Familial Risks and Proportions Describing Population Landscape of Familial Cancer

Background: Familial cancer can be defined through the occurrence of the same cancer in two or more family members. We describe a nationwide landscape of familial cancer, including its frequency and the risk that it conveys, by using the largest family database in the world with complete family structures and medically confirmed cancers. Patients/methods: We employed standardized incidence ratios (SIRs) to estimate familial risks for concordant cancer among first-degree relatives using the Swedish Cancer Registry from years 1958 through 2016. Results: Cancer risks in a 20–84 year old population conferred by affected parents or siblings were about two-fold compared to the risk for individuals with unaffected relatives. For small intestinal, testicular, thyroid and bone cancers and Hodgkin disease, risks were higher, five-to-eight-fold. Novel familial associations included adult bone, lip, pharyngeal, and connective tissue cancers. Familial cancers were found in 13.2% of families with cancer; for prostate cancer, the proportion was 26.4%. High-risk families accounted for 6.6% of all cancer families. Discussion/Conclusion: High-risk family history should be exceedingly considered for management, including targeted genetic testing. For the major proportion of familial clustering, where genetic testing may not be feasible, medical and behavioral intervention should be indicated for the patient and their family members, including screening recommendations and avoidance of carcinogenic exposure.

Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a

We describe the generation and characterization of camelid single-domain antibodies (nanobodies) raised against tumor suppressor protein p16INK4a (p16). p16 plays a critical role in the cell cycle by inhibiting cyclin-dependent kinases CDK4 and CDK6, and it is inactivated in sporadic and familial cancers. The majority of the p16 missense mutations cause loss of function by destabilizing the protein structure. We show that the nanobodies bind p16 with nanomolar affinities and restore the stability of a range of different cancer-associated p16 mutations located at sites throughout the protein. The nanobodies also bind and stabilize p16 in a cellular setting. The crystal structure of a nanobody-p16 complex reveals that the nanobody binds to the opposite face of p16 to the CDK-binding interface permitting formation of a ternary complex. These findings indicate that nanobodies could be used as pharmacological chaperones to determine the consequences of restoring the function of p16 in the cell.

WRN Germline Mutation Is the Likely Inherited Etiology of Various Cancer Types in One Iranian Family

BackgroundFamilial cancers comprise a considerable distribution of colorectal cancers (CRCs), of which only about 5% occurs through well-established hereditary syndromes. It has been demonstrated that deleterious variants at the newly identified cancer-predisposing genes could describe the etiology of undefined familial cancers.MethodsThe present study aimed to identify the genetic etiology in a 32-year-old man with early onset familial CRC employing several molecular diagnostic techniques. DNA was extracted from tumoral and normal formalin-fixed-paraffin-embedded (FFPE) blocks, and microsatellite instability (MSI) was evaluated. Immunohistochemistry staining of MMR proteins was performed on tumoral FFPE blocks. Next-generation sequencing (NGS), multiplex ligation-dependent amplification (MLPA) assay, and Sanger sequencing were applied on the genomic DNA extracted from peripheral blood. Data analysis was performed using bioinformatics tools. Genetic variants interpretation was based on ACMG.ResultsMSI analysis indicated MSI-H phenotype, and IHC staining proved no expressions of MSH2 and MSH6 proteins. MLPA and NGS data showed no pathogenic variants in MMR genes. Further analysis of NGS data revealed a candidate WRN frameshift variant (p.R389Efs*3), which was validated with Sanger sequencing. The variant was interpreted as pathogenic since it met the criteria based on the ACMG guideline including very strong (PVS1), strong (PS3), and moderate (PM2).ConclusionWRN is a DNA helicase participating in DNA repair pathways to sustain genomic stability. WRN deficient function may contribute to CRC development that is valuable for further investigation as a candidate gene in hereditary cancer syndrome diagnosis.

373 A Review of Microsatellite Instability (MSI) Testing: Real World Clinical Data

Introduction Colorectal cancers (CRC) are the second most common cause of death by cancer, in the UK. Microsatellite instability (MSI) analysis is novel yet important part of managing CRC and used as a tool for predicting prognosis, treatment and identifying lynch syndrome. Where lynch syndrome is identified, preventative screening can be utilised. Previous studies only focused tumour testing on high-risk cases. Method A retrospective study at Northumbria Health Care NHS Trust was performed on all new CRC patients between 2017-2020. Results A total of 965 patients with CRC were identified. After exclusion criteria was applied to the cohort, a total of 483 patients were identified as having undergone MSI analysis. The mean age was 73.5 years old, with the female to male ratio being 1:1.4. Patients were further grouped into MSI stable, low, and high. MSI High patients accounted for 10% of patients analysed. Further genetic testing was performed on these patients which highlighted 28 patients with BRAF positive genes who went on to screening for Lynch syndrome associated cancers. Conclusions MSI testing provides essential diagnostic, prognostic information and also guides treatment options. 2.9% of patients identified as high risk for familial cancers and went on to have genetic screening and surveillance.

Variable number tandem repeats mediate the expression of proximal genes

Variable number tandem repeats (VNTRs) account for significant genetic variation in many organisms. In humans, VNTRs have been implicated in both Mendelian and complex disorders, but are largely ignored by genomic pipelines due to the complexity of genotyping and the computational expense. We describe adVNTR-NN, a method that uses shallow neural networks to genotype a VNTR in 18 seconds on 55X whole genome data, while maintaining high accuracy. We use adVNTR-NN to genotype 10,264 VNTRs in 652 GTEx individuals. Associating VNTR length with gene expression in 46 tissues, we identify 163 “eVNTRs”. Of the 22 eVNTRs in blood where independent data is available, 21 (95%) are replicated in terms of significance and direction of association. 49% of the eVNTR loci show a strong and likely causal impact on the expression of genes and 80% have maximum effect size at least 0.3. The impacted genes are involved in diseases including Alzheimer’s, obesity and familial cancers, highlighting the importance of VNTRs for understanding the genetic basis of complex diseases.

Genetic predisposition to neural crest-derived tumors: revisiting the role of KIF1B

Objective We previously described a family in which predisposition to pheochromocytoma (PCC) segregates with a germline heterozygous KIF1B nucleotide variant (c.4442G>A, p.Ser1481Asn) in three generations. During the clinical follow-up, one proband’s brother, negative for the KIF1B nucleotide variant, developed a bilateral PCC at 31 years. This prompted us to reconsider the genetic analysis. Design and methods Germline DNA was analyzed by next-generation sequencing (NGS) using a multi-gene panel plus MLPA or by whole exome sequencing (WES). Tumor-derived DNA was analyzed by SnapShot, Sanger sequencing or NGS to identify loss-of-heterozygosity (LOH) or additional somatic mutations. Results A germline heterozygous variant of unknown significance in MAX (c.145T>C, p.Ser49Pro) was identified in the proband’s brother. Loss of the wild-type MAX allele occurred in his PCCs thus demonstrating that this variant was responsible for the bilateral PCC in this patient. The proband and her affected grandfather also carried the MAX variant but no second hit could be found at the somatic level. No other pathogenic mutations were detected in 36 genes predisposing to familial PCC/PGL or familial cancers by WES of the proband germline. Germline variants detected in other genes, TFAP2E and TMEM214, may contribute to the multiple tumors of the proband. Conclusion In this family, the heritability of PCC is linked to the MAX germline variant and not to the KIF1B germline variant which, however, may have contributed to the occurrence of neuroblastoma (NB) in the proband.

Systematic Screening for Familial Leukemia Based on Somatic Genomic Profiling Results

The incidence of familial acute leukemias (AL) and myelodysplastic syndrome (MDS) in the adult population is not well characterized, though recent estimates report that up to 4% of newly diagnosed individuals have a familial syndrome. Recognizing these syndromes is critical to proper clinical management of patients with an inherited susceptibility, and for genetic screening of family members. Within our tertiary care academic institution, less than 1% of AL/MDS cases are referred to genetic counseling, presenting an opportunity for improvement in practice. With the integration of next generation sequencing into standard clinical practice, we recently initiated a bi-monthly meeting to review these sequencing results, with the intent to detect possible familial AL/MDS syndromes and increase appropriate genetic counseling referrals. Here, we describe the potential value of this approach, through a retrospective analysis of somatic genomic profiling results in AL/MDS patients. We performed a retrospective, single-center analysis of all patients who underwent somatic genomic profiling with FoundationOne Heme for AL and MDS between May 2015 and July 2018. Genomic alterations implicated in familial leukemias or familial cancers and included in the FoundationOne Heme panel were as follows: RUNX1, CEBPA, ETV6, GATA2, TERC/TERT, PAX5, CHEK2, and TP53. We recorded baseline characteristics including age, sex, and diagnosis. The presence of the suspected germline variant and up 6 other genomic alterations were recorded. We described whether a comprehensive family history, defined as whether a family history of bleeding tendency, low blood counts, or cancers, was documented for all patients. All patients with a positive family history had the malignancies and blood disorders reported. Finally, we observed if a genetic counseling referral was placed. A total of 108 patients underwent genomic profiling during the study period. Pathogenic variants implicated in familial AL/MDS or familial cancers were detected in 41 of those patients. The number of patients under the age of 50 was 7. Twenty-nine patients had a diagnosis of AML and 12 patients had MDS. Of the reported relevant pathogenic variants, TP53 was seen in 20 patients, RUNX1 in 14 patients, CEBPA in 4 patients, ETV6 in 4 patients, and GATA2 in 3 patients. There were 5 patients that had 2 pathogenic variants noted on their genetic testing. Among the patients with positive pathogenic variant, 22/41 had a comprehensive family history performed. Family history was positive for malignancy in 26/41 patients. Of those 26, 9 patients had a first degree relative with a history of hematologic malignancy including leukemia. Only 2 patients overall were referred to genetic counseling. In AL/MDS patients who underwent somatic genomic profiling at our institution, nearly half of patients with suspected germline variants for familial AML-MDS syndromes had either a family history of malignancy or development of their malignancy at an earlier age, warranting genetic counseling referral. There also is room to improve comprehensive family history collection. Beginning in March 2018, we initiated a bi-monthly meeting to review somatic genomic profiling results in AL/MDS patients with a licensed geneticist. If a suspected germline variant is discovered, we now issue a statement to the primary oncologist to clarify family history if needed, and recommend a referral for formal genetic counseling in the presence of a suggestive family history or on the basis of age. In future investigations, we plan to study how this changes the rate of genetic counseling referrals, and whether this results in an increase in the detection of familial AL/MDS or familial cancer syndromes among this patient group. Disclosures Atallah: Abbvie: Consultancy; Pfizer: Consultancy; BMS: Consultancy; Jazz: Consultancy; Novartis: Consultancy.

Breast surgery (DRAFT)

Breast disease is a common surgical problem. It constitutes symptomatic disease, including breast lumps, nipple discharge, and breast abscesses, as well as asymptomatic disease detected on the NHS Breast Screening Programme (BSP) and patients identified at high risk of familial cancers. It is a busy subspecialty. Referrals for symptomatic breast disease primarily arise from primary care, where they constitute approximately 3% of general practice consultations. In addition, the NHS BSP screened over 2,000,000 women in 2014, of which 4.3% were referred for assessment. The cases in this chapter cover presentations that will be commonly encountered within the breast surgery unit, including the assessment of a breast lump and the surgical management of underlying benign and malignant pathology. It also covers the assessment and management of nipple discharge, as well as lactational and non-lactational breast abscess.