New procedures for genetic testing and counselling of patients with breast or ovarian cancer

The aim of this PhD project was to evaluate alternative procedures for genetic testing and counselling of patients newly diagnosed with breast or ovarian cancer, in order to meet the expected increasing need of this health service. We performed a prospective study, the DNA-BONus study, in which we consecutively offered BRCA testing and familial risk assessment to unselected patients with newly diagnosed breast (N=893) or ovarian (N=122) cancer between September 2012 and February 2015, without formal pre-test genetic counselling. Out of the 488 patients who underwent genetic testing 7 of 405 patients (2%) with breast cancer and 19 of 83 patients (22%) with ovarian cancer carried a germline pathogenic BRCA variant (Paper I). All carriers fulfilled at least one of the Norwegian BRCA test criteria (Paper I). There was a significant decline in the mean levels of anxiety symptoms (Paper I) and cancer related psychological distress (Paper II) from inclusion to six months after dissemination of the BRCA test result. Predictors of increased distress were young age, short time since diagnosis, low level of perceived social support, high level of decisional conflict, diagnosis of ovarian cancer, and living with a partner (Paper II). By investigating RNA splicing, we showed that the intronic BRCA1 c.5407-25T>A variant leads to partial skipping of exon 22, resulting in the truncated protein p.Gly1803GlnfsTer11. Combined with allele frequency data and clinical information from 20 families, this indicated that BRCA1 c.5407-25T>A is a likely pathogenic variant with reduced penetrance (Paper III). In conclusion, the current thesis showed that a simplified procedure for BRCA testing was accepted and overall well tolerated by women newly diagnosed with breast or ovarian cancer. However, we also identified more vulnerable subgroups that may need more counselling and support to benefit from diagnostic BRCA testing. Testing of large groups of individuals with low a priori risk of carrying a germline BRCA pathogenic variant, like unselected patients with breast cancer in our study, may lead to detection of more DNA variants with reduced penetrance

Ask Rosa – The making of a digital genetic conversation tool, a chatbot, about hereditary breast and ovarian cancer

Objective: We aimed at developing a pilot version of an app (Rosa) that can perform digital conversations with breast or ovarian cancer patients about genetic BRCA testing, using chatbot technology, to identify best practices for future patient-focused chatbots. Methods: We chose a commercial chatbot platform and participatory methodology with a team of patient representatives, IT engineers, genetic counselors and clinical geneticists, within a nationwide collaboration. An iterative approach ensured extensive user and formal usability testing during the development process. Results: The development phase lasted for two years until the pilot version was completed in December 2019. The iteration steps disclosed major challenges in the artificial intelligence (AI)-based matching of user provided questions with predefined information in the database, leading initially to high level of fallback answers. We therefore developed strategies to reduce potential language ambiguities (e.g. BRCA1 vs BRCA2) and overcome dialogue confusion. The first prototype contained a database with 500 predefined questions and 67 corresponding predefined answers, while the final version included 2257 predefined questions and 144 predefined answers. Despite the limited AI functionality of the chatbot, the testing revealed that the users liked the layout and found the chatbot trustworthy and reader friendly. Conclusions: Building a health chatbot is challenging, expensive and time consuming with today’s technology. The users had a positive attitude to the chatbot, and would use it in a real life setting, if given to them by health care personnel. Practice implications: We here present a framework for future health chatbot initiatives. The participatory methodology in combination with an iterative approach ensured that the patient perspective was incorporated at every level of the development process. We strongly recommend this approach in patient-centered health innovations.publishedVersio

Functional Analyses of Rare Germline Missense BRCA1 Variants Located within and outside Protein Domains with Known Functions

: The BRCA1 protein is implicated in numerous important cellular processes to prevent genomic instability and tumorigenesis, and pathogenic germline variants predispose carriers to hereditary breast and ovarian cancer (HBOC). Most functional studies of missense variants in BRCA1 focus on variants located within the Really Interesting New Gene (RING), coiled-coil and BRCA1 C-terminal (BRCT) domains, and several missense variants in these regions have been shown to be pathogenic. However, the majority of these studies focus on domain specific assays, and have been performed using isolated protein domains and not the full-length BRCA1 protein. Furthermore, it has been suggested that BRCA1 missense variants located outside domains with known function are of no functional importance, and could be classified as (likely) benign. However, very little is known about the role of the regions outside the well-established domains of BRCA1, and only a few functional studies of missense variants located within these regions have been published. In this study, we have, therefore, functionally evaluated the effect of 14 rare BRCA1 missense variants considered to be of uncertain clinical significance, of which 13 are located outside the well-established domains and one within the RING domain. In order to investigate the hypothesis stating that most BRCA1 variants located outside the known protein domains are benign and of no functional importance, multiple protein assays including protein expression and stability, subcellular localisation and protein interactions have been performed, utilising the full-length protein to better mimic the native state of the protein. Two variants located outside the known domains (p.Met297Val and p.Asp1152Asn) and one variant within the RING domain (p.Leu52Phe) were found to make the BRCA1 protein more prone to proteasome-mediated degradation. In addition, two variants (p.Leu1439Phe and p.Gly890Arg) also located outside known domains were found to have reduced protein stability compared to the wild type protein. These findings indicate that variants located outside the RING, BRCT and coiled-coiled domains could also affect the BRCA1 protein function. For the nine remaining variants, no significant effects on BRCA1 protein functions were observed. Based on this, a reclassification of seven variants from VUS to likely benign could be suggested

The intronic BRCA1 c.5407-25T>A variant causing partly skipping of exon 23—a likely pathogenic variant with reduced penetrance?

Rare sequence variants in the non-coding part of the BRCA genes are often reported as variants of uncertain significance (VUS), which leave patients and doctors in a challenging position. The aim of this study was to determine the pathogenicity of the BRCA1 c.5407-25T>A variant found in 20 families from Norway, France and United States with suspected hereditary breast and ovarian cancer. This was done by combining clinical and family information with allele frequency data, and assessment of the variant’s effect on mRNA splicing. Mean age at breast (n = 12) and ovarian (n = 11) cancer diagnosis in female carriers was 49.9 and 60.4 years, respectively. The mean Manchester score in the 20 families was 16.4. The allele frequency of BRCA1 c.5407-25T>A was 1/64,566 in non-Finnish Europeans (gnomAD database v2.1.1). We found the variant in 1/400 anonymous Norwegian blood donors and 0/784 in-house exomes. Sequencing of patient-derived cDNA from blood, normal breast and ovarian tissue showed that BRCA1 c.5407-25T>A leads to skipping of exon 23, resulting in frameshift and protein truncation: p.(Gly1803GlnfsTer11). Western blot analysis of transiently expressed BRCA1 proteins in HeLa cells showed a reduced amount of the truncated protein compared with wild type. Noteworthily, we found that a small amount of full-length transcript was also generated from the c.5407-25T>A allele, potentially explaining the intermediate cancer burden in families carrying this variant. In summary, our results show that BRCA1 c.5407-25T>A leads to partial skipping of exon 23, and could represent a likely pathogenic variant with reduced penetrance.publishedVersio

BRCA1 Norway: comparison of classifcation for BRCA1 germline variants detected in families with suspected hereditary breast and ovarian cancer between different laboratories

Pathogenic germline variants in Breast cancer susceptibility gene 1 (BRCA1) predispose carriers to hereditary breast and ovarian cancer (HBOC). Through genetic testing of patients with suspected HBOC an increasing number of novel BRCA1 variants are discovered. This creates a growing need to determine the clinical significance of these variants through correct classification (class 1–5) according to established guidelines. Here we present a joint collection of all BRCA1 variants of class 2–5 detected in the four diagnostic genetic laboratories in Norway. The overall objective of the study was to generate an overview of all BRCA1 variants in Norway and unveil potential discrepancies in variant interpretation between the hospitals, serving as a quality control at the national level. For a subset of variants, we also assessed the change in classification over a ten-year period with increasing information available. In total, 463 unique BRCA1 variants were detected. Of the 126 variants found in more than one hospital, 70% were interpreted identically, while 30% were not. The differences in interpretation were mainly by one class (class 2/3 or 4/5), except for one larger discrepancy (class 3/5) which could affect the clinical management of patients. After a series of digital meetings between the participating laboratories to disclose the cause of disagreement for all conflicting variants, the discrepancy rate was reduced to 10%. This illustrates that variant interpretation needs to be updated regularly, and that data sharing and improved national inter-laboratory collaboration greatly improves the variant classification and hence increases the accuracy of cancer risk assessment.publishedVersio

Recurrent candidiasis and early-onset gastric cancer in a patient with a genetically defined partial MYD88 defect

Gastric cancer is caused by both genetic and environmental factors. A woman who suffered from recurrent candidiasis throughout her life developed diffuse-type gastric cancer at the age of 23 years. Using whole-exome sequencing we identified a germline homozygous missense variant in MYD88. Immunological assays on peripheral blood mononuclear cells revealed an impaired immune response upon stimulation with Candida albicans, characterized by a defective production of the cytokine interleukin-17. Our data suggest that a genetic defect in MYD88 results in an impaired immune response and may increase gastric cancer risk

Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing

Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70. All included individuals were tested negative for germline CDH1 mutations before or during the study. Variants that were possibly deleterious according to in silico predictions were filtered using several independent approaches that were based on gene function and gene mutation burden in controls. Despite a rigorous search, no obvious candidate GC predisposition genes were identified. This negative result stresses the importance of future research studies in large, homogeneous cohorts

Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing

Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70. All included individuals were tested negative for germline CDH1 mutations before or during the study. Variants that were possibly deleterious according to in silico predictions were filtered using several independent approaches that were based on gene function and gene mutation burden in controls. Despite a rigorous search, no obvious candidate GC predisposition genes were identified. This negative result stresses the importance of future research studies in large, homogeneous cohorts

Ask Rosa – The making of a digital genetic conversation tool, a chatbot, about hereditary breast and ovarian cancer

Objective We aimed at developing a pilot version of an app (Rosa) that can perform digital conversations with breast or ovarian cancer patients about genetic BRCA testing, using chatbot technology, to identify best practices for future patient-focused chatbots. Methods We chose a commercial chatbot platform and participatory methodology with a team of patient representatives, IT engineers, genetic counselors and clinical geneticists, within a nationwide collaboration. An iterative approach ensured extensive user and formal usability testing during the development process. Results The development phase lasted for two years until the pilot version was completed in December 2019. The iteration steps disclosed major challenges in the artificial intelligence (AI)-based matching of user provided questions with predefined information in the database, leading initially to high level of fallback answers. We therefore developed strategies to reduce potential language ambiguities (e.g. BRCA1 vs BRCA2) and overcome dialogue confusion. The first prototype contained a database with 500 predefined questions and 67 corresponding predefined answers, while the final version included 2257 predefined questions and 144 predefined answers. Despite the limited AI functionality of the chatbot, the testing revealed that the users liked the layout and found the chatbot trustworthy and reader friendly. Conclusions Building a health chatbot is challenging, expensive and time consuming with today’s technology. The users had a positive attitude to the chatbot, and would use it in a real life setting, if given to them by health care personnel. Practice implications We here present a framework for future health chatbot initiatives. The participatory methodology in combination with an iterative approach ensured that the patient perspective was incorporated at every level of the development process. We strongly recommend this approach in patient-centered health innovations

Functional Analyses of Rare Germline Missense BRCA1 Variants Located within and outside Protein Domains with Known Functions

The BRCA1 protein is implicated in numerous important cellular processes to prevent genomic instability and tumorigenesis, and pathogenic germline variants predispose carriers to hereditary breast and ovarian cancer (HBOC). Most functional studies of missense variants in BRCA1 focus on variants located within the Really Interesting New Gene (RING), coiled-coil and BRCA1 C-terminal (BRCT) domains, and several missense variants in these regions have been shown to be pathogenic. However, the majority of these studies focus on domain specific assays, and have been performed using isolated protein domains and not the full-length BRCA1 protein. Furthermore, it has been suggested that BRCA1 missense variants located outside domains with known function are of no functional importance, and could be classified as (likely) benign. However, very little is known about the role of the regions outside the well-established domains of BRCA1, and only a few functional studies of missense variants located within these regions have been published. In this study, we have, therefore, functionally evaluated the effect of 14 rare BRCA1 missense variants considered to be of uncertain clinical significance, of which 13 are located outside the well-established domains and one within the RING domain. In order to investigate the hypothesis stating that most BRCA1 variants located outside the known protein domains are benign and of no functional importance, multiple protein assays including protein expression and stability, subcellular localisation and protein interactions have been performed, utilising the full-length protein to better mimic the native state of the protein. Two variants located outside the known domains (p.Met297Val and p.Asp1152Asn) and one variant within the RING domain (p.Leu52Phe) were found to make the BRCA1 protein more prone to proteasome-mediated degradation. In addition, two variants (p.Leu1439Phe and p.Gly890Arg) also located outside known domains were found to have reduced protein stability compared to the wild type protein. These findings indicate that variants located outside the RING, BRCT and coiled-coiled domains could also affect the BRCA1 protein function. For the nine remaining variants, no significant effects on BRCA1 protein functions were observed. Based on this, a reclassification of seven variants from VUS to likely benign could be suggested