category: Biospecimen deprecated: - is_ffpe - oct_embedded description: Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products. links: - label: Sample references the Case it is derived from. name: Case required: 'True' properties: biospecimen_anatomic_site: cde_id: 4742851 description: Text term that represents the name of the primary disease site of the submitted tumor sample. enum: - Abdomen - Abdominal Wall - Acetabulum - Adenoid - Adipose - Adrenal - Alveolar Ridge - Amniotic Fluid - Ampulla Of Vater - Anal Sphincter - Ankle - Anorectum - Antecubital Fossa - Antrum - Anus - Aorta - Aortic Body - Appendix - Aqueous Fluid - Arm - Artery - Ascending Colon - Ascending Colon Hepatic Flexure - Auditory Canal - Autonomic Nervous System - Axilla - Back - Bile Duct - Bladder - Blood - Blood Vessel - Bone - Bone Marrow - Bowel - Brain - Brain Stem - Breast - Broad Ligament - Bronchiole - Bronchus - Brow - Buccal Cavity - Buccal Mucosa - Buttock - Calf - Capillary - Cardia - Carina - Carotid Artery - Carotid Body - Cartilage - Cecum - Cell-Line - Central Nervous System - Cerebellum - Cerebral Cortex - Cerebrospinal Fluid - Cerebrum - Cervical Spine - Cervix - Chest - Chest Wall - Chin - Clavicle - Clitoris - Colon - Colon - Mucosa Only - Common Duct - Conjunctiva - Connective Tissue - Dermal - Descending Colon - Diaphragm - Duodenum - Ear - Ear Canal - Ear, Pinna (External) - Effusion - Elbow - Endocrine Gland - Epididymis - Epidural Space - Esophageal; Distal - Esophageal; Mid - Esophageal; Proximal - Esophagogastric Junction - Esophagus - Esophagus - Mucosa Only - Eye - Fallopian Tube - Femoral Artery - Femoral Vein - Femur - Fibroblasts - Fibula - Finger - Floor Of Mouth - Fluid - Foot - Forearm - Forehead - Foreskin - Frontal Cortex - Frontal Lobe - Fundus Of Stomach - Gallbladder - Ganglia - Gastroesophageal Junction - Gastrointestinal Tract - Groin - Gum - Hand - Hard Palate - Head & Neck - Head - Face Or Neck, Nos - Heart - Hepatic - Hepatic Duct - Hepatic Flexure - Hepatic Vein - Hip - Hippocampus - Humerus - Hypopharynx - Ileum - Ilium - Index Finger - Ischium - Islet Cells - Jaw - Jejunum - Joint - Kidney - Knee - Lacrimal Gland - Large Bowel - Laryngopharynx - Larynx - Leg - Leptomeninges - Ligament - Lip - Liver - Lumbar Spine - Lung - Lymph Node - Lymph Node(s) Axilla - Lymph Node(s) Cervical - Lymph Node(s) Distant - Lymph Node(s) Epitrochlear - Lymph Node(s) Femoral - Lymph Node(s) Hilar - Lymph Node(s) Iliac-Common - Lymph Node(s) Iliac-External - Lymph Node(s) Inguinal - Lymph Node(s) Internal Mammary - Lymph Node(s) Mammary - Lymph Node(s) Mesenteric - Lymph Node(s) Occipital - Lymph Node(s) Paraaortic - Lymph Node(s) Parotid - Lymph Node(s) Pelvic - Lymph Node(s) Popliteal - Lymph Node(s) Regional - Lymph Node(s) Retroperitoneal - Lymph Node(s) Scalene - Lymph Node(s) Splenic - Lymph Node(s) Subclavicular - Lymph Node(s) Submandibular - Lymph Node(s) Supraclavicular - Lymph Nodes(s) Mediastinal - Mandible - Maxilla - Mediastinal Soft Tissue - Mediastinum - Mesentery - Mesothelium - Middle Finger - Mitochondria - Muscle - Nails - Nasal Cavity - Nasal Soft Tissue - Nasopharynx - Neck - Nerve - Nerve(s) Cranial - Occipital Cortex - Ocular Orbits - Omentum - Oral Cavity - Oral Cavity - Mucosa Only - Oropharynx - Other - Ovary - Palate - Pancreas - Paraspinal Ganglion - Parathyroid - Parotid Gland - Patella - Pelvis - Penis - Pericardium - Periorbital Soft Tissue - Peritoneal Cavity - Peritoneum - Pharynx - Pineal - Pineal Gland - Pituitary Gland - Placenta - Pleura - Popliteal Fossa - Prostate - Pylorus - Rectosigmoid Junction - Rectum - Retina - Retro-Orbital Region - Retroperitoneum - Rib - Ring Finger - Round Ligament - Sacrum - Salivary Gland - Scalp - Scapula - Sciatic Nerve - Scrotum - Seminal Vesicle - Shoulder - Sigmoid Colon - Sinus - Sinus(es), Maxillary - Skeletal Muscle - Skin - Skull - Small Bowel - Small Bowel - Mucosa Only - Small Finger - Soft Tissue - Spinal Column - Spinal Cord - Spleen - Splenic Flexure - Sternum - Stomach - Stomach - Mucosa Only - Subcutaneous Tissue - Synovium - Temporal Cortex - Tendon - Testis - Thigh - Thoracic Spine - Thorax - Throat - Thumb - Thymus - Thyroid - Tibia - Tongue - Tonsil - Tonsil (Pharyngeal) - Trachea / Major Bronchi - Transverse Colon - Trunk - Umbilical Cord - Ureter - Urethra - Urinary Tract - Uterus - Uvula - Vagina - Vas Deferens - Vein - Venous - Vertebra - Vulva - White Blood Cells - Wrist - Unknown - Not Reported - Not Allowed To Collect - Sublingual Gland - Submandibular Gland - Paranasal Sinuses - Supraglottis - Subglottis - Glottis required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4742851%20and%20ver_nr=1.0 type: Enumeration biospecimen_laterality: cde_id: 2007875 description: For tumors in paired organs, designates the side on which the specimen was obtained. enum: - Bilateral - Left - Right - Unknown - Not Reported required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2007875%20and%20ver_nr=1.0 type: Enumeration case_id: key: 'yes' required: 'False' type: String case_submitter_id: key: 'yes' required: 'False' type: String catalog_reference: description: HCMI catalog reference number for cancer model. required: 'False' type: String composition: cde_id: 5432591 description: Text term that represents the cellular composition of the sample. enum: - 2D Classical Conditionally Reprogrammed Cells - 2D Modified Conditionally Reprogrammed Cells - 3D Organoid - 3D Air-Liquid Interface Organoid - 3D Neurosphere - Adherent Cell Line - Buccal Cells - Buffy Coat - Bone Marrow Components - Bone Marrow Components NOS - Control Analyte - Cell - Derived Cell Line - EBV Immortalized - Fibroblasts from Bone Marrow Normal - Granulocytes - Human Original Cells - Liquid Suspension Cell Line - Lymphocytes - Mononuclear Cells from Bone Marrow Normal - Peripheral Blood Components NOS - Pleural Effusion - Plasma - Peripheral Whole Blood - Serum - Saliva - Sputum - Solid Tissue - Sorted Cells - Whole Bone Marrow - Unknown - Not Reported - Not Allowed To Collect - Mixed Adherent Suspension required: 'True' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432591%20and%20ver_nr=1.0 type: Enumeration current_weight: cde_id: 5432606 description: Numeric value that represents the current weight of the sample, measured in milligrams. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432606%20and%20ver_nr=1.0 type: Number days_to_collection: cde_id: 3008340 description: Time interval from the date of biospecimen collection to the date of initial pathologic diagnosis, represented as a calculated number of days. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3008340%20and%20ver_nr=1.0 type: Integer days_to_sample_procurement: description: The number of days from the date the patient was diagnosed to the date of the procedure that produced the sample. required: 'False' type: Integer diagnosis_pathologically_confirmed: description: The histologic description of tissue or cells confirmed by a pathology review of frozen or formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used to extract analyte(s). enum: - 'Yes' - 'No' - Unknown - Not Reported - Not Allowed To Collect required: 'False' type: Enumeration distance_normal_to_tumor: cde_id: 3088708 description: Text term to signify the distance between the tumor tissue and the normal control tissue that was procured for matching normal DNA. enum: - Adjacent (< or = 2cm) - Distal (>2cm) - Unknown - Not Reported required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3088708%20and%20ver_nr=1.0 type: Enumeration distributor_reference: cde_id: 3088708 description: Distributor reference number for cancer model. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3088708%20and%20ver_nr=1.0 type: String freezing_method: cde_id: 5432607 description: Text term that represents the method used for freezing the sample. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432607%20and%20ver_nr=1.0 type: String gdc_project_id: description: Project identifier associated with the sample at the genomic data commons required: 'False' type: String gdc_sample_id: description: Sample identifier associated with the sample at the genomic data commons required: 'False' type: String growth_rate: description: Rate at which the model grows, measured as hours to time to split. required: 'False' type: Integer initial_weight: cde_id: 5432605 description: Numeric value that represents the initial weight of the sample, measured in milligrams. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432605%20and%20ver_nr=1.0 type: Number intermediate_dimension: description: Intermediate dimension of the sample, in millimeters. required: 'False' type: Number is_ffpe: cde_id: 4170557 description: Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in paraffin (FFPE). enum: - 'true' - 'false' required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4170557%20and%20ver_nr=1.0 type: Enumeration longest_dimension: cde_id: 5432602 description: Numeric value that represents the longest dimension of the sample, measured in millimeters. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432602%20and%20ver_nr=1.0 type: Number method_of_sample_procurement: description: The method used to procure the sample used to extract analyte(s). enum: - Abdomino-perineal Resection of Rectum - Anterior Resection of Rectum - Ascites Drainage - Aspirate - Autopsy - Biopsy - Blood Draw - Bone Marrow Aspirate - Core Biopsy - Cystectomy - Endo Rectal Tumor Resection - Endoscopic Biopsy - Endoscopic Mucosal Resection (EMR) - Enucleation - Excisional Biopsy - Fine Needle Aspiration - Full Hysterectomy - Gross Total Resection - Hand Assisted Laparoscopic Radical Nephrectomy - Hysterectomy NOS - Incisional Biopsy - Indeterminant - Laparoscopic Biopsy - Laparoscopic Partial Nephrectomy - Laparoscopic Radical Nephrectomy - Laparoscopic Radical Prostatectomy with Robotics - Laparoscopic Radical Prostatectomy without Robotics - Left Hemicolectomy - Liquid Biopsy - Lobectomy - Local Resection (Exoresection; wall resection) - Lumpectomy - Lymphadenectomy - Metastasectomy - Modified Radical Mastectomy - Needle Biopsy - Omentectomy - Oophorectomy - Open Craniotomy - Open Partial Nephrectomy - Open Radical Nephrectomy - Open Radical Prostatectomy - Orchiectomy - Other - Other Surgical Resection - Pan-Procto Colectomy - Pancreatectomy - Paracentesis - Partial Hepatectomy - Peritoneal Lavage - Pneumonectomy - Punch Biopsy - Radical Hysterectomy - Right Hemicolectomy - Salpingectomy - Salpingo-oophorectomy - Sigmoid Colectomy - Simple Hysterectomy - Simple Mastectomy - Subtotal Resection - Supracervical Hysterectomy - Surgical Resection - Thoracentesis - Thoracoscopic Biopsy - Total Colectomy - Total Hepatectomy - Total Mastectomy - Transplant - Transurethral resection (TURBT) - Transverse Colectomy - Tumor Debulking - Tumor Resection - Wedge Resection - Whipple Procedure - Unknown - Not Reported - Not Allowed To Collect - Endolaryngeal Excision - Laryngopharyngectomy - Radical Maxillectomy - Transoral Laser Excision - Lymph Node Dissection - Mandibulectomy - Radical Nephrectomy - Maxillectomy - Parotidectomy, NOS - Radical Prostatectomy - Superficial Parotidectomy - Palatectomy - Subtotal Prostatectomy - Tonsillectomy - Partial Laryngectomy - Deep Parotidectomy - Buccal Mucosal Resection - Partial Maxillectomy - Total Nephrectomy - Vertical Hemilaryngectomy - Supracricoid Laryngectomy - Glossectomy - Supraglottic Laryngectomy - Total Laryngectomy - Partial Nephrectomy - Transurethral Resection (TURP) required: 'False' type: Enumeration oct_embedded: cde_id: 5432538 description: Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432538%20and%20ver_nr=1.0 type: String passage_count: description: Number of passages (splits) between the original tissue and this model. required: 'False' type: Integer pathology_report_uuid: description: UUID of the related pathology report. required: 'False' type: String pool: description: Any biospecimen entity where multiple cases, samples or aliquots are combined to produce a reference. Sample pooling is commonly used for determining relative protein abundances in labeling experiments. enum: - 'Yes' - 'No' required: 'True' type: Enumeration preservation_method: cde_id: 5432521 description: Text term that represents the method used to preserve the sample. enum: - Cryopreserved - FFPE - Fresh - OCT - Snap Frozen - Frozen - Unknown - Not Reported - Not Allowed To Collect required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432521%20and%20ver_nr=1.0 type: Enumeration project_id: key: 'yes' required: 'False' type: String project_submitter_id: key: 'yes' required: 'False' type: String sample_id: key: 'yes' required: 'False' type: String sample_is_ref: description: A biospecimen entity which is used as a reference sample for determining relative protein abundances in labeling experiments. enum: - 'Yes' - 'No' required: 'False' type: Enumeration sample_ordinal: description: A number describing the samples place in an ordered sequence. required: 'False' type: Integer sample_submitter_id: key: 'yes' required: 'True' type: String sample_type: cde_id: 3111302 description: Text term to describe the source of a biospecimen used for a laboratory test. enum: - Additional Metastatic - Additional - New Primary - Benign Neoplasms - Blood Derived Cancer - Bone Marrow - Blood Derived Cancer - Bone Marrow, Post-treatment - Blood Derived Cancer - Peripheral Blood - Blood Derived Cancer - Peripheral Blood, Post-treatment - Blood Derived Liquid Biopsy - Blood Derived Normal - Bone Marrow Normal - Buccal Cell Normal - Cell Line Derived Xenograft Tissue - Cell Lines - Control Analyte - DNA - EBV Immortalized Normal - Expanded Next Generation Cancer Model - FFPE Recurrent - FFPE Scrolls - Fibroblasts from Bone Marrow Normal - GenomePlex (Rubicon) Amplified DNA - Granulocytes - Human Tumor Original Cells - In Situ Neoplasms - Lymphoid Normal - Metastatic - Mononuclear Cells from Bone Marrow Normal - Normal Adjacent Tissue - Neoplasms of Uncertain and Unknown Behavior - Next Generation Cancer Model - Primary Blood Derived Cancer - Peripheral Blood - Recurrent Blood Derived Cancer - Peripheral Blood - Pleural Effusion - Primary Blood Derived Cancer - Bone Marrow - Primary Tumor - Primary Xenograft Tissue - Post neo-adjuvant therapy - Recurrent Blood Derived Cancer - Bone Marrow - Recurrent Tumor - Repli-G (Qiagen) DNA - Repli-G X (Qiagen) DNA - RNA - Slides - Solid Tissue Normal - Total RNA - Tumor Adjacent Normal - Post Neo-adjuvant Therapy - Tumor - Xenograft Tissue - Unknown - Not Reported - Not Allowed To Collect - Next Generation Cancer Model Expanded Under Non-conforming Conditions - Mixed Adherent Suspension - Saliva - Serum required: 'True' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3111302%20and%20ver_nr=2.0 type: Enumeration sample_type_id: description: The accompanying sample type id for the sample type. enum: - '01' - '02' - '03' - '04' - '05' - '06' - '07' - 08 - 09 - '10' - '11' - '12' - '13' - '14' - '15' - '16' - '17' - '18' - '20' - '30' - '31' - '32' - '40' - '41' - '42' - '50' - '60' - '61' - '85' - '86' - '99' - '87' required: 'False' type: Enumeration shortest_dimension: cde_id: 5432603 description: Numeric value that represents the shortest dimension of the sample, measured in millimeters. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432603%20and%20ver_nr=1.0 type: Number status: description: Specifies if the sample is qualified or disqualified for any reason. required: 'True' type: String time_between_clamping_and_freezing: cde_id: 5432611 description: Numeric representation of the elapsed time between the surgical clamping of blood supply and freezing of the sample, measured in minutes. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432611%20and%20ver_nr=1.0 type: Number time_between_excision_and_freezing: cde_id: 5432612 description: Numeric representation of the elapsed time between the excision and freezing of the sample, measured in minutes. required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432612%20and%20ver_nr=1.0 type: Number tissue_collection_type: description: The text term used to describe the tyoe of collection used to obtain tissue. enum: - Prospective - Retrospective required: 'False' type: Enumeration tissue_type: cde_id: 5432687 description: Text term that represents a description of the kind of tissue collected with respect to disease status or proximity to tumor tissue. enum: - Tumor - Normal - Abnormal - Peritumoral - Unknown - Not Reported - Not Allowed To Collect required: 'True' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432687%20and%20ver_nr=1.0 type: Enumeration tumor_code: description: Diagnostic tumor code of the tissue sample source. enum: - Non cancerous tissue - Diffuse Large B-Cell Lymphoma (DLBCL) - Lung Cancer (all types) - Cervical Cancer (all types) - Anal Cancer (all types) - Acute Leukemia of Ambiguous Lineage (ALAL) - Acute lymphoblastic leukemia (ALL) - Acute myeloid leukemia (AML) - Induction Failure AML (AML-IF) - Neuroblastoma (NBL) - Osteosarcoma (OS) - Ewing sarcoma - Wilms tumor (WT) - Clear cell sarcoma of the kidney (CCSK) - Rhabdoid tumor (kidney) (RT) - CNS, ependymoma - CNS, glioblastoma (GBM) - CNS, rhabdoid tumor - CNS, low grade glioma (LGG) - CNS, medulloblastoma - CNS, other - NHL, anaplastic large cell lymphoma - NHL, Burkitt lymphoma (BL) - Rhabdomyosarcoma - Soft tissue sarcoma, non-rhabdomyosarcoma required: 'False' type: Enumeration tumor_code_id: description: BCR-defined id code for the tumor sample. enum: - '00' - '01' - '02' - '03' - '04' - '10' - '15' - '20' - '21' - '30' - '40' - '41' - '50' - '51' - '52' - '60' - '61' - '62' - '63' - '64' - '65' - '70' - '71' - '80' - '81' required: 'False' type: Enumeration tumor_descriptor: cde_id: 3288124 description: Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint. enum: - Metastatic - Not Applicable - Primary - Recurrence - Xenograft - NOS - Unknown - Not Reported - Not Allowed To Collect - Premalignant required: 'False' source: caDSR term_url: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3288124%20and%20ver_nr=1.0 type: Enumeration title: Sample type: object uniqueKeys: - - sample_id - sample_submitter_id