Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution

TCEAL1 Loss-of-Function Results in an X-Linked Dominant Neurodevelopmental Syndrome and Drives the Neurological Disease Trait in Xq222 Deletions

An Xq22.2 region upstream of PLP1 has been proposed to underly a neurological disease trait when deleted in 46,XX females. Deletion mapping revealed that heterozygous deletions encompassing the smallest region of overlap (SRO) spanning six Xq22.2 genes (BEX3, RAB40A, TCEAL4, TCEAL3, TCEAL1, and MORF4L2) associate with an early-onset neurological disease trait (EONDT) consisting of hypotonia, intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. None of the genes within the SRO have been associated with monogenic disease in OMIM. Through local and international collaborations facilitated by GeneMatcher and Matchmaker Exchange, we have identified and herein report seven de novo variants involving TCEAL1 in seven unrelated families: three hemizygous truncating alleles; one hemizygous missense allele; one heterozygous TCEAL1 full gene deletion; one heterozygous contiguous deletion of TCEAL1, TCEAL3, and TCEAL4; and one heterozygous frameshift variant allele. Variants were identified through exome or genome sequencing with trio analysis or through chromosomal microarray. Comparison with previously reported Xq22 deletions encompassing TCEAL1 identified a more-defined syndrome consisting of hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features include strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies. An additional maternally inherited hemizygous missense allele of uncertain significance was identified in a male with hypertonia and spasticity without syndromic features. These data provide evidence that TCEAL1 loss of function causes a neurological rare disease trait involving significant neurological impairment with features overlapping the EONDT phenotype in females with the Xq22 deletion

Workplace violence in a large correctional health servce in New South Wales, Australia: a retrospective review of incident management records

BackgroundLittle is known about workplace violence among correctional health professionals. This studyaimed to describe the patterns, severity and outcomes of incidents of workplace violenceamong employees of a large correctional health service, and to explore the help-seekingbehaviours of staff following an incident.MethodsThe study setting was Justice Health, a statutory health corporation established to providehealth care to people who come into contact with the criminal justice system in New SouthWales, Australia. We reviewed incident management records describing workplace violenceamong Justice Health staff. The three-year study period was 1/7/2007-30/6/2010.ResultsDuring the period under review, 208 incidents of workplace violence were recorded. Verbalabuse (71%) was more common than physical abuse (29%). The most (44%) incidents ofworkplace violence (including both verbal and physical abuse) occurred in adult maleprisons, although the most (50%) incidents of physical abuse occurred in a forensic hospital.Most (90%) of the victims were nurses and two-thirds were females. Younger employees andmales were most likely to be a victim of physical abuse. Preparing or dispensing medicationand attempting to calm and/or restrain an aggressive patient were identified as ‘high risk’work duties for verbal abuse and physical abuse, respectively. Most (93%) of the incidents ofworkplace violence were initiated by a prisoner/patient. Almost all of the incidents receivedeither a medium (46%) or low (52%) Severity Assessment Code. Few victims of workplaceviolence incurred a serious physical injury – there were no workplace deaths during the studyperiod. However, mental stress was common, especially among the victims of verbal abuse(85%). Few (6%) victims of verbal abuse sought help from a health professional.ConclusionsAmong employees of a large correctional health service, verbal abuse in the workplace wassubstantially more common than physical abuse. The most incidents of workplace violenceoccurred in adult male prisons. Review of the types of adverse health outcomes experiencedby the victims of workplace violence and the assessments of severity assigned to violentincidents suggests that, compared with health care settings in the community, correctionalsettings are fairly safe places in which to practice

The Use of Academic-Community Partnerships in Participant Accrual to an Inherited Cancer Registry

The Use of Academic-Community Partnerships in Participant Accrual to an Inherited Cancer RegistryDevon Bonner, Patrice Fleming, Sue Friedman, Susan Vadaparampil, Veronica Harville, Tuya PalBackground: The development of inherited cancer registries has provided for increased ascertainment of participants into genetic-based cancer research studies. Participants have mainly been recruited through academic-based genetic counseling and testing services. An Inherited Cancer Registry (ICARE) was established at Moffitt Cancer Center and participants were recruited through both an academic-community partnership with Facing Our Risks Empowered (FORCE), a non-profit organization for individuals and families affected by hereditary breast and ovarian cancer, and through academic-based high risk cancer clinics. This study sought to determine the efficacy of both methods in recruiting participants to the ICARE inherited cancer registry. Methods: Data was collected from a pre-existing dataset tracking accrual into the ICARE registry from June 2010 to November 2010. Frequencies were calculated for the number of participants accrued through each recruitment method as well as the number of subjects approached and number of participants consented to the registry through each method. Results: Of the 128 participants enrolled into ICARE, 82% (n=105) were enrolled through the academic-community partnership and 18% (n=23) were enrolled through the academic-based high risk cancer clinics. Of the 148 subjects approached for enrollment, 81% (n=116) were approached through the academic-community partnership and 19% (n=27) were approached through the academic-based high risk cancer clinics. 90.5% of subjects approached through the academic-community partnership were enrolled in the cancer registry while 85% of subjects approached through academic-based high risk cancer clinics enrolled.Conclusions: Although inherited cancer registries have historically recruited heavily through academic-based clinical services, recruitment through academic-community partnerships may prove to be a valuable tool in accruing registry participants as well

A Closer Look at Risk Perception among Black Women at Increased Risk for Hereditary Breast and Ovarian Cancer

Although Caucasian women are diagnosed with breast cancer more often than Black women, Black women are diagnosed at younger ages and experience higher mortality from breast cancer than any other racial/ethnic group

The Use of Academic-Community Partnerships in Participant Accrual to an Inherited Cancer Registry

The Use of Academic-Community Partnerships in Participant Accrual to an Inherited Cancer RegistryDevon Bonner, Patrice Fleming, Sue Friedman, Susan Vadaparampil, Veronica Harville, Tuya PalBackground: The development of inherited cancer registries has provided for increased ascertainment of participants into genetic-based cancer research studies. Participants have mainly been recruited through academic-based genetic counseling and testing services. An Inherited Cancer Registry (ICARE) was established at Moffitt Cancer Center and participants were recruited through both an academic-community partnership with Facing Our Risks Empowered (FORCE), a non-profit organization for individuals and families affected by hereditary breast and ovarian cancer, and through academic-based high risk cancer clinics. This study sought to determine the efficacy of both methods in recruiting participants to the ICARE inherited cancer registry. Methods: Data was collected from a pre-existing dataset tracking accrual into the ICARE registry from June 2010 to November 2010. Frequencies were calculated for the number of participants accrued through each recruitment method as well as the number of subjects approached and number of participants consented to the registry through each method. Results: Of the 128 participants enrolled into ICARE, 82% (n=105) were enrolled through the academic-community partnership and 18% (n=23) were enrolled through the academic-based high risk cancer clinics. Of the 148 subjects approached for enrollment, 81% (n=116) were approached through the academic-community partnership and 19% (n=27) were approached through the academic-based high risk cancer clinics. 90.5% of subjects approached through the academic-community partnership were enrolled in the cancer registry while 85% of subjects approached through academic-based high risk cancer clinics enrolled.Conclusions: Although inherited cancer registries have historically recruited heavily through academic-based clinical services, recruitment through academic-community partnerships may prove to be a valuable tool in accruing registry participants as well

Abstract A33: The utility of a state-wide cancer registry in recruiting a clinically representative population-based sample of young black women diagnosed with early-onset breast cancer.

Abstract Background: Black women have a higher incidence of and mortality from early-onset breast cancer than White women. This may partly be attributed to mutations in the breast cancer susceptibility genes, BRCA1 and BRCA2 (BRCA), as well as a greater proportion of the aggressive triple negative breast cancer subtype (TN). Recruitment of Black women with early onset breast cancer into etiologic studies is an important step toward identifying factors contributing to this health disparity and developing appropriate risk reduction and treatment strategies to reduce mortality in this underserved population. Objective: Within a registry-based sample of Black women diagnosed with breast cancer ≤ 50 years between 2009-2011, the purpose of this analysis was to examine differences in clinical characteristics between those 1) in whom contact was versus was not established and 2) among those contacted, those who indicated interest versus declined participation to a study investigating the etiology of breast cancer. Methods: The state-wide cancer registry, Florida Cancer Data System (FCDS) provided contact information and clinical characteristics (i.e. age at diagnosis, stage, grade, histology, TN status, nodes positive, primary site, and treatment [dates and types]) on eligible cases. Potential participants were approached using state-mandated recruitment methods consisting of two mailings sent three weeks apart followed by phone to discuss interest in participation. Study participation included completion of a risk-factor questionnaire, phone genetic counseling, and donation of a biological sample for BRCA testing. Bivariate analyses were used to analyze differences in contact and interest in participation. Results: Among 912 eligible women identified by FCDS, the average age at diagnosis was 42.6 ± 6.2 years and the majority of diagnoses were unilateral (96.4%), ductal (78.9%), stage1/2 (51.6%), and lymph node negative (58.6%). Furthermore, 13.2% were TN and 85.6%, 62.1%, and 23.7% had surgery, chemotherapy, and radiation therapy, respectively. Contact was established with 481 (52.7%) potential participants. Those in whom contact was not established were similar on all clinical and treatment characteristics other than a slightly younger age at diagnosis [42.1 ± 6.4 years versus 43.0 ± 5.9 years; p=0.03]. Of those contacted, 284 (59%) were interested, 100 (20.8%) declined participation, and 97 (20.2%) neither indicated interest nor declined or were deemed ineligible at first contact. Potential participants who indicated interest and those who declined participation at first contact were comparable based on all clinical and treatment factors. Conclusions: Our results suggest state-wide cancer registries are a feasible recruitment source to establish contact with a clinically representative population-based sample of Black women diagnosed with early-onset invasive breast cancer. Furthermore, contrary to prior reports, clinical features did not appear to affect interest in participation, highlighting the need to investigate the effects of socioeconomic, cultural, and behavioral factors on recruitment of minority populations. Citation Format: Devon Bonner, Tuya Pal, Christine Tallo, Susan T. Vadaparampil. The ut\ility of a state-wide cancer registry in recruiting a clinically representative population-based sample of young black women diagnosed with early-onset breast cancer. [abstract]. In: Proceedings of the Fifth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2012 Oct 27-30; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(10 Suppl):Abstract nr A33.</jats:p

Abstract A34: How important is comprehensive rearrangement testing for BRCA mutations in African American women with early-onset breast cancer?

Abstract Background: Young Black women are disproportionately afflicted with breast cancer, a proportion of which may be due to BRCA1 and BRCA2 (BRCA) gene mutations. Deleterious mutations in the BRCA genes include those identified by sequencing technology as well as large genomic rearrangements that are found with different technologies (i.e., multiplex ligation-dependent probe amplification (MLPA)). The sole provider of clinical BRCA genetic testing in the United States is Myriad Genetics Laboratories, the company which owns the patent on these genes. When BRCA testing is ordered through this company, the standard test is called ‘Comprehensive BRCAnalysis’, which includes BRCA sequencing and testing for five rearrangements in BRCA1. In addition, testing for large rearrangements has been available since 2006, but is ordered and billed as a separate test from Comprehensive BRCAnalysis (at a cost of $700, often as an out-of-pocket expense). Objectives: In a cancer registry-based sample of Black women with early onset breast cancer, we evaluated prevalence of: 1) BRCA mutations; and 2) individuals who had BRCA testing (+counseling) predating study enrollment. Methods: Black women diagnosed with invasive breast cancer &amp;lt; age 50 in 2009-2010 were recruited through the Florida Cancer Registry utilizing state-mandated recruitment methods. Participants completed genetic counseling and a comprehensive risk factor questionnaire which included uptake of clinical BRCA testing pre-dating study enrollment. All participants consented to medical record release, including release of prior genetic test results. Saliva specimens were collected and BRCA testing was performed on all individuals through full gene sequencing and comprehensive rearrangement testing. Results: Of the first 48 participants in whom results of genetic testing are currently available through the study, two mutations in the BRCA genes were detected. Both mutations were identified in women who had undergone comprehensive BRCAnalysis pre-dating study enrollment. This included one participant identified to have a deleterious BRCA2 mutation through prior clinical testing (BRCA2 exon11 5844del5), in whom the same mutation was detected through the study. The second mutation was identified through comprehensive rearrangement testing (BRCA1 delExon8) in a woman who had previously had clinical BRCA testing during her breast cancer treatment in whom no mutation was detected through ‘Comprehensive BRCAnalaysis’. Of note, 15 women overall (31.3%) had clinical BRCA testing pre-dating study enrollment, which included both women identified as mutation carriers. Conclusions: Our findings suggest that it is critical to offer comprehensive rearrangement testing as part of BRCA testing in African American women, as one of the two mutations identified in our study was only identified through MLPA. Furthermore, in contrast to prior publications which suggest low uptake of BRCA testing in African American women, our results suggest reasonable uptake of BRCA testing in a registry-based sample of African American women with rates comparable to that previously reported in White women. Citation Format: Tuya PalDevon Bonner, Mohammad Akbari, Steven Narod, Susan Vadaparampil. How important is comprehensive rearrangement testing for BRCA mutations in African American women with early-onset breast cancer? [abstract]. In: Proceedings of the Fifth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2012 Oct 27-30; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(10 Suppl):Abstract nr A34.</jats:p

Recruitment of a Population-Based Sample of Young Black Women with Breast Cancer through a State Cancer Registry

Given that Black women remain underrepresented in clinical research studies, we sought to recruit a population-based sample of young Black women with breast cancer through a state cancer registry. Demographic and clinical information on all Black women diagnosed with invasive breast cancer at or below age 50 between 2009 and 2012 in Florida was obtained through the state cancer registry. Survivors were invited to participate in the study through state-mandated recruitment methods. Participant demographic and clinical characteristics were compared using Chi-squared tests for categorical variables and the two sample t-test for continuous variables to identify differences between: (i) consented participants versus all other eligible; and (ii) living versus deceased. Of the 1,647 young Black women with breast cancer, mean age at diagnosis was 42.5, with the majority having localized or regional disease, unmarried, privately insured, and employed. There were no significant differences in demographic and clinical variables between the 456 consented study participants versus the remaining 1,191 presumed eligible individuals. Compared to potential participants, women determined to be deceased prior to recruitment (n = 182) were significantly more likely to have distant disease and a triple-negative phenotype. They were also significantly more likely to be unemployed, and uninsured or have public insurance (i.e., Medicaid or Medicare). Our results demonstrate that recruitment of a population-based sample of breast cancer survivors through a state cancer registry is a feasible strategy in this underserved and underrepresented population. However, survival bias, which was observed due to the lag time between diagnosis and recruitment, is important to adjust for when generalizing findings to all young Black breast cancer patients