Hereditary Colorectal Cancer Panel

Colorectal cancer (CRC) is one of the most common cancers worldwide with a marked hereditary component. Hereditary CRC syndromes can be divided into non-polyposis syndromes and polyposis syndromes (PMID: 25582351). The most common form of hereditary CRC is Lynch syndrome (also known as hereditary non-polyposis colorectal cancer, HNPCC). It is estimated to account for 5% of all CRCs. Lynch syndrome is an autosomal dominant syndrome caused by mutations in mismatch repair genes, mainly MLH1, MSH2, PMS2 and MSH6. Patients with MLH1 or MSH2 have approximately 50 – 80% lifetime risk of developing CRC and women have approximately 40% risk of endometrial cancer. Familial adenomatous polyposis (FAP) is characterized by the development of hundreds to thousands of adenomatous polyps throughout the large bowel. If untreated, patients with FAP have a nearly 100% chance of developing CRC by the age of 35-40 years. FAP is caused by germline mutations in the APC gene. FAP affects approximately 1 in 10 000 individuals and it accounts for 0.5-1% of all CRC cases. FAP patients may display extracolonic features such as papillary thyroid carcinoma and hepatoblastomas. Other rarer CRC predisposition syndromes include MUTYH-associated polyposis (MAP), Peutz-Jeghers syndrome (PJS), juvenile polyposis (JPS), and Cowden syndrome. The phenotype in MAP resembles that in FAP, but patients tend to develop fewer polyps (5-100) and are diagnosed at an older age. MAP is caused by biallelic germline mutations in the MUTYH gene. PJS is characterized by intestinal hamartomatous polyps and mucocutaneous pigmentation. The polyps in PJS are most commonly located in the small bowel but may also occur anywhere along the gastrointestinal tract. Patients have an increased risk of developing extraintestinal cancers. PJS is caused by germline mutations in the STK11 gene. The prevalence of PJS is approximately 1 in 200 000. The features in JPS are multiple hamartomatous polyps in the colon and rectum and an increased risk of colon, gastric, small intestine, and pancreatic cancers. The causative genes of JPS are SMAD4 and BMPR1A. The prevalence is estimated at 1:100 000. Cowden syndrome is characterized by multiple hamartomatous tumors that most commonly appear on the skin, intestine, breast and thyroid gland. Patients have a particularly high risk of breast and thyroid cancers. Germline mutations in PTEN have been described in 80% of Cowden syndrome patients. More recently, germline mutations in POLE, POLD1 and GREM1 have been associated with hereditary CRC predisposition (PMID: 23263490, 26493165).

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. If the test includes the mitochondrial genome the target region gene list contains the mitochondrial genes. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as  SIFT, PolyPhen,MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with suboptimal coverage (<20X for nuclear genes and <1000X for mtDNA) if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists, and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the cornerstone of clinical interpretation and resulting patient management decisions. Our classifications follow the ACMG guideline 2015.

The final step in the analysis is orthogonal confirmation. Sequence and copy number variants classified as pathogenic, likely pathogenic, and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing or by orthogonal methods such as qPCR/ddPCR when they do not meet our stringent NGS quality metrics for a true positive call.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes, and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene, and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts, and detailed information about related phenotypes. We also provide links to the references, abstracts, and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering healthcare provider at no additional cost, according to our latest follow-up reporting policy.