Report of IBDC Report of IBDC Breakout Session Breakout Session

on Clinical on Clinical Samples and Samples and

Mouse ModelsMouse ModelsIBDC ConferenceIBDC Conference

FHCRC, Seattle, WA, USAFHCRC, Seattle, WA, USA

12 October 200512 October 2005

ParticipantsParticipants

Yu-Sun Chang Yu-Sun Chang (Chang-(Chang-Gung U)Gung U)

Judith Clements Judith Clements (QueenslandUTSLS)(QueenslandUTSLS)

Michael Davis Michael Davis (FHCRC)(FHCRC)

Ken Evans Ken Evans (OCBN)(OCBN)

Michael Gillette Michael Gillette (Broad)(Broad)

Chris Kemp Chris Kemp (FHCRC)(FHCRC)

Jeong Heon Ko Jeong Heon Ko (KRIBB)(KRIBB)

Cheolju Lee Cheolju Lee (KIST)(KIST)

Lance Miller Lance Miller (GIS)(GIS)

Hal Moses Hal Moses (Vanderbilt)(Vanderbilt)

Nallisivam Nallisivam Palanisamy Palanisamy (GIS)(GIS)

Incheol Shin Incheol Shin (Hanyang U)(Hanyang U)

Khay-Guan Yeoh Khay-Guan Yeoh (U (U Singapore)Singapore)

MandateMandate

““The clinical members should The clinical members should identify best procedures for tissue identify best procedures for tissue procurement and handling. The procurement and handling. The mouse experts should identify best mouse experts should identify best mouse models for human cancer and mouse models for human cancer and optimum experimental paradigms optimum experimental paradigms for identifying mouse biomarkers for for identifying mouse biomarkers for disease and cross correlating them disease and cross correlating them with human biomarkers.”with human biomarkers.”

Mouse ModelsMouse Models

““Eliminate Red Herrings”Eliminate Red Herrings” FHCRC (McIntosh / Paulovich / FHCRC (McIntosh / Paulovich /

Kemp) dedicated to defining ideal Kemp) dedicated to defining ideal characteristics of mouse models, characteristics of mouse models, sample acquisition, storage, sample acquisition, storage, processingprocessing

FHCRC standards and protocols FHCRC standards and protocols available from Chris Kemp available from Chris Kemp (cjkemp@fhcrc.org)(cjkemp@fhcrc.org)

Sample MaterialsSample Materials Need for best practices and detailed protocolsNeed for best practices and detailed protocols Prospective Collection Prospective Collection Blood productsBlood products

PlasmaPlasma SerumSerum

UrineUrine Tumor tissueTumor tissue

Representative sections for HP reviewRepresentative sections for HP review Details per tumor type & project requirementDetails per tumor type & project requirement

““Pure” tumor vs. tumor with marginsPure” tumor vs. tumor with margins Heterogenous tumors (prostate) especially difficult caseHeterogenous tumors (prostate) especially difficult case

Disease specific materials: “proximal fluids”Disease specific materials: “proximal fluids” Gastric Juice (gastric ca); Semen (prostate ca); Gastric Juice (gastric ca); Semen (prostate ca);

pancreatic ductal lavage (pancreatic ca); CSF (CNS pancreatic ductal lavage (pancreatic ca); CSF (CNS malignancy)malignancy)

PlasmaPlasma

Ultimately BMs must survive vagaries of Ultimately BMs must survive vagaries of clinical laboratoriesclinical laboratories Discovery particularly challenging; standards Discovery particularly challenging; standards

more rigorousmore rigorous Citrate or EDTA, not heparinized tubesCitrate or EDTA, not heparinized tubes

Ideally single vendor, single lotIdeally single vendor, single lot Plan aliquots carefully at inceptionPlan aliquots carefully at inception

Available volume; requirements for intended Available volume; requirements for intended applications; storage constraints; FT applications; storage constraints; FT minimizationminimization

Consider “moderate” initial aliquots, eg 0.5 – 1 Consider “moderate” initial aliquots, eg 0.5 – 1 mL, allowing single FT cycle for subaliquotsmL, allowing single FT cycle for subaliquots

-80° C standard for storage-80° C standard for storage

All samples All samples

Barcoding from time of initial sample collectionBarcoding from time of initial sample collection System should track all steps in sample System should track all steps in sample

handling & processing (21 CFR adherence)handling & processing (21 CFR adherence) SOP adherence complemented by careful SOP adherence complemented by careful

documentation of collection / storage documentation of collection / storage parameters for each sample (stopwatch in OR)parameters for each sample (stopwatch in OR)

Samples may be used for initial validation as Samples may be used for initial validation as well as discoverywell as discovery Regulatory compliance: Agencies care about detailsRegulatory compliance: Agencies care about details *Rigorous adherence to GCP / GLP / GMP (Good *Rigorous adherence to GCP / GLP / GMP (Good

Clinical / Laboratory / Manufacturing Practice)Clinical / Laboratory / Manufacturing Practice)

Controls Controls criticalcritical Always imperfect; often inadequateAlways imperfect; often inadequate

Project-specific controlsProject-specific controls Minimize site / batch signaturesMinimize site / batch signatures Plasma requires “suitably matched” controlsPlasma requires “suitably matched” controls

HealthyHealthy Confounding diseaseConfounding disease

Tumor – consider multiple “orthogonal” controlsTumor – consider multiple “orthogonal” controls Distant histopathologically uninvolved (“non-tumor”)Distant histopathologically uninvolved (“non-tumor”) Contralateral uninvolved (eg prophylactic Contralateral uninvolved (eg prophylactic

mastectomy)mastectomy) Non-malignant diseasedNon-malignant diseased ““Healthy”Healthy” Other malignantOther malignant

The only missteps that are unrecoverable are The only missteps that are unrecoverable are those related to sample collection, storage, & those related to sample collection, storage, & annotationannotation

IBDC standing committee for sample IBDC standing committee for sample collection & storagecollection & storage Review / incorporate / disseminate best practices Review / incorporate / disseminate best practices

& protocols& protocols ? Limited empiric assessment across consortium? Limited empiric assessment across consortium

IBDC prospective longitudinal collection of IBDC prospective longitudinal collection of carefully annotated plasma / urine samples carefully annotated plasma / urine samples dedicated to BM validation (cf Women’s dedicated to BM validation (cf Women’s health initiative, nurses health study)health initiative, nurses health study)