Diagnostic Test Directory

Cancer Cytogenetics Laboratory

SMARCB1 (INI1) deletion/duplication analysis in tumor tissue

  • Synonyms: SMARCB1, BAF47, INI1
  • LIS Mnemonic: CMINI1MLPA


    Frozen tumor tissue. Formalin fixed tissue in blocks is acceptable as an alternative; however, the results may not be informative. Fixed sections on slides can not be submitted.

    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



Disease Information

Clinical Features:

Tumor with histology suggestive of atypical teratoid/rhabdoid tumor; malignant rhabdoid tumor or extra-renal rhabdoid tumor. The histologic diagnosis is based upon sheets of tumor cells with characteristic cytomorphology (eccentric nuclei, prominent nucleoli, eosinophilic cytoplasm with eosinophilic inclusions).1

Molecular Genetics:

Malignant rhabdoid tumors are aggressive, rare pediatric tumors, typically occurring in the brain, kidney or extrarenal sites. When these tumors occur in the central nervous system, they are referred to as atypical teratoid/rhabdoid tumors. The vast majority (98%) of malignant rhabdoid tumors and atypical teratoid/rhabdoid tumours have alterations of both copies of the SMARCB1 gene, that results in loss of function of the protein, 1 These alterations include loss of the chromosome 22q11.2 region encompassing SMARCB1, as well as intragenic duplications, deletions or mutations. as well as. Evaluation for SMARCB1 duplications and deletions using multiplex ligation dependent probe amplification (MLPA) of tumor DNA can be used for diagnosis as well as genetic risk assessment. A deletion or duplication may be a sporadic occurrence in the individual’s tumor cells, referred to as a somatic or acquired copy number alteration. This is different than a germline deletion or duplication: a genetic abnormality present in the sperm or egg at conception that results in the SMARCB1 alteration being present in all cells throughout the individual’s body. If SMARCB1 alterations are identified in tumor tissue, it is suggested that the individual be screened for the SMARCB1 abnormality in normal tissue (blood). Identifying the same genetic alteration in both the tumor tissue and within leukocytes would be consistent with a germline predisposing alteration and inform anticipatory guidance for the

Test Methods:


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