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Theme: Reproducible Genomics
April 12, 2017 SAS Institute, Cary, NC, USA
Massive Analysis and Quality Control Society Conference (MAQC2017)
Are They
Reproducible
???
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Table of Contents
Agenda at glance………………………………………………………………….3
About the MAQC Society ……………………………………………….……4
Key Information about the Conference ……………………………….5
MAQC Society Board and Committee ….………………………………6
Pre‐Conference Workshop (2nd SEQC2 workshop) …………….7
MAQC2017 Conference Program ….……………………………………11
o Future MAQC Society Conferences ……………………….… 16
o Biosketch of the Speakers …………….…………………………...17
Post‐Conference Workshop..………………………………………………33
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Program at Glance
7‐9 PM: The Board meeting
Page 3‐6: About MAQC Society and
Key Info
Page 7‐10: The pre‐conference
workshop on the 2nd SEQC2 working
group meeting Overview: The FDA‐led consortium project to evaluate WGS and target gene sequencing technologies. The previous workshop has led to the formation of 7 working groups to address specific areas of focus. In this workshop, each working group will provide update on (1) study design, (2) the progress, (3) data analysis plan, and (4) timeline.
Page 11‐32: The MAQC Society
meeting
Page 33: The post‐conference workshop on Advanced Data Analytics Overview: The workshop provides hands‐on practice of applying advanced statistical methods for clinical and genomics data analysis.
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About the Massive Analysis and Quality Control (MAQC) Society
The MAQC society is a new society and this is its first annual society meeting. The purposes of the Society are scientific, educational, literary, and charitable. The objective of the Society is to communicate, promote, and advance reproducible science principles and quality control for analysis of the massive data generated from the existing and emerging technologies in solving biological, health, and medical problems. The goals of the Society are to
Advocate and facilitate the development and application of quality control practice and standard analysis protocols of bioinformatics and biostatistics for enhanced reproducibility across multiple experiments, laboratories, and data analysis methods,
Advance our understanding and best practices in the analysis of massive data from emerging technologies applied in drug development, clinical application, and safety/risk assessment.
To achieve thes goals, the MAQC Society will:
Provide a platform for the members to address and discuss the issues related to the objective.
Coordinate activities that will contribute to the development of the objective.
Engage its dialog and cooperation with societies and organizations of similar interest and focus.
Facilitate the collaboration of researchers to develop projects related to the objective.
Promote education and communication of the objective with the national and international communities.
Inform the general public on the results and implications of current research related to the objective.
Support, encourage, and mentor the career development of young scientists and students deeply engaged in the objective.
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Key information: Conference Date: April 12 (Wednesday), 2017
Venue:
SAS Institute Inc., Building C 100 SAS Campus Drive, Cary, NC 27513, USA http://www.sas.com/, http://www.jmp.com/
Hotel (conference rate is available): Embassy Suites
201 Harrison Oaks Boulevard, Cary, North Carolina, 27513, USA TEL: +1‐919‐677‐1840 FAX: +1‐919‐677‐1841
Registration fee: $200 for all the participants Registration website: www.MAQCSociety.org
Contact persons: Weida Tong (NCTR/FDA)
o Email: [email protected], [email protected] o Tel: +1‐870‐543‐7142 (O), +1‐501‐200‐7370 (C)
Wenjun Bao (JMP/SAS) o Email: [email protected] o Tel: 1‐919‐531‐1484 (o), 1‐919‐244‐0260 (c)
Two adjacent events in the same location without registration fee:
1. April 10‐11 (Mon‐Tues): The pre‐conference workshop on the 2nd SEQC2 working group meeting Overview: The FDA‐led consortium project to evaluate WGS and target gene sequencing technologies. The previous workshop has led to the formation of 7 working groups to address specific areas of focus. In this workshop, each working group will provide update on (1) study design, (2) the progress, (3) data analysis plan, and (4) timeline.
2. April 13 (Thus): The post‐conference workshop on Advanced Data Analytics
Overview: The workshop provides hands‐on practice of applying advanced statistical methods for clinical and genomics data analysis.
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Steering Committee:
President: Weida Tong, Ph.D., National Center for Toxicological Research, FDA, USA
Local Organizing Committee Lead: Wenjun Bao, Ph.D., SAS Institute, Cary, NC, USA
President‐Elect: Leming Shi, Ph.D., Fudan University, Shanghai, China
President‐Elect: Cesare Furlanello, Ph.D., FBK, Trento, Italy
David Kreil, Ph.D., Boko University, Vienna, Austria
Pawel Labaj, Ph.D., Boko University, Vienna, Austria
Joaquin Dopazo, Ph.D., Clinical Bioinformatics Area, FPS, Seville, Spain
Rebecca Kusko, Ph.D., Immuneering Corporation
Wenzhong Xiao, Ph.D., Stanford University, MA, USA
Baitang Ning, Ph.D., NCTR/FDA, USA
Pierre Bushel, Ph.D., NIEHS, RTP, USA
James Willey, Ph.D., University of Toledo, Ohio, USA
MAQC Society Board of Directors and Officers: A Board of Directors is chartered to develop the Society and oversee the Society’s activities. Specifically, the Board is dedicated to building and strengthening the reproducible science practice by (1) engaging scientists in academia, industry, and government, (2) fostering collaboration and harmonization of education, research tools, and new technologies, and (3) building the global‐scientific infrastructure needed to advance and promote reproducible science.
President and Board Chairman: Weida Tong, Ph.D., National Center for Toxicological Research (NCTR), FDA, United States
President‐Elect: Leming Shi, Ph.D., Fudan University, China
President‐Elect: Cesare Furlanello, Ph.D., FBK, Trento, Italy
Russ Wolfinger, Ph.D., SAS Institute, USA
Chris Mason, Ph.D., Weill Cornell Medicine, New York, USA
Ben Haibe‐Kains, Ph.D., Princess Margaret Cancer Center in Toronto, Canada
Wendell Jones, Ph.D., Q2 lab solutions, USA
Matthias Fischer, Ph.D., Cologne University, Germany
Susanna Sansone, Ph.D., Oxford University., UK
Executive secretary: Becky Kusko, Ph.D., Immuneering Corporation, USA
Treasurer: Baitang Ning, NCTR/FDA, USA
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Brief overview of the Pre‐Conference SEQC2 workshop:
This is the fourth project of MicroArray Quality Control (MAQC) consortium, named Sequencing Quality Control Phase 2 (SEQC2). The primary objective is to develop standard analysis protocols and quality control metrics for fit‐for‐purpose use of next‐generation sequencing (NGS) data to enhance regulatory science research and precision medicine. The project consists of three specific aims: (1) to develop quality metrics for reproducible NGS results from both whole genome sequencing (WGS) and targeted gene sequencing (TGS), (2) to benchmark bioinformatics methods for WGS and TGS towards the development of standard data analysis protocols, and (3) to assess the joint effects of key parameters affecting NGS results and interpretation for clinical application. The figure below outlines the draft study design which is subject to change, revise and improve through this workshop.
About MAQC: It is the FDA‐led community wide consortium effort to address issues relating to the application of constantly evolving high‐throughput genomics technologies to either assess safety and efficacy of FDA regulated products or their safe and effective use in clinical applications as in vitro diagnostic devices. The MAQC consortium completed three projects between 2005 ‐2014 (namely MAQC I, II and III), resulting in ~30 publications and one third of which were published in Nature Biotechnology. Furthermore, two papers of these papers were among the most cited in Nature Biotechnology in the last 20 years (http://blogs.nature.com/tradesecrets/2016/03/04/most‐cited‐best‐papers‐sensors‐sequencing‐and‐arrays‐and‐imaging). More information about MAQC is available from (http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/default.htm).
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Pre Conference Workshop
“2nd SEQC2 working group meeting”
Monday, April 10, 2017
8:00 AM‐ Registration (Coffee and snack)
8:30 – 9:00 AM Welcome and Introduction
8:30 – 8:40 Welcome remark (Russ Wolfinger, Director of Scientific Discovery and Genomics, SAS Institute)
8:40 – 9:00 SEQC2 – An overview and update (Weida Tong, NCTR/FDA) 9:00 – 12:00 PM WG#1: Somatic Mutation Chair: Wenming Xiao (NCTR/FDA) and Zivana Tezak (CDRH/FDA) This session has 180 min (15 min for each speaker (150 min) + 15min break + 15min Q/A):
1. Overview (study objective/design), Wenming Xiao (NCTR/FDA) 2. ATCC cell lines, Maryellen de Mars/Liz Kerrigan, ATCC 3. Sequence quality and preprocessing (Yongmei Zhao, NCI) 4. Error fixing in sequence reads (Ping Gong, USACE) 5. Sequence alignment (Maggie Cam, NCI) 6. SNV/small indel calling (Chunhua Yuan, NCI) 7. Short reads and long reads (Litai Fang, Roche) 8. Mutation annotation (Mehdi Pirooznia, NHLBI) 9. Cross‐site comparison (Bin Zhu, NCI) 10. Single Cell sequencing (Malcolm Moos, CBER/FDA)
Panel Discussion and Q/A (15 min)
12:00 – 1:00 pm Lunch will be provided (in Building C Cafeteria)
1:00 – 4:30 PM WG#2: Target Gene Sequencing Chair: Joshua Xu (NCTR/FDA) and Wenjun Bao (SAS Institute)
This session has 210 min (with 20min break + 20min Q/A):
Overview (Study objective/design), Joshua Xu (20 minutes)
Pilot study and data analysis results (15 min each = 105min) 1. Agilent: Characterization of Universal Human Reference DNA with Agilent
ClearSeq Comprehensive Cancer panel (Natalia Novoradovskaya and Anne Bergstrom Lucas)
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2. IDT: Accurate detection of low frequency genetic variants using novel, molecular tagged sequencing adapters (Kristina Giorda)
3. Illumina (TBD) 4. Qiagen (TBD) 5. Roche NimbleGen (TBD) 6. Thermo Fisher (Simon Cawley) 7. TOMA (TBD)
Peripheral studies (15 minutes each = 45min) 1. Analysis of Cell line sequencing data to build consensus variant calls (TBD) 2. Deep sequencing of Neuroblastoma samples with IDT’s molecular tagging
technique (TBD) 3. Developing a liquid biopsy test for lung cancer (Don Johann, UAMS)
Panel discussion and Q/A (20min)
6:30 – Dinner (TBD)
Tuesday, April 11, 2017
8:00 AM‐ Registration (Coffee and snack)
8:30 – 10:00 AM WG#3: Germline Variants Chair: Huixiao Hong (NCTR/FDA) and Leming Shi (Fudan, China)
This session has 90 min (15 min for each speaker (5 speakers) + 15 min Q/A):
1. Study design / HapMap trio data, Huixiao Hong (NCTR/FDA) 2. Chinese quartet data / Agreement on data and results sharing, Leming Shi 3. ABRF data / Data analysis, Chris Mason 4. Downstream data analysis, Kelci Miclaus 5. Rare variant analysis using Whole Exome Sequencing data, Yingtao Bi 6. Panel Discussion and Q/A (15 min)
Coffee Break (20min) 10:20 – 12:00 PM WG#4: Difficult Genes Chair: Baitang Ning (NCTR/FDA) and Wenzhong Xiao (Harvard) This session has 100 min:
Update the working status of WG#4 and DMET Selection ( 10 min): Baitang Ning
HLA genotyping by NGS, challenges and strategies (20 min): Wenzhong Xiao
Finland Twin Cohort for Difficult Genes (20 min): Andreas Scherer and Chris
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Mason
HLA‐typing from RNA‐seq (20 min): Chad Brown
Panel Discussion and Q/A (30 min) 12:00 – 1:00PM Lunch will be provided (in Building C Cafeteria) 1:00 – 3:00 PM Additional Topics Chair: Chris Mason (Cornell U) and David Kreil () This session has 120 min (15 min for each speaker (8 speakers):
Epigenomics in SEQC2 (WG#7), Chris Mason
Targeted RNA‐seq for o Ontology and difficult genes, David Kreil o Pilot results, Paweł Łabaj
FFPE in SEQC2: Design of FFPE samples through cell line mixture and comparison study (Tom Blomquist)
Spike‐in in SEQC2: o Spike‐in DNAs for internal control (Tim Mercer??) o Design and Pilot study of competitive template spike‐in control mixtures
for targeted DNA‐seq quality control by Jim Willey and Tom Morrison
FDA activities in NGS: o CDER review process (Eric Donaldson, CDER/FDA) o NGS in CDRH review process (Zivana Tezak, CDRH/FDA)
NCBI data repository (Chunlin Xiao/Steve Sherry, NCBI)
3:00 – 5:00 PM Discussion and Decision Chair: Weida Tong (NCTR/FDA) and Leming Shi (Fudan U)
Next step
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MAQC2017 Conference Program
“Reproducible Genomics”
Tuesday, April 11, 2017
5:00 – 8:00 PM Registration Desk Open 6:30 – 8:30 PM Welcome reception Taipi 101 121 E Chatham St., Cary, NC 27511 (919) 388‐5885
Wednesday, April 12, 2017
8:00 – 12:00 AM Registration Desk Open 8:00 – 8:30 AM Coffee and Snacks
Morning Session
8:30 – 8:45 AM General Session
Welcome and Introductory Remarks Russ Wolfinger, Director of Scientific Discovery and Genomics, SAS Institute, USA MAQC Society – An Introduction Weida Tong, National Center for Toxicological Research, FDA, USA
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8:45 – 10:00 AM Session 1: Advancing Reproducible Genomics – Lessons Learned from the MicroArray and Sequencing Quality Control (MAQC/SEQC) Consortium
Session Chairs: Wenjun Bao (SAS Institute) and Leming Shi (Fudan University)
8:45 – 9:15 Keynote Address on “Reproducibility, Statistics, and MAQC/SEQC ” Russ Wolfinger, Director of Scientific Discovery and Genomics, SAS Institute, USA
9:15 – 9:30 Top 5 Lessons‐Learned from MAQC‐I
Wendell Jones, Q2 lab solutions, USA
9:30 – 9:45 Top 5 Lessons‐Learned from MAQC‐II Leming Shi, Fudan University, Shanghai, China
9:45 – 10:00 Top 5 Lessons‐Learned from MAQC‐III/SEQC Weida Tong, NCTR/FDA, USA
10:00 – 10:15 Coffee Break
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10:15 – 11:30 Session 2: Current Efforts Towards Reproducible
Genomics Session Chairs: Matthias Fisher (Colon University) and Andreas
Scherer (EATRIS)
10:15 – 10:30 RNA‐Seq Pipeline Evaluation May Wang, Georgia Institute of Technology and Emory University, Atlanta, USA
10:30 – 10:45 Best Practice for RNA‐Seq Analysis
David Kreil, Boko University, Vienna, Austria 10:45 – 11:00 Minimal Elements for Determination of Confidence Limits
Around NGS Measurement of DNA Variant Fraction James Willey, University of Toledo, Ohio, USA
11:00 – 11:15 The Least Common Denominator: Synthetic Spike‐In Modules
for Referencing NGS Pipelines, Experiments, and Individual Samples Torsten Reda, Lexogen, Vienna, Austria
11:15 – 11:30 Advancement in Metrology for Biomedical Science Jing Wang, National institute of metrology, Beijing, China
11:30 – 1:00 PM Lunch in Building C Cafeteria
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Afternoon Session
1:00 – 2:45 PM Session 3: Reproducible Genomics in Practice Session Chairs: Cesare Furlanello (FBK) and Joaquin Dopazo
(PFRC)
1:00 – 1:30 Keynote Address on “Standards in Genomics and Epigenomics for This World and Others” Chris Mason, Weill Cornell Medical College, USA
1:30 – 1:45 Towards Reproducible Cancer Genomics
Jian‐Liang Li, NIEHS, RTP, USA 1:45 – 2:00 Towards Reproducible Toxicogenomics: T‐Test versus ANOVA
Binsheng Gong, NCTR/FDA, USA 2:00 – 2:15 Mechanistic approach for Enhanced Reproducibility of
Genomics Joaquin Dopazo, Clinical Bioinformatics Area, FPS, Seville, Spain
2:15 – 2:45 Coffee Break
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2:45 – 4:30 PM Session 4: Reproducible Genomics in Application Session Chairs: Ben Haibe‐Kains (Princess Margaret Cancer
Center, Canada) and Chris Mason (Weill Cornell Medicine, USA)
2:45 – 3:00 The Importance of Data and Code Sharing and Transparent Pre‐ and Post‐Publication Review: A Case Study in Pharmacogenomics Ben Haibe‐Kains, Princess Margaret Cancer Center in Toronto, Canada
2:30 – 3:15 Training assay‐specific germline and somatic callers with deep
learning Fabien Campagne, Weill Cornell Medicine, New York, USA
3:15 – 3:30 Genomics In Vitro to In Vivo Extrapolation (GIVIVE) – A
Toxicogenomics Example Zhichao Liu, NCTR/FDA, USA
3:30 – 3:45 Of Human Diseases and Models: Examples in Inflammation
Wenzong Xiao, Stanford University, MA, USA
3:45 – 4:15 Closing Remarks and Future Society Conferences Weida Tong, President, NCTR/FDA, USA Leming Shi, President‐Elect, Fudan University, Shanghai, China President‐Elect: Cesare Furlanello, Ph.D., FBK, Trento, Italy
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Future Society Conferences: MAQC2018 (April 21‐23, 2018, Shanghai, China)
The 2018 MAQC Annual Meeting will be held in Shanghai with a tentative theme of "Facilitating Clinical Utilities of Genomics – Reproducibility in Practice".
MAQC2019 (April 08‐10, 2019, Trentino, Italy)
The 2019 MAQC Annual Meeting will be held in Riva del Garda (Trentino) with a tentative theme of “Machine Learning and Precision Medicine – Reproducibility in Big Data”.
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Russell D. Wolfinger, Ph.D.
Director of Scientific Discovery and Genomics SAS Institute Inc. Cary, NC USA E‐mail: [email protected] Russ leads a team in research and development of JMP‐based software solutions in the areas of genomics and clinical research. He joined SAS in 1989 after earning a PhD in Statistics from North Carolina State University (NCSU). For ten years he devoted his efforts to developing statistical procedures in the areas of linear and nonlinear mixed models, multiple testing, and density estimation. In 2000 he started the Scientific Discovery department at SAS. Wolfinger is co‐author of more than 100 publications and a fellow of both the American Association for the Advancement of Science and the American Statistical Association. He also is an adjunct faculty member at NCSU and the University of North Carolina at Chapel Hill and a Kaggle Master
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Weida Tong, Ph.D. Director Division of Bioinformatics and Biostatistics NCTR/FDA E‐mail: [email protected] Dr. Tong is Director of Division of Bioinformatics and Biostatistics at FDA’s National Center for Toxicological Research (NCTR/FDA). He has served a science advisory board member for several large projects involving multiple institutes in Europe and USA. He also holds several adjunct positions at universities in US and China. His division at FDA works to develop bioinformatic methodologies and standards to support FDA research and regulation and to advance regulatory science and personalized medicine. The most visible projects of his group are (1) leading the Microarray Quality Control (MAQC) consortium to develop standard analysis protocols and quality control metrics for emerging technologies to support regulatory science and precision medicine; (2) development of liver toxicity knowledge base (LTKB) for drug safety; (4) in silico drug repositioning for the enhanced treatment of rare diseases; and (4) development of the FDA bioinformatics system, ArrayTrackTM suite, to support FDA review and research on pharmacogenomics. In addition, his group also specializes in molecular modeling and QSARs with specific interest in estrogen, androgen, and endocrine disruptor. Dr. Tong has published more than 230 papers and book chapters.
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Wendell Jones, PhD Principal Bioinformaticist and Scientific Advisor EA Genomics A business unit of Q2 Solutions E‐mail: [email protected] Dr. Jones is currently Principal Bioinformaticist and Scientific Advisor at Q2 Solutions | EA Genomics. He conducts collaborative scientific research with clients in multiple areas, especially in oncology and immuno‐oncology. His background includes leading the analysis, development and validation of the bioinformatic and computational systems that process complex genomic assays, including next generation sequencing assays, evaluating new and emerging genomic technologies, and developing bioinformatic implementation strategies. He consults with clients and provides thought leadership in industry and public consortiums involved in genomic science and measurement. Dr. Jones has over 15 years of experience in advanced genomic technologies and 20 years of experience in scientific and technology leadership positions, including serving as Vice President of Statistics and Bioinformatics at Expression Analysis, Inc and Chief Science Officer at Reliametrics, a Nortel Networks business unit. He has authored over 30 peer‐reviewed publications and has presented at numerous scientific meetings and industry conferences and consortium workshops.
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Leming Shi, Ph.D. Professor and Director Center for Pharmacogenomics and Fudan‐Zhangjiang Center for Clinical Genomics School of Life Sciences, Fudan University Shanghai, China E‐mail: [email protected] Dr. Leming Shi is a professor at the School of Life Sciences of Fudan University in Shanghai, China where he established and directs the Center for Pharmacogenomics and Fudan‐Zhangjiang Center for Clinical Genomics. Dr. Shi’s research focuses on pharmacogenomics, bioinformatics, and cheminformatics aiming to realize precision medicine by developing biomarkers for early cancer diagnosis, prognosis, and personalized therapy. As a principal investigator at the US Food and Drug Administration (FDA) from 2003 to 2012, Dr. Shi conceived and led the MicroArray and Sequencing Quality Control (MAQC/SEQC) project aimed at realizing precision medicine by standardizing genomics and bioinformatics (www.nature.com/nbt/focus/maqc/, www.nature.com/focus/maqc2/, and www.nature.com/nbt/collections/seqc/), leading to the development of several FDA guidance documents. Dr. Shi was a co‐founder of Chipscreen Biosciences Ltd. in Shenzhen, China where he co‐developed a chemogenomics‐based drug discovery platform leading to several novel small‐molecule drug candidates with promising efficacy and safety profiles in anticancer and antidiabetic clinical trials in China, US, and Japan, with one novel compound (Chidamide) approved in 2014 by China FDA for treating T‐cell lymphoma and another candidate in Phase III clinical trials. Dr. Shi is a co‐inventor on nine issued patents about novel therapeutic molecules and has published over 200 peer‐reviewed papers (11 of them appeared in Nature Biotechnology) with >8,000 citation by SCI journals. Dr. Shi received his Ph.D. in computational chemistry from the Chinese Academy of Sciences in Beijing, M.Sc. in computational chemistry from the University of Science and Technology of China in Hefei, and B.Sc. in analytical chemistry from Hunan University in Changsha, China. Dr. Shi conducted postdoctoral training at Case Western Reserve University and the NIH/NCI. Dr. Shi was a senior research scientist at Wyeth (now Pfizer) and BASF before co‐founding Chipscreen in 2001.
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David P. Kreil, Ph.D. Chair of Bioinformatics Boku University Vienna E‐mail: [email protected]
Interests: Development of computational and quantitative experimental methods to allow the investigation of complex biological questions that are hard to examine using traditional gene‐by‐gene approaches alone. Background: Analysis of life‐science data using probabilistic and statistical methods, sequence analysis(Research Fellow of Darwin College and the Medical Research Council UK, Dept of Genetics & Cavendish Laboratory, Univ. of Cambridge). Integration of heterogeneous databases and bioinformatics tools, comparative genome analysis (EMBL fellow, European Bioinformatics Institute, Cambridge). Theory of dynamic properties at phase transitions (Dept of Physics, Technical University of Munich)
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James C. Willey, M.D. George Isaac Professor for Cancer Research Professor of Medicine and Pathology University of Toledo College of Medicine Toledo, OH 43614 E‐Mail: [email protected] Dr. James Willey is George Isaac Professor for Cancer Research at Director of Research for the Eleanor N. Dana Cancer Center at the University of Toledo College of Medicine in Toledo OH. Dr Willey has participated in several national and international consortia comprising academic, governmental, and industrial groups aiming to improve quantification and standardization of transcript abundance measurement and next generation sequencing methods. Dr. Willey’s research has been funded by NIH for more than twenty years. His primary area of research is development of quantitative methods for transcript abundance measurement and quantitative analysis of the relationship between transcript abundance level, promoter DNA sequence, and functional status of proteins that interact with the promoter DNA sequence. His applied research involves applying this quantitative approach to understanding how a particular combination of common inherited DNA variants in promoter regions and/or regulatory protein coding regions may increase risk for disease or alter individual response to therapeutics by decreasing optimal regulation of key genes responsible for the normal phenotype. Dr. Willey has over 13 patents for molecular diagnostics technology, and the technology is licensed to Accugenomics, Inc. Dr. Willey is a Co‐Founder of Accugenomics, Inc., located in Wilmington, North Carolina, USA. Prior to joining the University of Toledo Medical Center and University of Toledo College of Medicine in 1994, Dr. Willey was Assistant Professor of Medicine and Environmental Medicine at the University of Rochester School of Medicine, Rochester, N.Y. He did his post‐doctoral training at the National Cancer Institute with Curt Harris. He completed training in Pulmonary Medicine at the Pulmonary Branch of the National Heart, Lung, and Blood Institute in Bethesda, MD, and the University of Rochester Strong Memorial Hospital.
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Torsten Reda, Ph.D.
Chief Scientific Officer Lexogen Vienna, Austria
E‐mail [email protected]
Torsten is a biophysicist and joined Lexogen in September 2009 to become its CSO. Lexogen’s mission is to develop innovative technologies to resolve the complexity of transcriptomes by accurate and reproducible RNA measurements. Here, Torsten is leading a multidisciplinary team which bridges the gap between fundamental research and applied sciences. Under his aegis the R&D team filed 12 patents in the field of RNA segregation, solid phase amplification, RNA sequencing, and data evaluation, and developed a portfolio of diverse RNA analysis tools. Before, Torsten worked for 5 years in the area of bioelectrochemistry and electron spin resonance at the MRC Mitochondrial Biology Unit in Cambridge (UK) to research the structure and function of NADH‐Dehydrogenase. He also continued with fundamental research in reversible interconversion of carbon dioxide by electroactive enzymes, a topic which started during his time as a postdoctoral fellow at the CSIRO Industrial Physics in Sydney (Australia) where he investigated the biophysical principles of organic electrocatalysts and nanoparticle carriers for artificial photosynthesis reactions. In 1999 Torsten received his PhD from the Technical University Munich (Germany), Department of Biological Chemistry with his thesis about biomimetic molecular switches on basis of redoxactive compounds, after having studied Biophysics at the Humboldt University Berlin (Germany). Torsten has written 20 scientific publications, and is co‐inventor of 8 patents.
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Jing Wang, Ph.D. Deputy director of division of medical and biological measurement, National institute of metrology (NIM), China. E‐mail: [email protected] She is an academic leader of bio‐metrology, responsible for establishing national bio‐metrological standard and bio‐measurement technology platform. From 2003, she embarked on the national measurement and metrology on bioanalysis. Until 2005 she finally established a bio‐measurement technology research platform of nucleic acid, protein, microbiology, cell, bio‐active components, fatty acid and biotoxin. From 2003, as a representatives of county, she first attend the meeting of BIPM/CCQM bio analyze working group (BAWG) and becoming BAWG member. She is ISO members of the Council Task Force on Biotechnology in 2009. Now she also is co‐chair of Quantity group in Microbial Measurements Steering Group (MBSG), the National Technical Committee of Biometrology (NTCB)’s secretary‐general, Members of a council in Chinese Society for Measurement (CSM) and Beijing Food Institute (BFI). She has done many studies on the safety and life sciences. Principal Investigator and Head of National science and technology key project of Study on the tracebility and delivery technology of bio‐safety. Topic Responsible Person of National project of research on the measurement technology and standard of Food, Chinese traditional medication and natural products effective ingredient. She gained S&T Award of AQSIQ and Beijing 7 times from 2005 to 2015 and have finished 11 national standards. She has published four books.
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Christopher E. Mason, Ph.D . Associate Professor Department of Physiology and Biophysics Weill Cornell Medical College, New York, USA E‐mail: [email protected] Dr. Mason, is an associate professor of Computational Genomics at Weill Cornell Medical College. He completed his B.S In Genetics and Biochemistry from University of Wisconsin‐Madison and Ph.D. in Genome Evolution and postdoctoral in Neuroscience from Yale University. His laboratory work utilizes computational and experimental methodologies to identify and characterize the essential genetic elements that guide the function of the human genome. He perform research in three principal areas: (1) the functional annotation of the human genome by mutational profiling in families with brain malformations and cancer patients, (2) the examination of the elements that orchestrate the development of the human brain and their evolutionary changes, and (3) the development of models for systems and synthetic biology. Mason Lab uses high‐throughput methods to generate cell‐specific molecular maps of genetic, epigenetic, and transcriptional activity and we use them to create multi‐dimensional molecular portraits of development and disease. He also develops algorithms to detect, catalog and functionally annotate variants in the genetic pathways that control developmental processes. He has more than 130 publications.
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Jian‐Liang Li, Ph.D. Director, Integrative Bioinformatics Group Division of Intramural Research National Institute of Environmental Health Sciences 111 T.W. Alexander Drive Research Triangle Park, NC 27709 E‐mail: [email protected] Dr. Jian‐Liang (Jason) Li is Director of Integrative Bioinformatics group at National Institute of Environmental Health Sciences (NIEHS). Dr. Li has extensive experience in both academia and pharmaceutical industry. His major interests include developing and applying bioinformatics and statistical approaches to analyze and integrate high‐throughput omic data. Before joining the NIEHS, he was Director of Applied Bioinformatics core at Sanford Burnham Medical Research Institute at Lake Nona, where he established a bioinformatics group in collaboration with basic research groups for supporting cancer genomics researches. Dr. Li received his Ph.D. in Bioinformatics from Boston University and has published more than 50 papers.
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Binsheng Gong, Ph.D. Visiting Scientist Division of Bioinformatics and Biostatistics NCTR/FDA E‐mail: [email protected]
Dr. Gong is a Visiting Scientist in Division of Bioinformatics and Biostatistics at FDA’s National Center for Toxicological Research (NCTR/FDA), with expertise in next‐generation sequencing technologies and high‐throughput data analysis. His studies have significantly advanced the application of bioinformatics methods and systems biology strategies in basic biological study and translational medicine and his research achievements have been recognized with several awards from U.S. FDA and from China. He has served as reviewer for multiple prestigious journals such as Oncotarget, PLoS ONE, Scientific Reports, etc. Dr. Gong has been involved as one of the major investigators in the FDA led SEquencing Quality Control (SEQC) project, and he is the leading author of one Nature Biotechnology paper and co‐authors of several others produced by SEQC project. Dr. Gong has more than 30 research papers published in prestigious journals such as Nature Biotechnology, Genome Biology, Nucleic Acid Research, etc. His researches have received more than 350 citations from government agencies, armies, pharmaceutical and food companies and research institutes. Dr. Gong was one of the chapter editors of the first bioinformatics text book for higher institutions in China.
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Joaquin Dopazo, Ph.D. Director Clinical Bioinformatics Area, Fundación Progreso y Salud, Andalusian Ministry of Health, Spain E‐mail: [email protected] Dr. Joaquin Dopazo heads the Clinical Bioinformatics Area of the Ministry of health of Andalucia, Spain. He leads the Bioinformatics groups of the Spanish network for Rare Diseases and is part of the Spanish Institute of Bioinformatics. He has a BSc in Chemistry and a PhD in Biology (University of Valencia, 1989). He was previously leading Bioinformatics teams at the Computational Genomics Department at CIPF, Valencia, the Bioinformatics unit of the CNIO (Madrid, Spain) and the Bioinformatics Unit of Glaxo Wellcome (Madrid, Spain), as well as in some other private and academic institutions. He has published more than 270 papers in international peer‐reviewed journals. Dr. Dopazo’s interests revolve around functional genomics, systems biology as well as development of algorithms and software for the analysis of high‐throughput genomic data and its application to personalized and precision medicine. He is particularly interested in studying disease mechanisms and drug action mechanisms by modeling complex cellular systems in which signaling, regulation and metabolism information are integrated. He has participated in numerous European and International consortiums and in Spain has promoted initiatives such as the Medical Genome Project in which more than 1000 exomes of patients of familiar diseases were sequenced to find disease genes.
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Benjamin Haibe‐Kains, PhD
Scientist Princess Margaret Cancer Center University Health Network
Assistant Professor Department of Medical Biophysics University of Toronto
Adjunct Professor Department of Computer Science University of Toronto
OICR Associate
Ontario Institute of Cancer Research
E‐mail: [email protected]
Dr. Haibe‐Kains earned my PhD in Bioinformatics at the Université Libre de Bruxelles (Belgium), for which he was awarded the Solvay Award (Belgium). Supported by the Fulbright Award, Dr. Haibe‐Kains did his postdoctoral fellowship at the Dana‐farber Cancer Institute and Harvard School of Public Health (USA). He started his laboratory at the Institut de Recherches Cliniques de Montréal (Canada) and moved to PM in November 2013. His research focuses on the integration of high‐throughput data from various sources to simultaneously analyze multiple facets of carcinogenesis. His team is analyzing high‐throughput (pharmaco)genomic datasets to develop new prognostic and predictive models and to discover new therapeutic regimens in order to significantly improve disease management. Dr. Haibe‐Kains’ main scientific contributions include several prognostic gene signatures in breast cancer, subtype classification models for ovarian and breast cancers, as well as genomic predictors of drug response in cancer cell lines.
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Zhichao Liu, Ph.D. Principal investigator Division of Bioinformatics and Biostatistics NCTR/FDA Email: [email protected] Dr. Liu's background is across Chemistry, Biology and Computer Science. In past ten years, he led and took part in several cutting‐edge projects from both industry and academia. Specifically, he developed innovative approaches for in silico drug repositioning framework to seek for novel opportunities for rare disease treatment development. Furthermore, Dr. Liu’s research is also focused on toxicogenomics for facilitating the drug safety evaluation. One remarkable research is to investigate Genomics In Vitro to In Vivo Extrapolation (GIVIVE) for drug‐induced liver injury. His interests widely covers (1) development of flexible and integrative risk prediction systems for drug safety evaluation; (2) development and application of standard pipeline for genomic data (e.g. microarray/NGS) analysis for drug safety and efficacy questions; (3) development of strategies and frameworks to facilitate text‐mining performance for diverse of document types and infrastructures; (4) Design and development of databases and visualization systems that allow interactive exploration of complex interior relationship embedded in biological data profiles. Dr. Liu has published more than 50 papers in the prestigious journals.
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Wenzhong Xiao, Ph.D. Stanford Genome Technology Center Stanford University School of Medicine E‐mail: [email protected] Wenzhong Xiao is Director of the Immuno‐Metabolic Computational Center at Massachusetts General Hospital, Harvard Medical School. His research is at the interface of computation, genomics and medicine. A major bottleneck of genome medicine today is no longer data generation but computational challenges around data analysis, interpretation, and integration. His research interest is to develop approaches to address these challenges and to help translate genome technologies to better disease diagnosis, prevention and therapeutics, especially in the studies of the human immune and metabolic diseases. His lab developed several algorithms for the statistical analysis and integration of omic data for biomarker identification in large scale disease studies, and the knowledge‐based network analysis for the interpretation and integration of genomic data. He also directs the Computational Genomics Lab at Stanford Genome Technology Center, and is responsible for the computational developments in multiple new applications in genome technology.
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Post Conference Workshop
“Advanced Data Analysis”
Thursday, April 13, 2017
Data scientists from the SAS / JMP Life Sciences division will offer a free advanced level hands‐on workshop to MAQC Society conference attendees with limited seats available right after the conference. We will analyze one or more complex experiments together and discuss various statistical methods and concepts. You will be able to follow along on your laptop. When: April 13, 2017, afternoon Where: SAS Institute Inc. Data: Submit your omics, NGS, clinical trial, or laboratory data before March 24,
2017. We will select representative data sets to demonstrate analyses. Your data set must be publicly shareable, but we will request that other attendees keep it confidential until you provide permission to use it more broadly.
Analysis: Depending on the problems, topics can include: Design of Experiments, Quality Assessment, Normalization, ANOVA and Mixed Modeling, Reproducibility, Pattern Discovery, Predictive Modeling, Genetic Marker Screening, Genome‐Wide Association Study, Population Analysis, Marker‐Assisted Breeding and Cross‐Evaluation, Best Linear Unbiased Prediction, Linkage Mapping, Quantitative Trait Loci, Bioassay, Clinical Trials, Bioequivalence, Method Comparison, Calibration Curves, Limit of Quantification.
Software: JMP, with dashboards created by JMP Genomics and/or JMP Clinical Instructors: Dr. Russ Wolfinger(JMP/ SAS), a fellow of the American Association for
the Advancement of Science and the American Statistical Association, will lead the workshop with assistance from other data scientists on the JMP Life Sciences Team.
Contact: Dr. Wenjun Bao (JMP/SAS) Email: [email protected] to register Tel: 1‐919‐531‐1484 (0), 1‐919‐244‐0260
