, performing research in the area of genetic diseases. As initiator of the Leiden Genome Technology Center (LGTC) he focuses on the development and application of high-throughput genome technology in research and diagnosis of genetic disease. He started his career to work on Duchenne and Becker muscular dystrophy for which his group developed several diagnostic tests as well as invented the “exon skipping” technology for the treatment for DMD/BMD and other diseases. His current focus is on next generation sequencing and data analysis pipelines, especially exome/genome sequencing and RNA-expression profiling and gene variant databases (the LOVD platform): trying to make sense of a genome. He is active for several international organizations promoting standardized variant reporting (HGVS nomenclature to describe sequence variants) and data sharing. DNA diagnostics is based on sharing data on genes, variants and phenotypes. Without sharing DNA diagnostics is not possible.

ETH Zurich, Switzerland

Gunnar Rätsch leads the Biomedical Informatics group at the Institute of Machine Learning at the ETH Zurich since May 2016. Before that he was an Associate Professor at Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College in New York City, where he will continue to hold adjunct positions for the coming years.

He studied computer science and physics and obtained his Ph.D. degree in Machine Learning in 2001 at the National Institute for Data Analysis in Berlin. As a postdoctoral fellow he was at the Research School of Information Sciences and Engineering of the Australian National University in Canberra (Australia) and at the Max Planck Institute for Biological Cybernetics in Tübingen (Germany). Between 2005 and 2011 he also led a research group at the Friedrich Miescher Laboratory of the Max Planck Society in Tübingen (Germany). In 2002, he received the Michelson award for his Ph.D. work with in Machine Learning and in 2007 he was awarded the Olympus prize from the German Association for Pattern Recognition for his work on Boosting.

His group’s research at ETH lies at the interface between methods research in machine learning & sequence analysis and relevant application areas in biology & medicine. In interdisciplinary collaborations, his group has significantly contributed to the understanding of several RNAdependent processes including RNA splicing and translation.

University of Melbourne, Australia

Professor Winship completed her medical training and postgraduate training in genetics and dermatology at the University of Cape Town, followed by a combined academic and clinical position there. In 1994, she joined the University of Auckland where she later became Professor of Clinical Genetics, Associate Dean Research, and Clinical Director of the Northern Regional Genetic Service.

Professor Winship has a wide range of clinical and research interests in inherited disorders, particularly those with adult onset, including familial cancer, and where foreknowledge of genotype may influence clinical or lifestyle measures to create positive patient outcomes. She has experience in gene discovery and in the translation of discovery into clinical practice. She has also highlighted the societal implications with research into the ethical, legal, cultural and psychosocial domains of genetic technology.

The Cyprus Institute of Neurology and Genetics, Cyprus

Dr Lederer is researcher and head of unit in the Department of Molecular Genetics Thalassemia (MGTD; head: Marina Kleanthous) at the Cyprus Institute of Neurology and Genetics (CING), where he is the organiser of the CING Lectures site seminar series. As assistant professor at the Cyprus School for Molecular Medicine he is course coordinator and faculty member for the courses Introduction to Molecular Biomedical Sciences and Molecular Basis of Monogenic Diseases, respectively.

Dr Lederer received his MSc from the Friedrich-Wilhelm University, Bonn, Germany and his PhD from the University of East Anglia, Norwich, UK. After postdoctoral work at the University of Cyprus and the CING on cell biology and functional genomics of amyotrophic lateral sclerosis he turned to development of advanced therapies and electronic infrastructures for thalassaemia. He has since set up a gene-therapy research programme at the CING, where he now heads the MGTD Gene Therapy and Genome Editing unit, and has achieved competitive funding for and continues to contribute to the ITHANET Portal for haemoglobinopathies, the largest repository for data related to haemoglobinopathies. Dr Lederer is member of the steering committee for the Global Globin 2020 Challenge, a global initiative of the Human Variome Project for the haemoglobinopathies, is board member and web content developer of the Cyprus Society of Human Genetics and a member of the European Society of Human Genetics and the Hellenic Society of Gene Therapy and Regenerative Medicine.

Imperial College London, UK

Andrea Crisanti is professor of molecular parasitology at Imperial College and Professor of Clinical Microbiology at the University of Perugia, Italy. He graduated in Medicine at the University of Rome "la Sapienza', and carried his doctoral work at the Basel Institute for Immunology. After the doctorate he was awarded a three years EMBO fellowship at the University of Heidelberg, Germany. Thereafter he was employed as medical consultant at the University of Rome Institute of Parasitology. Prof. Crisanti has pioneered the molecular biology of the human malaria vector Anopheles gambiae and has made a number of important scientific contributions that advanced the genetic and molecular knowledge of the malaria parasite and its mosquito vector. More recently Prof. Crisanti has applied concepts of synthetic biology for the development of genetic vector control measures aimed at either eliminating wild type mosquito populations or at interfering with their ability to transmit malaria. This resulted in the development and validation of a CRISPR based genetic drive system capable of spreading, into wild type mosquitoes, mutations impairing female fertility genes. The development of gene drive is generating a growing scientific interest as well as the attention of policy makers, media and pressure groups as a consequence of its implication in manipulating the genetic make up of wild species.

The University of Edinburgh, Scotland

Professor David Hume is an international authority in genome sciences, with a particular focus on the function of macrophages, specialised cells of the immune system involved in infection, inflammatory disease and cancer. He was Director of The Roslin Institute and Research Director of the Royal (Dick) School of Veterinary Studies between 2007 and 2017. He was previously Director of the ARC Special Centre for Functional and Applied Genomics at the Institute for Molecular BioScience at the University of Queensland.

University of Western Australia, Australia

Professor Alistair Forrest is the inaugural Cancer Research Trust Senior Fellow and head of the systems biology and genomics lab at the Harry Perkins Institute of Medical Research, University of Western Australia. He also holds a visiting senior scientist position at RIKEN Japan. He is an expert in transcriptomics and as scientific coordinator of the FANTOM5 consortium led an international team to global maps of human promoters, enhancers and long non-coding RNAs. These are landmark resources that are being used world-wide to build transcriptional regulatory networks, understand the effect of regulatory variant polymorphisms and for identifying cancer biomarkers. In 2016 he and the FANTOM5 team were awarded the Eureka Prize for Excellence in International Scientific Collaboration by the Australian Museum. He was also awarded the 2016 Millennium Science mid-career award at Lorne Genome. His lab is currently using bioinformatic and genomic approaches to study the relationship between tissue specific expression and tissue specific disease phenotypes, ligand-receptor mediated cell-to-cell communication networks and to build enhancer aware transcriptional regulatory network models.

RIKEN, Japan

Dr. Jay W. Shin acquired his PhD at ETH Zurich, Switzerland after his research training at Harvard Medical School (HMS) under Prof. Michael Detmar. During this period, Jay investigated Transcriptional Regulatory Network controlling tumor angiogenesis. Passionate for transcriptome, Jay continued his research at the RIKEN Institute under Dr. Yoshihide Hayashizaki as a postdoctoral fellow. Now, as a team leader, Jay is co-leading FANTOM6 – investigating the functional role of long non-coding RNAs – together with Dr. Michiel de Hoon. Jay enjoys developing new technologies and functional genomics platforms to decipher the molecular mechanisms involved in cellular plasticity and reprogramming. 

Time Thursday, 15 March 2018
8:00 - 09:00

What are the Critical Factors to Publish Well?
Meet the Editors Session from Science, Nature, CSHL, EMBO and Human Genomics
Chair: Karen Avraham, Tel Aviv University, Israel

9:00 - 09:45

Plenary 2: Adrian Krainer, Cold Spring Harbor Laboratory, US
"Development of Spinraza for the treatment of spinal muscular atrophy"
Chair: Sanghyuk Lee, South Korea

09:45 – 10:45

Chen Award for Distingushed Scientist - Aravinda Chakravarti
"The noncoding genome and its contribution to human disease"

Chen Award of Excellence - Ami Bhatt
"Translating the human microbiome in medicine"

Chair: Charles Lee, USA

10:45 - 11:15

HUGO African Prize - Collen Masimirembwa
Chair: Stylianos Antonarakis, Switzerland

11:15 - 12:30

Lunch

11:30 - 12:30

Luncheon Session by Fluidigm K.K.

High-resolution characterization of drug-induced cellular response
Speaker

Erik Arner, MSc, PhD

Unit Leader, CLST, RIKEN, Yokohama

Talk Title:

High-resolution characterization of drug-induced cellular response

Abstract:

Drug response expression profiling has emerged as a powerful method for characterizing the cellular response to drug treatment at a molecular level. In this approach, cells are treated with various drugs and changes in expression compared to negative control are measured. Using this method, it is possible to gain insight into the mode of action (MOA) of drugs, distinguish direct from indirect targets and also assess off target effects. Currently existing resources lack in several important aspects, regarding the resolution they can achieve and which kinds of cell types can be profiled. Firstly, the response measure is biased by only considering a fixed set of genes to profile. This may leave out genes that are very specific to the pathways involved, and also RNAs not commonly present on microarrays such as lncRNAs and enhancer RNAs. By using a sequencing based method it would be possible to get an unbiased response measure, and also get specific response profiles at different genomic elements such as enhancers and promoters. Secondly, studies of drug response in bulk cell culture do not address the heterogeneity in the drug response. Several studies have shown that cells do not react to drug treatment in a uniform way, including at the transcriptional level. If done at the single cell level, it is possible to get a more precise characterization of the response, and to identify genes and pathways that enable or disable an efficient response, by using advanced gene network reverse-engineering approaches, which require multiple expression profiles to work properly. Thirdly, existing resources are mainly done in cancer cell lines, which are not always good models for in vivo situations. In particular, rare cell types are impossible to profile using bulk cell approaches.

We will here present a project where we measure the transcriptional drug response at promoters and enhancers using C1 CAGE, a newly developed method for doing CAGE in single cells. C1 CAGE is able to detect expression at promoters in a quantitative way, as well as enhancer expression. By using C1 CAGE, we can address the shortcomings of currently used cell population and array based methods: achieving unbiased expression measurements with high genomic resolution, assess population response heterogeneity, and profile rare cell types. Initially we profile the response of two HDAC inhibitors, VPA and TSA, in three cell types (two cell lines, HepG2 and MCF-7, and one primary cell type, fibroblasts). In the second phase of the project, we focus on Acute Myeloid Leukemia (AML) and profile the response in AML cells and leukemic stem cells to a novel drug with potential AML relevance (BRD inhibitor OTX-015), with hematopoietic stem cells (HSC) and hematopoietic progenitor cells (HPCs) from healthy donors used as control. The final goal is to have a set of transcriptional response profiles to highly relevant drugs in primary cells, stem cells, cancer stem cells and IPS derived cell models of rare cell types.

Luncheon Session 6
12:30 - 14:00

Symposium 11 - Population and Evolutionary Genetics
Chair: Juergen Reichardt, Ecuador

Symposium 12 - Model Organisms for Human Diseases
Chair: Aki Minoda, Japan

(30 min)

Svante Pääbo, Max Planck Institute, Germany
"Archaic Genomics"

Peter Koopman, U of Queensland, Australia
"Disorders of Sex Development: What we’re learning from CRISPR/Cas9 in mice"

(30 min)

Michel Georges, Universite de Liege, Belgium
"Risk loci for inflammatory bowel disease are enriched in multigenic regulatory modules that act across cell types and encompass causative genes"

Nadia Rosenthal, The Jackson Laboratory, US
"The mouse ascending: prospects for gene discovery through diversity"

(30 mins each)

Peter Visscher, U of Queensland, Australia
"Using GWAS data to estimate selection and adaptation on complex traits"

Teresa Nicolson, Oregon Hearing Research Center, US
"Using zebrafish to gain basic insights into human deafness"

14:00 - 14:45

Coffee Break & Exhibition

14:45 - 15:30

Plenary 3: Yuan-Tsong Chen, Academia Sinica, Taiwan
"Therapies for genetic diseases: Lessons learned from Pompe disease"
Chair: Ed Liu, USA

15:30 - 16:00

Student Award

16:00 - 16:30

Closing Remarks

17:00 - 20:00 Council Meeting (Invitation Only)
Thursday, 15 March 2018
Plenary Speaker
Cold Spring Harbor Laboratory, US

Dr. Adrian Krainer is the St Giles Professor of Molecular Genetics and Program Chair of Cancer & Molecular Biology at Cold Spring Harbor Laboratory, which he joined in 1986. He received a B.A. in Biochemistry from Columbia University and a Ph.D. in Biochemistry from Harvard University. His laboratory studies pre-mRNA splicing regulation, and is also engaged in developing targeted therapies to correct or modulate alternative splicing in genetic diseases and cancer. Together with Ionis Pharmaceuticals, they developed nusinersen (Spinraza), an antisense-oligonucleotide drug that corrects defective splicing of the SMN2 gene and is the first FDA/EMA-approved therapy for spinal muscular atrophy, an inherited motor-neuron disease. Prof. Krainer is a Pew Biomedical Scholar, a MERIT-award recipient from the NIH, a past President of the RNA Society, and a member of the American Academy of Arts and Sciences and the Royal Society of Medicine. He has authored ~200 publications and 18 patents.

Academia Sinica, Taiwan

Professor Yuan-Tsong (Y-T) Chen received his MD degree from National Taiwan University (Taipei) and PhD from Columbia University (USA). He is Director Emeritus and Distinguished Research Fellow of the Institute of Biomedical Sciences, Academia Sinica, Taiwan and also Professor Emeritus of Pediatrics of Duke University.

Professor Chen is a physician and scientist, recognized for his work on human genetic disorders. His translational research leads to the development of now standard therapies for two devastating inherited metabolic diseases: a simple and effective cornstarch therapy for severe hypoglycemia in glycogen storage diseases and an enzyme replacement therapy, the first ever treatment, for a debilitating, progressive and often fatal myopathy called Pompe disease. He has also identified susceptibility genes for several human diseases, including genes for diabetes, Kawasaki disease and severe adverse drug reactions.

Professor Chen has published more than 280 peer-review journal articles and contributed numerous book chapters in textbook, such as Harrison’s Principles of Internal Medicine and Nelson’s Pediatrics.

Professor Chen is an elected member of Academia Sinica, Taiwan and an elected member of the World Academy of Sciences.

Chen Award Winner
Johns Hopkins University School of Medicine, USA

Aravinda Chakravarti, Ph.D. is Professor of Medicine, Pediatrics, Molecular Biology & Genetics, and, Biostatistics at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health. He was the 2008 President of the American Society of Human Genetics, is a member of the US National Academy's Institute of Medicine and an Honorary Fellow of the Indian Academy of Sciences. He has been a key participant and architect of the Human Genome, HapMap and 1000 Genomes project. His research is aimed at genome-scale analysis of humans and computational analysis of gene variation and function to understand the molecular genetic basis of complex human disease.

Aravinda Chakravarti received his doctoral degree in human genetics in 1979 and started his faculty career at the University of Pittsburgh (1980 - 1993), was the James H. Jewell Professor of Genetics at Case Western Reserve University (1994-2000), and the Director and Henry J. Knott Professor of the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins (2000-2007). He is one of the founding Editors-in-Chief of Genome Research and Annual Reviews of Genomics & Human Genetics, and serves on the boards of numerous international journals, academic societies, the NIH and biotechnology companies.

Stanford University, USA

Prof. Ami Bhatt is a physician scientist with a strong interest in microbial genomics and metagenomics. She received her MD and PhD from the University of California, San Francisco where she was inducted into the Alpha Omega Alpha Medical Honors Society. She then carried out her residency and fellowship training at Harvard’s Brigham and Women’s Hospital and Dana-Farber Cancer Institute, and served as Chief Medical Resident from 2010-2011. She joined the faculty of the Departments of Medicine (Divisions of Hematology and Bone marrow transplantation) and Genetics at Stanford University in 2014 after completing a post-doctoral fellowship focused on genomics at the Broad Institute of Harvard and MIT. Prof. Bhatt is a current Damon Runyon Clinical Investigator and has received multiple awards for her academic scholarship and global health leadership, including a Union for International Cancer Control-Young Leader Award and the Rosenkranz Prize for Global Health.

Her team’s research program seeks to illuminate the interplay between the microbial environment and host/clinical factors in human diseases. Her translational laboratory develops and applies novel molecular and computational tools to study strain level dynamics of the microbiome, to understand how microbial genomes change over time and predict the functional output of microbiomes. These innovations facilitate much improved (1) measurement of the types and functions of microbes in patients with non-communicable diseases, (2) understanding of the interactions between microbial genes, gene products, and host cells and (3) testing of the impact of microbially targeted interventions in clinical trials.

HUGO African Prize Winner
African Institute of Biomedical Science and Technology, Zimbabwe

Collen Masimirembwa graduated with an Honours degree in Biochemistry (1989) and completed DPhil studies in Biochemistry (1993) at the University of Zimbabwe focusing on the metabolism of anti-parasitic drugs. The work led to the elucidation of the metabolism of the anti-schistosomicidal drug, praziquantel. Fascinated by the then emerging field of pharmacogenetics, he conducted studies leading to a PhD in Medical Biochemistry & Biosphysics (1995) at the Karolinska Institute (Sweden) focusing on pharmacogenetics in African populations. The work led to the discovery of the molecular genetic basis of why people of African origin have a reduced capacity to metabolise and eliminate drugs which are substrates of the enzyme CYP2D6. During a two year postdoctoral fellowship at the Biomedical Centre (BMC) at Uppsala University, he worked on the discovery of molecular targets in plasmodium falciparum (1996-1997). In 1998 he joined AstraZeneca Pharmaceutical company (Sweden) where he worked as a Principal Scientist (1998-2007) in preclinical drug metabolism and pharmacokinetics and bioanalytical chemistry (DMPK &BAC). Collen made many innovative contributions to in slico and in vitro drug absorption, distribution, metabolism, excretion and toxicology (ADMET) especially in understanding molecular aspects of drug-enzyme interactions. In 2007 Collen assumed a permanent of position as the President and Chief Scientific officer of AiBST in Zimbabwe, an institute he had founded in 2002. Human capacity building in Africa is at the core of his scientific drive hence the training of many postgraduates (MSc and PhD) and prolific publication of original research findings that have relevance to Africa’s healthcare challenges. He has received many awards for his research work including a certificate of Distinction in Biochemistry from the Government of Zimbabwe and the Innovation Award from ANDi.

Symposium Speaker
Max Planck Institute, Germany

Svante Pääbo has developed techniques and approaches that allow DNA sequences from archaeological and paleontological remains to be determined. This has allowed ancient DNA from extinct organisms, humans, animals and pathogens to be studied. He determined a high-quality Neandertal genome sequence, allowing for the reconstruction of the recent evolutionary history of our species and the realization that Neandertals contributed DNA to present-day humans who live outside Africa. By studying DNA sequences from a small Siberian bone he discovered Denisovans, a previously unknown hominin group distantly related to Neandertals. He also works on the comparative and functional genomics of humans and apes, particularly the evolution of genetic features such as the FOXP2 ‘speech and language’ gene that may underlie aspects of traits specific to humans.

Svante Pääbo has received several honorary doctorates and scientific prizes and is a member of numerous academies. He is currently a Director at the Max-Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Universite de Liège, Belgium

Michel Georges received his Doctor of Veterinary Medicine from the University of Liège in 1983, followed by a Master of Science in Molecular Biology from the Free University of Brussels in 1985. Since 1994 he has been heading the Unit of Animal Genomics at the University of Liège. He played an instrumental role in establishing the GIGA (Interdisciplinary Cluster for Applied Genoproteomics) Research Institute within the University of Liege. In 2006, the Unit of Animal Genomics became part of GIGA, and Michel Georges is now the Research Director of GIGA.

Michel is well known for his research in the field of animal genetics and genomics. He is one of the world leaders in the development of tools and strategies for increasing the efficiency of genome analysis for livestock improvement. He has been instrumental in the identification and mapping of genes affecting both single gene and complex multi‐gene economically important traits in livestock, double‐muscling in cattle among the best known. Among his present activities is research on the processes of gene mutation and recombination. These processes have a direct impact on phenotypes and traits such as lethality and fertility.

University of Queensland, Australia

Peter Visscher’s undergraduate studies were in the Netherlands. He moved to Edinburgh (UK) in 1987 for an MSc and subsequent PhD in animal breeding and genetics, working on the estimation of genetic parameters in large livestock pedigrees. A postdoctoral period in Melbourne (Australia) was followed by a return to Edinburgh, where he developed methods to map genetic loci underlying complex traits. In 1995 he moved to a faculty position at the Institute of Evolutionary Biology of the University of Edinburgh, developing gene mapping methods and software tools, with practical applications in livestock and human populations. Visscher joined the Queensland Institute of Medical Research in Brisbane (Australia) in 2005 and in 2011 moved to the University of Queensland where he is Professor and Chair of Quantitative Genetics and Director of the Program in Complex Trait Genomics. Visscher is a Senior Principal Research Fellow of the Australian National Health and Medical Research Council and was elected a Fellow of the Australian Academy of Science in 2010. Visscher’s research interests are focussed on a better understanding of genetic variation for complex traits, including quantitative traits and disease, and on systems genomics.

University of Queensland, Australia

Dr. Koopman was awarded a PhD from the University of Melbourne in 1986, for research in sstem cell differentiation. He undertook two postdoctdoral appointments in London, first at the Medical Research Council’s Mammalian Development Unit, where he conducted a molecular analysis of mouse embryo development. His second postdoc was undertaken at the MRC National Institute for Medical Research, isolating the mouse Y-chromosomal gene Sry and demonstrated its role as the testis-determining gene by reversing the sex of XX transgenic mice. In 1992 he took up a research group leader position at the University of Queensland, Brisbane. From 2007-2012, he was a Federation Fellow of the ARC, and in 2008 was elected a Fellow of the Australian Academy of Science.

Dr.Koopman is in the Division of Genomics of Development and Disease at the Institute for Molecular Bioscience, The University of Queensland, Australia. He was part of the team that discovered the Y-chromosomal sex-determining gene Sry in 1990, recognized as one of the most important breakthroughs in 20th century genetics. He heads a research team whose current work focuses on genes that regulate embryonic development, with special emphasis on the molecular genetics of sex development, fertility, gonadal cancers and intersex conditions.

The Jackson Laboratory, US

Rosenthal’s research uses mammalian genetics to explore the embryonic development of heart and skeletal muscle and the regeneration of adult tissues. She focuses on muscle and cardiac developmental genetics and the role of growth factors, stem cells and the immune system in tissue regeneration.

She is a global leader in the use of targeted mutagenesis in mice to investigate muscle development, disease and repair, and is a participant in EUCOMM, the European Conditional Mouse Mutagenesis Program, where she coordinates the selection and production of new Cre driver strains for the international mouse genetics community.

After earning her Ph.D. in biochemistry at Harvard Medical School, she started collaborating with JAX researchers, developing her longstanding focus on mammalian genetics using the mouse as model. As her career progressed, through faculty appointments at Harvard Medical School and Boston University School of Medicine, Rosenthal’s network with the JAX faculty and Board of Trustees continued to grow.In 2001 Rosenthal moved to Rome to establish the mouse biology program for the European Molecular Biology Laboratory (EMBL).

Oregon Hearing Research Center, US

After receiving her B.S. in Biochemistry at Western Washington University, Teresa Nicolson received her Ph.D. in Biological Chemistry in 1995 from the University of California, Los Angeles. She then trained as a post-doctoral fellow at the Max Planck Institute for Developmental Biology in Tuebingen, Germany. In 1999, Teresa became an independent Group Leader at the same institute. In 2003, she was appointed as an assistant professor to the Oregon Hearing Research Center with a joint appointment in the Vollum Institute. She was promoted to associate professor in 2005 and professor in 2014. Teresa was an HHMI Investigator from 2005 to 2013.

For her graduate thesis work, she received training in basic aspects of cell biology, which was helpful for later studies in zebrafish that included analyses of phenotypes at the molecular and cellular level. As a post-doctoral fellow and later as an independent group leader at the Max-Planck-Institute in Tübingen, Germany, she received training that enabled her to positionally clone genes, and characterize defects in hair-cell morphology and function in zebrafish models of human deafness. During this time, she participated in forward genetic screens that were unprecedented in scale, and collected a large group of mutants that specifically affect auditory/vestibular function in larvae.