OCTANE (Ontario-wide Cancer Targeted Nucleic Acid Evaluation): a platform for intraprovincial, national, and international clinical data-sharing

Cancer is a genetic disease resulting from germline or somatic genetic aberrations. Rapid progress in the field of genomics in recent years is allowing for increased characterization and understanding of the various forms of the disease. The Ontario-wide Cancer Targeted Nucleic Acid Evaluation (octane) clinical trial, open at cancer centres across Ontario, aims to increase access to genomic sequencing of tumours and to facilitate the collection of clinical data related to enrolled patients and their clinical outcomes. The study is designed to assess the clinical utility of next-generation sequencing (ngs) in cancer patient care, including enhancement of treatment options available to patients. A core aim of the study is to encourage collaboration between cancer hospitals within Ontario while also increasing international collaboration in terms of sharing the newly generated data. The single-payer provincial health care system in Ontario provides a unique opportunity to develop a province-wide registry of ngs testing and a repository of genomically characterized, clinically annotated samples. It also provides an important opportunity to use province-wide real-world data to evaluate outcomes and the cost of ngs for patients with advanced cancer. The octane study is attempting to translate knowledge to help deliver precision oncology in a Canadian environment. In this article, we discuss the background to the study and its implementation, current status, and future directions.

SU-E-T-260: Radiation Exposure Estimation for 131Cs Prostate Implant Patient Release Determination

PURPOSE

Due to the short half-life and high energy of Cesium-131 (131Cs), the exposure rate outside the patient could potentially increase radiation exposure to hospital staff and exceed the maximum patient release exposure rate limit. A calculation technique has been developed to estimate the exposure rate at 1 meter from the patient, for prostate patients receiving 131Cs implants.

METHODS

In our calculation for each patient, all 131Cs sources were treated as one single source, and the point on the prostate with the shortest distance to skin surface was selected as the effective source position. Attenuation inside the patient was calculated based on the attenuation coefficient of 30 keV photons in water, assuming homogeneous patient density. This calculation technique was evaluated on our first 25 131Cs implant patients. For comparison, the exposure rate at approximately 1 meter inferior to patient perineum was measured prior to patient release using the Inovision 451P-RYR survey meter.

RESULTS

The distance from the edge of the prostate to skin surface along the inferior direction was the shortest in all 25 patients. The mean of the calculated exposure rates at 1 meter from skin surface was 0.53 mR/hr, 0.53 mR/hr, 0.04 mR/hr, 0.04 mR/hr and 1.5 mR/hr along the anterior, posterior, left, right and inferior directions, respectively. The mean of the measured exposure rate at 1 meter inferior to patient perineum was 1.1 mR/hr. The mean ratio of the measured versus calculated exposure rate was 0.74 (standard deviation = 0.23).

CONCLUSIONS

Our calculation technique is useful in determining in advance whether a patient may require hospitalization after his implant. The exposure rate at 1 meter inferior to patient perineum is a good indicator for determining whether the exposure rate along any direction might exceed the maximum allowed patient release exposure rate of 6 mR/hr.

Prostate cancer–specific mortality after definitive radiation therapy: Who dies of disease?

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Background: A competing risks analysis was undertaken to identify patient subgroups at greatest risk of dying from prostate cancer (CAP) after treatment with definitive external beam radiation therapy (RT) +/− androgen deprivation therapy (ADT) in the PSA era, and to determine which factors predict for survival from disease.

Methods: A total of 2,675 men with localized CAP treated with RT +/− ADT at M. D. Anderson Cancer Center from 1987-2007 were evaluated. Prostate cancer-specific mortality (PCSM) and other cause mortality rates were calculated after stratifying patients according to NCCN risk group, RT dose, use of ADT, and age at treatment. In total, 21% had low-risk, 40% had intermediate-risk, and 39% had high-risk disease. Multivariate analysis (MVA) was performed using Cox regression modeling.

Results: Median age was 68.5 years and median follow-up was 6.4 years. For patients with low-risk disease, only 0.2% died of CAP 10 years after treatment. None of the low-risk patients <70 years old who received ≥72 Gy died of CAP. The majority of deaths in the intermediate-risk group were also due to other causes; men ≥70 years old who received <72 Gy had the highest 10-year PCSM (5%). High-risk patients <70 years old who received <72 Gy without ADT had similar 10-year rates of CAP (15.2%) and non-CAP (18.5%) mortality. Men with high-risk disease <70 years old treated with higher doses >72 Gy were twice as likely to die from non-CAP causes (15.9%) than die from CAP (8.6%). In older men ≥70 years old with high risk disease, dose-escalation with ADT reduced 10-year PCSM from 14% to 4%, and most deaths were due to other causes (41% and 20%). On MVA, dose (p=0.002), ADT (p=0.007), PSA (p<0.0001) and Gleason score (p<0.0001) were predictive of PCSM in the high-risk group.

Conclusions: Men with low- and intermediate-risk CAP treated with definitive RT are unlikely to die of disease. PCSM is higher in men with high-risk disease but can be reduced with dose escalation and ADT, although patients are still twice as likely to die of other causes.

No significant financial relationships to disclose.

Breast Cancer Risk Asssessment in the High Risk Marin County Population Using OncoVue® Compared to SNPs from Genome Wide Association Studies

Background: Models for accurate assessment of individualized risk of developing breast cancer are important for effectively guiding clinical decisions regarding early detection and prevention. Marin County (MC), California (located immediately north of San Francisco) has long been recognized as a population with high incidence rates of breast cancer. In a population-based case-control study conducted from 1997 to 1999 in MC, no classical epidemiological risk factors such as age at menarche, age at first live birth, number of first-degree relatives with breast cancer, and history/outcome of previous breast biopsies were associated with breast cancer risk. Thus, the widely used National Cancer Institute-Breast Cancer Risk Assessment Tool (BCRAT) or Gail Model is not an effective risk assessment tool for this population. Recently, we found that a new breast cancer risk assessment model (OncoVue) that integrates information from 22 single nucleotide polymorphisms (SNPs) and 5 personal risk factors effectively stratified risk in the MC population. Several genome wide association studies (GWAS) have also recently derived a consensus of seven independent candidate SNPs strongly associated with breast cancer risk that are not included in the OncoVue model. Here we have evaluated these SNPs from GWAS to determine their utility in risk estimation and stratification of the high risk MC population.Materials and Methods: Study DNAs were genotyped for the following SNPs in seven genes: rs2981582 (FGFR2), rs3817198 (LSP1), rs889312 (MAP3K), rs4415084 (MRPS30), rs13281615 (POU5F1P1), rs13387042 (TNP1), and rs3803662 (TOX3, formerly TNRCR9). The analyses were performed on white women ages 30-69 and included 164 cases and 173 controls that were genotyped for all seven SNPs. Association of individual genotypes with breast cancer risk was evaluated by calculating odds ratios (ORs). Composite risk for each individual in the study was calculated by assigning risks from published studies for each genotype and multiplying them. The clinical utility of composite risk scores was evaluated by calculating positive likelihood ratios (PLR) as the proportion of patients with breast cancer with an elevated risk estimate divided by the proportion of disease-free individuals with an elevated risk estimate.Results: Carriers of the rare allele for FGFR2, MAP3K, and TNP1 exhibited statistically significant associations with breast cancer risk. Over a range of risk levels, composite risk scores exhibited PLRs of approximately 1.0 but at the highest end of the risk spectrum a PLR of 2.3 indicates useful risk stratification. The women at this risk level represent &lt;10% of the control population.Conclusions: In the high risk MC population the seven GWAS SNPs stratify risk at the highest end of the risk. In contrast, overall OncoVue exhibits higher PLRs at high risk levels and may prove to be more clinically useful for directing prevention and screening decisions.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3057.

Breast Cancer Risk Estimation Using the OncoVue® Model Compared to Combined GWAS Single Nucleotide Polymorphisms

Background: We have developed a new breast cancer risk assessment model (OncoVue) that integrates information from 22 single nucleotide polymorphisms (SNPs) and 5 personal risk factors. It has been shown to effectively stratify risk in three independent validation populations. Genome wide association studies (GWAS) have identified seven candidate SNPs independently associated with breast cancer risk. Using estimates of relative risks and allele frequencies derived from these studies, a theoretical examination of these SNPs has concluded that they have the potential to modestly improve clinical risk estimation. We have examined both the OncoVue model and these GWAS SNPs in the same case-control population to determine their utility in risk estimation.Materials and Methods: A randomly selected subset of participants (376 cases and 982 controls) that had enrolled in a larger case-control study conducted in six distinct geographic regions of the United States were examined. DNAs were genotyped for the 22 SNP variants in OncoVue and combined with personal factors to calculate the risk scores for the individual participants. DNAs were also genotyped for the following GWAS SNPs: rs2981582 (FGFR2), rs3817198 (LSP1), rs889312 (MAP3K), rs4415084 (MRPS30), rs13281615 (POU5F1P1), rs13387042 (TNP1), and rs3803662 (TOX3, formerly TNRCR9). Association of individual GWAS SNP genotypes with breast cancer risk was evaluated by calculating odds ratios (ORs). Assuming independent contribution of each SNP to risk, a combined GWAS risk score was calculated using a multiplicative model. Positive likelihood ratios (PLRs) were calculated using a risk threshold of 1.5-fold the control population mean risk to evaluate the proportion of individuals placed at elevated risk by OncoVue compared to the combined GWAS risk scores.Results: OncoVue exhibited significant ability to stratify risk at the 1.5-fold mean with a PLR of 2.2 and at a risk level of 2.5-fold mean the PLR increased to 5.0. In analyses of individual GWAS SNPs, statistically significant associations with breast cancer were identified for homozygous carriers of the rare allele for the FGFR2, MAP3K and TOX3 genes. However, the PLR for the combined GWAS risk scores at 1.5-fold mean was 1.0 indicating no ability to discriminate risk in this study population.Conclusions: In this case-control population OncoVue effectively stratified risk by accurately assigning elevated risk to breast cancer cases. In the same population, a combined risk score produced from seven GWAS SNPs did not effectively stratify risk. These results indicate that the OncoVue model has clinical utility for identifying elevated risk women who might benefit from additional screening and prevention.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3177.

Transcriptome-wide mutation discovery in patients in a phase II clinical trial of first-line erlotinib for clinically selected patients with advanced non-small cell lung cancer

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Background: The purpose of this study was to clinically select a population of patients (pts) likely to benefit from erlotinib and to perform extensive genetic profiling of fresh tissue tumour to identify predictive biomarkers. Methods: Treatment was erlotinib 150 mg p.o. daily until disease progression. Eligibility criteria included: stage IIIB/IV NSCLC; no prior chemo; ECOG ≤2; at least 2 of the following 4 criteria: women, never-smokers, Southeast Asian origin, adenocarcinoma and/or BAC. All pts had baseline serum samples and a fresh frozen tumour biopsy. EGFR and KRAS were sequenced using traditional methods to identify known mutations of erlotinib. Transcribed coding regions of all other expressed genes were sequenced to uncover novel mutations and other genetic features. Results: From Sept-06 to Oct-08, 65 pts have been enrolled. Of these 60 have completed at least 8 wks of erlotinib (or progressed before 8 wks). 49F and 11M; 45 never smokers. PS 0/1/2: 10/39/11. 18 Caucasian and 42 Asian. Pathology: 44 ACA; 3 BAC;1 squamous carcinoma; 13 NSCLC NOS. Responses: PR - 21 (35%); SD - 24 (DCR 75%); PD - 10; NE - 5. 85% did not progress at 8 weeks. 19 of 51 (37%) pre-treatment samples had an EGFR mutation. 10 of the 28 pts with response data (24pts still on drug) had a PR and 7 of these had either an LREA deletion or L858R point mutation. 1 of 3 post-treatment samples developed a T790M mutation on erlotinib. 3 of 51 pts have KRAS mutations. Analysis of over 21 Giga basepairs of aligned transcriptome sequencing data from 20 tumour samples has uncovered 1089 putative non-conservative gene mutations of which 15 are seen in multiple tumours: TUBA1C, EPS8L1, ARID4B, RPL22, C20orf52, CCT8, HLA-DRB5, TRIP6, and PLP2 in 4 tumours, C20orf52 and CTSL1 in 5 tumours, and SERF2, TMEM173, and an uncharacterized gene in 6 tumours. Conclusions: Clinical selection of pts enriches the EGFR mutation positive and KRAS mutation negative population and leads to high rates of non-progression. Full tumour RNA analysis identified several recurrent mutations that may describe mechanisms of erlotinib response and resistance. The discovery of novel mutations in multiple pts suggests patterns that may shed light on lung cancer specific behaviour.

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Previously documented mutations in the epidermal growth factor receptor (EGFR) gene in a non-small cell lung cancer (NSCLC) population treated with gefitinib are not associated with response

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Background: Mutations in the tyrosine kinase domain of EGFR that may correlate with clinical features and response of NSCLC to EGFR tyrosine kinase inhibitors have been described. But, varying methodologies have contributed to an uncertain relationship between EGFR mutational status and response. This study sought to characterize EGFR mutations in microdissected tumour tissue from pts with advanced NSCLC treated with gefitinib and correlate their clinical data. Methods: Biopsy material from pts treated with gefitinib for advanced NSCLC at the British Columbia Cancer Agency was analyzed. Malignant cells (cytology specimens) or tissue (paraffin embedded biopsies) was reviewed and tumour cells isolated by laser- capture microdissection or manual scrape. Genomic DNA was extracted and exons coding for the EGFR tyrosine kinase domain (18 - 24) were amplified by PCR and sequenced. When insufficient, the priority was 18, 19, 21, followed by 20, 23, 22, and 24. EGFR mutational analyses were correlated with response to gefitinib and clinical features. Results: 61 pts were identified, 14 (23%) radiological responders (CR, PR): 10 Asian, 10 female, 8 non-smokers, 8 adenocarcinoma, 2 BAC. Of 51 tumour samples available, 39 had adequate tissue for sequencing analysis. EGFR copy number by FISH is pending. Laser-capture microdissection allowed for high quality DNA to be extracted almost exclusively from tumour. Exons 18, 19, 20, 21, 22, 23 and 24 have been sequenced in 37, 34, 30, 33, 12, 10, and 13 patients, respectively. 4 mutations were identified: 2 in 2 non-smoking Asian pts (exon 19; deletion or substitution of L747-T751) and 2 in Caucasians (exon 20 point mutation resulting in a L798F substitution). None of these pts had a response to gefitinib. Conclusions: As with other series, most responders were female, non-smokers of Asian origin. Our results support the relationship between Asian ethnicity and EGFR mutations but question the role of EGFR mutational status in predicting response. Prospective studies will need to focus the detection of additional genetic features using accurate and reproducible techniques before recommendations for selecting populations to be treated can be made.

No significant financial relationships to disclose.

A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers

A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resistance and defence gene analogs (Rgenes-RFLP) previously mapped in cacao. A genomic library enriched for (GA)(n) and (CA)(n) was constructed, and 201 new microsatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Amazon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identification and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.

Facilitated loading of horizontal gels using a capillary comb loader

Manual loading of samples into horizontal gels, such as the agarose gels commonly used for DNA fragment sizing and quantification, is laborious and prone to errors. Manual-loading times for highthroughput gels can reach 10 min/gel, and human error can result in incorrect identification of samples because of reverse loading or other errors in the loading process. To reduce gel-loading times and to improve reliability, a novel comb has been developed that uses glass capillaries and hydrostatic pressure to simplify sample loading from microplates. Accurate sample metering is ensured by the uniform length and volume of the capillaries. The loaded comb is placed in the gel boat over a pre-cast agarose gel, and buffer is added to a reservoir at the top of the comb. Once the buffer rises over the ends of the capillaries, the samples are pushed into the wells by hydrostatic pressure. This technique was successfully demonstrated for a 24-lane comb. This capillary comb loader reduces loading time, maintains well-to-well uniformity, and retains the same geometry and appearance of manually loaded bands, making this loading method compatible with existing downstream processes and software for subsequent analysis of the gel image.

Dietary restriction attenuates age-related increases in rat skeletal muscle antioxidant enzyme activities

Dietary restriction (DR) retards aging in rodents, but its mechanism of action remains unclear. Free radicals have been hypothesized to be involved in aging and in DR's actions. We investigated the influences of age and DR on the antioxidant enzymes catalase (CAT), glutathione peroxidase (GPX), and superoxide dismutase (SOD) in skeletal muscle from 11-, 26- and 34-mo-old (BN x Fischer 344) F1 rats fed either ad libitum (AL) or subjected to a 30% DR from 14 weeks of age. The mass of the upper hindlimb muscles recoverable in 34-mo-old AL rats was only 52% that of 11-mo-old AL rats, whereas rats on DR showed a stable, intermediate value at both ages. CAT and GPX activities increased progressively and markedly in muscle of AL animals with aging. The increase in CAT activity was partially attenuated by DR, while that of GPX was entirely prevented. These effects of aging and DR were more profound in 12,000 x g pellets than in cytosolic fractions. SOD activities were more variable and not clearly influenced by age or DR. These data agree with prior reports of an age-related increase in skeletal muscle antioxidant enzyme activities. Further, DR attenuates this alteration and does so most profoundly in the 12,000 x g pellet, the fraction which is enriched in mitochondria.