AMP Core Labs FAQs

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.

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.

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.

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.

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-order/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.

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.

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.

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.

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.

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.

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

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.

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.

Core Antibodies are optimized reagents with active protocols that are used with sufficient frequency to ensure 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 ensure that reagents will be consumed prior to their expiration date.

Core Antibodies are listed on the website.

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.

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.

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.

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 optimization is still required. The Lab no longer supports semi-automated assays that require technical intervention during a run or manual assays.

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.

Detailed information about antibody selection can be accessed under Links:

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 a 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.

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.

It is necessary to formally collaborate with a staff pathologist who can assist with the 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 ensure 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.

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

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.

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.

Some investigators include various control tissues, e.g., positive controls for planned immunohistochemical stains, or non-neoplastic tissues from the same 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 the harvest of DNA/RNA/protein. The cored tissues for each case/donor block can be stored in appropriately labeled sterile tubes.

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

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.

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

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 minimized. However, some tissues may require modification of the standard processing cycle. Many common staining problems are caused by inadequate fixation, usually under fixation. If experiencing such problems, we recommend that you read our introductory document on formalin fixation.

GUIDE SLIDE & FORM 4800-R: To obtain reliable sequencing data for a tumor, there must be sufficient cellularity as compared to surrounding or associated non-neoplastic cells.  The current cut-off for clinical studies is 10% and assumes that most of the cells are viable. A guide slide assists with selecting areas of high cellularity suitable for coring and sequencing. If the tissue shows uniform and sufficiently high tumor cellularity, scrolls could be ordered

1. If an H&E stained slide is available, create a guide slide by circling the area for testing using an ultrafine dotting pen. Note: if only blocks are available it will be necessary to first order an H&E stained slide for each block via the AMP Core Labs web site; this will be used to generate the guide.
2. Each specimen for sequencing will also require completion of a GPS Form 4800-R. This research form is much simpler than the corresponding clinical form. However, like the clinical form, it provides an assessment of specimen quality and suitability for testing. Copies can be downloaded from this site.
3. If questions there are questions about creating a guide slide or completing the form consult with a pathologist on the GPS Intake Service or collaborate with someone on that service.
4. If you do not have a collaborating GPS pathologist, the guide slides and form will need to be reviewed by a pathologist on the service, or by Dr. Crouch.

SAMPLING THE TISSUE: Ordering coring on this web site is essentially the same as for ordering any histochemical or immunohistochemical stain, but is detailed here. The same general workflow applies to scrolls (thick sections of paraffin block) or microdissections of sections on unstained slides of FFPE tissue.

1. Via the AMP Core Labs web site select Request Service.
2. Log in with your network username and password (not WUSTL key).
3. Choose a project or create a name.
4. Using the Type of Service drop-down select “Procedures beginning with tissue or tissue block”.
5. Describe the specimen as needed using the form and indicate that all blocks will be treated identically from the drop-down.
6. Indicate the number of blocks submitted.
7. Enter “1” in the # of Different Types of Procedures text box.
8. Select Molecular Pathology from the Process/Stain drop-down.
9. In the Instructions text box indicate that you want the blocks to be cored for NGS using the provided guide slide(s). Alternatively, If scrolls or microdissections are required this can be indicated in the box.
10. Select the Submit button at the bottom of the window and print out a copy of the requisition.
11. Deliver the blocks, corresponding guide slides, a printed copy of the requisition, and printed copies of the completed 4800-R forms to the AMP Core Labs on 4th floor West Building.
12. You can track the status of your order on the web site. In any case, you will receive email notification once the cores, blocks, and guide slides are available for pickup. Cores are provided in labeled specimen tubes ready for extraction.

Deliver the specimens and the corresponding 4800-R forms to Cortex according to GPS instructions.