Ovarian Cancer and Rhabdoid Tumor Predisposition Syndrome via the SMARCA4 Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 3173 | SMARCA4 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare aggressive form of ovarian cancer found in young women (i.e. < 40 years of age). Even though it is often detected at an early stage, there is a high relapse rate within 2 years of diagnosis and a poor survival rate (Jelinic et al. 2014). SCCOHT can often be difficult to distinguish from other primary and metastatic ovarian cancers, and morphologically, clinically and molecularly resemble atypical teratoid/rhabdoid tumors (ATRTs) and malignant rhabdoid tumors (MRTs) (Foulkes et al. 2014). Rhabdoid tumors are rare aggressive tumors found in children and can be involved in rhabdoid tumor predisposition syndrome, especially when a family history is present. These tumors are histologically confirmed by having large cells with eccentrically located nuclei and abundant eosinophilic cytoplasm (Beckwith and Palmer 1978). Originally, rhabdoid tumors were found in the kidney, but have since been found in the liver, soft tissue, lung, skin, heart and the central nervous system (CNS). Approximately 10-15% of patients with malignant rhabdoid tumors have synchronous or metachronous brain tumors. In the CNS, where rhabdoid tumors are termed ATRT (atypical teratoid, rhabdoid tumor), the most affected area is in the cerebellum (Bourdeaut et al. 2011).
Genetics
SCCOHT is an autosomal dominant disease caused by mutations in the SMARCA4 gene (Witkowski et al. 2014). Pathogenic variants in this gene also cause autosomal dominant rhabdoid tumor predisposition syndrome (Schneppenheim et al. 2010) and Coffin-Siris syndrome (Tsurusaki et al. 2012). The SMARCA4 gene encodes a member of the SWI/SNF family that has helicase and ATPase activities that regulate transcription by altering chromosome structure surrounding genes (Sredni and Tomita 2015). Missense pathogenic variants appear to be responsible for Coffin-Siris syndrome whereas nonsense, splicing, indels, small insertions and deletion variants are reportedly responsible for SCCOHT and rhabdoid tumor predisposition syndrome (Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PG-Select
Pathogenic variants in the SMARCA4 gene have been reported in 25% of individuals with Coffin-Siris syndrome (Schrier Vergano et al. 2013), but the proportion of individuals with small cell carcinoma of the ovary of hypercalcemic type or tumor predisposition syndrome who have a SMARCA4 causative variant is not known.
Testing Strategy
This test provides full coverage of all coding exons of the SMARCA4 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Individuals who are clinically suspected or diagnosed with SCCOHT, individuals with rhabdoid tumor predisposition syndrome who have been found to be negative for pathogenic variants in the SMARCB1 gene, and individuals with a family history of a pathogenic variant in SMARCA4 may be tested. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.
Individuals who are clinically suspected or diagnosed with SCCOHT, individuals with rhabdoid tumor predisposition syndrome who have been found to be negative for pathogenic variants in the SMARCB1 gene, and individuals with a family history of a pathogenic variant in SMARCA4 may be tested. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| SMARCA4 | 603254 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Rhabdoid Tumor Predisposition Syndrome 2 | AD | 613325 |
Citations
- Beckwith JB, Palmer NF. 1978. Histopathology and prognosis of Wilms tumors: results from the First National Wilms’ Tumor Study. Cancer 41: 1937–1948. PubMed ID: 206343
- Bourdeaut F, Lequin D, Brugières L, Reynaud S, Dufour C, Doz F, André N, Stephan J-L, Pérel Y, Oberlin O, Orbach D, Bergeron C, Rialland X, Fréneaux P, Ranchere D, Figarella-Branger D, Audry G, Puget S, Evans DG, Pinas JC, Capra V, Mosseri V, Coupier I, Gauthier-Villars M, Pierron G, Delattre O. 2011. Frequent hSNF5/INI1 germline mutations in patients with rhabdoid tumor. Clin. Cancer Res. 17: 31–38. PubMed ID: 21208904
- Foulkes WD, Clarke BA, Hasselblatt M, Majewski J, Albrecht S, McCluggage WG. 2014. No small surprise - small cell carcinoma of the ovary, hypercalcaemic type, is a malignant rhabdoid tumour: Whole exome sequencing unites rare tumours. The Journal of Pathology 233: 209–214. PubMed ID: 24752781
- Human Gene Mutation Database (Bio-base).
- Jelinic P, Mueller JJ, Olvera N, Dao F, Scott SN, Shah R, Gao J, Schultz N, Gonen M, Soslow RA, Berger MF, Levine DA. 2014. Recurrent SMARCA4 mutations in small cell carcinoma of the ovary. Nature Genetics 46: 424–426. PubMed ID: 24658004
- Schneppenheim R, Frühwald MC, Gesk S, Hasselblatt M, Jeibmann A, Kordes U, Kreuz M, Leuschner I, Subero JIM, Obser T, Oyen F, Vater I, Siebert R. 2010. Germline Nonsense Mutation and Somatic Inactivation of SMARCA4/BRG1 in a Family with Rhabdoid Tumor Predisposition Syndrome. The American Journal of Human Genetics 86: 279–284. PubMed ID: 20137775
- Schrier Vergano SA, Santen G, Wieczorek D, Wollnik B, Matsumoto N, Deardorff MA. 2013. Coffin-Siris Syndrome. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 23556151
- Sredni ST, Tomita T. 2015. Rhabdoid Tumor Predisposition Syndrome. Pediatric and Developmental Pathology 18: 49–58. PubMed ID: 25494491
- Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, Hibi-Ko Y, Kaname T, Naritomi K, Kawame H, Wakui K, Fukushima Y, Homma T, Kato M, Hiraki Y, Yamagata T, Yano S, Mizuno S, Sakazume S, Ishii T, Nagai T, Shiina M, Ogata K, Ohta T, Niikawa N, Miyatake S, Okada I, Mizuguchi T, Doi H, Saitsu H, Miyake N, Matsumoto N. 2012. Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Nat. Genet. 44: 376–378. PubMed ID: 22426308
- Witkowski L, Carrot-Zhang J, Albrecht S, Fahiminiya S, Hamel N, Tomiak E, Grynspan D, Saloustros E, Nadaf J, Rivera B, Gilpin C, Castellsagué E, Silva-Smith R, Plourde F, Wu M, Saskin A, Arseneault M, Karabakhtsian RG, Reilly EA, Ueland FR, Margiolaki A, Pavlakis K, Castellino SM, Lamovec J, Mackay HJ, Roth LM, Ulbright TM, Bender TA, Georgoulias V, Longy M, Berchuck A, Tischkowitz M, Nagel I, Siebert R, Stewart CJ, Arseneau J, McCluggage WG, Clarke BA, Riazalhosseini Y, Hasselblatt M, Majewski J, Foulkes WD. 2014. Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type. Nature Genetics 46: 438–443. PubMed ID: 24658002
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
Requisition Form
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
For Requisition Forms, visit our Forms page
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
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