OHSU

OHSU Biolibrary FAQ

Frequently Asked Questions

 

Answers


How does the Biolibrary Search Engine work?

The Biolibary Search Engine is a user-friendly, online tool that allows OHSU researchers to search the data of certain biospecimen collections.  All OHSU researchers can access the Biolibrary Search Engine from a computer on the OHSU network. (Completion of some basic training is required, but the system will let you know if you need to complete online training.)

Currently, the Search Engine accesses data from the Knight Tissue Bank and the Department of Pathology Shared Archives.

 

What are some examples of how researchers can use the Search Engine?

The Biolibrary Search Engine offers a simple way for researchers to gather deidentified information about biospecimens in two major OHSU biorepositories: the Knight Tissue Bank and the Department of Pathology Shared Archives.

There are two main ways in which researchers can utilize the Search Engine: conducting feasibility analyses and identifying samples for analysis.

Example #1 | Feasibility Analysis for Proposals
A researcher can use the Search Engine to determine if her research question can form the basis for a grant proposal or industry-sponsored project. She can search for ‘Barrett’s esophagus’ to see how many samples from women are available.   In addition to finding out whether there are enough samples, she can use associated data to strengthen the aims of her proposal.

Example #2 | Finding Enough Samples for Genotyping
A researcher interested in nodal metastasis in thyroid carcinoma could use the Biolibrary Search Engine to identify node-negative and node-positive cases. She can then download a lot of information about these samples, including: deidentified pathology reports, full TNM staging, treatments and follow-up status, and the availability of fresh-frozen or archival tissue. Statistical analysis can be done to determine whether the available samples and matching data meet power requirements for the study. If the statistical analysis is promising, the researcher can obtain IRB approval and access the samples for genotyping.

Example #3 | Finding Matching Samples for Antibody Testing
A researcher needs to test an antibody to determine whether it can detect a protein in the metastatic adenocarcinomas. He uses the Search Engine to explore adenocarcinoma samples, and he is able to find matched sets of primary and metastatic tumor samples. With IRB approval (or exemption), the researcher is able to access the samples in order to test the antibody.

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Are there plans to add repositories to the Search Engine?

Yes, we are currently evaluating repositories to be added to the Search Engine. The summary table of OHSU collections is updated to indicate which collections are pending to be added.

Have a suggestion for the Search Engine?

Please contact the OCTRI Research Navigator Program.

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Do I need to submit an IRB protocol for research on human biospecimens?

The answer depends on the types of biospecimens being studied and the experiments that will be performed on them. 

No IRB oversight is required if the study: 

  • is on coded or anonymized biospecimens from patients who did not select the genetic opt out;
  • does not require knowledge of the patient’s identity;

  • does not involve genetic data generated from DNA (genomic or mitochondrial), RNA or protein sequence.

Example: a study of hormone or cytokine levels in cellular lysates of coded samples, without need for clinical chart review

IRB exemption can be obtained if the study: 

  • is on coded or anonymized biospecimens from patients who did not select the genetic opt out; 
  • does not require knowledge of the patient’s identity;

  • involves genetic data generated from DNA (genomic or mitochondrial), RNA or protein sequence.

Example: a study of oncogene mutation frequency in a particular tumor, without need for clinical chart review

A full IRB protocol is required if the study:

  • is on coded biospecimens from patients who did not select the genetic opt out;
  • requires knowledge of the patient’s identity for clinical correlation.

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Will I be charged for biospecimens?

Each biospecimen collection has its own policy in regard to fees for biospecimens. Contact the PI of the collection for additional information.

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How do I obtain biospecimen samples?

For each biospecimen collection on the OHSU campus there is a contact person. See Biospecimen Collections.

Note: depending on the type of study you plan to perform, you may be required to submit an IRB protocol before biospecimens are made available to you.

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What is the Oregon genetic ’opt out’ and how does it affect the use of biospecimens for research?

In 2005, the Oregon state legislature enacted several amendments and clarifications to the so-called genetic privacy law, which was first passed in 1995.

  • The law stipulates that genetic information and DNA samples are considered private, and that an individual has a right to the protection of this privacy.
  • All patients have the opportunity to ’opt out’ if they do not wish their genetic information or DNA to be used in research.
  • Research organizations are required to offer patients the research opt out, and to keep track of each patient’s response. Patients can change their opt out status at anytime.
  • Research is permitted on coded specimens and anonymized specimens originating from patients who have not opted out, provided that the researcher submits a protocol to the IRB.

See additional information on the Oregon Genetic Privacy Law.

 

How is genetic information defined in the Oregon genetic privacy law?

  • Genetic information is any information about an individual or the individual’s blood relatives obtained from a genetic test.
  • A genetic test is a test for determining the presence or absence of genetic characteristics in a human individual or the individual’s blood relatives, including tests of nucleic acids such as DNA, RNA, and mitochondrial DNA, chromosomes or proteins in order to diagnose or determine a genetic characteristic.
  • A genetic characteristic includes a gene, chromosome or alteration thereof that may be tested to determine the existence or risk of a disease, disorder, trait, propensity or syndrome or to identify an individual or a blood relative. Genetic characteristic does not include family history or a genetically transmitted characteristic whose existence or identity is determined other than through a genetic test.
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What is a ’coded’ biospecimen?

Biospecimens that have a unique identifier that is not derived from any patient identifiers are termed ‘coded’ samples. Coded samples can be linked back to the patients from which they were obtained. An example of a biospecimen code would be a tissue bank number (e.g. TB-1234).

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What is an ’anonymized’ biospecimen?

Biospecimens that are labeled with an identifier that cannot be linked back to the originating patient, not even by the PI who collected them, are considered anonymized.

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What are the limitations to using formalin-fixed, paraffin-embedded (FFPE) tissue for research studies?

Nucleic acids in formalin-fixed, paraffin-embedded (FFPE) tissue are highly degraded, but a surprising amount of information can still be gained from studies on FFPE material. The average length of DNA or RNA from FFPE tissue is between 200 and 400 bp. If amplicons are kept short (80 to 200 bp), genomic DNA can be accurately assessed for the presence of specific SNPs or mutations of interest by any sequencing technology (ABI, pyrosequencing, and even high throughput next-gen sequencing). Similarly, short amplicons can be used to measure RNA (cDNA) elements in a sample by real-time PCR, microarrays or high-throughput next-gen sequencing. In addition to nucleic acid studies, FFPE tissue can be used for histologic, immunohistochemical and fluorescence in-situ hybridization experiments.  

 

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Tissue Samples and OHSU Biolibrary Director Christopher Corless

OCTRI and the Knight Cancer Institute have joined to create the OHSU Biolibrary program.