Abstract P3-07-05: Frequent BRCA1 and BRCA2 mutations are found in Mexican and Mexican-American women with breast cancer

Background: The Arizona Cancer Registry has shown that in Pima County, AZ, breast cancer diagnosed in young Latinas increased 40% from 2004-2008, compared to 1999-2003, and Latinas more likely to die of their cancer. This study seeks to characterize genetic variation in women of Mexican ancestry with breast cancer using next generation sequencing, with the goal of providing prevalence information to help guide screening and cancer prevention efforts.

Methods: The ELLA Binational Breast Cancer Study enrolled women of Mexican ancestry living in either U.S. or Mexico within 24 months of breast cancer diagnosis. Mexican women from the state of Jalisco were collected through collaboration with the Universidad de Guadalajara and women of Mexican ancestry were recruited from Tucson and Phoenix, AZ. Genomic DNA from 92 ELLA study participants (49 from the U.S. and 43 from Mexico) was enriched for breast cancer influencing gene sequence using the BROCA panel with standard techniques. Samples were sequenced with next generation sequencing and variants identified.

Results: Sequencing of breast cancer risk genes in 92 Mexican and Mexican-American women with breast cancer revealed the presence of deleterious mutations in 15% of women (14/92). Five carry mutations in BRCA1, 5 in BRCA2, 2 in CHEK2, 1 in PALB2 and 1 in RAD51C. An additional 9% of participants (8/92) carry rare mutations of unknown functional consequence in the same genes. Four carry mutations in BRCA1 or BRCA2 at sites predicted to alter splice enhancers and four carry missense mutations in CHEK2 that are predicted to damage to kinase function. None of these variants appear in public databases or are characterized functionally in gene-specific databases. Dozens of women carry VUS or novel variants.

Women carrying BRCA1 mutations are significantly more likely to have had triple negative pathology. Women carrying other mutations known or thought to be deleterious are also more likely to have been younger at diagnosis, to have more aggressive breast cancer or to report a family history of breast cancer.

Table 1. Deleterious MutationsGeneEffectTotalBRCA1185delAG1BRCA12569delC2BRCA1Del Complete Gene1BRCA1Del Exons 9-121BRCA2c.658delGT1BRCA2c.3264insT2BRCA2c.5195delT1BRCA2c.6024insG1CHEK2R160G2PALB2S779 Stop1RAD51CDel Exons 4-91

Conclusion: Deleterious BRCA1 and BRCA2 gene mutations are common among women of Mexican ancestry diagnosed with breast cancer. Within this cohort, the prevalence of BRCA1/2 mutations is 11%, and 4% of women carry mutations in other genes increasing breast cancer risk. This is higher than the 10% mutation prevalence estimated for Ashkenazi Jewish women with breast cancer. An additional 9% of women carry variants likely to disrupt gene function and dozens of VUS and novel variants are found in these women. Further analysis of samples from the remaining 942 women using genetic sequencing will help further elucidate the role of genetic risk factors in women of Mexican ancestry with breast cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-07-05.

Parallel Simulation of Population Balance Model-Based Particulate Processes Using Multicore CPUs and GPUs

Computer-aided modeling and simulation are a crucial step in developing, integrating, and optimizing unit operations and subsequently the entire processes in the chemical/pharmaceutical industry. This study details two methods of reducing the computational time to solve complex process models, namely, the population balance model which given the source terms can be very computationally intensive. Population balance models are also widely used to describe the time evolutions and distributions of many particulate processes, and its efficient and quick simulation would be very beneficial. The first method illustrates utilization of MATLAB's Parallel Computing Toolbox (PCT) and the second method makes use of another toolbox, JACKET, to speed up computations on the CPU and GPU, respectively. Results indicate significant reduction in computational time for the same accuracy using multicore CPUs. Many-core platforms such as GPUs are also promising towards computational time reduction for larger problems despite the limitations of lower clock speed and device memory. This lends credence to the use of highfidelity models (in place of reduced order models) for control and optimization of particulate processes.

A combined experimental and modeling approach to study the effects of high-shear wet granulation process parameters on granule characteristics

The purpose of the current work is to study the effects of high-shear wet granulation process parameters on granule characteristics using both experimental and modeling techniques. A full factorial design of experiments was conducted on three process parameters: water amount, impeller speed and wet massing time. Statistical analysis showed that the water amount has the largest impact on the granule characteristics, and that the effect of other process variables was more pronounced at higher water amount. At high water amounts, an increase in impeller speed and/or wet massing time showed a decrease in granule porosity and compactability. A strong correlation between granule porosity and compactability was observed. A three-dimensional population balance model which considers agglomeration and consolidation was employed to model the granulation process. The model was calibrated using the particle size distribution from an experimental batch to ensure a good match between the simulated and experimental particle size distribution. The particle size distribution of three other batches were predicted, each of which was manufactured under different process parameters (water amount, impeller speed and wet massing time). The model was able to capture and predict successfully the shifts in granule particle size distribution with changes in these process parameters.

Isolation, speciation, and antibiogram of clinically relevant non-diphtherial Corynebacteria (Diphtheroids)

PURPOSE

Coryneform or the non-diphtherial Corynebacterium species largely remains a neglected group with the traditional consideration of these organisms as contaminants. This concept, however, is slowly changing in the light of recent observations. This study has been done to find out the species distribution and antibiogram of various members of the clinically relevant Coryneform group, isolated from various clinical materials.

MATERIALS AND METHODS

One hundred and fourteen non-duplicate isolates of diphtheroids from various clinical isolates were selected for the study. The isolates were identified to the species level by using a battery of tests; and antimicrobial susceptibility was tested by using a combination of Clinical and Laboratory Standards Institute (CLSI) and the British Society for Antimicrobial Chemotherapy (BSAC) guidelines, in the absence of definitive CLSI guidelines.

RESULTS

Corynebacterium amycolatum was the predominant species (35.9%) in our series followed by the CDC Group G organisms (15.7%). Each of the remaining 19 species comprised of less than 10% of the isolates. More than half the total isolates were resistant to the penicillins, erythromycin, and clindamycin; while excellent activity (all the strains being susceptible) was shown by vancomycin, linezolid, and tigecycline. Chloramphenicol and tetracycline also had good activity in inhibiting more than 80% of the isolates. Multiply drug resistance was exhibited by all the species.

CONCLUSION

This study was an attempt to establish the clinical significance of coryneform organisms. The high level of resistance shown by this group to some of the common antibacterial agents highlights the importance of processing these isolates in select conditions to guide the clinicians towards an appropriate therapy.

Isolation of Legionella pneumophila from clinical & environmental sources in a tertiary care hospital

BACKGROUND & OBJECTIVES

Legionella pneumophila and other members of this genus are important respiratory pathogens but legionellosis often remains a neglected and under reported condition. Hence, this study was done to find out the presence of this organism in patients admitted to a tertiary care hospital with community-acquired pneumonia (CAP).

METHODS

A total of 470 lower respiratory tract samples and 24 water samples from hospital outlets were examined. Culture was done on buffered charcoal yeast extract agar with supplements and identification of the isolates was done by microscopy and biochemical tests.

RESULTS

L. pneumophila could be isolated from 12 (2.55%) patients suffering from community-acquired lower respiratory tract infection, unassociated with other aetiological agents of bacterial pneumonia. Of the 24 water samples tested, 8 (33.3%) grew the same organism.

INTERPRETATION & CONCLUSION

Our study has shown that Legionella is present in the hospital environment and was the aetiological agent of lower respiratory tract infection in 2.55 per cent of patients. A larger study and reports from other parts of the country may help in determining the true significance of legionellosis in India.