Biomarkers

The Biomarkers Shared Resource (Biomarkers SR) is a joint resource of the Herbert Irving Comprehensive Cancer Center and Columbia’s NIEHS Center for Environmental Health in Northern Manhattan. It provides a centralized, efficient, and cost-effective resource for receiving, handling, and storing human samples that are collected as part of research studies in molecular epidemiology and other types of cancer-related research. Services provided include:

• Consultation on sample processing
• Preparation of kits for bio-specimen collection
• Processing and storage of blood components, including cells and plasma
• Storage of other body fluids, including urine, sputum, and oral cells
• Isolation of DNA/RNA with quality controls
• Maintenance of a sample inventory
• Analysis of candidate single nucleotide polymorphisms (SNPs) by Taqman assays
• ELISA with commercially available kits

Consultation is provided on all aspects of sample collection and processing for specific studies including the types of tubes needed for sample collection, shipment methods, separation of specific fractions, number of aliquots, etc. The samples processed and/or stored include blood, urine, oral cells, and sputum. Coded samples are received by the facility and processed into appropriate fractions (e.g., plasma, mononuclear cells, granulocytes, total white blood cells, and red blood cells) and frozen in multiple aliquots in more than one freezer whenever possible. A web-based database of the sample inventory is maintained and samples retrieved as specified in the governing protocol. A telephone alarm system is used to ensure sample safety. 

Additional services include:

• DNA isolation from buccal and white blood cells and plasma and serum
• RNA isolating including microRNAs
• Whole genome amplification of limited DNA samples
• Genotyping for single nucleotide polymorphisms in candidate genes

Commercial ELISA kits can also be run by the SR. Samples from over 34,000 subjects participating in 112 different studies, 78 cancer-related, are currently stored.

Location and Contacts

The Biomarkers laboratory is located at:
Black Building, 650 West 168th Street, Room 1608

Hui-Chen Wu, DrPH, Faculty Director
Phone: 212-305-6960
Email: hw2057@cumc.columbia.edu

Irina Gurvich, MS, Manager
Phone: 212-305-8158
Email: ig112@cumc.columbia.edu

User Fees 

Guidelines for Use of the Biomarkers Shared Resource

Prior to use of the Biomarkers SR, the Principal Investigator will fill out the “Request for sample processing/storage” providing information on the number of samples to be processed, the maximum number expected per day, and details about number and type of aliquots for short and long term storage. A protocol will be developed in conjunction with the PI for processing and aliquoting of samples and any special handling procedures (e.g., any additives such as ascorbic acid for later folate measurement). Costs will vary based on estimated technician time and supplies needed. 

A coding system for labeling collection material can be developed in conjunction with the PI and preprinted bar code labels (which also contain the readable number) provided for sample collection tubes and paperwork. If random digit numbers are required for the study, they must be provided to the facility on a disc. 

In studies where it is clear that certain vials will be used reasonably soon, they will not be placed with other samples for long term storage but be stored separately. This will allow for rapid retrieval of samples when needed. Thus, the PI needs to inform the facility of the short-term usage of samples. Samples will be split into two freezers if feasible. 

For sample retrieval, the PI fills out a “Request for Sample Retrieval” form indicating the number of samples requested and type. The PI must also provide a computerized list of the sample IDs. To the extent possible, samples will be retrieved within 2-3 weeks of the request. 

For DNA/RNA extractions, an electronic list of sample IDs must be provided and the preferred method of extraction, if any. For sample analysis such as ELISA with commercial kits, the PI should discuss the request with the BSR director. 

ALL requests must be finalized through iLab before a project can be initiated. 

How to Conduct Research on Samples Stored in the Biomarkers Shared Resource by Another Investigator

• Discuss with the PI who deposited samples the appropriateness of the proposed study, availability of biospecimens needed and any specific procedures the study requires for obtaining permission to use samples.
• Obtain written approval for use of the samples.
• Obtain IRB approval.
• Provide Shared Resource Director with approvals and completed biospecimen retrieval form.