INTRODUCTION

We are excited to announce the second computational cancer genomics event in SVAI's Collaborative Research Series. This event will focus on papillary renal-cell carcinoma type 1 (p1RCC), in partnership with RareKidneyCancer.org, Salesforce, Google, NIH, and NCBI.

We will invite 150 researchers, engineers and enthusiasts to join us at Salesforce in San Francisco for an intense weekend of exploration in computational biomedicine. Interdisciplinary teams will work to further understand, develop potential interventions and advance the standard of care for p1RCC. In addition to sequencing a patient for this event, we will use genomic datasets for p1RCC through the NIH's Cancer Genome Atlas. 

BACKGROUND

Papillary renal-cell carcinoma, accounts for between 15 to 20% of all kidney cancers. It occurs in the cells lining the small tubules in the kidney that filter waste from the blood and make urine. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist.

PURPOSE

• Advance papillary renal-cell carcinoma research.

• Contribute to real, ongoing patient case.

• Create interdisciplinary opportunities for computer scientists and biologists.

• Learn and develop skills in AI/ML, computational biology and cancer genomics.

• Build an open community for collaborative biomedicine discovery.

DATASETS

[1] SVAI facilitated sequencing for one p1RCC patient (paid for by UCSF Health): RNA and DNA Whole Genome Sequencing for Tumor and Blood samples, sequenced at 90x using a BGISEQ-500. The data will be available as .bam and .vcf files.

Detailed write up on the dataset

Register your team to get access to the dataset (For accepted in-person and remote participants)

[2] NIH Cancer Genome Atlas (TCGA) for data for Papillary Renal Cell Carcinoma which includes: RNA-Seq gene expression, identifiable germ-line mutations and some clinical information:

Cases (291)

Genes (12,063)

Mutations (25,723)

PROBLEM TRACKS

• Exploration of disease pathology and current development efforts/ongoing clinical trials

• Identification of genomic characteristics and driver events of p1RCC.

• Ranking somatic mutations of p1RCC.

• Targeting methods for getting constructs into the RCC cells.

• Identifying gene locations where CRISPR or zinc finger can be applied for treatment.

• Identifying off-label therapeutics through mutational homogeneity.

• Orthogonal assessment of mutated alleles by tumour RNA.

• In Silico HLA Typing Using Standard RNA-Seq Sequence Reads.

• Predicting likelihood of mutated peptides binding autologous HLA-A or HLA-B proteins.

• Create a novel drug intervention with DeepChem.

• Create a pRCC clonal evolution model using sequencing info from individual pRCC cases. Here's an similar model for chRCC.

• Analyze the gene expression signature and come up with a treatment regimen. See here.

SUGGESTED READINGS

We've put together a list of (optional) selected readings to help you prepare for this event. 

WHY YOU SHOULD COME

• Advanced learning in computational biology and cancer genomics.

• Great mentoring sessions.

• Make new friends.

• Connect with us and our event partners.

• Our first research event was amazing, and this one will be even better.

Ben Busby, PhD

Computational Biology Branch, NCBI, NLM, NIH

[MC, Mentor, Judge]

Ben leads the NIH's efforts to partner with Genomics hackathons. His research interests include generation of clustering algorithms for analysis of large gene families and whole genomes and Phylomic Analysis of Gene Transfer Events. Ben holds a PhD in Biochemistry and Molecular Biology from University of Maryland, Baltimore.

LinkedIn    NIH.gov

Dr. James Hsieh, MD, PhD

Professor, Washington University in St. Louis
Department of Medicine, Oncology Division, Molecular Oncology, Medical Oncology

Dr. James Hsieh, MD, PhD, one of North America’s foremost Kidney cancer experts, will be providing the keynote address. Dr. Hsieh is a professor at Washington University's School of Medicine. His research spans Kidney cancer metabolomics, Genomics, Epigenetics, Therapeutics, Precision Medicine, drug development and more.

LinkedIn

Dr. Alex Feltus

Professor, Clemson University, Bioinformatics

Clemson University has been working on Translating gene-chemical molecular signature interactions between six tumor subtypes, and will present their findings for:

1. Sorting the entire TCGA panCancer Atlas with t-SNE.

2. Identifying TCGA gene expression signatures that are common and unique between Kidney Chromophobe (KICH), Kidney Renal Clear Cell Carcinoma (KIRC), and Kidney Renal Papillary Cell Carcinoma (KIRP).

3. Characterizing KIRP-specific molecular signatures including interactions with possible therapeutics.

Linkedin

Jyotika (Jo) Varshney, DVM, Ph.D.

Co-founder and CEO, VeriSIM Life

Jyotika is a doctor of veterinary medicine (DVM). She received her M.S. in Veterinary Pathology and Pathobiology from Penn State University, focusing on gut microbiome analysis for colitis patients. She received her Ph.D. in Comparative Oncology/ Genomics/CS from University of Minnesota-Twin Cities in 2015, where she identified small compounds for Osteosarcoma that is in Phase 1 trials.

She has worked on biotechnological solutions for mental and physical health issues, using machine learning to forecast colon cancer as a Scientific Advisor at CounteractIO, and was a UCSF Postdoctoral Fellow working on developing techniques to interrogate behaviors of pancreatic and lung cancer. Jyotika also served as a Visiting Research Scientist at Genentech working on understanding the mechanisms of toxicities induced by antibody drug conjugates. 

Dr. Varshney is currently the CEO and co-founder of VeriSIM Life.

She led one of the winning teams from our previous NF2 Research Hackathon.

LinkedIn

Avantika Lal, Ph.D.

BRCA Foundation Young Investigator at Stanford University

[Speaker, Mentor and Judge: Attending Sunday]

Avantika is a BRCA Foundation Young Investigator at Stanford University. Previously, Avantika discovered clinically relevant subtypes of 21 cancers by developing CIMLR, a novel clustering algorithm for multi-mic data, while working as a Postdoctoral Researcher at Stanford University. Avantika also developed a machine learning algorithm to identify mutational process active in cancer and neural networks to identify potential antimalarial drug targets. Avantika received her Ph.D. in Genomics from the National Centre for Biological Sciences in India.

Avantika led one of the winning teams form our NF2 Research Hackathon.

LinkedIn

Steven Tamm

CTO, Salesforce

Steven is the CTO of Salesforce, where he develops and oversees overall technical strategy across the company to unify the experience for end-users, administrators and developers. Steven’s experience spans Software Architect for Cloud Computing, eCommerce, Virtualization, Developer Tools, and Software as a Service. Extensive experience in Technical M&A, Corporate Development, Integration, Market Strategy, and advising ground-level startups. He is a graduate from MIT and started his career at Calico Commerce.

LinkedIn  Twitter

Bill Paseman

Founder, RareKidneyCancer.org

Bill Paseman has been in Silicon Valley since 1980. He was the Founder and Chairman of Calico Commerce from 1994-2000 and currently focuses on Angel Investing through Paseman & Associates, and advancing rare kidney cancer research and patient advocacy  through RareKidneyCancer.org.

LinkedIn  Twitter   Personal Site

Ioana L. Aanei, Ph.D.

Entrepreneurship Program Manager & Scientific Analyst, UCSF QB3

Ioana is the Entrepreneurship Program Manager and a Scientific Analyst at QB3 Startup in a Box program. Previously, Ioana was a Graduate Student Research Affiliate at Lawrence Berkeley National Laboratory, where she optimized existing radiolabeling procedure two fold, streamlined data analysis to allow for more facile radioactive decay correction and specific activity calculations, and more. Prior to that, she worked as the Vice-chair of Graduate Student Liaison at BPEP. Ioana received her Ph.D. in Chemical Biology from University of California, Berkeley and B.S. in Chemistry with Honors from California Institute of Technology.

LinkedIn

Onno Faber

Founder, RDMD

Onno is the Founder of RDMD, formerly NF2 Project He previously founded several other startup companies (such as Tapstack), and now focuses full time on RDMD, a patient organization focused on research and treatment options for Neurofibromatosis type 2 and other rare diseases. He will talk about his experience from the first SVAI research event. Onno has engaged in a life long pursuit of creating things and solving problems. He studied architecture, receiving his degree in 2006 ( honors).

 Twitter   LinkedIn

Sam De Brouwer

Co-founder and COO, doc.ai

Sam is the cofounder and Chief Operating Officer at doc.ai, a blockchain AI platform that enables deep learning computations on quantified biology to develop personalized health insight and predictive models. Prior to doc.ai, Sam co-founded Scanadu where she served as VP for Communications. As a member of TED, Sam has ogranized TEDxBrussels and she has been organizing TEDxSanFrancisco since 2016.

LinkedIn

Sean Davis, Ph.D.

Staff Scientist, National Cancer Institute

[Speaker, Mentor]

Bioinformatics and cancer researcher, pediatric oncologist, Bioconductor developer,

LinkedIn  Twitter   GitHub 

Bharath Ramsundar PhD

Stanford; UC Berkeley; DeepChem Author

[Attending Saturday]

Bharath Ramsundar received a BA and BS from UC Berkeley in EECS and Mathematics and was valedictorian of his graduating class in mathematics. He recently completed his PhD in computer science at Stanford University with the Pande group. His research focuses on the application of deep-learning to drug-discovery. In particular, Bharath is the creator and lead-developer of DeepChem, an open source package that aims to democratize the use of deep-learning in drug-discovery and quantum chemistry. He is supported by a Hertz Fellowship, the most selective graduate fellowship in the sciences.

 LinkedIn  Twitter  GitHub

Patrick Hop

Principal Deep Learning Engineer, Numerate, Inc.

[Speaker, Mentor]

Patrick is leading AI research at Numerate, a computational drug design company. Previously Patrick founded DeepCrystal, and Artificial Intelligence company that catered to the pharmaceutical sector. DeepCrystal worked with some of the most iconic companies in the industry and was acquired by Numerate. Patrick graduated from UC Berkeley in Applied Mathematics: Computer Science.

LinkedIn

Pete Kane

Director, SVAI, Founder, Healthcare.mn

Peter has done a lot of work building healthcare and technology communities in Minnesota and the SF Bay Area. His academic background is Chinese Language and Literature.

LinkedIn

Vladimir Vacic, Ph.D.

Senior Scientist, Computational Biology, 23andMe Therapeutics

Vladimir joined 23andMe in 2015 and manages the Computational Biology group within the Research team. He leads the analysis of research sequencing data and works closely with the Therapeutics team on computational analysis of candidate drug targets. Prior to joining 23andMe, he was one of the founding scientists at the New York Genome Center, where he was leading a cancer genome analysis and computational biology group. Vladimir earned his Ph.D. in Computer Science from the University of California, Riverside and trained as a postdoctoral fellow in computational genetics at Cold Spring Harbor Laboratory and Columbia University.

LinkedIn

Alex Furman

Co-founder & Culture and People Analytics, Invitae

Alex is a co-founder at Invitae where he works on software development, people analytics, and business strategy. Alex is also on the Board of Directors for EcoShift Development. Previously, Alex was a Lead Software Engineer where he oversaw the design and implementation of the Navigenics technology platform; he also leveraged this platform to launch Navigenics Health Compass, Navigenics Annual insight, and Scripps Genomic Health Initiative. Prior to this,  Alex worked as a Senior Software Engineer at Iris Financial Solutions to guide business analysts in technical requirements definition and planning and laid foundation of a performance team. Alex also worked as a Principal Engineer at GuidedChoice under Nobel Prize Winner Harry Markowitz where he managed a distributed team of developers and guided the integration platform.

LinkedIn

Shiva Amiri, Ph.D.

Director, Data Science, Zymergen, Inc.

[Attending Saturday Morning]

Shiva Amiri is the Director of Data Science at Zymergen Inc. a technology company in the San Francisco Bay Area focused on Biology, Automation and Data Science. She was previously the CEO at BioSymetrics Inc., a machine learning company specializing in complex biomedical data. Prior to BioSymetrics she was the Chief Product Officer at Real Time Data Solutions Inc., she has led the Informatics and Analytics team at the Ontario Brain Institute and she was the head of the British High Commission’s Science and Innovation team in Canada. Shiva completed her Ph.D. in Computational Biochemistry at the University of Oxford and her undergraduate degree in Computer Science and Human Biology at the University of Toronto.

LinkedIn  Twitter

Keith Nykamp, Ph.D.

Senior Scientist Group Lead, Invitae

Dr. Nykamp has been studying the influence of genetic variation on phenotype in academic and diagnostic settings for more than 15 years. He’s been with Invitae since 2013 and leads the effort to establish and maintain a reliable evidence-based system for variant classification. Before joining Invitae, Dr. Nykamp worked as a molecular geneticist and director of next-generation sequencing at Prevention Genetics.

Avanti Shrikumar

Stanford; MIT

Avanti is a Ph.D student in the Department of Computer Science at Stanford, advised by Professor Anshul Kundaje. She has develop broadly-applicable methods to make deep learning models interpretable, and has applied these methods to study regulatory genomics. Avanti has a Bachelor's in Computer Science with Molecular Biology from MIT and spent a year working as a developer for the Healthcare team of Palantir Technologies before starting her PhD. Read more at Avanti's Stanford page.

LinkedIn  Twitter  GitHub

Liezl Puzon

Software Engineer, Facebook

Liezl is a Software Engineer at Facebook where she works on Neural Machine Translation. Previously she was a Software Engineer at Kiron Open Higher Education and interned at Facebook, Google, and Fidelity National Information Services. Liezl is the winner of Generation Google Scholarship winner and Google Code-In Grand Prize. Liezl received her B.S. in Computer Science from Stanford University.

Linkedin Twitter

Clayton Mellina

Google Cloud AI

"My current interests are primarily in deep learning for computer vision, image search, and visual similarity search. I am also particularly interested - both from a research perspective as well as a productization perspective - in intelligent systems that allow users to express search intentions or information-needs in nuanced ways that are otherwise difficult to express by language or classical search tools." Clay complted his graduate studies at Stanford University with a dual focus in Human-Computer Interaction and Artificial Intelligence. Prior to joining Google, he worked on Computer Vision and Machine Learning Team at Yahoo on many topics, including scaling deep learning and computer vision technologies for Yahoo products, product integrations, large-scale approximate nearest neighbor search, deep learning for visual similarity search, and visualization tools."

LinkedIn   Twitter  GitHub

Clinton Mielke, Ph.D.

Founder, infinome ; Data Scientist, UCSF Memory and Aging Center

Clinton is the Founder of infinome and a data scientist at UCSF Memory and Aging Center. Previously he worked as a Research Associate at the Mayo Clinic and the Biodesign Institute in Arizona State University, and an Analyst at the Shadowserver Foundation, a Staff Research at the Artificial Intelligence Lab at the University of Arizona. Prior to these positions, Clinton worked at NASA Ames Research Center as a Software Engineer, at Steward Observatory as a Scientist and a Scientific Programmer at the Arecibo Observatory. Clinton received his Ph.D. in Biomathematics, Bioinformatics, and Computational Biology from the Biodesign Institute of Mayo Clinic.

LinkedIn

Marianne Camargo, MD. MSCR.

Nephrologist

[Attending Saturday and Sunday Afternoon]

Marianne graduated from UMDNJ-New Jersey Medical School and did her residency in Internal Medicine at Cornell. After finishing her residency she joined a research fellowship track and developed projects in health literacy, quality improvement and communication skills, at Mount Sinai Hospital in New York. She then pursued nephrology sub-specialty fellowship training to diagnose and treat kidney diseases. As part of her fellowship, she is currently engaged in biomedical clinical research with a focus on understanding the complex link between kidney disease and cancer, including the potential nephrotoxic effects of anti-neoplastic treatments. She has been practicing clinical medicine for almost 10 years and is board certified in Internal Medicine and Nephrology.

Ryan Leung

Director of Research & Partnerships, SVAI; Technical Development Engineer,  Genentech

Ryan leads Research and Partnerships at SVAI and is an Engineer in Pharma Technical Operations at Genentech. At Genentech, his work spans the complete end-to-end development process of biologics, ranging from bioanalytical protein characterization to global manufacturing campaigns. Previously, Ryan was a researcher at the SENS Research Foundation and the Tufts University School of Medicine focused on applications of biomaterials and tissue-engineered constructs as human therapeutic and disease modeling platforms, as well as enabling technologies for such products.

LinkedIn

Nina Sardesh

Research, Partnerships and Fundraising Member, SVAI;  Clinical Trial Assistant for Aerotek, Verily Life Sciences

Nina is a Clinical Trial Associate at Verily LIfe Sciences and a Product Management Consultant at LynxCare Clinical Informatics. Previously, Nina worked as a Clinical Research Coordinator at UCSF and a Research Associate at NASA Ames Research Center.

LinkedIn

Parikshit Sharma

Analyst, IndieBio

Parikshit is an Analyst at IndieBio where he leads analysis, modeling, and automation for the IndieBio data pipeline and portfolio, researches life science VC and market landscape, assists investment committee with due-diligence on computational biology startups, and supports portfolio companies with fundraising and financial modeling. 

LinkedIn

Ankita Das

Marketing Manager, MEDGENOME, Inc

[Attending Saturday Afternoon]

Ankita specializes in studying Epigenetic mechanisms that regulate stem and progenitor cell differentiation during development. She has extensive experience in studying various vertebrate organisms including zebrafish and mice to study in vivo developmental processes, using imaging & genetic strategies. She is enthusiastic about entrepreneurship, and has designed a mentoring program serving Hopkins fellows considering careers in entrepreneurship / start-ups and venture capital strategists. She also serves on the board of Innovation Factory at JHU Carey School of Business to facilitate team building and peer mentoring between business school and science students interested in Entrepreneurship.

LinkedIn