STAT Comprehensive Cancer Panel

This comprehensive panel includes genes associated with the following hereditary cancers and cancer syndromes:

• Bloom Syndrome
• Breast Cancer
• Carney Complex
• Costello Syndrome
• DICER1 Tumor Predisposition Syndrome
• Familial Meningioma
• Gastrointestinal and Colorectal Cancers
• Gynecological Cancers
• Hereditary Breast and Ovarian Cancer Syndrome
• Hereditary Thrombocytopenia and Hematologic Cancer Predisposition Syndrome
• Hyperparathyroidism with Jaw Tumor Syndrome
• Leukemia
• Li-Fraumeni Syndrome
• Lynch Syndrome
• Melanoma
• Mismatch Repair Cancer Syndrome
• Multiple Endocrine Neoplasia 
• Myelodysplastic Syndrome
• Neuroblastoma
• Neurofibromatosis
• Nevoid Basal Cell Carcinoma Syndrome
• Nijmegen Breakage Syndrome
• Non-Small Cell Lung Cancer
• NTHL1-Deficiency Tumor Predisposition Syndrome
• Pancreatic Cancer
• Paraganglioma
• Perlman Syndrome
• Peutz-Jeghers Syndrome
• Pheochromocytoma
• Pleuropulmonary Blastoma
• POT1 Tumor Predisposition Syndrome
• Prostate Cancer
• PTEN Hamartoma Tumor Syndrome
• Renal Cancer
• Retinoblastoma
• Rhabdoid Tumor Predisposition Syndrome
• Rothmund-Thomson Syndrome
• Tuberous Sclerosis
• Von Hippel-Lindau Syndrome
• Werner Syndrome
• Wilms Tumor

Please see professional society guidelines, including the National Comprehensive Cancer Network (NCCN), for the most up-to-date testing criteria.

Sequencing is performed on genomic DNA using a targeted sequence capture method to enrich for the exome. Captured regions are sequenced on a short-read next-generation sequencing (NGS) system. Coverage requirements are based on validation data. An exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered. Alignment to the human reference genome is performed, and annotated variants within the targeted region are identified. Variants are reviewed based on minimum coverage and alternate allele frequency cutoffs defined as per laboratory procedure. Indel and single-nucleotide variants (SNVs) may be confirmed by Sanger sequencing analysis before reporting, based on laboratory requirements.

This assay cannot detect variants in regions that are not targeted, including deep intronic, promoter, or enhancer regions. Exons with nonunique sequences, such as those containing pseudogene regions, are not analyzed in this assay. Copy number variation (CNV) analysis detects deletions and duplications in genes on this panel; however, in some instances, due to exon size, sequence complexity, or other factors, certain CNVs may be difficult to detect and analyze. When reported, copy number variant size is approximate, and actual breakpoint locations may lie outside of the targeted regions. Only CNVs identified in genes included in the panel will be reported. This assay does not interrogate CNVs in mitochondrial DNA. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, or genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; however, possible cases of mosaicism may be detected and reported if laboratory requirements are met.

Primary data analysis is performed using standard FASTQ conversion tools appropriate to the sequencing platform. Secondary analysis is conducted using a high-performance genomic analysis pipeline. Tertiary analysis incorporates established annotation tools together with Revvity Omics' internal software. Copy number variation and absence of heterozygosity assessments are performed using a clinical cytogenomics platform.