Session Abstract – PMWC 2024 Silicon Valley

Track 4 - January 26 9.00 A.M.-4.00 P.M.


Track Chair: Stacey Gabriel, Broad Institute and Steve Turner, PacBio

  • New Frontiers in Genomic Analysis & Interpretation
    - Robert Sebra, ISMMS
    - Anshul Kundaje, Stanford
    - Chaz Langelier, UCSF
    - Orly Alter, Prism AI Inc
  • From Potential to Reality: Bringing Nanopore Sequencing to Clinical Practice (PANEL)
    Chair: Emma Stanton, Oxford Nanopore Tech - Charles Chiu, UCSF
    - Billy Tsz Cheong Lau, Stanford
  • Population Sequencing at Scale: Impact and Future Path of Genomic Programs (PANEL)
    Chair: Stacey Gabriel, Broad Institute
    - Heidi Rehm, MGH
    - Cindy Lawley, Olink
    - John M. Gaziano, Million Veterans Program (MVP)
  • New Frontiers in Genomic Analysis & Interpretation continues: AI in Spatial Transcriptomics in Patient Response
    - David. W. Craig, City of Hope Cancer Center
    - Premal Shah, MyOme
  • The Economic Perspective on Genomics (PANEL)
    Chair: Bill Hyun, UCSF
    - Steve Turner, PacBio
    - Alex de Winter, Danaher Ventures
    - Kandaswamy (Swamy) Vijayan, Zafrens
  • Using AI for Scalable Phenotyping and Discovery
    - Andrew Carroll, Google
  • Building Bridges: Precision Medicine Communities
    - Kumar Prashant, Karkinos
  • NCI Showcase
    - Xiaofeng Xie, MicrOmics Technologies

 Speaker Profile

PhD, Chief Genomics Officer, Broad Inst.

Biography
Stacey Gabriel is a human geneticist with a research interest in large scale genomics research. The organization that she leads operates as one of the largest sequencing centers in the world and continually explores, validates, optimizes, and implements new technologies, methods, and analysis tools to meet the needs of the scientific community. She has played a central role in the development of methods for generating and analyzing data using genomic technologies for both cancer and medical genetics studies. Her research on the haplotype structure of the human genome provided the foundation for the Human HapMap Project. She directs the Broad Institutes execution in flagship large scale projects including the Human HapMap, the 1000 Genomes Project, The Cancer Genome Atlas, and the All of Us Research Program. During the covid19 pandemic Dr. Gabriel led the development and execution of a commercial scale diagnostic testing and viral surveillance activity.


 Speaker Profile

PhD, Professor, Genetics and Genomic Sciences Director, ISMMS

Biography
Dr. Robert Sebra is the founding Director of the Center for Advanced Genomics Technology (CAGT) which is focused on accelerating innovation and commercial platform application to ensure that the scientific and medical communities have access to a broad toolbox to enable technology driven omics research. Dr. Sebra has built a unique technology development program that focuses on cutting edge single molecule, bulk, single cell, and spatial multi omics molecular and analytical methods development for community application and datasets for translational science and medicine research with over 200 publications and patents, to date. His research program focuses on applying these technologies to study development, tumor progression, and infectious disease to better characterize health and disease progression. Recent research interests include discovery of biomarkers of tumor initiation, novel gene discovery in human preimplantation development, and engineering of accelerated AI foundation models to facilitate cellular and gene expression signatures of disease.


Talk
Improving Transcriptomics Data Interpretability Via Single-Cell Informed Machine Learning
This talk will cover the integration of single-cell data from 1500 studies via Unicell Deconvolve. Well delve into the future implications of single-cell and spatial data, presenting a universal model applicable to all human systems. The focus centers on interpretable machine learning approaches to reveal cellular and transcriptional signatures affecting patient outcomes.


 Speaker Profile

PhD, Chief Scientific Officer, Karkinos

Biography
Dr. Prashant Kumar brings along with him vast expertise accomplishments in the field of Cancer Biology and has done extensive research to enhance the translational merits of cancer research. He worked in several path breaking research initiatives that include establishing a novel mouse model of malignant breast cancers, optimization of a culture method to assess CTCs, implementation of cutting edge technologies in genomics, proteomics to investigate biomarkers and therapeutic targets to accelerated discovery in the advancement towards cancer vaccines, precision medicine, molecular diagnostics. Dr. Kumar received his Ph.D. in 2009 from the Max Planck Institute for Infection Biology, Berlin, Germany. Following this, he did his postdoctoral work at the Department of Cancer Biology, UMASS, Worcester, USA. To further advance his research stint, he joined Prof. JeanPaul Thiery, a world renowned authority in the area of EMT at IMCB, ASTAR Singapore. Currently he is the Chief Scientific Officer (CSO) of Karkinos Healthcare.


 Speaker Profile

PhD, Professor, MGH & Broad Inst.

Biography
Heidi Rehm is a renowned human geneticist and genomic medicine researcher who has made significant contributions to the field of genomics including developing and implementing new approaches, standards and resources to improve genetic testing and diagnosis for rare diseases. She holds several prominent positions including a chief genomics officer role to apply genomics to clinical care across MGH. She is also the codirector of the Program in Medical and Population Genetics at the Broad Institute of MIT and Harvard, where she coleads several initiatives to advance genomic medicine research including the Broad Center for Mendelian Genomics involved in rare disease gene discovery, as well as the Clinical Genome Resource (ClinGen) and Genome Aggregation Database (gnomAD), providing free and publicly accessible resources to support the interpretation of genes and variants. She is the recipient of the Curt Stern Award from the American Society of Human Genetics and has published over 250 peer reviewed papers.


 Speaker Profile

Vice President Clinical, Oxford Nanopore

Biography
As Head of Oxford Nanopore Diagnostics (OND), Emma supports Oxford Nanopores ambitions for growth in healthcare applications. Until November 2020, Emma was Director for Supplies and Innovation as part of the British government's NHS Test and Trace response to COVID19. Prior to this, Emma was CEO of Four Eyes Insight, Chief Partnership Officer for Beacon Health Options (Northeast USA) and CEO of Beacon in the UK. Emma has also been a Commonwealth Fund Harkness Fellow in Healthcare Policy and Practice and a Senior Associate at the Institute for Strategy and Competitiveness, both at Harvard University. Prior to this, Emma was a practicing clinician in the UK's National Health Service (NHS).


 Speaker Profile

PhD, Director, Population Health, Olink

Biography
Cindy is passionate about innovation to make genetic and multi omic technologies easier and cheaper to measure. She sees such innovation as pivotal to lower the barrier of entry for implementing scalable, reproducible solutions advancing individualized medicine and health equity. In over 14 years at Illumina and together with customers, she helped develop solutions to advance the understanding of genetic risk and holds several USDA Excellence in Technology Transfer awards for her work leading Illuminas Consortia Program. She joined Olink in 2020 soon after the launch of the Explore Platform that leverages next generation sequencing as a high throughput proteomic readout. Ask her about how high throughput proteomics are helping translate the impact our genetics has on more real time health.


 Speaker Profile

MD, MPH, National PI, Million Veterans Program (MVP)

Biography
Dr. Gaziano, Professor of Medicine at Harvard Medical School, is a prominent chronic disease epidemiologist and trialist with a focus on the study of chronic diseases, particularly the influences of lifestyle choices, metabolic factors, and biochemical and genetic markers on coronary artery disease and stroke. He is the Executive Director of the Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) at the VA Boston Healthcare System. He is one of the PI for the Million Veteran Program (MVP), an observational cohort with stored biospecimens. Enrollment currently stands at 980,000 veterans and is quickly approaching its target of 1,000,000 enrollees. He also serves as the Chief of the Division of Aging at Brigham and Women's Hospital, where he is the PI of the Physicians Health Study, a large scale trial exploring the role of vitamins in preventing chronic diseases. He has a prolific publication record with over 750 original reports, reviews, and book chapters.


 Speaker Profile

MD, PhD, Professor, Laboratory Medicine and Infectious Diseases, UCSF

Biography
Charles Chiu, M.D. Ph.D. is a Professor at UCSF, Director of the UCS-FAbbott Viral Diagnostics and Discovery Center (VDDC), and Associate Director of the UCSF Clinical Microbiology Laboratory. Chiu currently leads a translational research laboratory focused on clinical metagenomic sequencing assay development for infectious diseases and genomic investigation and surveillance of emerging pathogens, including the SARSCoV2 coronavirus. He also uses RNASeq transcriptome profiling to develop predictive models using machine learning for host response based diagnosis of COVID19 and other infections. Chius work is supported by funding from the National Institutes of Health (NIH), Department of Defense, US Centers for Disease Control and Prevention (CDC), philanthropy, and the California Initiative to Advance Precision Medicine. He has authored more than 100 peer reviewed publications (20 on COVID19), holds over 15 patents and patent applications, and serves on the scientific advisory board for Mammoth Biosciences, Danaher Dx, Biomesense, and Flightpath.


 Speaker Profile

PhD, Manager, MicrOmics Tech

Biography
Dr. Xie possesses a distinct expertise in the development and commercialization of innovative instruments for microcolumn separations in life science research. During his doctoral work under Prof. Milton Lee, two of his projects resulted in patented innovations that were subsequently commercialized. Later, he became a key member of the startup Axcend Technologies, where he played a pivotal role in commercializing field portable liquid chromatography tools he had a hand in developing. In 2021, he partnered with Ryan Kelly's laboratory as a postdoctoral research associate. By 2022, he ascended to the position of Manager at MicrOmics Technologies. In this capacity, he made significant strides in the creation of robotic platforms for single cell proteomics and pioneering the next generation LCMS platform tailored for single cell proteomics.


NCI Showcase:
MicrOmics Technologies

MicrOmics Technologies LLC was founded to make advanced technologies available to scientists seeking to extend the capabilities of their LC-MS workflow, particularly for increased sensitivity and analysis of smaller samples (e.g., single-cell proteomics).

 Speaker Profile

PhD, Director, Genoa Ventures

Biography
Bill is a respected expert in both basic research and clinical lab technology development as faculty in UCSF Laboratory Medicine and Venture Partner at Genoa Ventures. Academically, Bill directed several labs with a strong concentration on cytometry and genomic technologies implementing a myriad of research, translational and clinical applications. His career includes joint appointments at UC Berkeley and LBNL, three honorary doctorates, and authorship of over 100 peer reviewed publications. Bill has been directly involved in the conception, engineering, and validation of more than 20 commercially successful analytical instruments, consumable products, and software programs, often in collaboration with strategic partners like Zeiss, Danaher, Thermo, BD, and Sony. Bill is an investor, and or advisor to more than 50 companies, cofounder of 11 startups, shepherding 14 exits. Bill joined Genoa Ventures at its inception to invest in unique opportunities and to further capitalize on his ability to repeatedly identify disruptive science in transformative markets.


 Speaker Profile

PhD, Founder and Chief Technology Officer, PacBio

Biography
Dr. Turner founded PacBio in 2004. He was awarded a Ph.D. in Physics by Cornell University in 2000, where he worked with Prof. Harold Craighead to study the behavior of biomolecules in nanofabricated structures. He was a member of the project team at Cornell which developed the technology now employed by PacBio and was coauthor of the cover story in Science magazine (13103) that introduced the technology to the scientific community. Dr. Turner's undergraduate work was at the University of Wisconsin, Madison, where he received a B.S. in Applied Mathematics, Electrical Engineering and Physics. He is the author of over 50 scientific papers in fields ranging from DNA sequencing technology and biophysics to genomics and epigenomics. He is listed as the inventor on over 50 U.S. patents and numerous published patent applications. Dr. Turner was recipient of the MIT Technology Review TR100 Award in 2003 and the UW Madison Distinguished Young Alumnus Award in 2008.


 Speaker Profile

PhD, Associate Professor, Stanford

Biography
Anshul Kundaje's primary research area is large scale computational regulatory genomics. The Kundaje lab specializes in developing statistical and machine learning methods for large scale integrative analysis of heterogeneous, highthroughput functional genomic and genetic data to decipher regulatory elements and long range regulatory interactions, learn predictive regulatory network models across individuals, cell types and species and improve detection and interpretation of natural and disease associated genetic variation. Previously as a postdoc at Stanford and Research Scientist at MIT, Anshul was the lead computational analyst of the ENCODE Project and the Roadmap Epigenomics Project. Anshul is also a recipient of the 2016 NIH Director's New Innovator Award and the 2014 Alfred Sloan Fellowship.


Talk
Deep Learning Regulatory Sequence Syntax and Variation


 Speaker Profile

MD, PhD, Associate Professor of Medicine, Division of Infectious Diseases, UCSF

Biography
Dr. Chaz Langelier is an Associate Professor of Medicine in the Division of Infectious Diseases at UCSF. His work seeks to advance the understanding and management of pneumonia, sepsis, and other infectious and inflammatory diseases. His laboratory combines host gene expression profiling, metagenomic pathogen detection and profiling of the microbiome to develop novel molecular diagnostics, study host pathogen biology, and advance methods for emerging infectious diseases surveillance.


Talk
Integrated Host-Microbe Metagenomics for Diagnosis of Sepsis and Pneumonia
Combining host transcriptional profiling and unbiased microbial metagenomics affords accurate diagnosis and detection of probable pathogens in critically ill patients with sepsis and pneumonia.


 Speaker Profile

PhD, CSO and Co-Founder, Prism AI

Biography
Orly Alter is a USTAR associate professor at the Scientific Computing and Imaging Institute and the Huntsman Cancer Institute at the University of Utah, a scientific advisory board member of the NCI-DOE Cancer Moonshot collaboration on predictive oncology, and the CSO and a co-founder of Prism AI. Her Ph.D. thesis in applied physics at Stanford University is recognized as crucial to quantum computing. Inventor of the “eigengene," Alter develops AI/ML to compare and integrate datasets of any types, number and dimensions, and sizes. She demonstrated that her algorithms, the multi-tensor comparative spectral decompositions, discover interpretable and actionable predictors, applicable to the general population from as few as 50–100 patients, and her predictors outperform all others, where they exist. Her retrospective clinical trial experimentally validated a genome-wide pattern in brain cancer tumors as the most accurate and precise predictor of life expectancy and response to standard of care.


Talk
AI-Powered Biomarker Discovery for Personalized Medicine
The ability to detect complex multi-omic differential signatures is the basis for personalized medicine. But with typical AI this process rarely converges into an effective solution. We will present a powerful and novel AI approach for the discovery of biomarkers and drug targets from real-life, small-cohort, multi-omic, and noisy data.


Clinical & Research Tools Showcase:
Prism AI

Prism AI offers an AI-first clinical multi-omic data management and analytics platform that allows biotech companies and health systems to unlock the potential of their own data and create the next generation of drugs and biomarkers.

 Speaker Profile

MD, Managing Partner, Recode Health Ventures

Biography
Dr Vishal Gulati is a venture capitalist investing globally in companies applying Moore's Law-based technologies to solve unmet healthcare needs. His investments include companies using generative AI, semiconductors and deep learning to improve gene therapies, cancer detection, and antibody discovery. Before developing a career in venture capital investing, Vishal trained as a medical doctor and clinical scientist at the University of Oxford and at Imperial College, London as a UNESCO Fellow and a Rhodes Scholar. He then worked at the Wellcome Trust on strategy and policy around the Human Genome Project. In addition to his venture capital investing, Vishal also serves on the boards and investment committees of several funds, foundations, research bodies and academic institutions.


 Speaker Profile

PhD, CEO, Zafrens

Biography
Swamy is a serial entrepreneur in interdisciplinary technologies. Having worked on novel sequencing methodologies and small molecule drug discovery platforms previously, he currently guides the integration of genomics tools in drug discovery at Zafrens. Swamy's interests are in decentralized and simplified access to high-resolution, high-throughput insights into biology.


 Speaker Profile

Ph.D., Professor and Chair, Department of Integrative Translational Sciences, City of Hope

Biography
David W. Craig is an internationally recognized leader in developing and applying novel bioinformatics and genomics tools as well as in translating genomic discoveries from bench to bedside. Craig leads an integrative translational sciences department at City of Hope comprehensive cancer center that focuses on precision measurement, data science and diversity. His team seeks to further improve both translational outcomes as well as the science underpinning the use of precision medicine.Craig collaborates with regulatory agencies, industry partners, researchers and health care professionals to integrate scientific findings and translate potentially practice-changing discoveries into improved patient care and human health. He has spearheaded collaborative computational and data science efforts within large and small research consortiums, including the 1000 Genomes Project and the Bipolar Genome Study. His exceptional expertise has resulted in more than 200 publications, four patents and two founded companies.


Talk
AI-Driven Individualized Analysis of Spatial Transcriptomics
Novel methods in spatial transcriptomics methods offer deep insights into disease biology, advancing the field beyond single-cell genomics to incorporate the spatial context. Craig describes use of AI, deep learning and graph-based networks to merge histology and genomic sequencing, enhancing understanding of tumor biology and guiding analysis for broader research.


 Speaker Profile

PhD, Product Lead, Google

Biography
Andrew leads product development for the genomics team in Google Health. The genomics team develops methods that improve real-world applications in clinical genomics, population-level sequencing, drug discovery, and the combination of genomic and clinical data. Prior to Google, Andrew was Chief Scientific Officer at DNAnexus, where he supported many of the first large-scale genomics projects, such as the CHARGE Consortium, Regeneron-Gesinger and Regeneron-UKBiobank cohorts, the 3000 Rice Genomes Project, PrecisionFDA, and the St. Jude Pediatric Cancer Cloud. Andrew holds a PhD in Molecular Biology from Stanford University and a Bachelors degree in Physics from the University of Virginia.


Talk
As sequencing becomes more scalable and affordable, the ability to accurately phenotype large cohorts becomes increasingly important.This talk will explore how AI methods can solve this problem by using AI approaches on retinal images and spiromtery to discover new associates for glaucoma, COPD, and asthma. Additionaly, using mutli-modal LLMs to integrate phenotype information.


 Speaker Profile

Ph.D., CEO, MyOme

Biography
Dr. Premal Shah leads MyOme's efforts to make clinical grade whole genome sequencing available to everyone. Before MyOme, Dr. Shah was President, COO and Co-Founder at Ciitizen (acquired by Invitae), where he led the company's efforts to develop the core Ciitizen technology enabling patients to seamlessly acquire and codify their personal health records from structured and unstructured data. Prior to Ciitizen, Dr. Shah was CEO of Applied Proteomics, a proteomics platform company that developed a blood-based colorectal cancer screening test. In addition, Dr. Shah has held leadership positions at Genomic Health and was a management consultant at Booz Company, serving clients throughout the healthcare ecosystem. Dr. Shah completed his graduate work at the California Institute of Technology.


Talk
Clinical Grade Whole Genome Sequencing
For the first time, a sub $500 clinical-grade whole genome is available to everyone, enabling on-going analysis throughout a patient's life, including use of polygenic risk scores for assessing risk of common diseases (e.g., CAD, T2D) that integrate a patient's clinical risk factors.


 Speaker Profile

Ph.D., Instructor, Medicine - Oncology, Stanford

Biography
Dr. Billy Lau is an Instructor in the Division of Oncology at Stanford University School of Medicine. His research focus is on leveraging genome technology for cancer detection, and for studying human genomic variation. Dr. Lau received his doctorate from Harvard University in Engineering Sciences, and completed his postdoctoral training with Dr. Hanlee Ji at Stanford University. He has also received the NHGRIs Genomic Innovator Award, where he focuses on building tools to maximize information from single molecules and cells.


 Speaker Profile

Ph.D., Vice President of New Ventures, Danaher Ventures

Biography
Alex de Winter invests in life sciences tools and clinical diagnostic startups for Danaher Ventures. Prior to Danaher, he was a managing director at GE Ventures, where he invested in precision medicine startups like Labcyte, Raindance, Singular Genomics, Syapse, and Veracyte. Alex previously worked at Mohr Davidow Ventures, and was a research scientist at Pacific Biosciences and 454 Life Sciences.


 Speaker Profile

Ph.D., Professor of Pathology, Genetics and, by courtesy, Computer Science, Stanford

Biography
Dr. Stephen Montgomery is the Stanford Medicine Endowed Professor of Pathology and Professor of Genetics, Biomedical Data Science and, by courtesy, Computer Science at Stanford University. He leads a dynamic lab where his team blends functional genomics and sophisticated bioinformatics to unravel the molecular roots of genetic diseases. His research prominently features in numerous large-scale consortia, such as GTEx and MoTrPAC. Dr. Montgomery's laboratory is renowned for developing innovative transcriptome-based methods. These breakthroughs are pivotal for uncovering impactful rare variants in diverse groups, ranging from individuals and families to broader populations. His approaches are also unique in their ability to measure gene-by-environment interactions. His expertise extends to multi-omics studies of global populations showcasing his labs commitment to inclusive and diverse genomics research. Dr. Montgomery is a leader in the discovery and interpretation of rare variants using multiomics, and his work in building genomic databases for RNA diagnostics sets him apart in the field. He is also a key contributor to the integration of long-read sequencing and RNA sequencing for more accurate variant interpretation, a technique crucial in precision medicine.


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