2017 Program Workshops

Sunday, June 11, 2017


Small Core to Large Core: Recruiting, Retaining and Expanding Core Staff​

Kathleen Brundage

First Steps As An Innovator: Generate Your Value Proposition 

Betsy Ohlsson-Wilhelm, SciGro, Inc.
Paul J Smith, OncoTherics Ltd.
Gary Durack, The TEKMILL, Univ. Illinois at Urbana-Champaign
Renold Capocasale, FlowMetric, Inc.

Problem Focus and Key Questions:
  1. What is a value proposition?
  2. Who will use your invention?
  3. What is the value to the user of that invention? What specific benefit will they obtain?
  4. Why should the user buy your product instead of that of a competitor?
  5. How will your value proposition affect your business plan?
Desired Outcomes:
  1. List of specific DIY tasks that can be carried out while still at your “day job”.
  2. List of information that attendees would like to see on the CytoInnovation page of the ISAC website to assist those interested in making their innovations available to the rest of the community.
  3. Feedback on the direction of the Innovation program within ISAC.
  4. List of mechanisms to enhance the general awareness on the part of the cytometry community of the potential for commercialization of innovations/inventions, whether the inventor is based in a research institution or a commercial site.
Photon Calibration and Advanced Photon Detection in Flow Cytometry

Paul Robinson

Strategies, instrumentation, and best practices for NextGeneration characterization of single cells and nuclei flow sorted from complex tissues and organs 
David Galbraith, Monica DeLay, and Byoung Koh.  
Flow cytometry and cell sorting was originally devised for the analysis of natural single cell suspensions, prototypically cells of the mammalian erythropoietic system, and has ultimately developed to the point that cells can be analyzed for type and function at very high dimensionalities.
We now face two challenges. First, many eukaryotic cells do not naturally occur in the form of cell
suspensions, instead being complex three-dimensional assemblies of different cell types associated in the form of organs and tissues. Strategies for dissociation of tissues and organs into the individual cellular components therefore are needed. Second, the types of downstream analyses to be applied have developed considerably in sophistication, particularly those involving various ‘omics platforms and
methods applied at the level of single cells.
This workshop will outline strategies and provide examples that address both of these concerns when initiating and implementing NextGeneration analyses of cellular functions in organs and tissues, following flow cytometry and sorting to define and isolate single cells and nuclei. It will comprise short presentations to set the stage, followed by longer periods of open discussion to define concerns, reach
consensus, and establish best-practices.
Workshop Agenda: (90 mins)
Part 1: Overview
David Galbraith and Monica Delay: Overview and identification of major concerns.
Part 2:  Specific Examples
David Galbraith: Flow sorting of nuclei and characterization of transcripts within these nuclei.
Byoung Koh:  Isolation of gastrointestinal cells by FACS and downstream applications.
Monica DeLay:  Cell sorting to single cell RNASeq using commercial platforms
Presentations will be no more than 15 minutes each, including active audience participation, followed by a 30 minute question-and-answer session and general discussion.
Building a quantitative flow cytometry (FCM) measurement system 

Lili Wang, NIST
Robert Hoffman, Consultant, CA
Gerald Marti, FDA
John Nolan, Scintillon Institute, CA

Focus and Key Questions:
Building a quantitative cytometry measurement system requires proper controls and standards, e.g. particles for instrument standardization and calibration, and biological cell reference materials.  The purpose of this workshop is to foster the dialogue between ISAC standards committee/task force, NIST, FDA, NIH, CDC and user communities and address key questions: 1) how best to standardize flow cytometers using calibration beads with ERF value assigned traceable values according to NIST SRM 1934? 2) will any bead controls with ERF value assigned be of interest to assay manufacturers to be included in their assay kits? 3) is it useful to send out flow cytometry raw data files obtained from the reference cell characterization project to test users’ comparability of cytometry data analysis? 4) what types of evaluation study are of interest to general/specific user communities using reference bead and cell controls/standards?

Workshop Agenda:
The workshop will be formatted with three 10-15 minute presentations that are composed of current state of traceable calibration beads and characterized commercially produced cell reference materials, and applications needing these reference materials for ultimately building a quantitative flow cytometry measurement system. Presentations will be followed by discussion and conclusion.

Finding the Needle in the Haystack: Rare Event Detection and Validation of the Lower Limit of Quantification​

Workshop Leaders:
Virginia Litwin, Hematology/Flow Cytometry, Covance Inc., virginia.litwin@covance.com
Steven Eck,, MedImmune, One MedImmune Way, Gaithersburg, MD 20876, USA  EckS@MedImmune.com
Alessandra Vitaliti, BioMarker Development, Novartis Pharma AG, Postfach CH-4002 Basel, Switzerland alessandra.vitaliti@novartis.com
Jennifer Stewart, Flow Contract Site Laboratory, LLC,      18311 Bothell Everett Highway, Suite 180, Bothell, WA 98012, USA   jennifer.stewart@fcslaboratory.com
 This workshop is intended for translational and clinical researchers wishing to tap into current thoughts around trends in ensuring that the performance of rare event analyses assays are well characterized and fit-for-purpose, particularly in regulated environments such as for lab developed clinical tests, toxicology studies and clinical trials.  This workshop is aimed at producing a recommendation paper on the validation of rare event and establishing a LLOQ.
Both the American Association of Pharmaceutical Scientists (AAPS) and the International Clinical Cytometry Society (ICCS) have published white papers on the analytical validation of flow cytometric methods (1, 2).  But neither of these publications has adequately addressed best practices for the validation of rare event and establishing a lower limit of quantification (LLOQ). 
Key Topics:
  1. How do the concepts of LLOQ, limit of blank (LOB), and limit of detection (LOD) apply to flow cytometry?
  2. What defines a ‘blank’ sample?
  3. Experimental design for LLOQ validation and creation of validation samples
  4. LLOQ vs total number of events collected.
    1. What is the minimal acceptable number of events?
  5. Application of quantitative validation principles to rare event analyses 
    1. Data review
    2. Acceptance criteria
    3. Application of cut-point approaches and presenting ranges of numbers.
  • Introduction—Overview and Definitions (15 min)
  • Topic 1.  How do the concepts of LLOQ, limit of blank (LOB), and limit of detection (LOD) apply to flow cytometry? What defines a ‘blank’ sample
    • Introduction (5 min)
    • Open discussion (20 min)
  • Topic 2.    Experimental design for LLOQ validation and creation of validation samples.  LLOQ vs total number of events collected
    • Introduction (5 min)
    • Open discussion (15 min)
  • Topic 3.  Application of quantitative validation principles to rare event analyses 
    • Introduction (5 min)
    • Open discussion (15 min)
  • Summary and Next Steps (10 min)

Lifting the ‘curse of dimensionality’ from single-cell data

Nikolay Samusik, Stanford School of Medicine, USA
Zinaida Good, Stanford School of Medicine, USA

Topics covered:
Modern cytometry devices provide an ever-expanding number of detection channels, which on one hand enables comprehensive survey of complex biological systems, but on the other hand presents significant challenges for data analysis and visualization. One of the common problems is the ‘curse of dimensionality’, which manifests in that some cell populations that can be easily separated by biaxial gating become inseparable by clustering methods and invisible in dimensionality reduction techniques, such as single-cell force-directed layouts or tSNE. Here we will recast the ‘curse of dimensionality’ as a signal-to-noise problem and discuss potential methods to overcome it: noise filtering, nonlinear data compression and specially designed distance measures.
Introductory talk and a review code examples (30 minutes), facilitated group discussion (30 minutes), brainstorming session (15 minutes). 

Monday, June 12, 2017

Self-Service Cell Sorting in an SRL: User Training, Implementation and Other Concerns​

Michael Gregory, DART Cytometry, NYULMC
Benjamin Daniel, Microbiology and Immunology, UTHealth San Antonio  
This workshop aims to discuss the placement of self-serve sorters in SRLs, focusing on the training and support that needs to be provided by SRLs for their proper use.

Multilaser Cytometry 2017 - Optimising Wavelength, Power and Optics for High Parameter Flow Cytometry​

Adrian Smith

Single Cell Genomics​

Michael Stadinsky

For Whom the Bead Tolls: real-life benefits and challenges of quantitative flow cytometry​

Nathan Bays

Automated Flow Cytometry Data Analysis

Ryan Brinkmann

Detecting and Characterizing Heterogeneity in Single Cell Data

David Gebhard

Launching and Supporting Basic and Translational Studies Incorporating Mass Cytometry

Jonathan Irish

Tuesday, June 13, 2017



Developing an ISAC Shared Resource Laboratory Recognition Program

Adrian Smith, Rui Gardner, Joanne Lannigan, Michael Gregory

Overview: In November 2016 a group of SRL staff serving on the ISAC Shared Resource Lab Taskforce published ‘International Society for Advancement of Cytometry (ISAC) Flow Cytometry Shared Resource Laboratory (SRL) Best Practices’ in Cytometry A.  The purpose of this publication was to ‘define minimal standards for a flow cytometry shared resource laboratory (SRL) and provide guidance for best practices in several important areas.’  This was also the first step in the development of a program to recognize SRL’s that adhere to these best practices and provide an example of a level of excellence  to which other facilities can aspire.   This workshop will provide a forum for discussion and to gain feedback and ideas that will help inform the development, implementation and benefits of this new ISAC program.

Panel members will introduce the idea of the ISAC SRL recognition program, give a brief history of its inception and share the progress made thus far.  Topics of discussion will be introduced including:
·         Application and evaluation process, 
·         Selection criteria
·         Potential benefits for participating SRLs  
·         Renewal process

Feedback will be gathered by audience members via either online tools or in app tools using the CYTO app.  Depending on attendance levels, the workshop may be broken out into smaller discussion groups that focus on particular topics before reporting back to the whole group.

Cytometry Via High Throughput Single Cell RNA Seq, Why All the Fuss About Microfluidics?​

David Weitz, Experimental Soft Condensed Matter Group, Harvard, Boston, MA, United States
Rob Salomon, Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, Australia

This workshop will focus on the use of microfluidics to perform  high throughput single cell transcriptomic characterisation  of cells.  Whilst there are various ways to achieve  high-throughput Single cell RNAseq, this tutorial will  allow attendees to  physically see  many of the components of a microfluidics system and will focus on the setup, operations and expected results from the inDrop system (as published by Klein et. Al., Cell 2015). 

Optimizing Biomarkers for Immunotherapy and Adoptive Cell Therapy

Workshop Leaders
  1. Virginia Litwin, Hematology/Flow Cytometry, Covance Inc., Indianapolis, IN
  2. Cherie Green, Flow Cytometry Biomarker Development Sciences, Genentech, Inc., a Member of the Roche Group, South San Francisco, CA, USA
  3. Ulrike Sommer, BioMarker Development, Novartis Pharma AG, Basel, Switzerland
This workshop will address the challenges associated with analyzing cellular biomarkers for Immunotherapy and Adoptive Cell Therapy.  The workshop is applicable to non-regulated as well as regulated laboratories.  This workshop is aimed at producing recommendation papers on the optimal processes and controls for cellular biomarkers and monitoring cellular therapies.
Key Topics:
  • Standardization.  We will discuss approaches to standardizing assays and instruments between laboratories.  The focus will be on establishing standards that will facilitate successful assay and data exchange.
  • Beads and Controls for Believable Biomarkers.  The use –and usefulness- of various beads, assay controls, quality controls, etc. will be discussed.  The focus will be on ensuring robust data sets from multicenter, longitudinal studies.
  • Biomarkers Supporting Adoptive Cellular Therapies.  Strategies and challenges associated with successfully measuring biomarkers for adoptive cellular therapies and rare event detection will be tackled!  CAR-T therapeutic monitoring will be emphasized.
  • Introduction—Overview of biomarkers for Immunotherapy and Adoptive Cell Therapy (5 min)
  • Topic 1.  Standardization
    • Introduction (5 min)
    • Open discussion (20 min)
  • Topic 2.  Beads and Controls for Believable Biomarkers
    • Introduction (5 min)
    • Open discussion (20 min)
  • Topic 3.  Unique Requirements for Adoptive Cell Therapy and Rare Event Detection
    • Introduction (5 min)
    • Open discussion (20 min)
  • Summary and Next Steps (10 min)
3-Dimensional Image Analysis and Image Cytometry

Silas Leavesley

Flow Cytometry for Multicenter Studies # 2

Anis Larbi

Moving Towards Reproducible Flow Cytometry-based Extracellular Vesicles Measurements

John Nolan