AMP Core Labs FAQs

Registration

Why do I need to register?

Investigators complete a one-time registration for each research project. This includes contact, billing, IRB and other information. Registration minimizes re-entry of identifying information on subsequent order forms and allows tracking by project. For subsequent projects, most of the information will auto-fill from the previous registration.

Why do I need a username and password?

This facilitates updating of contact information and makes it possible to provide a personalized display of past orders. Members of the Department of Pathology and Immunology can use their network username and password; most of the contact information will auto-fill. Other users should select Register. If desired, laboratories can create a shared username and password.

How do I register for lab services?

Select the Register button on the Request Lab Service page or select the Profile (Update Registration) tab on the Order Form. Department investigators simply log in using their network username and password.

How do I update my registration information?

Select the Profile (Update Registration) tab on the Order Form. Make changes and then hit the Submit button. If you have to change the funding source or billing number for a project, it is necessary to create a new project.

Ordering

What is my order number?

An alphanumeric order identifier is shown at the top of your order form and under View Past Requests. The format is as follows:

PI initials – year project initiated – assigned project number – sequential experiment number. For example, JD09-453-2 describes the second oredr/experiment submitted by John Doe under project 453, which was registered in 2009. Because the project number is randomly generated, orders can be unambiguously identified even if multiple users have the same initials.

What is the project number?

Each project has a unique number that is assigned at the time of registration. In many cases, the project corresponds to a specific funded research. Every grant or named project should have its own project number.

Each project can have many associated experiments or orders. When a new order is placed you will be asked to select from among existing projects or create a new project. Orders for each project are numbered chronologically. However, an optional name or description can also be entered. Past orders are grouped by project number when you select the View Past Requests tab.

How do I submit a new project?

Select the Projects Tab and select New from the Please Choose A Project or Select New drop down list. Provide the requested information.

How do I request new lab services for a previously registered project?

Select the Request Service tab on the Order Form and then select the specific project from the Choose Project drop-down list.

How and where do I submit my specimens?

Labeled specimens and a printed copy of the requisition form should be delivered to Room 4721 in the West Building at South Campus. Please see Contact Us for more information.

How do I modify a submitted work order?

It is necessary to contact the laboratory for modifications or add-ons. Modifications may or may not be possible depending on the nature and status of the work order. In some cases, it will be easier to submit a follow up order.

How will I know when my order is complete?

You will receive an auto-generated e-mail when all parts of the order have been completed. However, you can visually track the status of the order or individual specimens by selecting the Request Status tab.

How can I utilize banked tumor tissues?

Investigators must retrieve and deliver their banked materials to the AMP Core Labs.

How do I review my previously submitted orders?

Select the View Past Requests tab on the Request Lab Services Order Form. Orders are grouped by project. Click on the title, then click on the specific order you wish to view. If you entered an experiment name or description when you placed the order, this information will be displayed.

Immunohistochemistry

What is a User Antibody?

A User Antibody is any antibody that is not listed on the AMP Core Labs list or that has not been previously optimized by the Lab. It is usually provided by the requestor or user. Testing with a User Antibody requires prior optimization via an optimization order. An Optimized User Antibody is a User Antibody that has already been optimized by the Core, i.e., it has an existing protocol.

What is a Core Antibody?

Core Antibodies are optimized reagents with active protocols that are used with sufficient frequency to insure their use before expiration. Nearly all Core Antibodies are pre-diluted Ventana or Cell-Marque reagents and are intended to be used with the Ventana autostainer. An Optimized User Antibody can become a Core Antibody if utilization is sufficiently high to insure that reagents will be consumed prior to their expiration date.

How do I find out what antibodies are currently available via the Core?

Core Antibodies are listed on the web site.

Does the Core perform immunohistochemical assays on mouse tissues?

Many mouse tissues contain abundant endogenous Igs that are detected by the secondary reagents used with the Ventana platform. In fact, the detection reagents are specifically designed to allow similar detection of rabbit and mouse antibodies. This results in a high background. Mouse tissues with cells containing abundant Fc receptors can show remarkably specific appearing nonspecific cellular staining.

Where can I check the antibody prices?

Click on the “cost of antibody” link in the price listing. The price is based on the actual cost per slide of the antibody. Most antibodies are pre-diluted reagents from Ventana, and the pricing is taken directly from their price listing.

What is the turnaround time for immunohistochemistry orders?

Clinical testing always has priority. Turnaround time depends on clinical volume, order size, and the number of research orders already in the queue. Note: orders are not assigned to a queue until all specimens and required reagents have been delivered to the lab.

What is a routine versus optimization order?

Pre-diluted antibodies that have been previously characterized by the Core can be selected by name or clone from the drop-down list. Note that essentially all of the listed antibodies are intended for use on human tissues. If you have another antibody that has been previously characterized by the Core you can select the Optimized User Antibody option and enter the antibodies name/clone in the text field.

An optimization order is required for the initial characterization of antibodies that do not have an existing lab protocol. Optimizations involve one or more experiments designed to define the optimal conditions for assay. In most cases, the experiments use pre-defined optimization matrices to examine key variables, including retrieval conditions. If the results are not promising, the optimization project will usually be discontinued. Optimizations are usually very straightforward for new Ventana and most Ventana/Cell-Marque antibodies, but an optimization is still required. The Lab no longer supports semi-automated assays that require technical intervention during a run or manual assays.

How do I submit a work order for optimization of an antibody?

When placing the order, select “Antibody or Probe optimization” from the list of service types. Provide all the information asked for and submit the order. Completion of the order requires the requestor to provide additional information about the antibody and scientific objectives. You will receive a confirmation e-mail with additional information about the process. See the price listing for information on optimization charges. Users are expected to cover the total cost of the antibody.

How do I select the best antibody for my project?

Detailed information about antibody selection can be accessed under Links:

Tissue microarray (TMA)

What is a tissue microarray (TMA)?

TMAs are paraffin blocks that contain cores of tissue derived from other (so-called “donor”) paraffin blocks. Thus, a TMA allows many tissues to be examined on the same slide, facilitating the comparison of protein or nucleic acid expression in various tissues or tumors. For expensive reagents, TMAs can provide cost savings because a single TMA can substitute for large number of individual slides. TMAs are routinely used by the Core Lab for validation of antibodies because each array can provide many potential positive and negative controls.

How do I request a new TMA?

TMA projects can only be initiated with prior approval by the Lab Director. The process of design and fabrication is quite complex and other demands can preclude an acceptable turnaround time.

TMA projects can be initiated using the online order form. Select Tissue Microarray from the Type of Service drop-down box. You will be asked to provide some basic information, which will be forwarded to the Core Labs.

What is required to design a TMA?

It is necessary to formally collaborate with a staff pathologist who can assist with design of the array, identify suitable blocks, and select areas for sampling. It is the responsibility of the investigator to obtain the required IRB approval, identify a collaborating pathologist, identify appropriate specimens, and arrange for retrieval of the blocks.

Depending on the objectives, you will need to make decisions regarding the number and size of cores, the number of replicate cores from the same block, and the placement of cores in the microarray. It is important to carefully select the region to sample and to insure that there is sufficient thickness of tissue in the block to provide a usable core. Each TMA can contain many cores, but the number depends on the size of the individual cores.

What is the cost to design and fabricate a TMA?

Pricing depends on the nature and scope of the project. However, the minimum cost is approximately $5 per core of tissue.

How long does it take to fabricate a new TMA?

Once the TMA has been designed, blocks have been selected, and sites for coring have been identified, the order will be placed in a TMA work queue. The turnaround for the order will depend on the position in the queue, the number of cores per TMA, the number of separate blocks that will constitute the TMA, and the test volume in other areas of the lab. The Lab Manager will work with the investigator to establish a tentative but non-binding schedule for each order.

How many slides can be obtained from a single TMA?

This depends on the thickness of the tissue in the source blocks. The thinnest core will determine the maximum number of complete arrays that can be obtained. Because tissue is lost every time a block is mounted on the microtome and faced, and because it is not advisable to store unstained sections for extended periods of time, care must be taken when planning experiments. In order to conserve tissue, the lab does not routinely section and stain arrays for quality control. Nevertheless, this is the only way the Lab can guarantee the suitability of each core in the block.

What other tissues should I consider including on my TMA?

Some investigators include various control tissues, e.g., positive controls for planned immunohistochemical stains, or non-neoplastic tissues from the sames sites as the sampled tumors. The investigator can determine the placement of these cores on the TMA. For some studies, it is possible to perform sterile punches for harvest of DNA/RNA/protein. The cored tissues for each case/donor block can be stored in appropriately labeled sterile tubes.

Histology

How do I find out what special stains are currently available via the Core?

Special stains are listed in the drop-down box on the order form.

What is the turnaround time for histology orders?

Orders are placed in different queues depending on the type of order, and then processed on a first come first served basis. However, clinical testing always has the highest priority and we cannot guarantee a specific turnaround. Research orders from the Department of Pathology and Immunology are scheduled for Monday-Tuesday, orders from other users are scheduled for Wednesday-Friday. Turnaround time depends on the clinical volume, order size, and the number of research orders already in the queue. Orders are not assigned to a queue until all specimens have been delivered and can be reconciled with the order form.

Where can I check on current histology prices?

Routine charges are given in our price listing. Prices are re-evaluated annually.

What should I do if the quality of my stained sections is sub-optimal?

Please arrange to review your slides together with the Histology Supervisor or Lab Manager. Stain quality can be influenced by many factors. Because the lab uses automatic tissue processing and well-maintained autostainers, analytical problems are minimimized. However some tissues may require modification of the standard processing cycle. Many common staining problems are caused by inadequate fixation, usually underfixation. If experiencing such problems, we recommend that you read our introductory document on formalin fixation.