Unrecognised actionability for breast cancer risk variants identified in a national-level review of Australian familial cancer centres.

Breast cancer remains a significant global health challenge. In Australia, the adoption of publicly-funded multigene panel testing for eligible cancer patients has increased accessibility to personalised care, yet has also highlighted the increasing prevalence of variants of uncertain significance (VUS), complicating clinical decision-making. This project aimed to explore the spectrum and actionability of breast cancer VUS in Australian familial cancer centers (FCCs). Leveraging data from 11 FCCs participating in the Inherited Cancer Connect database, we retrieved VUS results from 1472 patients. Through ClinVar crosschecks and application of gene-specific ACMG/AMP guidelines, we showed the potential for reclassification of 4% of unique VUS as pathogenic or likely pathogenic, and 80% as benign or likely benign. Surveys conducted with FCCs and diagnostic laboratories described current practices and challenges in variant reclassifications, highlighting resource constraints preventing periodic VUS review and notifications from the laboratories to the FCCs. Our study suggests there are benefits to routine VUS review and reclassification, particularly in publicly-funded healthcare systems. Future research should focus on assessing the clinical impact and cost-effectiveness of implementing routine variant review practices, alongside efforts to enhance communication between FCCs and laboratories.

A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome.

Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). SLS cases (n = 135) were recruited from Family Cancer Clinics across Australia and New Zealand. Targeted panel sequencing was performed on tumor (n = 137; 80×CRCs, 33×ECs and 24xSSTs) and matched blood-derived DNA to assess for microsatellite instability status, tumor mutation burden, COSMIC tumor mutational signatures and to identify germline and somatic MMR gene variants. MMR immunohistochemistry (IHC) and MLH1 promoter methylation were repeated. In total, 86.9% of the 137 SLS tumors could be resolved into established subtypes. For 22.6% of these resolved SLS cases, primary MLH1 epimutations (2.2%) as well as previously undetected germline MMR pathogenic variants (1.5%), tumor MLH1 methylation (13.1%) or false positive dMMR IHC (5.8%) results were identified. Double somatic MMR gene mutations were the major cause of dMMR identified across each tumor type (73.9% of resolved cases, 64.2% overall, 70% of CRC, 45.5% of ECs and 70.8% of SSTs). The unresolved SLS tumors (13.1%) comprised tumors with only a single somatic (7.3%) or no somatic (5.8%) MMR gene mutations. A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.

A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome.

Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). SLS cases (n=135) were recruited from Family Cancer Clinics across Australia and New Zealand. Targeted panel sequencing was performed on tumor (n=137; 80xCRCs, 33xECs and 24xSSTs) and matched blood-derived DNA to assess for microsatellite instability status, tumor mutation burden, COSMIC tumor mutational signatures and to identify germline and somatic MMR gene variants. MMR immunohistochemistry (IHC) and MLH1 promoter methylation were repeated. In total, 86.9% of the 137 SLS tumors could be resolved into established subtypes. For 22.6% of these resolved SLS cases, primary MLH1 epimutations (2.2%) as well as previously undetected germline MMR pathogenic variants (1.5%), tumor MLH1 methylation (13.1%) or false positive dMMR IHC (5.8%) results were identified. Double somatic MMR gene mutations were the major cause of dMMR identified across each tumor type (73.9% of resolved cases, 64.2% overall, 70% of CRC, 45.5% of ECs and 70.8% of SSTs). The unresolved SLS tumors (13.1%) comprised tumors with only a single somatic (7.3%) or no somatic (5.8%) MMR gene mutations. A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.

Aligning intuition and theory: enhancing the replicability of behaviour change interventions in cancer genetics.

BACKGROUND: Despite considerable encouragement for healthcare professionals to use or be clear about the theory used in their improvement programmes, the uptake of these approaches to design interventions or report their content is lacking. Recommendations suggest healthcare practitioners work with social and/or behavioural scientists to gain expertise in programme theory, ideally before, but even during or after the work is done. We aim to demonstrate the extent to which intuitive intervention strategies designed by healthcare professionals to overcome patient barriers to communicating genetic cancer risk information to family members align with a theoretical framework of behaviour change. METHODS: As part of a pre-post intervention study, a team of genetic counsellors aimed to understand, and design interventions to overcome, the major barriers a group of familial cancer patients face around communicating hereditary cancer risk information to their relatives. A behavioural change specialist worked with the team to review and recode barriers and interventions according to the Theoretical Domains Framework (TDF) and 93 behaviour change techniques (BCTs). Resulting BCTs were cross-referenced against the Theory and Techniques Tool to examine whether evidence-based mechanistic links have been established to date. RESULTS: Five themes emerged from the genetic counsellor coded barriers, which when recoded according to the TDF represented seven domains of behaviour change. Forty-five experiential and intuitive interventions were used to tackle key barriers. These were represented by 21 BCTs, which were found to be used on 131 occasions. The full mapping exercise is presented, resulting in a suite of intervention strategies explicitly linked to a theoretical framework. Structured, written reflections were provided retrospectively by the core clinical team. CONCLUSIONS: Although the ideal is to use theory prospectively, or even whilst a project is underway, making links between theory and interventions explicit, even retrospectively, can contribute towards standardising intervention strategies, furthering understanding of intervention effects, and enhancing the opportunities for accurate replicability and generalisability across other settings. Demonstrating to healthcare professionals how their intuition aligns with theory may highlight the additional benefits that theory has to offer and serve to promote its use in improvement.

Quantifying family dissemination and identifying barriers to communication of risk information in Australian BRCA families.

PurposeRecommendations for BRCA1 and BRCA2 mutation carriers to disseminate information to at-risk relatives pose significant challenges. This study aimed to quantify family dissemination, to explain the differences between fully informed families (all relatives informed verbally or in writing) and partially informed families (at least one relative uninformed), and to identify dissemination barriers.MethodsBRCA1 and BRCA2 mutation carriers identified from four Australian hospitals (n=671) were invited to participate in the study. Distress was measured at consent using the Kessler psychological distress scale (K10). A structured telephone interview was used to assess the informed status of relatives, geographical location of relatives, and dissemination barriers. Family dissemination was quantified, and fully versus partially informed family differences were examined. Dissemination barriers were thematically coded and counted.ResultsA total of 165 families participated. Information had been disseminated to 81.1% of relatives. At least one relative had not been informed in 52.7% of families, 4.3% were first-degree relatives, 27.0% were second-degree relatives, and 62.0% were cousins. Partially informed families were significantly larger than fully informed families, had fewer relatives living in close proximity, and exhibited higher levels of distress. The most commonly recorded barrier to dissemination was loss of contact.ConclusionLarger, geographically diverse families have greater difficulty disseminating BRCA mutation risk information to all relatives. Understanding these challenges can inform future initiatives for communication, follow-up and support.

Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing.

Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg2+-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) is a unique recessive syndrome characterized by neurodegeneration and ambiguous genitalia. We studied 12 human families with PCH7, uncovering biallelic, loss-of-function mutations in TOE1, which encodes an unconventional deadenylase. toe1-morphant zebrafish displayed midbrain and hindbrain degeneration, modeling PCH-like structural defects in vivo. Surprisingly, we found that TOE1 associated with small nuclear RNAs (snRNAs) incompletely processed spliceosomal. These pre-snRNAs contained 3' genome-encoded tails often followed by post-transcriptionally added adenosines. Human cells with reduced levels of TOE1 accumulated 3'-end-extended pre-snRNAs, and the immunoisolated TOE1 complex was sufficient for 3'-end maturation of snRNAs. Our findings identify the cause of a neurodegenerative syndrome linked to snRNA maturation and uncover a key factor involved in the processing of snRNA 3' ends.

A Relational Approach to Genetic Counseling for Hereditary Breast and Ovarian Cancer.

Ethical issues arise for genetic counselors when a client fails to disclose a genetic diagnosis of hereditary disease to family: they must consider the rights of the individual client to privacy and confidentiality as well as the rights of the family to know their genetic risk. Although considerable work has addressed issues of non-disclosure from the client's perspective, there is a lack of qualitative research into how genetic counselors address this issue in practice. In this study, a qualitative approach was taken to investigate whether genetic counselors in Australia use a relational approach to encourage the disclosure of genetic information from hereditary breast and ovarian cancer (HBOC) clients among family members; and if so, how they use it. Semi-structured qualitative interviews were conducted with 16 genetic counselors from selected states across Australia. Data collection and analysis were guided by a basic iterative approach incorporating a hybrid methodology to thematic analysis. The findings provide indicative evidence of genetic counselors employing a relational approach in three escalating stages--covert, overt and authoritative--to encourage the disclosure of genetic information. The findings lend credence to the notion that genetic counselors envision a form of relational autonomy for their clients in the context of sharing genetic information, and they depart from individualistic conceptions of care/solely client-centered counseling when addressing the needs of other family members to know their genetic status.

Breast and ovarian cancer referrals to the ACT Genetic Service: are we meeting guidelines?

BACKGROUND: The ACT Genetic Service at The Canberra Hospital evaluates the genetic risk of individuals for inherited diseases, and provides counselling and genetic testing where appropriate. AIM: To evaluate the current referral practice for patients with a personal and/or family history of breast and/or ovarian cancer, and to assess whether these referrals are made according to eviQ cancer referral guidelines. METHODS: A retrospective clinical audit of patients seen by the ACT Genetic Service for evaluation of genetic risk of breast and/or ovarian cancer between 1 January 2013 and 30 June 2015. Statistical analysis included Chi-squared and Poisson distribution tests. RESULTS: Of the 711 patients referred during the 30-month period, 671 were seen by the service. The number of patients seen increased steadily over the time period, as did waiting times. The majority of referrals were made by general practitioners (403/711; 57%) and oncologists (172/711; 24%). Of note, 300 of 711 (42%) of all referrals made to the service during this time period did not meet eviQ referral guidelines. Patients who met guidelines for referral were more likely both to be offered genetic testing and to have a positive result. CONCLUSION: Demand on the ACT Genetic Service increased over the time period assessed. As a significant proportion of patients did not meet eviQ cancer referral guidelines, it is worth reviewing the referral process in order to optimise utility of this limited resource.

Consequences of germline variation disrupting the constitutional translational initiation codon start sites of MLH1 and BRCA2: Use of potential alternative start sites and implications for predicting variant pathogenicity.

Variants that disrupt the translation initiation sequences in cancer predisposition genes are generally assumed to be deleterious. However, few studies have validated these assumptions with functional and clinical data. Two cancer syndrome gene variants likely to affect native translation initiation were identified by clinical genetic testing: MLH1:c.1A>G p.(Met1?) and BRCA2:c.67+3A>G. In vitro GFP-reporter assays were conducted to assess the consequences of translation initiation disruption on alternative downstream initiation codon usage. Analysis of MLH1:c.1A>G p.(Met1?) showed that translation was mostly initiated at an in-frame position 103 nucleotides downstream, but also at two ATG sequences downstream. The protein product encoded by the in-frame transcript initiating from position c.103 showed loss of in vitro mismatch repair activity comparable to known pathogenic mutations. BRCA2:c.67+3A>G was shown by mRNA analysis to result in an aberrantly spliced transcript deleting exon 2 and the consensus ATG site. In the absence of exon 2, translation initiated mostly at an out-of-frame ATG 323 nucleotides downstream, and to a lesser extent at an in-frame ATG 370 nucleotides downstream. Initiation from any of the downstream alternative sites tested in both genes would lead to loss of protein function, but further clinical data is required to confirm if these variants are associated with a high cancer risk. Importantly, our results highlight the need for caution in interpreting the functional and clinical consequences of variation that leads to disruption of the initiation codon, since translation may not necessarily occur from the first downstream alternative start site, or from a single alternative start site.

Multifactorial likelihood assessment of BRCA1 and BRCA2 missense variants confirms that BRCA1:c.122A>G(p.His41Arg) is a pathogenic mutation.

Rare exonic, non-truncating variants in known cancer susceptibility genes such as BRCA1 and BRCA2 are problematic for genetic counseling and clinical management of relevant families. This study used multifactorial likelihood analysis and/or bioinformatically-directed mRNA assays to assess pathogenicity of 19 BRCA1 or BRCA2 variants identified following patient referral to clinical genetic services. Two variants were considered to be pathogenic (Class 5). BRCA1:c.4484G> C(p.Arg1495Thr) was shown to result in aberrant mRNA transcripts predicted to encode truncated proteins. The BRCA1:c.122A>G(p.His41Arg) RING-domain variant was found from multifactorial likelihood analysis to have a posterior probability of pathogenicity of 0.995, a result consistent with existing protein functional assay data indicating lost BARD1 binding and ubiquitin ligase activity. Of the remaining variants, seven were determined to be not clinically significant (Class 1), nine were likely not pathogenic (Class 2), and one was uncertain (Class 3).These results have implications for genetic counseling and medical management of families carrying these specific variants. They also provide additional multifactorial likelihood variant classifications as reference to evaluate the sensitivity and specificity of bioinformatic prediction tools and/or functional assay data in future studies.

Are videoconferenced consultations as effective as face-to-face consultations for hereditary breast and ovarian cancer genetic counseling?

PURPOSE: Videoconferencing is increasingly used to deliver family cancer services for hereditary breast and ovarian cancer to outreach areas. This study compared the effectiveness and acceptability of genetic counseling for hereditary breast and ovarian cancer through videoconferencing (hereafter referred to as "telegenetics"). METHODS: One hundred six women seen by telegenetics and 89 women seen face-to-face completed self-administered questionnaires before, and 1 month after, genetic counseling. Telegenetics consultations involved a genetic clinician via telegenetics in addition to a local genetic counselor present with the patient. RESULTS: No significant differences were found between telegenetics and face-to-face genetic counseling in terms of knowledge gained (P = 0.55), satisfaction with the genetic counseling service (P = 0.76), cancer-specific anxiety (P = 0.13), generalized anxiety (P = 0.42), depression (P = 0.96), perceived empathy of the genetic clinician (P = 0.13), and perceived empathy of the genetic counselor (P = 0.12). Telegenetics performed significantly better than face-to-face counseling in meeting patients' expectations (P = 0.009) and promoting perceived personal control (P = 0.031). CONCLUSION: Telegenetics seems to be an acceptable and effective method of delivering genetic counseling services for hereditary breast and ovarian cancer to underserved areas.

Women's experience of telehealth cancer genetic counseling.

Telegenetics offers an alternative model of delivering genetic counseling to rural and outreach areas; however there is a dearth of qualitative research into the patient's experience. Twelve women who had received telemedicine genetic counseling for hereditary breast and/or ovarian cancer (HBOC) within the previous 12 months participated in a semi-structured telephone interview. The interview explored women's experience with telegenetics, satisfaction, perceived advantages and disadvantages and quality of the interaction with their genetic professionals. Overall women were highly satisfied with telegenetics. Telegenetics offered them convenience and reduced travel and associated costs. The majority of women described feeling a high degree of social presence, or rapport, with the off-site genetic clinician. One woman with a recent cancer diagnosis, reported that telemedicine was unable to meet her needs for psychosocial support. This finding highlights the need to be mindful of the psychosocial support needs of women with a recent diagnosis being seen via telegenetics. Patients attending for HBOC genetic counseling are generally highly satisfied with the technology and the interaction. Care should be taken, however, with patients with more complex psychosocial needs.

Neuropsychological functioning in children with early-treated phenylketonuria: impact of white matter abnormalities.

Impact of white matter abnormalities (WMAs) on neuropsychological functioning in children with early-treated phenylketonuria (ETPKU) was examined. Children with ETPKU (20 males, 12 females, mean age 11 years 2 months, SD 3 years 6 months) and controls (20 males, 14 females, mean age 10 years 4 months, SD 3 years 1 month) aged 7 to 18 years were assessed using tests of attention, processing speed, memory and learning, executive function, and academic achievement. Those with ETPKU, exhibiting WMAs extending into subcortical/frontal regions (n=14), displayed significant impairments in a number of domains. Children with ETPKU but no WMAs (n=6), or pathology restricted to the posterior periventricular region (n=12), displayed only mild deficits. Concurrent phenylalanine levels correlated weakly with cognitive parameters, whereas lifetime phenylalanine levels were associated with deficits in several cognitive domains. Impairments in children with extensive WMAs are consistent with compromised neural transmission, which is characterized by dysmyelination. However, children with no detectable, or mild WMAs, also displayed cognitive problems, indicating that neuropsychological functioning in children with ETPKU is determined by a complex interaction of biological and environmental factors.