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What happens to biopsy and cytology specimens?

Standard procedures and methods are used to process nearly all types of biopsy samples. These procedures are the usual ways that a sample is prepared in the lab. Other procedures, which are described later,  may also be done on certain types of samples (such as lymph nodes and bone marrow).

How biopsies are processed routinely

After its removal, the biopsy specimen is put in a container with a mixture of water and formaldehyde (formalin) or some other fluid to preserve it. The container is labeled with the patient’s name and other identifying information (hospital number and birth date, for example) and the site of biopsy (exactly where on the body it was taken from). It’s then sent to the pathology lab. Next, the pathologist or a trained lab assistant looks at the specimen without a microscope. This is called gross examination. (In medicine, gross means seen without a microscope.) This is done to record what is seen by simply looking at, measuring, or feeling the tissue. The gross examination includes the tissue sample’s size, color, consistency, and other characteristics. The lab staff may even take a picture of the sample as part of the record. The gross examination is important since the pathologist may see features that suggest cancer. It also helps the pathologist decide which parts of a large biopsy are the most critical to look at under a microscope.

For small biopsies, such as a punch biopsy or a core needle biopsy, the entire specimen is usually looked at under a microscope. The tissue is put into small containers called cassettes. The cassettes hold the tissue securely while it’s processed. After processing, which may take a few hours (but is usually done overnight), the tissue sample is put into a mold with hot paraffin wax. The wax cools to form a solid block that protects the tissue.

This paraffin wax block with the embedded tissue is cut into very thin slices using an instrument called a microtome. These thin slices of the specimen are placed on glass slides, and dipped into a series of stains or dyes to change the color of the tissue. The color makes cells easier to see under a microscope. For most biopsy specimens, this routine processing is all that’s needed. At this point (usually the day after the biopsy was done), the pathologist looks at the tissue under a microscope. Looking at the solid specimens in this way is called histology, which is the study of the structures of cells and tissues.

Special biopsy processing: Frozen section (intra-operative consultation)

Sometimes information about a tissue sample is needed during surgery to make immediate decisions. If the surgeon can’t wait the day or more that it takes for routine processing and histology, they will request an intra-operative (during surgery) pathology consult. This is often called a frozen section exam.

How is a frozen section done?

When a frozen section exam is done, fresh tissue is sent from the operating room right to the pathologist. Because the patient is often under general anesthesia (kept asleep with drugs) it’s important that the tissue be looked at quickly. It usually takes 10 to 20 minutes. The fresh tissue is grossly examined by the pathologist to decide which part of it should be looked at under the microscope. Instead of processing the tissue in wax blocks, the tissue is quickly frozen in a special solution that forms what looks like an ice cube around the tissue. It’s then thinly sectioned (sliced) on a special machine, quickly stained (dipped in a series of dyes), and looked at under the microscope. The frozen sections usually do not show features of the tissue as clearly as sections of tissue embedded in wax, but they are good enough to help the surgeon make decisions during the operation.

When is a frozen section done?

To find out if a tumor is cancer: Sometimes the type of operation needed depends on whether the tumor is cancer (malignant). For instance, just removing the tumor could be enough to treat a tumor that is not cancer (benign), but more tissue and/or lymph nodes may need to be removed if the tumor is cancer. In a case like this, the surgeon might send the tumor for a frozen section exam. This often can give enough information to help the surgeon decide what type of operation, if any, is best for the patient. Sometimes, though, the frozen section doesn’t give a definite answer and the piece of tissue will need to go through routine or even special processing to get a clear answer. When this happens the surgeon usually stops the operation and closes the surgical incision (cut). After the results are back, another operation may be needed.

To make sure all of the cancer is removed: Surgical treatment of cancer is often a difficult balance between removing enough tissue to feel that the cancer has been removed completely and leaving enough normal tissue to limit damage. If the surgeon is concerned that a cancer has not been removed completely, a slice from the edge of the tissue that was removed (called a margin) is sent for a frozen section diagnosis. If there are no cancer cells at the margin, more surgery usually isn’t needed. But if cancer cells are found, it can be assumed that some are still in the tissue left in the patient. If this happens, the surgeon will usually remove more tissue to try to get all the cancer cells and reduce the chance of cancer coming back. If it’s not possible to remove more tissue, there may be other options, such as radiation to kill the remaining cancer cells.

Process for Mohs surgery (microscopically controlled surgery)

This procedure is used to treat certain kinds of skin cancer. In Mohs surgery, the surgeon removes a thin layer of the skin that the tumor might have invaded and then checks the sample under a microscope. If cancer cells are seen, more layers are removed and checked until no cancer cells are found in the skin samples. This process is slow, but it means that more normal skin near the tumor can be saved. Mohs surgery is a highly specialized technique that should only be used by doctors who have been trained to do it.

How cytology specimens are processed

How cytology specimens are processed depends on the type of specimen. Some specimens are smeared on glass microscope slides by the doctor who gets the sample. These slides, which are called smears, are then sent to the cytology lab where they’re dipped into a series of stains (colored dyes), much like those used for biopsy samples.

Other specimens, such as body fluids, can’t be placed on a glass microscope slide easily because they are too diluted (there are too few cells in a large volume of fluid). Procedures are used to concentrate these cells on a glass slide before they are stained.

After processing and staining, the samples are examined under a microscope. The abnormal cells are found and marked with a special pen. A pathologist will then examine the marked cells to make a diagnosis.

How long are pathology specimens kept?

A federal law called CLIA (Clinical Laboratory Improvement Amendments) guides the regulation and certification of clinical labs. To be CLIA accredited, labs must keep human specimens for the minimum amount of time. For instance, CLIA says that labs must keep:

  • Cytology slides for at least 5 years
  • Histopathology slides for at least 10 years
  • Paraffin blocks for at least 2 years

Some states have their own laws that require labs to keep pathology specimens longer than the time specified in the CLIA regulations. And some labs have policies for keeping specimens longer than required by federal or state laws.

What this means for you

Some people want to get a second opinion on the diagnosis made from their tissue sample (specimen). This is called a pathology review. It means getting another doctor to look at your biopsy tissue and make a diagnosis on what’s seen.

Human tissue samples are not discarded right after testing. So, in most cases, if there’s enough tissue, the sample can be sent to another doctor or lab.

Sometimes keeping specimens for a longer time can be helpful in other ways. For instance, if a cancer survivor develops a tumor several years after the first one was removed, doctors will want to know if this new tumor is the old one coming back (a recurrence) or a completely new cancer.

This can often be figured out based on the locations of the 2 tumors and by comparing the histopathology slides from both specimens. But sometimes, more tests (such as immunohistochemical stains) that can be done using tissue from the original specimen’s paraffin block are also helpful.

The American Cancer Society medical and editorial content team

Our team is made up of doctors and oncology certified nurses with deep knowledge of cancer care as well as journalists, editors, and translators with extensive experience in medical writing.

Last Revised: July 30, 2015