Diagnostic Test Directory

Cancer Cytogenetics Laboratory

SMARCB1 (INI1) Sequencing in Tumor Tissue

  • Synonyms: SMARCB1, BAF47, INI1
  • LIS Mnemonic: CMINI1SMARCB1


    Frozen tumor tissue. Formalin-fixed tissue is accepted for analysis but may not yield informative results.

    Volume Required

    0.5 X 0.5 X 0.5 cm tumor tissue

    Minimum Required

    0.5 X 0.2 X 0.2 cm tumor tissue


    tumor on dry ice

Days Performed

Monday through Friday


3 weeks

Reflex Testing

Deletion/duplication analysis



Disease Information

Clinical Features:

Malignant rhabdoid tumors are aggressive, rare pediatric tumors, typically occurring in the brain, kidney (renal) or extrarenal sites. When these tumors occur in the central nervous system, they are referred to as atypical teratoid/rhabdoid tumors. The histologic diagnosis is based upon sheets of tumor cells with characteristic cytomorphology (eccentric nuclei, prominent nucleoli, eosinophilic cytoplasm with eosinophilic inclusions). The tumors will typically demonstrate loss of nuclear expression of the SMARCB1 protein by immunohistochemistry.1

Molecular Genetics:

The vast majority (98%) of malignant rhabdoid tumors and atypical teratoid/rhabdoid tumours have alterations of both copies of the SMARCB1 gene resulting in loss of function of the protein, consistent with the two-hit hypothesis for tumor suppressor genes.2 These alterations include whole gene or intragenic deletions and duplications and mutations.2 Evaluation for a SMARCB1 mutation in tumor tissue may assist in diagnosing the tumor type. An alteration in the SMARCB1 gene that is a sporadic occurrence in the individual’s cancer cells is referred to as a somatic or acquired mutation. This is different than a germline mutation- a gene mutation present in the sperm or egg and/or at conception that results in the SMARCB1 mutation throughout the individual’s body. If SMARCB1 mutations are identified in tumor tissue, a blood sample from the individual should be screened for the same SMARCB1 mutation(s). Identifying the same genetic alteration present in both tumor tissue and leukocytes would be consistent with a germline mutation and inform anticipatory guidance for the patient and genetic counseling for the family. If a germline mutation is identified in the patient, parental studies to rule out an inherited mutation are recommended. 1. Judkins AR. Immunohistochemistry of INI1 expression: a new tool for old challenges in CNS and soft tissue pathology. Adv Anat Pathol. 2007 Sept; 14(5): 335-9 2. Eaton KW, Tooke LS, Wainwright LM, Judkins AR, Biegel JA. Spectrum of SMARCB1/INI1

Test Methods:

Direct sequence analysis of 9 coding exons and promoter region of SMARCB1

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