Genomic Testing

Gene profile testing, which is done by microarray assay or reverse transcription-polymerase chain, is done to help with treatment decisions and is part of precision medicine.

The Brain and CNS schemas have several SSDIs that cover molecular markers.

Brain Molecular Markers [NAACCR Data Item #3816]

When the 5th edition of the WHO Blue Book for CNS tumors was released, a lot of new terms were added that included different molecular markers; however, there were no new histology codes to capture these molecularly defined histologies.

This data item was first introduced in 2018, and was updated/expanded in 2023. It allows registrars to assign the base histology code and then in this SSDI, indicate the specific molecular marker, as applicable.

For example

• Diagnosis: Astrocytoma, IDH-mutation, grade 3
• Histology code: 9401/3: Astrocytoma, anaplastic
• Brain molecular markers: 03: 9401/3: Astrocytoma, IDH-mutant, grade 3

When ICD-O-4 is implemented in the US, this SSDI will be discontinued, since the ICD-O-4 codes will be able to capture the specific molecular markers with a unique histology code.

• Not all histologies are covered in the Brain Molecular Markers data item. For those that are not covered, there is a specific code which states “Not applicable, histology NOT 9385/3, 9396/3, 9400/3, 9401/3, 9430/3, 9440/3, 9450/3, 9451/3, 9471/3, 9478/3, 9721/1, 9430/3, 9500/3.
• All benign/borderline cases (except for 9421/1) also have a NA code.
• For these two groups above, the NA code is always to be used regardless of how the diagnosis was made. Never code unknown for these two groups.

Note: This SSDI is applicable for Brain and CNS Other. Intracranial Gland schema has no SSDIs.

Chromosome 1p and 19q [NAACCR Data Items #3801, 3802]

Loss of Heterozygosity Chromosome 1p and Chromosome 19q are two genetic tests that are frequently done at the same time and reported together. Loss of heterozygosity (LOH) in a chromosome means that genetic material normally found in a specific area of a chromosome is missing. This damage to the chromosome results in failure of tumor suppression, which may cause the development or progression of a malignancy. For 1p LOH, the specific chromosomal defect is on the short arm (p) of chromosome 1. For 19q LOH, the specific chromosomal defect is on the long arm (q) of chromosome 19.

To code this SSDI, you must have a pathological confirmation of the histology and tissue to run the genetic testing on. If there is no histological examination, code unknown.

There are certain histologies where this test is frequently done. A list of those histologies is available in the schema, which can be found on SEER*RSA. 1p and 19q can be assessed on other histologies, so if the tests are done on a histology not listed, go ahead and record those results.

There are also default codes for the benign and borderline tumors.

Methylation of O6-Methylguanine-Methyltransferase (MGMT) [NAACCR Data Item #3889]

O6-Methylguanine-Methyltransferase (MGMT) is an enzyme in cells that repairs DNA. DNA repair is undesirable in tumors, because it may enable them to overcome the DNA damage done by chemotherapy. With methylation, less MGMT enzyme is produced, which may lead to prolonged survival compared to unmethylated MGMT.

There are three major categories for MGMT

• None (unmethylated)
• Low (hypomethylated, partial methylated)
• High (hypermethylated, MGMT methylation present)

To code this SSDI, you must have a pathological confirmation of the histology and tissue to run the genetic testing on. If there is no histological examination, code unknown.

There are certain histologies where this test is frequently done. A list of those histologies is available in the Schema, which can be found on SEER*RSA. MGMT can be assessed on other histologies, so if the tests are done on a histology not listed, go ahead and record those results.

There are also default codes for the benign and borderline tumors.

Updated: September 23, 2026