Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.

SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia

Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.

A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network

PURPOSE

Next-generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultrarare conditions. However, diagnosis rates differ between analytical pipelines. In the National Institutes of Health-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice.

METHODS

A retrospective review was performed at 2 UDN clinical sites to compare the variants and diagnoses/candidate genes identified with the dual analyses of the NGS data.

RESULTS

In total, 95 individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, whereas the clinical sites prioritized more research variants/candidate genes (P < .001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the 2 pipelines were more often because of variant prioritization disparities than variant detection.

CONCLUSION

The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provided a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.

Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment

Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.

Continuing a search for a diagnosis: the impact of adolescence and family dynamics

The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.

TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 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.

DPP9 deficiency: An inflammasomopathy that can be rescued by lowering NLRP1/IL-1 signaling

Dipeptidyl peptidase 9 (DPP9) is a direct inhibitor of NLRP1, but how it affects inflammasome regulation in vivo is not yet established. Here, we report three families with immune-associated defects, poor growth, pancytopenia, and skin pigmentation abnormalities that segregate with biallelic DPP9 rare variants. Using patient-derived primary cells and biochemical assays, these variants were shown to behave as hypomorphic or knockout alleles that failed to repress NLRP1. The removal of a single copy of Nlrp1a/b/c, Asc, Gsdmd, or Il-1r, but not Il-18, was sufficient to rescue the lethality of Dpp9 mutant neonates in mice. Similarly, dpp9 deficiency was partially rescued by the inactivation of asc, an obligate downstream adapter of the NLRP1 inflammasome, in zebrafish. These experiments suggest that the deleterious consequences of DPP9 deficiency were mostly driven by the aberrant activation of the canonical NLRP1 inflammasome and IL-1β signaling. Collectively, our results delineate a Mendelian disorder of DPP9 deficiency driven by increased NLRP1 activity as demonstrated in patient cells and in two animal models of the disease.

Characterization of HNRNPA1 mutations defines diversity in pathogenic mechanisms and clinical presentation

Mutations in HNRNPA1 encoding heterogeneous nuclear ribonucleoprotein (hnRNP) A1 are a rare cause of amyotrophic lateral sclerosis (ALS) and multisystem proteinopathy (MSP). hnRNPA1 is part of the group of RNA-binding proteins (RBPs) that assemble with RNA to form RNPs. hnRNPs are concentrated in the nucleus and function in pre-mRNA splicing, mRNA stability, and the regulation of transcription and translation. During stress, hnRNPs, mRNA, and other RBPs condense in the cytoplasm to form stress granules (SGs). SGs are implicated in the pathogenesis of (neuro-)degenerative diseases, including ALS and inclusion body myopathy (IBM). Mutations in RBPs that affect SG biology, including FUS, TDP-43, hnRNPA1, hnRNPA2B1, and TIA1, underlie ALS, IBM, and other neurodegenerative diseases. Here, we characterize 4 potentially novel HNRNPA1 mutations (yielding 3 protein variants: *321Eext*6, *321Qext*6, and G304Nfs*3) and 2 known HNRNPA1 mutations (P288A and D262V), previously connected to ALS and MSP, in a broad spectrum of patients with hereditary motor neuropathy, ALS, and myopathy. We establish that the mutations can have different effects on hnRNPA1 fibrillization, liquid-liquid phase separation, and SG dynamics. P288A accelerated fibrillization and decelerated SG disassembly, whereas *321Eext*6 had no effect on fibrillization but decelerated SG disassembly. By contrast, G304Nfs*3 decelerated fibrillization and impaired liquid phase separation. Our findings suggest different underlying pathomechanisms for HNRNPA1 mutations with a possible link to clinical phenotypes.

Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science

PURPOSE

The NIH Undiagnosed Diseases Network (UDN) evaluates participants with disorders that have defied diagnosis, applying personalized clinical and genomic evaluations and innovative research. The clinical sites of the UDN are essential to advancing the UDN mission; this study assesses their contributions relative to standard clinical practices.

METHODS

We analyzed retrospective data from four UDN clinical sites, from July 2015 to September 2019, for diagnoses, new disease gene discoveries and the underlying investigative methods.

RESULTS

Of 791 evaluated individuals, 231 received 240 diagnoses and 17 new disease-gene associations were recognized. Straightforward diagnoses on UDN exome and genome sequencing occurred in 35% (84/240). We considered these tractable in standard clinical practice, although genome sequencing is not yet widely available clinically. The majority (156/240, 65%) required additional UDN-driven investigations, including 90 diagnoses that occurred after prior nondiagnostic exome sequencing and 45 diagnoses (19%) that were nongenetic. The UDN-driven investigations included complementary/supplementary phenotyping, innovative analyses of genomic variants, and collaborative science for functional assays and animal modeling.

CONCLUSION

Investigations driven by the clinical sites identified diagnostic and research paradigms that surpass standard diagnostic processes. The new diagnoses, disease gene discoveries, and delineation of novel disorders represent a model for genomic medicine and science.

De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation

EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.

Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing

BACKGROUND

Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored.

METHODS

We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated.

RESULTS

Sixty-six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty-two of 66 (64%) received insurance denial for clinician-ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%).

CONCLUSIONS

These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.

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.

A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing

There are approximately 7,000 rare diseases affecting 25-30 million Americans, with 80% estimated to have a genetic basis. This presents a challenge for genetics practitioners to determine appropriate testing, make accurate diagnoses, and conduct up-to-date patient management. Exome sequencing (ES) is a comprehensive diagnostic approach, but only 25%-41% of the patients receive a molecular diagnosis. The remaining three-fifths to three-quarters of patients undergoing ES remain undiagnosed. The Stanford Center for Undiagnosed Diseases (CUD), a clinical site of the Undiagnosed Diseases Network, evaluates patients with undiagnosed and rare diseases using a combination of methods including ES. Frequently these patients have non-diagnostic ES results, but strategic follow-up techniques identify diagnoses in a subset. We present techniques used at the CUD that can be adopted by genetics providers in clinical follow-up of cases where ES is non-diagnostic. Solved case examples illustrate different types of non-diagnostic results and the additional techniques that led to a diagnosis. Frequent approaches include segregation analysis, data reanalysis, genome sequencing, additional variant identification, careful phenotype-disease correlation, confirmatory testing, and case matching. We also discuss prioritization of cases for additional analyses.

Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students

With the wide adoption of next-generation sequencing (NGS)-based genetic tests, genetic counselors require increased familiarity with NGS technology, variant interpretation concepts, and variant assessment tools. The use of exome and genome sequencing in clinical care has expanded the reach and diversity of genetic testing. Regardless of the setting where genetic counselors are performing variant interpretation or reporting, most of them have learned these skills from colleagues, while on the job. Though traditional, lecture-based learning around these topics is important, there has been growing need for the inclusion of case-based, experiential training of genomics and variant interpretation for genetic counseling students, with the goal of creating a strong foundation in variant interpretation for new genetic counselors, regardless of what area of practice they enter. To address this need, we established a genomics and variant interpretation rotation for Stanford's genetic counseling training program. In response to changes in the genomics landscape, this has now evolved into three unique rotation experiences, each focused on variant interpretation in the context of various genomic settings, including clinical laboratory, research laboratory, and healthy genomic analysis studies. Here, we describe the goals and learning objectives that we have developed for these variant interpretation rotations, and illustrate how these concepts are applied in practice.

Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay

SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.

Racial disparities in BRCA testing and cancer risk management across a population-based sample of young breast cancer survivors

BACKGROUND

Breast cancer (BC) disparities may widen with genomic advances. The authors compared non-Hispanic white (NHW), black, and Hispanic BC survivors for 1) cancer risk-management practices among BRCA carriers and 2) provider discussion and receipt of genetic testing.

METHODS

A population-based sample of NHW, black, and Hispanic women who had been diagnosed with invasive BC at age 50 years or younger from 2009 to 2012 were recruited through the state cancer registry. Multiple logistic regression was used to compare cancer risk-management practices in BRCA carriers and associations of demographic and clinical variables with provider discussion and receipt of testing.

RESULTS

Of 1622 participants, 159 of 440 (36.1%) black women, 579 of 897 (64.5%) NHW women, 58 of 117 (49.6%) Spanish-speaking Hispanic women, and 116 of 168 (69%) English-speaking Hispanic women underwent BRCA testing, of whom 90 had a pathogenic BRCA mutation identified. Among BRCA carriers, the rates of risk-reducing mastectomy and risk-reducing salpingo-oophorectomy were significantly lower among black women compared with Hispanic and NHW women after controlling for clinical and demographic variables (P = .025 and P = .008, respectively). Compared with NHW women, discussion of genetic testing with a provider was 16 times less likely among black women (P < .0001) and nearly 2 times less likely among Spanish-speaking Hispanic women (P = .04) after controlling for clinical and sociodemographic factors.

CONCLUSIONS

The current results suggest that the rates of risk-reducing salpingo-oophorectomy are lower among black BRCA carriers compared with their Hispanic and NHW counterparts, which is concerning because benefits from genetic testing arise from cancer risk-management practice options. Furthermore, lower BRCA testing rates among blacks may partially be because of a lower likelihood of provider discussion. Future studies are needed to improve cancer risk identification and management practices across all populations to prevent the widening of disparities. Cancer 2017;123:2497-05. © 2017 American Cancer Society.

Racial disparities in BRCA testing and cancer risk management across a population-based sample of young breast cancer survivors

BACKGROUND

Breast cancer (BC) disparities may widen with genomic advances. The authors compared non-Hispanic white (NHW), black, and Hispanic BC survivors for 1) cancer risk-management practices among BRCA carriers and 2) provider discussion and receipt of genetic testing.

METHODS

A population-based sample of NHW, black, and Hispanic women who had been diagnosed with invasive BC at age 50 years or younger from 2009 to 2012 were recruited through the state cancer registry. Multiple logistic regression was used to compare cancer risk-management practices in BRCA carriers and associations of demographic and clinical variables with provider discussion and receipt of testing.

RESULTS

Of 1622 participants, 159 of 440 (36.1%) black women, 579 of 897 (64.5%) NHW women, 58 of 117 (49.6%) Spanish-speaking Hispanic women, and 116 of 168 (69%) English-speaking Hispanic women underwent BRCA testing, of whom 90 had a pathogenic BRCA mutation identified. Among BRCA carriers, the rates of risk-reducing mastectomy and risk-reducing salpingo-oophorectomy were significantly lower among black women compared with Hispanic and NHW women after controlling for clinical and demographic variables (P = .025 and P = .008, respectively). Compared with NHW women, discussion of genetic testing with a provider was 16 times less likely among black women (P < .0001) and nearly 2 times less likely among Spanish-speaking Hispanic women (P = .04) after controlling for clinical and sociodemographic factors.

CONCLUSIONS

The current results suggest that the rates of risk-reducing salpingo-oophorectomy are lower among black BRCA carriers compared with their Hispanic and NHW counterparts, which is concerning because benefits from genetic testing arise from cancer risk-management practice options. Furthermore, lower BRCA testing rates among blacks may partially be because of a lower likelihood of provider discussion. Future studies are needed to improve cancer risk identification and management practices across all populations to prevent the widening of disparities. Cancer 2017;123:2497-05. © 2017 American Cancer Society.

Disparities in cancer risk management among BRCA carriers across a diverse sample of young black, Hispanic, and non-Hispanic white breast cancer survivors

LBA1504

Background: Rates of risk-reducing bilateral mastectomy (RRM) or risk-reducing prophylactic oophorectomy (RRSO) among BRCA carriers are based on studies of non-Hispanic whites (NHW), with little known among blacks or Hispanics. Methods: A population-based sample of NHW, black, and Hispanic women diagnosed with invasive BC < age 50 in 2009-12 were recruited through the Florida State Cancer Registry and completed a baseline survey. Among the subset of BRCA carriers, we compared risk management for: 1) ovarian cancer (OC) through RRSO; and 2) BC through RRM or MRI screening, by calculating percentages and conducting logistic regression to control for other variables. Results: Of 1570 participants, 884 reported BRCA testing. Of the 91 BRCA carriers, 1) RRSO was 71% (36/51) among NHW, 32% (9/28) among blacks, and 83% (10/12) among Hispanics; 2) either breast MRI or RRM was 98% (50/51) among NHW, 85.7% (24/28) among blacks, and 100% (12/12) among Hispanics. BC risk management modality differed across groups, with lower rates of RRM among blacks (67%) compared to Hispanics (83%) and NHW (94%). After controlling for age at enrollment, time since diagnosis, income, family history of BC, family history of OC and private insurance at diagnosis: 1) Hispanics and NHW were significantly more likely than blacks to have RRSO (p = 0.01 and 0.02 respectively); and 2) NHW were also significantly more likely than blacks to have RRM (p = 0.03), although Hispanic race approached statistical significance (p = 0.10). Conclusions: The racial disparities in uptake of RRSO observed among blacks is particularly concerning given that RRSO is strongly recommended as the main OC prevention option due to the absence of effective OC early detection methods. The benefit from genetic testing comes from uptake of cancer risk management options, rather from testing itself. Future studies are needed to better understand and develop methods to improve cancer risk management practices across all populations.

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.

A high frequency of BRCA mutations in young black women with breast cancer residing in Florida

BACKGROUND

Black women are disproportionately affected with triple-negative breast cancer and have relatively poor survival. To the authors' knowledge, it is not known to what extent differences in the clinical presentation of breast cancer between non-Hispanic white women and black women can be accounted for by the presence of mutations in the BRCA1 and BRCA2 genes. The authors sought to evaluate the frequency of BRCA pathogenic variants in a population-based sample of young black women with breast cancer.

METHODS

Black women diagnosed with invasive breast cancer at age ≤50 years from 2009 to 2012 were recruited to the study through the Florida Cancer Registry. Participants underwent genetic counseling, completed a study questionnaire, and consented to release of their medical records. Saliva specimens were collected for BRCA sequencing and large rearrangement testing through multiplex ligation-dependent probe amplification.

RESULTS

A DNA sample was evaluated for 396 women, 49 of whom (12.4%) had a mutation in BRCA1 or BRCA2. Eight recurrent mutations accounted for 49% of all pathogenic variants.

CONCLUSIONS

To the authors' knowledge, the prevalence of BRCA mutations among the Florida-based sample of young black women with breast cancer in the current study exceeds that previously reported for non-Hispanic white women. It is appropriate to recommend BRCA testing in all young black women with invasive breast cancer.

Factors associated with genetic counseling and BRCA testing in a population-based sample of young Black women with breast cancer

Concerns about the potential for genomic advances to increase health disparities have been raised. Thus, it is important to assess referral and uptake of genetic counseling (GC) and testing in minority populations at high risk for hereditary breast and ovarian cancer (HBOC). Black women diagnosed with invasive breast cancer ≤age 50 in 2009-2012 were recruited through the Florida State Cancer Registry 6-18 months following diagnosis and completed a baseline questionnaire. Summary statistics, Chi-square tests, and path modeling were conducted to examine which demographic and clinical variables were associated with referral and access to genetic services. Of the 440 participants, all met national criteria for GC, yet only 224 (51 %) were referred for or received GC and/or HBOC testing. Variables most strongly associated with healthcare provider referral for GC included having a college education (OR 2.1), diagnosis at or below age 45 (OR 2.0), and triple negative tumor receptor status (OR 1.7). The strongest association with receipt of GC and/or HBOC testing was healthcare provider referral (OR 7.9), followed by private health insurance at diagnosis (OR 2.8), and household income greater than $35,000 in the year prior to diagnosis (OR 2.0). Study findings suggest efforts are needed to improve genetic services access among a population-based sample of high-risk Black women. These results indicate that socioeconomic factors and physician referral patterns contribute to disparities in access to genetic services within this underserved minority population.

Abstract C43: Health-related quality of life among younger black breast cancer survivors

Purpose: Of an estimated 3 million breast cancer survivors in the U.S, the median age at diagnosis is 61 years for all racial/ethnic groups combined. Although the overall incidence of breast cancer is lower in Black women compared to White women, they are more likely to develop and die from early onset (age 50 years or younger) aggressive disease. As a result, young Black women with invasive breast cancer may experience poorer quality of life after breast cancer diagnosis; yet, few studies have focused on this subset of younger Black breast cancer survivors. As part of an ongoing population-based case-only study to investigate etiology and outcomes of early-onset breast cancer in Black women, we sought to evaluate baseline predictors of health-related quality of life (HRQOL) at time of study entry.

Methods: Black women with invasive breast cancer at age 50 or younger diagnosed between 2009-2012 were recruited through the Florida State Cancer Registry utilizing state-mandated recruitment methods. Participants completed a comprehensive baseline questionnaire which included sociodemographic, clinical, and psychosocial characteristics. In the current study, we used multiple regression analysis to examine predictors of HRQOL measured with the FACT-G instrument. Predictors were selected based on the Contextual Model of HRQOL and included individual clinical (e.g., age at diagnosis) and psychosocial (e.g., anxiety) as well as macro/systemic (e.g., social support) level variables.

Results: This report includes the first 206 women who completed the baseline questionnaires. The mean age at diagnosis was 42.5 years (SD=6.2; range=21-50). The mean HRQOL score was 74.4 (SD=21.6; range= 25-108), which is lower than ranges reported in normative samples of both healthy females (mean: 79.6, SD=18.6; range=25-108) and cancer patients (mean: 82.1, SD=16.3; range=15-108). In bivariate analyses, HRQOL was significantly associated with 19 predictor variables (p &lt; .05). In multiple regression, these variables accounted for about 78% of the variance in HRQOL. Adjusting for other model variables, self-reported current general health (beta=.15); role limitations for moderate activities (.12) and climbing stairs (.15); and social support (.14) were significantly associated with higher HRQOL, whereas life stress (-.37) was inversely associated with HRQOL.

Conclusions: Individual-level factors such as better self-reported general health, more social support, and less stress were associated with higher HRQOL. Conversely, women with moderate role limitations reported higher HRQOL. These findings document baseline characteristics among a sample of younger Black breast cancer survivors and provide an important benchmark by which to compare subsequent changes in HRQOL in this cohort.

Citation Format: Susan T. Vadaparampil, Teri L. Malo, Chanita Hughes-Halbert, Cheryl L. Holt, Shalanda A. Bynum, Jongphil Kim, Devon Bonner, Linda Bomboka, Courtney Scherr, Kimlin Ashing, Tuya Pal. Health-related quality of life among younger black breast cancer survivors. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C43. doi:10.1158/1538-7755.DISP13-C43

BRCA sequencing and large rearrangement testing in young Black women with breast cancer

Young Black women in the United States are disproportionately afflicted with breast cancer, a proportion of which may be due to BRCA1 and BRCA2 (BRCA) gene mutations. In a cancer registry-based sample of young Black women with breast cancer, we evaluated: (1) the prevalence of BRCA mutations detected through full gene sequencing and large rearrangements testing and (2) proportions that accessed genetic services pre-dating study enrollment. Black women diagnosed with invasive breast cancer ≤age 50 years in 2009-2012 were recruited through the Florida Cancer Registry. Participants completed genetic counseling, a study questionnaire, and consent for medical record release. Saliva specimens were collected for BRCA testing. Overall, 13 participants (9 %) had BRCA mutations detected (including 11 through full gene sequencing and two through large rearrangements testing). One of these large rearrangements, BRCA1 (delExon8), was identified in a participant who had previously tested negative on clinical comprehensive BRCAnalysis that was performed prior to undergoing a lumpectomy. Although all 144 participants met national criteria for referral for cancer genetic risk assessment, 61 (42 %) were referred for genetic counseling and/or had genetic testing preceding study enrollment, and only 20 (14 %) received genetic counseling. Our findings emphasize the importance of large rearrangements testing to increase detection of deleterious BRCA mutations in young Black women with breast cancer. The registry-based design of our study increase the generalizability of findings compared with efforts focused on clinic-based populations. Furthermore, results suggest efforts are needed to improve access to genetic counseling and testing.

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

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.

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

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 &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.

Abstract A71: BRCA mutations and surgical decision making in a sample of young black women with invasive breast cancer

Background: On average, Black women develop breast cancer ten years earlier than White women and are more likely to die from the disease. Early onset breast cancer is a hallmark feature of the BRCA1 and BRCA2 (BRCA) gene mutations and may contribute to a portion of breast cancers in Black women. Widespread availability of genetic testing for hereditary breast cancer has resulted in an increasing number of women considering their BRCA test results prior to surgical treatment decisions for their breast cancer surgery (e.g., consideration of a risk-reducing bilateral mastectomy, contralateral prophylactic mastectomy). However, little is known about use of BRCA testing prior to definitive surgery specifically among Black women. The purpose of this abstract is to describe baseline utilization of BRCA testing in Black breast cancer patients prior to surgery and to document the prevalence of BRCA mutations in a cohort of Black women with early onset breast cancer.

Methods: Black women diagnosed with invasive breast cancer ≤ age 50 between the years of 2005 and 2006 were recruited through the Florida Cancer Registry utilizing state-mandated recruitment methods. Participants completed genetic counseling and a comprehensive risk factor questionnaire including 7 items specific to referral and uptake of genetics clinical services. Biological specimens (either blood or saliva) were collected, and BRCA testing was performed.

Results: Of the 209 eligible cases, 48 women consented to study participation. Of the 46 women with usable biological specimens: the average age of diagnosis was 42.8 ±6.14 and 50% (n=23) reported a positive family history of breast cancer (i.e., ≥ 1 first and/or second-degree relative with breast cancer). A previous BRCA test was reported by 30.4% (n=14) of those completing the study with only 2 participants (4.3%) receiving a genetic test result prior to making a breast surgery decision. Seven women (15.2 %) chose a bilateral mastectomy, 4 of which were risk reducing. No association was observed between family history and the type of breast surgery elected. Mutations in the BRCA genes were identified in three participants (including 1 in BRCA1 and 2 in BRCA2). In 16 additional participants, there were a total of 28 variants of uncertain significance (VUS) identified.

Conclusions: Our results suggest that few Black women utilized genetic test results and/or family history to make surgical decisions for their breast cancer treatment despite data documenting similar BRCA prevalence rates in Black women with early onset breast cancers as those previously reported in White women. These findings highlight an important health disparity in access to and utilization of genetics services among Black women with breast cancer.

Citation Information: Cancer Epidemiol Biomarkers Prev 2011;20(10 Suppl):A71.

Synergistic activities of gatifloxacin in combination with other antimicrobial agents against Pseudomonas aeruginosa and related species

Drug combinations have been used to treat serious infections caused by Pseudomonas, Burkholderia, Stenotrophomonas, and Acinetobacter. In this study, the combined drug effects of gatifloxacin (GAT) and nonquinolones were determined by time-kill analysis at clinically achievable drug concentrations. Synergy (>or=2 log(10)-enhanced killing at 24 h) was observed with GAT plus amikacin or a beta-lactam against 50 to 75% of strains, including strains nonsusceptible to one or both drugs.

Correlation between genotype and phenotypic categorization of staphylococci based on methicillin susceptibility and resistance

Positive correlation between methicillin and oxacillin susceptibility test results and the detection of the mecA gene was observed for Staphylococcus aureus, S. epidermidis, and S. haemolyticus as well as among mecA(+) strains of other species of coagulase-negative staphylococci (CNS). However, at least 50% of the mecA-negative strains of these other species of CNS were falsely classified as methicillin and oxacillin resistant.

Comparative killing kinetics of the novel des-fluoro(6) quinolone BMS-284756, fluoroquinolones, vancomycin and beta-lactams

The primary bactericidal classes used therapeutically as single agents, are the quinolones and the cell-wall active agents. In this study, their rates of killing were compared. The des-fluoro(6) quinolone BMS-284756 (T-3811ME), fluoroquinolones (trovafloxacin, levofloxacin) and cell wall-active agents (beta-lactams, vancomycin) were evaluated against Enterobacteriaceae, Staphylococcus aureus, streptococci, and Enterococcus faecalis. Time-kill analysis was done at 10x the MIC, using Mueller-Hinton broth (supplemented with 7% lysed horse blood for Streptococcus pneumoniae and the viridans streptococci), or Brain Heart Infusion broth for beta-haemolytic streptococci. Using a 3-log(10) decrease in viable count as an index of bactericidal activity, BMS-284756 and the fluoroquinolones killed Enterobacteriaceae rapidly, requiring < 2 h versus > or =6 h for beta-lactams. The staphylococcal cell counts generally decreased more rapidly with quinolone exposure, compared with those treated with vancomycin or the beta-lactams. The antimicrobial agents killed streptococci and enterococci more slowly, requiring > 6 h to decrease the viable count by 99.9%. In summary, BMS-284756 killing rates are similar to those of recent fluoroquinolones and are bacterial group-dependent. Overall, the quinolones are more rapidly bactericidal than vancomycin and the beta-lactam antibiotics.

Regulation of Pyk2 expression by p56(Lck) in Jurkat T lymphocytes

Lysates from the Jurkat T lymphocyte cell line were immunoblotted with anti-Pyk2, and two major forms of Pyk2 were identified. When lysates from the p56(Lck) negative (J.CaM1/Rep3) and CD45 negative Jurkat cell line derivatives were immunoblotted with anti-Pyk2, only the lower mobility form of Pyk2 was predominant. Transfection of J.CaM1 cells with p56(Lck) restored expression of the multiple forms of Pyk2. Using RT-PCR, we found that both species of the alternatively spliced mRNA for Pyk2 were present in all of the lines regardless of their ability to express CD45 or p56(Lck) protein. When p56(Lck) immunoprecipitates were immunoblotted with anti-Pyk2, only the higher mobility form of Pyk2 immunoprecipitated with p56(Lck). These data demonstrate that certain members of the Src family of kinases interact preferentially with the different isoforms of Pyk2 and may have a role in the regulation of the Pyk2 protein in lymphocytes.

Susceptibility of bacterial isolates to gatifloxacin and ciprofloxacin from clinical trials 1997-1998

MICs of gatifloxacin and ciprofloxacin against 3482 pre-treatment, clinical trial isolates collected during 1997-1998 are reported. These data suggested that gatifloxacin was four- to eight-fold more active than ciprofloxacin against Gram-positive bacteria, with gatifloxacin MIC(90)s < or = 0.33 mg/l against Staphylococcus aureus and Streptococcus pneumoniae, and < or = 1.0 mg/l versus viridans streptococci and Enterococcus faecalis. Both quinolones had similar MIC(90)s versus Enterobacteriaceae (generally < or = 0.38 mg/l, except 0. 7-0.8 mg/l for Citrobacter freundii) and Pseudomonas aeruginosa ( approximately 8 mg/l). A total of 78% P. aeruginosa had gatifloxacin MICs < or = 2 mg/l. Gatifloxacin was more active than ciprofloxacin against Acinetobacter species and non-P. aeruginosa pseudomonads. Both had exceptional activity versus Haemophilus spp, Moraxella catarrhalis and Neisseria gonorrhoeae. In summary, compared to ciprofloxacin, gatifloxacin had improved activity against Gram-positive bacteria and comparable activity against Gram-negative bacteria.

Voices, Opportunities & Choices Employment Club: transforming sheltered workshops using an affirmative business approach. The VOCEC Board of Directors

Voices, Opportunities & Choices Employment Club (VOCEC) is a non-profit "umbrella" corporation that facilitates the development of affirmative businesses to create jobs for consumers of mental health services. To date, 5 independent businesses have been developed by transforming the resources of sheltered workshops within Kingston Psychiatric Hospital and 2 businesses have been established in collaboration with a local public library. This paper provides a description of VOCEC, including an overview of the affirmative business approach, the structure of the organization, and the process of business development. Personal reflections provide insights into the experiences of consumers, staff, and Board members associated with the corporation.

In vitro antibacterial spectrum of a new broad-spectrum 8-methoxy fluoroquinolone, gatifloxacin

The in vitro antibacterial spectrum of gatifloxacin was compared with those of ciprofloxacin and ofloxacin. Gatifloxacin was two- to four-fold more potent than comparator quinolones against staphylococci, streptococci, pneumococci and enterococci (gatifloxacin MIC90s, < or =1 mg/L, except 4 mg/L against methicillin-resistant Staphylococcus aureus and Enterococcus faecium). Gatifloxacin was two-fold less potent than ciprofloxacin, and the same as or two-fold more potent than ofloxacin against Enterobacteriaceae (MIC90s, 0.06-0.5 mg/L against most members of the Enterobacteriaceae and < or =1 mg/L against Proteus/Morganella spp.). Relative to the comparator quinolones, gatifloxacin was two- to four-fold more potent against Providencia spp., and had good potency against Acinetobacter spp. (MIC90s, 0.25-1 mg/L). Gatifloxacin and ofloxacin had similar anti-pseudomonal potency, with corresponding MIC90s of 4, 8 and 0.25 mg/L for Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas stutzeri, while ciprofloxacin had two- to eight-fold more potency. The three quinolones were equipotent against Burkholderia cepacia (MIC90s, 8 mg/L), but gatifloxacin was two-fold more potent against Stenotrophomonas maltophilia (MIC90, 4 mg/L). Gatifloxacin was highly potent (MIC90s, 0.03-0.06 mg/L) against Haemophilus influenzae, Legionella spp., Helicobacter pylori and had at least eight-fold better anti-chlamydial and anti-mycoplasma potency (gatifloxacin MIC90s, 0.13 mg/L). The higher quinolone MICs for ureaplasma (MIC90s, 4-8 mg/L) may be due to the acidic pH of the ureaplasma test medium, which antagonizes quinolones. Like other quinolones, gatifloxacin had poor potency against Mycobacterium avium-intracellulare, though it was eight- to 16-fold more potent against Mycobacterium tuberculosis (MIC90, 0.25 mg/L). Of the three quinolones, only gatifloxacin had activity against Bacteroides fragilis and Clostridium difficile. In summary, gatifloxacin is a broad-spectrum 8-methoxy fluoroquinolone that is more potent than ciprofloxacin and ofloxacin against Gram-positive bacteria, chlamydia, mycoplasma, mycobacteria and anaerobes.

Antibacterial activity of BMS-180680, a new catechol-containing monobactam

The in vitro activities of a new catechol-containing monobactam, BMS-180680 (SQ 84,100), were compared to those of aztreonam, ceftazidime, imipenem, piperacillin-tazobactam, ciprofloxacin, amikacin, and trimethoprim-sulfamethoxazole. BMS-180680 was often the most active compound against many species of the family Enterobacteriaceae, with MICs at which 90% of the isolates were inhibited (MIC90s) of < or = 0.5 microg/ml for Escherichia coli, Klebsiella spp., Citrobacter diversus, Enterobacter aerogenes, Serratia marcescens, Proteus spp., and Providencia spp. BMS-180680 had moderate activities (MIC90s of 2 to 8 microg/ml) against Citrobacter freundii, Morganella morganii, Shigella spp., and non-E. aerogenes Enterobacter spp. BMS-180680 was the only antibiotic evaluated that was active against >90% of the Pseudomonas aeruginosa (MIC90, 0.25 microg/ml), Burkholderia cepacia, and Stenotrophomonas maltophilia (MIC90s, 1 microg/ml) strains tested. BMS-180680 was inactive against most strains of Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas diminuta, and Burkholderia pickettii. BMS-180680 was moderately active (MIC90s of 4 to 8 microg/ml) against Alcaligenes spp. and Acinetobacter lwoffii and less active (MIC90, 16 microg/ml) against Acinetobacter calcoaceticus-Acinetobacter baumanii complex. BMS-180680 lacked activity against gram-positive bacteria and anaerobic bacteria. Both tonB and cir fiu double mutants of E. coli had greatly decreased susceptibility to BMS-180680. Of the TEM, PSE, and chromosomal-encoded beta-lactamases tested, only the K1 enzyme hydrolyzed BMS-180680 to any measurable extent. Like aztreonam, BMS-180680 bound preferentially to penicillin-binding protein 3. The MICs of BMS-180680 were not influenced by the presence of hematin or 5% sheep blood in the test medium or with incubation in an atmosphere containing 5% CO2. BMS-180680 MICs obtained under strict anaerobic conditions were significantly higher than those obtained in ambient air.

Acute frontal lobe syndrome and dyscontrol associated with bilateral caudate nucleus infarctions

BACKGROUND

A 67-year-old man presented with acute onset of spatial and temporal disorientation, memory loss and associated episodic dyscontrol. Investigations showed infarctions of both caudate nuclei. This patient presented a unique opportunity to study the relationship between the lesions, his behaviour, and neuropsychological testing.

METHOD

Single case report. Investigations included interviews to determine cognitive impairment, i.e. WAIS-R, MMSE, and neurological examination.

RESULTS

Extensive neuropsychological testing revealed severe impairment on tasks requiring planning, memory or abstract thought. These findings are very similar to those seen in Huntington's disease.

CONCLUSIONS

A neurobiological hypothesis is proposed to account for his symptoms, and recent discoveries in the basic sciences used to inform his management.

Magnetic resonance imaging volumetric measurements of the superior temporal gyrus, hippocampus, parahippocampal gyrus, frontal and temporal lobes in late paraphrenia

Quantified magnetic resonance measurements were made of superior temporal gyrus, parahippocampal gyrus, hippocampal, frontal and temporal lobe volumes and of the planar area of the thalamus and basal ganglia structures in 47 late paraphrenic patients and 33 healthy elderly controls. The late paraphrenics were divided into 31 schizophrenics and 16 patients with delusional disorder according to ICD-10 guidelines. Patients with delusional disorder tended to have smaller left temporal volumes compared with control subjects and patients with schizophrenia, but this difference failed to reach accepted levels of statistical significance after correction for the effects of multiple statistical comparisons, age and total brain size. Physiological right-left asymmetry, reported for temporal and frontal lobe volumes, was present in control, schizophrenic and delusional disorder subjects but delusional disorder patients had a significantly greater degree of temporal lobe asymmetry. The results add to the evidence for heterogeneity among late-onset psychoses and emphasize the subtle nature of any structural brain abnormalities in these patients.

Antibacterial activities of cefprozil compared with those of 13 oral cephems and 3 macrolides

Thirteen oral cephems (cefprozil, loracarbef, cefaclor, cefuroxime axetil, cefpodoxime proxetil, cefetamet pivoxil, cefixime, cefdinir, cefadroxil, cephradine, cephalexin, cefatrizine, and cefroxadine), the cephalosporin class representative cephalothin, cefazolin, and the macrolides erythromycin, clarithromycin, and azithromycin were compared for their antibacterial activities against 790 recent clinical isolates. These oral agents differed in their spectra and antibacterial potencies against community-acquired pathogens.

Treatment-resistant depression in the elderly

Apparent treatment-resistant depression (TRD) is frequently encountered by and poses particular challenges for the old-age psychiatrist. The prevalence of true nonresponse to treatment is not known with accuracy but reports put it at 18% to 40% for the elderly. This article reviews the concept of TRD in the elderly, discussing the factors involved in apparent resistance and the treatment of this group. We suggest that absolute TRD may be a rarer entity than the estimated 18% to 40% if depressed patients are treated carefully and vigorously.