The Biorepository of this consortium provides the necessary infrastructure for all the projects to achieve their potential and expedite their findings. It is an integral component of the CRC since it processes and banks specimens that are needed for all projects and furnishes an accurate and complete characterization of each CLL specimen and allows for hypothesis-driven basic and clinical studies to be performed by the members of the consortium.

The CRC Biorepository performs all the studies with the patient’s informed consent that is approved by the Institutional Review Board (IRB) of each CRC site and maintained according to the guidelines established by the Health Insurance Portability and Accountability Act (HIPAA). Patient privacy is maintained throughout all activities of the biorepository.

The Tissue Core of the CRC  serves as the central biorepository for all CLL samples diagnosed and collected from the participating CRC sites and used for the studies described in this proposal. The Tissue Core self-evaluation process (via the rigorous QA/QC) facilitates the development of the quality management systems that are essential to maintain biospecimen quality. This Tissue Core also follows the recommendations of the NCI “Best Practices for Biospecimen Resource” to promote excellent tissue banking, biospecimen data quality, and to adhere to all ethical and legal requirements: (http://biospecimens.cancer.gov)  Biorepositories and Biospecimen Research Branch(BBRB).

This centralized, organized, and characterized sample distribution lowers the threshold for research and discoveries for the CRC program and EXPEDITES the development of novel CLL therapies and enables the understanding the cause of RESISTANCE to specific therapies.

 

Tissue Core Duties

1. The Tissue Core serves as the central repository for all CLL samples diagnosed and collected from the participating CRC sites and used for all CRC studies.

The processing and storage of each sample is performed according to established standard operating procedures, given a unique identifier number and logged into a sample-accrual database with its corresponding clinical, cytogenetics, and demographic data. All patients are consented in accordance with the Declaration of Helsinki, for the collection and use of their samples for institutional review board-approved research purposes. 

Clinical data is de-identified in compliance with HIPAA regulations.

The CLL samples are collected close to diagnosis, pre-treatment, as specified by CRC clinical protocols, and from affected family members with CLL for targeted genetic studies. QA/QC procedures are in place for all SOPs and equipment used by this biorepository. The Tissue Core performs all activities according to the NIH “Best Practices for Biospecimen Resources Guidelines”.
 

2. The Tissue Core performs a basic set of assays, using established SOPs, on the viably stored CLL samples to determine specific sample characteristics.

The surface antigen phenotype of each sample is determined by multiparameter flow cytometric analysis. In addition, the expression of of ZAP-70 the IgVH mutation status is determined on all samples received. Additional project-specific flow cytometry testing are performed on specific samples for hypothesis-driven studies as requested by the CRC investigators.
 

3. The Tissue Core acquires serial samples during the disease progression of all CLL patients that are registered in the CRC.

This enables the CRC investigators to examine for longitudinal changes in the leukemia cell's genotype, biochemistry, and/or immunologic phenotype and correlate these data to clinical outcome.
 

4. The Tissue Core obtains the interphase Fluorescence in situ Hybridization (FISH) and karyotype data that is associated with the acquired CLL sample according to the established SOPs and QA/QCs this data on a quarterly basis.

The acquisition of this data occurs when the patient is first enrolled in the CRC and for all subsequent blood draws (serial samples.)

This standardized cytogenetics data provides accurate and uniform interphase FISH studies for CRC clinical trials and research investigators. 
 

5. The Tissue Core distributes specific banked and characterized samples to the CRC investigators for hypothesis-driven studies. 

The distribution of these characterized samples occurs when an investigator requests the number and type of samples required and completes a Sample Acquisition Form. This form requires a description of the proposed hypothesis, the outcome of the project, and the number and type of samples requested. Other requested data such as clinical and demographic data also can be made available to the investigator via the electronic database. 

This trafficking and distribution of uniformly characterized CLL samples, with their associated surface phenotype, IgVH mutation status, cytogenetics, clinical, and demographic data, facilitates and expedites the CRC investigators in their studies of the biology and evolution of CLL.

 

The merits and justifications of the CRC Tissue Core (Biorepository): 

1) Uniform distribution of characterized samples/reduction in cost. 

2) Continued sample accrual enables the capture of CLL patients with unique/low incidence mutations(P1,P2), & enables accurate/significant statistical correlations.

3) SERIAL samples acquisition: enable longitudinal studies, disease evolution, Collection of SERIAL samples at Dx, pre & post of various therapies from the SAME patient (including NOVEL therapies) enables the CRC investigators to study longitudinal changes in cases who have not progressed vs those who do progress and correlate to various biological markers and resistance to treatment

4) Relative expression data on novel antigens can facilitate & expedite correlations between biological markers  and therapy outcome(resistance vs response) for CRC clinical trials 

5) The managed & centralized FISH data(including the % of abnormal cells carrying the FISH abnormality) and karyotype data is associated with each CLL sample date. This enables the retrieval of a particular sample associated with this data & the use of this physical sample to answer a particular question biology, resistance, & disease correlations 

 

Sample Acquisition Request

The CLL Research Consortium (CRC) welcome new collaborators. Please complete the two documents below and email it to Dr. Laura Rassenti (lrassenti@ucsd.edu), she will get back to you promptly.

CRC TissueCore Sample Request Letter.doc

CRC Sample Acquisition Form.doc

 

Resources Generated by the Tissue Core

The resources generated by the Tissue Core include a large number of banked CLL samples from patients diagnosed at different institutions across the country. In addition, the basic set of data collected on each of these samples allows CRC investigators to retrieve desired samples for specific hypothesis-driven studies. The data on each sample (including longitudinal time points on each patient) comprises clinical data, demographic data, immunophenotyping, IgVH, karyotype, and data from the hypothesis-driven studies. This interactive information on each CLL sample allows CRC investigators and clinicians to better understand the biology of CLL and perform improved prognosis and clinical trials for this leukemia. In addition, the standardization and validation of FISH studies will allow for accurate and uniform FISH data for clinical trials and CRC research investigators. The cytogenetics data (FISH & karyotype) in the CRC Core A-TCMS database) that is associated with each CLL patient sample is a crucial added value to each CLL sample.

Click here to view the resources generated by the Tissue Core are reflected in the publications by the CRC investigators.

 Tissue Core Team:  Tuan Tran, Charlene Gutierrez, Monica Spydell, Laura Rassenti
Tissue Core Team: 
Tuan Tran, Charlene Gutierrez, Monica Spydell, Laura Rassenti

References

Best Practices for Repositories I: Collection, Storage, and Retrieval of Human Biological Materials for Research. Vol. 3 5-48 (Cell Preservation Technology, 2005).

Eiseman E, Bloom G, Brower J, Clancy N & Olmsted SS. Case studies of existing human tissue repositories: "best practices" for a biospecimen resource for the genomic and proteomic era, (RAND Corporation, Santa Monica, CA, 2003).

Eiseman E & Haga S. Handbook of human tissue sources a national resource of human tissue samples, (Rand Corporation, Santa Monica, CA, 1999).

Friede A, Grossman R, Hunt R, Li RM & Stern S. Biospecimen and data collection and distribution. in National Biospecimen Network Blueprint[online] (Constella Group, Inc., Durham, NC., 2003).

Grizzle W. Practical factors in collecting tissues for research. in Tissue Procurement Training Manual [unpublished] (Cooperative Tissue Network, 2004).

Mager R, Ratcliffe C & Knox K. Developing an operational framework: Standard workflows, operating, and quality control policies and procedures for the collection, storage, and distribution of frozen and paraffin-embedded tissue and blood.  (ed. Prepared on behalf of DJ Kerr, D., National Translational Cancer Research Network and National Cancer Research Institute) (2004).

Merz JF, Sankar P, Taube SE & Livolsi V. Use of human tissues in research: clarifying clinician and researcher roles and information flows. J Investig Med 45:252-257 (1997)

Stoneburner G, Goguen A & Feringa A. Risk Management Guide for Information Technology Systems [online].  (National Institute of Standards and Technology, Gaithersburg, MD, 2002).

Biosafety in Microbiological and Biomedical Laboratories [online].  (U.S. Government Printing Office, Washington, DC, 2007).

Caporaso N & Vaught J. Collection, processing, and analysis of preneoplastic specimens. in Cancer precursors: epidemiology, detection, and prevention (eds. Franco, E.L. & Rohan, T.E.) xx, 430 (Springer, New York, 2002).

Grizzle WE & Fredenburgh J. Avoiding biohazards in medical, veterinary and research laboratories. Biotech Histochem 76:183-206 (2001)

Landi MT & Caporaso N. Sample collection, processing and storage. IARC Sci Publ:223-236 (1997)

Holland NT, Smith MT, Eskenazi B & Bastaki M. Biological sample collection and processing for molecular epidemiological studies. Mutat Res 543:217-234 (2003)

Hallek M, Cheson BD, Catovsky D, Caligaris-Cappio F, Dighiero G, Dohner H, Hillmen P, Keating MJ, Montserrat E, Rai KR & Kipps TJ. Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute-Working Group 1996 guidelines. Blood 111:5446-5456 (2008) 

 

CRC Tissue Biorepository Workflow
CRC Tissue Biorepository Workflow

Cytogenetic abnormalities in B-cell CLL are important prognostic indicators for predicting disease progression and treatment response. Interphase FISH (Fluorescence In Situ Hybridization) is widely used in clinical practice to study patients with CLL. This technology is useful to detect specific gene anomalies and various aneuploid conditions in neoplastic cells. FISH can be performed on blood and bone marrow aspirates or smears, paraffin embedded tissues, touch preparations, and many other tissue preparations. Interphase FISH can be used to establish the percentage of neoplastic and normal cells in both interphase and metaphase cells before and after therapy, and therefore can be used to assess therapy and monitor remission. Some FISH tests can detect levels of disease that are less than 1% and are therefore particularly useful to study minimal residual disease, though most FISH assays for CLL have a normal cutoff of approximately 7%.

The most common cytogenetic anomalies in CLL involve chromosomes 6, 11, 12, 13, 14 and 17.

Chromosomal anomalies detected by interphase FISH are among the most important factors predicting survival in B-CLL(21). FISH-detected chromosome anomalies have also been associated with different clinical outcomes and may be associated with IGHv mutation status, CD38 expression, ZAP 70, antigen expression on leukemic B-lymphocytes, cell morphology and other biological features(2,3,27,29). Today many investigators use the following hierarchical risk model of FISH anomalies in B-CLL defined by Dohner et al. (27) and Dewald et al (21) with 17p- as the most aggressive and 13q-x1 as the least aggressive: 17p- ® 11q- ® 6q- ® +12 ® normal ® 13q-x2 ® 13q-x1.

The Tissue Core has standardized interphase FISH among the CRC cytogenetics sites (uniform scoring and data-entry). This validation has provided accurate interphase FISH studies for CRC clinical trials and CRC research investigators across the United States. In addition, the CRC FISH information associated with each CRC CLL patient has used for genetic studies by Project 1 of this consortium.

 

References

Van Dyke DL, Werner L, Rassenti LZ, Neuberg D, Ghia E, Heerema NA, Dal Cin P, Dell Aquila M, Sreekantaiah C, Greaves AW, Kipps   TJ & Kay NE. The Dohner fluorescence in situ hybridization prognostic classification of chronic lymphocytic leukemia (CLL): the CLL  Research Consortium experience. Br J Haematol 173:105-113 (2016) PMC4963001

International Standing Committee on Human Cytogenetic Nomenclature., Shaffer LG, Slovak ML & Campbell LJ. ISCN 2009: an international system for human cytogenetic nomenclature (2009), (Karger, Basel; Unionville, CT, 2009). 

Van Dyke DL, Shanafelt TD, Call TG, Zent CS, Smoley SA, Rabe KG, Schwager SM, Sonbert JC, Slager SL & Kay NE. A comprehensive evaluation of the prognostic significance of 13q deletions in patients with B-chronic lymphocytic leukemia. Br J Haematol 148:544-550 (2010)

Dewald G, Brockman SR & Paternoster SF. Molecular cytogenetics studies in hematological malignancies. in Hematopathology in oncology: Cancer treatment and research; v. 121 (eds. Finn, W.G. & Peterson, L.C.) 69-112 (Kluwer Academic Publishers, Boston, 2004).

Nowakowski GS, Dewald GW, Hoyer JD, Paternoster SF, Stockero KJ, Fink SR, Smoley SA, Remstein ED, Phyliky RL, Call TG, Shanafelt TD, Kay NE & Zent CS. Interphase fluorescence in situ hybridization with an IGH probe is important in the evaluation of patients with a clinical diagnosis of chronic lymphocytic leukemia. Br J Haematol 130:36-42 (2005)

Shanafelt TD, Witzig TE, Fink SR, Jenkins RB, Paternoster SF, Smoley SA, Stockero KJ, Nast DM, Flynn HC, Tschumper RC, Geyer   S, Zent CS, Call TG, Jelinek DF, Kay NE & Dewald GW. Prospective evaluation of clonal evolution during long-term follow-up of
 
Heerema NA, Byrd JC, Dal Cin PS, Dell' Aquila ML, Koduru PR, Aviram A, Smoley SA, Rassenti LZ, Greaves AW, Brown JR, Rai KR, Kipps TJ, Kay NE, Van Dyke DL & Chronic Lymphocytic Leukemia Research C. Stimulation of chronic lymphocytic leukemia cells with CpG oligodeoxynucleotide gives consistent karyotypic results among laboratories: a CLL Research Consortium (CRC) Study. Cancer Genet Cytogenet 203:134-140 (2010) PMC3018693

Wiktor AE, Van Dyke DL, Stupca PJ, Ketterling RP, Thorland EC, Shearer BM, Fink SR, Stockero KJ, Majorowicz JR & Dewald GW. Preclinical validation of fluorescence in situ hybridization assays for clinical practice. Genet Med 8:16-23 (2006)