Glossary

AD: Alzheimer’s Disease (also sometimes ALZ)

ALK biomarker: Anaplastic Lymphoma Kinase. http://www.ncbi.nlm.nih.gov/pubmed/21642865 and http://www.cancernetwork.com/lung-cancer/content/article/10165/154050

Biomarker: Though this term has a different meaning in other areas of science (genetics for instance), in pathology, biomarkers indicate the presence of a substance that can identify a particular disease state or infection, yield information about the characteristics of a disease or disease potential, or suggest possible patient outcomes or treatment responses. Biomarkers tell us something about the genetic and molecular characteristics of affected cells and individuals and are important in personalized medicine. See also: Cluster of differentiation.

CLIA: Clinical Laboratory Improvement amendments. http://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/index.html?redirect=/CLIA/

Common Rule: (45-CFR-46): The "Common Rule" is a set of federal regulations governing patient protection for research conducted with federal funds, or at sites supported with federal funds. As a result, the Common Rule generally applies to every US academic medical center. The code describes requirements for conducting ethically sound research, such as informed consent and institutional review of research proposals. http://www.hhs.gov/ohrp/

Cluster of differentiation: The cluster of differentiation (cluster of designation) (often abbreviated as CD) is a protocol used for the identification and investigation of cell surface molecules providing targets for immunophenotyping of cells. Physiologically, CD molecules can act in numerous ways, often acting as receptors or ligands (the molecule that activates a receptor) important to the cell. A signal cascade is usually initiated, altering the behavior of the cell (see cell signaling). Some CD proteins do not play a role in cell signaling, but have other functions, such as cell adhesion. For a list of known human CDs see: http://en.wikipedia.org/wiki/List_of_human_clusters_of_differentiation

COD: Cause of Death.

CMS: Center for Medicare and Medicaid Services (CMS)

Consent: An important regulatory element for biorepositories is the ability to demonstrate that donors have given informed consent for the tissues they donate to be used in scientific studies. Ethical guidelines for how tissues are collected and used at a given organization are usually determined by the organization’s IRB.

CSLI: Clinical and Laboratory Standards Institute

CSF: Cerebrospinal fluid. http://www.nlm.nih.gov/medlineplus/ency/article/003428.html

CTC: Circulating Tumor Cell. http://en.wikipedia.org/wiki/Circulating_tumor_cell

CTCL: Cutaneous T-cell lymphoma. http://en.wikipedia.org/wiki/Cutaneous_T-cell_lymphoma

CRO: Contract Research Organization

DIG Staining: Digoxigenin, a hapten, can be bound to nucleotides and sugars. http://en.wikipedia.org/wiki/Digoxigenin

EGFR: Epidermal Growth Factor Receptor. Upregulation of this can be involved with some cancers. Related biomarkers can be used to predict responsiveness of some cancers to certain treatments. See also HER2.

FFPE: Formalin Fixed Paraffin Embedded tissues

FISH: fluorescence in situ hybridization. A common staining / screening technique used by Phylogeny. Fluorescent probes are used to indicate target sequences on chromosomes. Compare with ISH

Functional Genomics: http://en.wikipedia.org/wiki/Functional_genomics

Gleason Score: prostate cancer prognosis tool. http://en.wikipedia.org/wiki/Gleason_Grading_System

H&E staining: Hematoxylin and eosin stain. http://en.wikipedia.org/wiki/H%26E_stain

HER2: HER2-positive breast cancer is a breast cancer that tests positive for a protein called human epidermal growth factor receptor 2 (HER2), which promotes the growth of cancer cells. In about 1 of every 5 breast cancers, the cancer cells make an excess of HER2 due to a gene mutation. This gene mutation and the elevated levels of HER2 that it causes can occur in many types of cancer — not only breast cancer. This is a gene mutation that occurs only in the cancer cells and is not a type of mutation that you can inherit from a parent. HER2-positive breast cancers tend to be more aggressive than other types of breast cancer. http://www.mayoclinic.org/breast-cancer/expert-answers/faq-20058066

HIPAA: Health Insurance Portability and Accountability Act. Originally designed in the early 1990s, HIPPA is a federal regulation that standardizes electronic data exchanged within health care transactions, specifies security requirements for stored or exchanged health information, and establishes privacy regulations for health information. http://privacyruleandresearch.nih.gov/

IHC: Immunohistochemistry. http://en.wikipedia.org/wiki/Immunohistochemistry

IQCP: Individualized Quality Control Program

IRB: Internal Review Board.

ISH: In Situ hybridization. A common staining / screening techniques used by Phylogeny. Probes are used to show the physical location of target molecules on within sectioned tissue. Compare with FISH: fluorescence in situ hybridization.

ISO: International Organization for Standardization. See also International Electrotechnical Commission (IEC) The ISO and the IEC define common standards that are often used as guidelines by organizations working in the histology, pathology and biorepository industries. Examples of standards that may be relevant include:

ISO9001: 2000 QM Systems

ISO/IEC 17025: 2005 quality testing and calibration

ISO/IEC 15186: 2007 medical labs

ISO/IEC 27002: 2005 information security

KRAS: A membrane bound GTPase involved in signaling. http://en.wikipedia.org/wiki/KRAS

LC codes: Laboratory Certification Codes. http://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/Downloads/lccodes.pdf

Metastasis: The spread of cancer to other organs of the body. Typically in cancers, the cancer will move to a lymph node first, and then more distant areas of the body. This spread of the tumor from its primary site is considered a “metastasis.”

Mets: metastatic cells at a secondary location

NAT: Normal Adjacent Tissue. Obtaining “normal” tissue for control purposes is sometimes difficult because normal, healthy tissue is seldom removed from a healthy patient. Two common solutions are NAT from resected material and cadaveric, also called post-mortem specimens.

OCT: Optimum cutting temperature. A medium used to mount tissue for sectioning in a cryostat.

Pathology: 1) Study of the essential nature of diseases and especially of the structural and functional changes produced by them 2) Anatomic and physiological deviations from the normal that constitute disease or characterize a particular disease. 3) Treatise on or compilation of abnormalities

Pathologic (or Histologic) Grade: (of cancer cells) The scoring of tumor cells to show how far they have evolved from a normal cell pattern. The lower the number, the closer the cells are to normal. Normal cells tend to grow and multiply slowly to form well-organized tissues made up of differentiated cells. Cancer cells are more “generic” (i.e., less differentiated into the specific cell type usually found in that tissue).

G1: Well differentiated – low grade, tends to grow slowly

G2: Moderately differentiated – Intermediate grade

G3: Poorly differentiated – High grade

G4: Undifferentiated – High grade, tends to be highly invasive.

Pathologic Stage: (of a cancer tumor or event) This categorization system has the same 1-4 scoring scheme as “grade” but uses TNM scores to determine the STAGE of the cancer. The stage of the cancer does not consider cells at a cytological level the way grading does and is more concerned with the characteristics of the tumor(s) and the prognosis for the patient. This scoring is used to describe how the whole tumor has developed in the body. Various TNM scores will fall into each stage. Note: this system is used for most forms of cancer except brain tumors and hematological (related to the blood, bone marrow and lymph nodes) malignancies. Stage may be impossible to determine if very limited samples or biopsies are the only thing available for reexamination.

PBMC: Peripheral Blood Mononuclear Cells. See http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell

PD: Parkinson’s Disease

PMI: Post-mortem intervalPost-mortem interval (PMI) is the time that has elapsed since a person died. http://en.wikipedia.org/wiki/Post-mortem_interval

QA: Quality assurance. Making sure specimens meet QC criteria and that all SOPs and QC processes are actually followed.

QC: Quality Control. Specific criteria and processes designed to insure good quality.

Remnant Tissue: Tissue left over from a surgical procedure. Remnant tissue may qualify for exempt status (i.e. from the need for patient consent to be used in research) if it was removed as part of a required medical procedure.

Resection: A surgical procedure to remove part of an organ or gland. It may also be used to remove a tumor and normal tissue around it. In lung cancer surgery, segmental resection refers to removing a section of a lobe of the lung.

RIN: RNA Integrity Number. RIN is a metric offered by the Agilent Bioanalyzer as an estimate of the extent of degradation of total RNA.

Secondary Score: Any scoring used in a particular cancer type. For instance, prostate cancer uses a Gleason scoring system for helping determine the course of treatment for the patient.

Section Planes: Sagittal (longitudinal, side), Coronal (longitudinal, frontal), Transverse (dorsal-ventral cross section). See “planes” section of http://en.wikipedia.org/wiki/Anatomical_terms_of_location

SOP: Standard Operating Procedure. A formal process that has been established and should be strictly followed to insure compliance with company standards.

SNOMED CT: A systematically organized collection of medical terms providing codes, terms, synonyms and definitions covering diseases, findings, procedures, microorganisms, substances, etc. http://en.wikipedia.org/wiki/SNOMED_CT

TMA: Tissue Microarray. See http://tissuearray.org/yale/tisarray.html

TNM: Type of tumor scoring relating to

T: Tumor size

N: Lymph node involvement

M: Metastasis to other organs

The higher the number following the T, N and M, the more aggressive the cancer is.

TKI: Tyrosine Kinase Inhibitor. Class of anti cancer drugs. Erlotinib (Tarceva) andgefitinib (Iressa) are examples. http://www.mesothelioma-aid.org/kinhibitors.htm