Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios

Background: Missense (amino-acid changing) variants found in cancer predisposition genes often create difficulties when clinically interpreting genetic testing results. Although bioinformatics has developed approaches to predicting the impact of these variants, many of these approaches have not been readily applicable in the clinical setting. Bioinformatics approaches for predicting the impact of these variants have not yet found their footing in clinical practice because 1) interpreting the medical relevance of predictive scores is difficult; 2) the relationship between bioinformatics “predictors” (sequence conservation, protein structure) and cancer susceptibility is not understood.Methodology/Principal Findings: We present a computational method that produces a probabilistic likelihood ratio predictive of whether a missense variant impairs protein function. We apply the method to a tumor suppressor gene, BRCA2, whose loss of function is important to cancer susceptibility. Protein likelihood ratios are computed for 229 unclassified variants found in individuals from high-risk breast/ovarian cancer families. We map the variants onto a protein structure model, and suggest that a cluster of predicted deleterious variants in the BRCA2 OB1 domain may destabilize BRCA2 and a protein binding partner, the small acidic protein DSS1. We compare our predictions with variant “re-classifications” provided by Myriad Genetics, a biotechnology company that holds the patent on BRCA2 genetic testing in the U.S., and with classifications made by an established medical genetics model [1]. Our approach uses bioinformatics data that is independent of these genetics-based classifications and yet shows significant agreement with them. Preliminary results indicate that our method is less likely to make false positive errors than other bioinformatics methods, which were designed to predict the impact of missense mutations in general.Conclusions/Significance: Missense mutations are the most common disease-producing genetic variants. We present a fast, scalable bioinformatics method that integrates information about protein sequence, conservation, and structure in a likelihood ratio that can be integrated with medical genetics likelihood ratios. The protein likelihood ratio, together with medical genetics likelihood ratios, can be used by clinicians and counselors to communicate the relevance of a VUS to the individual who has that VUS. The approach described here is generalizable to regions of any tumor suppressor gene that have been structurally determined by X-ray crystallography or for which a protein homology model can be built

Pharmacogenetic testing affects choice of therapy among women considering tamoxifen treatment

Abstract Background Pharmacogenetic testing holds major promise in allowing physicians to tailor therapy to patients based on genotype. However, there is little data on the impact of pharmacogenetic test results on patient and clinician choice of therapy. CYP2D6 testing among tamoxifen users offers a potential test case of the use of pharmacogenetic testing in the clinic. We evaluated the effect of CYP2D6 testing in clinical practice to determine whether genotype results affected choice of hormone therapy in a prospective cohort study. Methods Women planning to take or currently taking tamoxifen were considered eligible. Participants were enrolled in an informational session that reviewed the results of studies of CYP2D6 genotype on breast cancer recurrence. CYP2D6 genotyping was offered to participants using the AmpliChip CYP450 Test. Women were classified as either poor, intermediate, extensive or ultra-rapid metabolizers. Results were provided to clinicians without specific treatment recommendations. Follow-up was performed with a structured phone interview 3 to 6 months after testing to evaluate changes in medication. Results A total of 245 women were tested and 235 completed the follow-up survey. Six of 13 (46%) women classified as poor metabolizers reported changing treatment compared with 11 of 218 (5%) classified as intermediate, extensive or ultra-rapid metabolizers (P < 0.001). There was no difference in treatment choices between women classified as intermediate and extensive metabolizers. In multi-variate models that adjusted for age, race/ethnicity, educational status, method of referral into the study, prior knowledge of CYP2D6 testing, the patients' CYP2D6 genotype was the only significant factor that predicted a change in therapy (odds ratio 22.8; 95% confidence interval 5.2 to 98.8). Genetic testing did not affect use of co-medications that interact with CYP2D6. Conclusions CYP2D6 genotype testing led to changes in therapy among poor metabolizers, even in the absence of definitive data that an alternative medicine improved outcomes. Pharmacogenetic testing can affect choice of therapy, even in the absence of definitive data on clinical impact

Declines in risk behaviour and sexually transmitted infection prevalence following a community-led HIV preventive intervention among female sex workers in Mysore, India.

OBJECTIVE: To investigate the impact on sexual behaviour and sexually transmitted infections (STI) of a comprehensive community-led intervention programme for reducing sexual risk among female sex workers (FSW) in Mysore, India. The key programme components were: community mobilization and peer-mediated outreach; increasing access to and utilization of sexual health services; and enhancing the enabling environment to support programme activities. METHODS: Two cross-sectional surveys among random samples of FSW were conducted 30 months apart, in 2004 and 2006. RESULTS: Of over 1000 women who sell sex in Mysore city, 429 participated in the survey at baseline and 425 at follow-up. The median age was 30 years, median duration in sex work 4 years, and the majority were street based (88%). Striking increases in condom use were seen between baseline and follow-up surveys: condom use at last sex with occasional clients was 65% versus 90%, P < 0001; with repeat clients 53% versus 66%, P < 0.001; and with regular partners 7% versus 30%, P < 0.001. STI prevalence declined from baseline to follow-up: syphilis 25% versus 12%, P < 0.001; trichomonas infection 33% versus 14%, P < 0.001; chlamydial infection 11% versus 5%, P = 0.001; gonorrhoea 5% versus 2%, P = 0.03. HIV prevalence remained stable (26% versus 24%), and detuned assay testing suggested a decline in recent HIV infections. CONCLUSION: This comprehensive HIV preventive intervention empowering FSW has resulted in striking increases in reported condom use and a concomitant reduction in the prevalence of curable STI. This model should be replicated in similar urban settings across India

A Pilot study of the Sharing Risk Information Tool (ShaRIT) for Families with Hereditary Breast and Ovarian Cancer Syndrome

<p>Abstract</p> <p>Background</p> <p>Individuals who carry deleterious BRCA mutations face significantly elevated risks of breast, ovarian, and other cancers. These individuals are also responsible for informing relatives of their increased risk for carrying the family BRCA mutation. Few interventions have been developed to facilitate this family communication process.</p> <p>Methods</p> <p>We developed the Sharing Risk Information Tool (ShaRIT), a personalized educational intervention, to support BRCA carriers as they discuss BRCA positive results and their implications with relatives. We conducted a pilot study of 19 BRCA carriers identified through the University of California San Francisco Cancer Risk Program. Our study had two aims: 1) to assess the feasibility and acceptability of ShaRIT, and 2) describe characteristics associated with increased family communication and BRCA testing. Participants in our study were divided into two groups: those who had not received ShaRIT as part of their genetic counseling protocol (control group, n = 10) and those who received ShaRIT (n = 9).</p> <p>Results</p> <p>All 9 women who received ShaRIT reported that it was a useful resource. Characteristics associated with increased sharing and testing included: female gender, degree of relationship, and frequency of communication. Increased pedigree knowledge showed a trend toward higher rates of sharing.</p> <p>Conclusions</p> <p>Both participants and genetic counselors considered ShaRIT a well-received, comprehensive tool for disseminating individual risk information and clinical care guidelines to Hereditary Breast and Ovarian Cancer Syndrome families. Because of this, ShaRIT has been incorporated as standard of care at our institution. In the future we hope to evaluate the effects of ShaRIT on family communication and family testing in larger populations of BRCA positive families.</p

Beaten but not down! Exploring resilience among female sex workers (FSWs) in Nairobi, Kenya.

BACKGROUND: In Kenya sex work is illegal and those engaged in the trade are stigmatized and marginalized. We explored how female sex workers in Nairobi, Kenya, utilize different resources to navigate the negative consequences of the work they do. METHODS: Qualitative data were collected in October 2019 from 40 FSWs who were randomly sampled from 1003 women enrolled in the Maisha Fiti study, a 3-year longitudinal mixed-methods study exploring the relationship between HIV risk and violence and mental health. All interviews were audio-recorded, transcribed and translated. Data were thematically coded and analyzed using Nvivo 12. RESULTS: Participants' age range was 18-45 years. Before entry into sex work, all but one had at least one child. Providing for the children was expressed as the main reason the women joined sex work. All the women grew up in adverse circumstances such as poor financial backgrounds and some reported sexual and physical abuse as children. They also continued to experience adversity in their adulthood including intimate partner violence as well as violence at the workplace. All the participants were noted to have utilised the resources they have to build resilience and cope with these adversities while remaining hopeful for the future. Motherhood was mentioned by most as the reason they have remained resilient. Coming together in groups and engaging with HIV prevention and treatment services were noted as important factors too in building resilience. CONCLUSION: Despite the adverse experiences throughout the lives of FSWs, resilience was a key theme that emerged from this study. A holistic approach is needed in addressing the health needs of female sex workers. Encouraging FSWs to come together and advocating together for their needs is a key resource from which resilience and forbearance can grow. Upstream prevention through strengthening of education systems and supporting girls to stay in school and complete their secondary and/or tertiary education would help them gain training and skills, providing them with options for income generation during their adult lives

Longitudinal experiences and risk factors for common mental health problems and suicidal behaviours among female sex workers in Nairobi, Kenya

Abstract Background Female sex workers (FSWs) are at high risk of mental health problems and suicide risk. Few longitudinal studies have examined risk factors for poor mental health among FSWs. Methods Maisha Fiti is a longitudinal study among FSWs randomly selected from Sex Worker Outreach Programme clinics across Nairobi. Behavioural-biological survey data were collected at baseline (n = 1003, June–December 2019), midline (n = 366) (Jan–March 2020) and endline (n = 877) (June 2020–Jan 2021). Women reporting mental health problems were offered counselling services. Multivariable mixed logistic regression models were used to examine factors associated with mental health problems and suicidal behaviours. Results There was a decline in the proportion of women reporting any mental health problem (depression and/or anxiety and/or PTSD) (baseline: 29.9%, midline: 13.3%, endline: 11.8%). There was strong evidence that any mental health problem was associated with recent hunger (aOR 1.99; 95% CI 1.37–2.88) and recent violence from non-intimate partners (2.23; 95% CI 1.55–3.19). Recent suicidal behaviour prevalence was similar across survey rounds (baseline: 10.2%; midline: 10.2%; endline: 10.4%), and was associated with recent violence from non-intimate partners (aOR 1.96; 95% CI 1.31–2.95), recent hunger (aOR 1.69; 95% CI 1.15–2.47) and having an additional employment to sex work (aOR 1.50; 95% CI 1.00–2.23). Conclusions Our study found a decline in mental health problems but high levels of persistent suicidal behaviours among FSWs. Syndemic risk factors including food insecurity and violence were longitudinally associated with mental health problems and recent suicidal behaviours. There is a need for accessible mental health services for FSWs, alongside structural interventions addressing poverty and violence. </jats:sec

Childhood and adolescent factors shaping vulnerability to underage entry into sex work: a quantitative hierarchical analysis of female sex workers in Nairobi, Kenya

OBJECTIVE: To explore factors associated with early age at entry into sex work, among a cohort of female sex workers (FSWs) in Nairobi, Kenya. BACKGROUND: Younger age at sex work initiation increases the risk of HIV acquisition, condom non-use, violence victimisation and alcohol and/or substance use problems. This study aimed to understand factors in childhood and adolescence that shape the vulnerability to underage sex work initiation. DESIGN: Building on previous qualitative research with this cohort, analysis of behavioural-biological cross-sectional data using hierarchical logistic regression. PARTICIPANTS AND MEASURES: FSWs aged 18-45 years were randomly selected from seven Sex Workers Outreach Programme clinics in Nairobi, and between June and December 2019, completed a baseline behavioural-biological survey. Measurement tools included WHO Adverse Childhood Experiences, Alcohol, Smoking and Substance Involvement Screening Test and questionnaires on sociodemographic information, sexual risk behaviours and gender-based violence. Descriptive statistics and logistic regression were conducted using hierarchical modelling. RESULTS: Of the 1003 FSWs who participated in the baseline survey (response rate 96%), 176 (17.5%) initiated sex work while underage (<18 years). In the multivariable analysis, factors associated with entering sex work while underage included incomplete secondary school education (aOR=2.82; 95% CI=1.69 to 4.73), experiencing homelessness as a child (aOR=2.20; 95% CI=1.39 to 3.48), experiencing childhood physical or sexual violence (aOR=1.85; 95% CI=1.09 to 3.15), young age of sexual debut (≤15 years) (aOR=5.03; 95% CI=1.83 to 13.79) and being childless at time of sex work initiation (aOR=9.80; 95% CI=3.60 to 26.66). CONCLUSIONS: Lower education level and childhood homelessness, combined with sexual violence and sexual risk behaviours in childhood, create pathways to underage initiation into sex work. Interventions designed for girls and young women at these pivotal points in their lives could help prevent underage sex work initiation and their associated health, social and economic consequences

Prevalence and correlates of common mental health problems and recent suicidal thoughts and behaviours among female sex workers in Nairobi, Kenya.

BACKGROUND: Adverse childhood experiences (ACEs), poverty, violence and harmful alcohol/substance use are associated with poor mental health outcomes, but few studies have examined these risks among Female Sex Workers (FSWs). We examine the prevalence and correlates of common mental health problems including suicidal thoughts and behaviours among FSWs in Kenya. METHODS: Maisha Fiti is a longitudinal study among FSWs randomly selected from Sex Worker Outreach Programme (SWOP) clinics across Nairobi. Baseline behavioural-biological survey (n = 1003) data were collected June-December 2019. Mental health problems were assessed using the Patient Health Questionnaire (PHQ-9) for depression, the Generalised Anxiety Disorder tool (GAD-7) for anxiety, the Harvard Trauma Questionnaire (HTQ-17) for Post-Traumatic Stress Disorder (PTSD) and a two-item tool to measure recent suicidal thoughts/behaviours. Other measurement tools included the WHO Adverse Childhood Experiences (ACE) score, WHO Violence Against Women questionnaire, and the Alcohol, Smoking and Substance Involvement Screening Test (ASSIST). Descriptive statistics and multivariable logistic regression were conducted using a hierarchical modelling approach. RESULTS: Of 1039 eligible FSWs, 1003 FSWs participated in the study (response rate: 96%) with mean age 33.7 years. The prevalence of moderate/severe depression was 23.2%, moderate/severe anxiety 11.0%, PTSD 14.0% and recent suicidal thoughts/behaviours 10.2% (2.6% suicide attempt, 10.0% suicidal thoughts). Depression, anxiety, PTSD and recent suicidal thoughts/behaviours were all independently associated with higher ACE scores, recent hunger (missed a meal in last week due to financial difficulties), recent sexual/physical violence and increased harmful alcohol/substance. PTSD was additionally associated with increased chlamydia prevalence and recent suicidal thoughts/behaviours with low education and low socio-economic status. Mental health problems were less prevalent among women reporting social support. CONCLUSIONS: The high burden of mental health problems indicates a need for accessible services tailored for FSWs alongside structural interventions addressing poverty, harmful alcohol/substance use and violence. Given the high rates of ACEs, early childhood and family interventions should be considered to prevent poor mental health outcomes

Genetic variation in insulin-like growth factor signaling genes and breast cancer risk among BRCA1 and BRCA2 carriers

Abstract Introduction Women who carry mutations in BRCA1 and BRCA2 have a substantially increased risk of developing breast cancer as compared with the general population. However, risk estimates range from 20 to 80%, suggesting the presence of genetic and/or environmental risk modifiers. Based on extensive in vivo and in vitro studies, one important pathway for breast cancer pathogenesis may be the insulin-like growth factor (IGF) signaling pathway, which regulates both cellular proliferation and apoptosis. BRCA1 has been shown to directly interact with IGF signaling such that variants in this pathway may modify risk of cancer in women carrying BRCA mutations. In this study, we investigate the association of variants in genes involved in IGF signaling and risk of breast cancer in women who carry deleterious BRCA1 and BRCA2 mutations. Methods A cohort of 1,665 adult, female mutation carriers, including 1,122 BRCA1 carriers (433 cases) and 543 BRCA2 carriers (238 cases) were genotyped for SNPs in IGF1, IGF1 receptor (IGF1R), IGF1 binding protein (IGFBP1, IGFBP2, IGFBP5), and IGF receptor substrate 1 (IRS1). Cox proportional hazards regression was used to model time from birth to diagnosis of breast cancer for BRCA1 and BRCA2 carriers separately. For linkage disequilibrium (LD) blocks with multiple SNPs, an additive genetic model was assumed; and for single SNP analyses, no additivity assumptions were made. Results Among BRCA1 carriers, significant associations were found between risk of breast cancer and LD blocks in IGF1R (global P = 0.011 for LD block 2 and global P = 0.012 for LD block 11). Among BRCA2 carriers, an LD block in IGFBP2 (global P = 0.0145) was found to be associated with the time to breast cancer diagnosis. No significant LD block associations were found for the other investigated genes among BRCA1 and BRCA2 carriers. Conclusions This is the first study to investigate the role of genetic variation in IGF signaling and breast cancer risk in women carrying deleterious mutations in BRCA1 and BRCA2. We identified significant associations in variants in IGF1R and IRS1 in BRCA1 carriers and in IGFBP2 in BRCA2 carriers. Although there is known to be interaction of BRCA1 and IGF signaling, further replication and identification of causal mechanisms are needed to better understand these associations