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Introduction A high tumor mutational burden (TMB) (≥10 mut/Mb) has been associated with improved clinical benefit in non-small cell lung cancer (NSCLC) treated with immune checkpoint inhibitors (ICI) and is a tumor agnostic indication for pembrolizumab across tumor types. We explored whether combining TMB with programmed cell death ligand 1 (PD-L1) and pretreatment neutrophil-lymphocyte ratio (NLR) was associated with improved outcomes in ICI-treated NSCLC. Methods We retrospectively analyzed patients treated with ICI with Foundation One genomic testing, including TMB. Optimal cutoff for prediction of response by TMB was determined by receiver operating characteristic analysis, and area under the curve (AUC) was calculated for all 3 biomarkers and combinations. Cox model was used to assess prognostic factors of overall survival (OS) and time to progression (TTP). Survival cutoffs calculated with Kaplan-Meier survival curves were TMB ≥10 mut/Mb, PD-L1 ≥50%, NLR Results Data from 88 patients treated were analyzed. The optimal TMB cutoff was 9.24 mut/Mb (AUC, 0.62), improving to 0.74 combining all 3 biomarkers. Adjusted Cox model showed that TMB ≥10 mut/Mb was an independent factor of OS (hazard ratio [HR], 0.31; 95% confidence interval; 0.14-0.69; P = .004) and TTP (HR, 0.46; 95% CI, 0.27-0.77; P = .003). The combination of high TMB with positive PD-L1 and low NLR was significantly associated with OS (P = .038) but not TTP. Conclusions TMB has modest predictive and prognostic power for clinical outcomes after ICI treatment. The combination of TMB, PD-L1, and NLR status improves this power.

PURPOSE Comprehensive genomic profiling to inform targeted therapy selection is a central part of oncology care. However, the volume and complexity of alterations uncovered through genomic profiling make it difficult for oncologists to choose the most appropriate therapy for their patients. Here, we present a solution to this problem, The Molecular Registry of Tumors (MRT) and our Molecular Tumor Board (MTB). PATIENTS AND METHODS MRT is an internally developed system that aggregates and normalizes genomic profiling results from multiple sources. MRT serves as the foundation for our MTB, a team that reviews genomic results for all Duke University Health System cancer patients, provides notifications for targeted therapies, matches patients to biomarker-driven trials, and monitors the molecular landscape of tumors at our institution. RESULTS Among 215 patients reviewed by our MTB over a 6-month period, we identified 176 alterations associated with therapeutic sensitivity, 15 resistance alterations, and 51 alterations with potential germline implications. Of reviewed patients, 17% were subsequently treated with a targeted therapy. For 12 molecular therapies approved during the course of this work, we identified between two and 71 patients who could qualify for treatment based on retrospective MRT data. An analysis of 14 biomarker-driven clinical trials found that MRT successfully identified 42% of patients who ultimately enrolled. Finally, an analysis of 4,130 comprehensive genomic profiles from 3,771 patients revealed that the frequency of clinically significant therapeutic alterations varied from approximately 20% to 70% depending on the tumor type and sequencing test used. CONCLUSION With robust informatics tools, such as MRT, and the right MTB structure, a precision cancer medicine program can be developed, which provides great benefit to providers and patients with cancer.

Cancer transmission from a donor organ to a transplant recipient is a rare but not infrequently fatal event. We report a case of lung cancer transmission from a deceased donor to 2 kidney recipients. Approximately 1 year after uneventful kidney transplantation, both recipients developed acute kidney failure. Computed tomography imaging of abdomen and pelvis for both recipients showed masses in the transplanted kidneys along with innumerable masses in the livers. Pathologic examinations for both cases demonstrated high-grade neuroendocrine carcinoma with "mirror image" histologic findings in the transplant kidneys with liver metastases. Short tandem repeat (STR) analyses were performed to determine the origin of the tumors. STRs of both tumors were nearly identical to that of the donor, proving that both tumors were from the same donor. Immunohistochemical analyses showed that both tumors were positive for thyroid transcription factor 1, supporting a lung primary. One recipient died as a direct sequela to metastatic tumor, and the other required transplant nephrectomy and chemotherapy. Awareness of this largely nonpreventable complication and prompt molecular testing if cancer transmission is suspected are important.

Recent advances in next-generation sequencing have allowed for an increase in molecular tumor profiling. We sought to assess the actionability and clinical utilization of molecular tumor profiling results obtained via Foundation Medicine tumor sequencing tests in uterine and ovarian cancers. We performed a single-institution retrospective chart review to obtain demographic and clinical information in patients with uterine and ovarian cancer whose tumors were submitted to Foundation Medicine for molecular tumor profiling over a 7-year period. Alterations identified on testing were stratified according to the OncoKB database actionability algorithm. Descriptive statistics were primarily used to analyze the data. Tumors from 185 women with gynecologic cancer were submitted for molecular tumor profiling between 2013 and 2019. The majority of tests (144/185; 78%) were ordered after a diagnosis of recurrence. In 60 (32%), no actionable molecular alteration was identified. Thirteen (7%) identified an alteration that directed to a US Food and Drug Administration-approved therapy in that tumor type, while 112 (61%) had alterations with investigational or hypothetical treatment implications. In patients with any actionable finding, treatment was initiated in 27 (15%) based on these results. The majority of uterine and ovarian cancers (93%) did not have molecular alterations with corresponding Food and Drug Administration-approved treatments. Even in patients with a potentially actionable alteration, gynecologic oncologists were more likely to choose an alternative therapy. Further investigation is warranted to determine which patients with uterine and ovarian cancer are most likely to benefit from molecular tumor profiling and the ideal timing of testing. The potential to identify effective therapeutic options in a minority of patients needs to be balanced with the current limited clinical applicability of these results in most cases.

We implemented universal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing of patients undergoing surgical procedures as a means to conserve personal protective equipment (PPE). The rate of asymptomatic coronavirus disease 2019 (COVID-19) was

Background: Data describing therapeutic outcomes in patients with non-small cell lung cancers (NSCLC) with BRAF mutations remains limited. Methods: We conducted a retrospective cohort study of 31 patients with metastatic NSCLC treated at Duke University Hospital who had been identified by next-generation sequencing methods to bear a BRAF mutation in their tumor in order to evaluate clinical response to immunotherapy and chemotherapy. Results: Sixty-five percent of patients identified in this cohort were current or former smokers. Fourteen (45.2%) of patients had a BRAF V600E mutation and 17 (54.8%) had a non-V600E mutation. Median progression-free survival (PFS) in the 23 patients who received first-line chemotherapy was 6.4 months [95% confidence interval (CI), 2.3 to 13.0]. Overall survival (OS) in patients who received first-line chemotherapy showed a median survival of 18 months (95% CI, 7.4 to 28.6). OS comparing patients who had never received immunotherapy at any point was 18.4 months (95% CI, 4.1 to NE) compared to 19.0 months (95% CI, 9.9 to 28.6) in those who had received immunotherapy. We did not find a statistically significant difference in OS in patients with BRAF V600E, BRAF amplification, or non-V600E mutations. There was also no difference in OS in patients treated with targeted BRAF inhibitors compared to those who were not treated with targeted BRAF inhibitors. Conclusions: We describe therapeutic outcomes for patients with metastatic NSCLC with BRAF mutations treated with either cytotoxic chemotherapy or immunotherapy. Although the sample size is small, the survival curves do not suggest improved clinical activity in this population when treated with immunotherapy.

On university campuses and in similar congregate environments, surveillance testing of asymptomatic persons is a critical strategy (1,2) for preventing transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). All students at Duke University, a private research university in Durham, North Carolina, signed the Duke Compact (3), agreeing to observe mandatory masking, social distancing, and participation in entry and surveillance testing. The university implemented a five-to-one pooled testing program for SARS-CoV-2 using a quantitative, in-house, laboratory-developed, real-time reverse transcription-polymerase chain reaction (RT-PCR) test (4,5). Pooling of specimens to enable large-scale testing while minimizing use of reagents was pioneered during the human immunodeficiency virus pandemic (6). A similar methodology was adapted for Duke University's asymptomatic testing program. The baseline SARS-CoV-2 testing plan was to distribute tests geospatially and temporally across on- and off-campus student populations. By September 20, 2020, asymptomatic testing was scaled up to testing targets, which include testing for residential undergraduates twice weekly, off-campus undergraduates one to two times per week, and graduate students approximately once weekly. In addition, in response to newly identified positive test results, testing was focused in locations or within cohorts where data suggested an increased risk for transmission. Scale-up over 4 weeks entailed redeploying staff members to prepare 15 campus testing sites for specimen collection, developing information management tools, and repurposing laboratory automation to establish an asymptomatic surveillance system. During August 2-October 11, 68,913 specimens from 10,265 graduate and undergraduate students were tested. Eighty-four specimens were positive for SARS-CoV-2, and 51% were among persons with no symptoms. Testing as a result of contact tracing identified 27.4% of infections. A combination of risk-reduction strategies and frequent surveillance testing likely contributed to a prolonged period of low transmission on campus. These findings highlight the importance of combined testing and contact tracing strategies beyond symptomatic testing, in association with other preventive measures. Pooled testing balances resource availability with supply-chain disruptions, high throughput with high sensitivity, and rapid turnaround with an acceptable workload.

Background The ThyroSeq mutational panel and Afirma gene expression classifier (GEC) are used to risk stratify cytologically indeterminate thyroid nodules. In the current study, the authors evaluated the performance of these tests within the context of ultrasonographic features and with the incorporation of the noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) nomenclature. Methods The authors reviewed nodules using ThyroSeq or Afirma GEC testing. For nodules that were surgically resected, both tests were studied within the context of ultrasound findings, comparing performance stratified by the 2015 American Thyroid Association guideline (ATA 2015) sonographic patterns and assessing the positive predictive value (PPV) of these tests both including and excluding NIFTP in the malignant category. Results A total of 304 cases were identified, 119 of which were resected. All cases that met the criteria for NIFTP on excision demonstrated either high-risk mutations on ThyroSeq or a "suspicious" result on Afirma GEC. When NIFTP cases were shifted from the malignant to nonmalignant category, the PPV of "positive" tests for both ThyroSeq and Afirma GEC decreased from 42.9% to 14.3% (an absolute decrease of 28.6%) and 30.1% to 25.3% (an absolute decrease of 4.8%), respectively. No cases of malignancy were found in the ATA 2015 "very low suspicion" group, even with a "suspicious" Afirma GEC result. Conclusions Both the ThyroSeq and Afirma GEC tests demonstrated decreases in the PPV when NIFTP was considered nonmalignant. In the era of NIFTP, a "positive" test result for either the Afirma GEC or ThyroSeq should be interpreted in light of clinical factors and should not exclude conservative (ie, lobectomy) surgical management. ATA 2015 "very low suspicion" nodules, even with "suspicious" Afirma GEC results, were not found to demonstrate malignancy in this series. Cancer Cytopathol 2018. © 2018 American Cancer Society.

Widespread clinical laboratory implementation of next-generation sequencing–based cancer testing has highlighted the importance and potential benefits of standardizing the interpretation and reporting of molecular results among laboratories. A multidisciplinary working group tasked to assess the current status of next-generation sequencing–based cancer testing and establish standardized consensus classification, annotation, interpretation, and reporting conventions for somatic sequence variants was convened by the Association for Molecular Pathology with liaison representation from the American College of Medical Genetics and Genomics, American Society of Clinical Oncology, and College of American Pathologists. On the basis of the results of professional surveys, literature review, and the Working Group's subject matter expert consensus, a four-tiered system to categorize somatic sequence variations based on their clinical significances is proposed: tier I, variants with strong clinical significance; tier II, variants with potential clinical significance; tier III, variants of unknown clinical significance; and tier IV, variants deemed benign or likely benign. Cancer genomics is a rapidly evolving field; therefore, the clinical significance of any variant in therapy, diagnosis, or prognosis should be reevaluated on an ongoing basis. Reporting of genomic variants should follow standard nomenclature, with testing method and limitations clearly described. Clinical recommendations should be concise and correlate with histological and clinical findings.

BACKGROUND Molecular testing provides an important ancillary study for thyroid nodules with indeterminate cytology. The nomenclature shift to “noninvasive follicular thyroid neoplasm with papillary-like nuclear features” (NIFTP) will impact the performance of molecular tests. For the current study, the authors reviewed the performance of the Afirma gene-expression classifier (GEC) and the University of Pittsburgh Medical Center (UPMC) targeted mutation panel tests in thyroid nodules that were subsequently diagnosed as NIFTP on surgical resection. METHODS In total, 302 nodules were sent for molecular testing between June 2012 and June 2016. These cases were retrospectively reviewed to identify patients who underwent subsequent surgical resection and were diagnosed with follicular variant of papillary thyroid carcinoma (FVPTC). Twenty-five nodules that were diagnosed as FVPTC met the initial inclusion criteria. These cases were reviewed using strict criteria to identify NIFTP. RESULTS Eight cases met criteria for NIFTP, and 4 NIFTPs underwent Afirma testing. Cytology diagnoses were all Bethesda category III, with 3 diagnosed as atypia of undetermined significance (AUS) and 1 diagnosed as follicular lesion of undetermined significance (FLUS). All of these nodules were identified as “suspicious” using GEC. Four NIFTPs underwent testing at UPMC, all using ThyroSeq V2. The cytology diagnoses for these nodules also were category III, with the exception of 1 nodule that was category IV, suspicious for follicular neoplasm. All NIFTPs were positive for mutations, all of which were RAS mutations (NRAS, KRAS). One patient who had a nodule classified as NIFTP had metastatic carcinoma identified in a lymph node. Another who had a 6-cm tumor had coexisting NRAS and TERT mutations. CONCLUSIONS The current results indicate that NIFTP is a rare tumor if defined by strict criteria, that both the GEC and UPMC methods indicate abnormalities in NIFTP, and further independent study will be needed to better characterize the molecular and clinical characteristics of NIFTP. Cancer (Cancer Cytopathol) 2016. © 2016 American Cancer Society.

This diagnostic study describes an online tool created with actual severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus copy number data to help policy makers understand how pooled testing compares with single-sample testing in different populations.

1516 Background: The proportion of germline versus somatic mutations identified on genomic tumor testing of solid malignancies is not well characterized. We compared somatic and germline testing results in patients with breast, ovarian, pancreatic or prostate cancer with a genomic alteration identified on tumor testing. Methods: Retrospective chart review was performed using a tertiary care academic center’s database of somatic tumor testing results obtained via FoundationOne and Guardant testing. Patients with breast, ovarian, pancreatic or prostate cancer who had a genomic alteration identified on tumor testing, including pathogenic and VUS variants, in BRCA1or BRCA2, CHEK2, ATM, BRIP1, RAD51C, RAD51D, PALB2and CDH1and who had also received germline testing were identified. Analysis was performed to assess prevalence of germline results. The association between mutant allele fraction (MAF) and germline mutation status was also assessed. Results: Results: 124 patients with breast, ovarian, pancreatic or prostate cancer were identified who had a genomic alteration of interest also tested for via germline testing. 54 (32.5%) of tumor mutations were also identified on germline testing. Proportion of genomic results that were germline was wide, ranging from 0-85.7% depending on the gene and variant classification (Table). Germline mutations were present in 36.4% of breast, 25% of ovarian, 53.3% of pancreatic, and 20.9% of prostate cancer patients who had a tumor alteration present. Alterations that were found to be concordant in both somatic and germline testing had an average MAF of 0.54, and alterations identified on somatic testing only had an average MAF of 0.30. Conclusions: Our findings suggest that approximately one-third of genomic alterations on tumor testing will be of germline origin. However, concordance rates may be gene and variant dependent. Higher MAF may be associated with germline alteration status, but further evaluation is needed. Thus, while information provided by genomic tumor testing may be suggestive of a correlating germline mutation, no single alteration type or MAF value is reliably predictive. [Table: see text]

80 Background: TMB is a promising predictive biomarker for ICB, but recent studies have shown that TMB varies substantially between tumor types. We examined the association between TMB and clinical response to ICB in metastatic urothelial carcinoma (mUC), renal cell carcinoma (mRCC), and non-small cell lung cancer (mNSCLC). Methods: We conducted a single center retrospective study inclusive of 1444 consecutive patients (pts) initiating ICB prior to 1/2019, cross-referenced with pts with Foundation One testing with TMB (mut/Mb), resulting in 17 mUC, 10 mRCC, and 60 mNSCLC. PD-L1 status was determined by the Dako 22C3 antibody. Pts were divided into clinical responders (R) and non-responders (NR) based on clinical assessment per their oncologist. The primary outcome of the study was to describe the relationship between TMB and clinical benefit, including duration of clinical response and overall survival (OS). A t-test was performed between R groups. Kaplan Meier (KM) curves and Cox-Mantel log rank tests were performed for PFS/OS comparing high TMB (≥ median) to low TMB pts. Results: For mUC, 8/17 (47%) were R with median TMB 7.74 (Interquartile range or IQR 6.04-9.78) compared to 9 NR, median TMB 7.57 (IQR 3.78-11.41) [p = 0.36]. For mRCC, 4/10 (40%) were R with median TMB 1.75 (IQR 1.75-1.97), versus 6 NR with median TMB 5.79 (IQR 3.07-7.48) [p = 0.02]. For mNSCLC, 30/60 (50%) were R with median TMB 11.38 (IQR 9.65-16.24), significantly higher than 30 NR with median TMB 9.46 (IQR 7.65-13.87) [p = 0.05]. For mNSCLC, no difference in PD-L1 positivity was found between R (17/30, 56%) and NR (16/30, 53%), and concurrent chemotherapy with ICB was the same in both R (10/30 (33%)) and NR (10/30 (33%)). KM analysis showed equivocal results for duration of clinical response and OS between high TMB vs low TMB in the three solid tumors, except OS in mUC which favored high TMB (p = 0.03) [cutoff TMB: mUC 7.57, mRCC 2.63, mNSCLC 11.35]. Conclusions: Higher TMB was associated with a greater likelihood of clinical benefit to ICB in our cohort of NSCLC patients and mUC. This correlation was not detected among mRCC patients, although these data are limited by relatively small number of cases.

e14291 Background: Low-density lipoprotein receptor-related protein 1B (LRP1B) is a putative tumor suppressor gene spanning > 500 kb on chromosome 2. A melanoma study previously reported enrichment of LRP1B mutations in responders (34%) to immune checkpoint inhibitors (ICIs) compared with non-responders (3%). Deep deletions in LRP1B are frequently observed in non-small cell lung cancer (NSCLC, 12%), head and neck (11%), cervical (9%), bladder (8%), and prostate cancers (8%). This study examines the clinical response to ICIs in a diverse group of tumor types with LRP1B alterations. Methods: We conducted a single center retrospective study inclusive of all patients (pts) with tumors containing any LRP1B variant who were treated with an ICI between 01/2015 and 11/2018. The primary outcome of the study was to describe the clinical outcomes of patients with LRP1B alterations, with respect to radiographic response to therapy, time on therapy, duration of response, and overall survival. Results: 44 pts with an LRP1B variant were treated with an ICI at Duke between 01/2015 and 11/2018. The most common ICIs were pembrolizumab (29/44, 66%) and nivolumab (12/44, 27%). Tumor types included NSCLC (24/44, 55%), renal cell carcinoma (RCC, 5/44, 11%), and prostate cancer (5/44, 11%). 14 (32%) pts had pathogenic variants (PVs) and 30 pts (68%) had variants of uncertain significance (VUS). Among pts with LRP1b PVs, 36% (95%CI 14%-64%) had radiographic responses (5/14, 2 lung, 1 prostate, 1 RCC, 1 endometrial carcinoma), two of whom were MSI high. As a control, the radiographic response rate among patients with a LRP1b VUS was 10% (95%CI 3%-28%). Of those with PVs, 3 pts had stable disease, one of whom has been on CPI therapy for > 22 months and 5 (36%) remain on therapy, with 2 (14%) pts discontinued due to immune toxicities, and 7 (50%) pts discontinued due to disease progression. The median TMB among responders was 12 (2-150.05 mut/Mb) and the median TMB amongst non-responders was 9.5 (6-18 mut/Mb). Conclusions: In a tumor agnostic population of pts harboring LRP1B PVs, 36% of pts have responses to ICI. The majority of responders were MSS and TMB low, which may suggest that PV in LRP1B may independently predict for response to ICI. Prospective and multicenter validation is now needed.

Background: Numerous gene-expression signatures have been developed for breast cancer. However, assessments of their validity continue to largely ignore the impact of intratumor heterogeneity and technical variation on clinical utility. Here, the collection of replicate specimen in Barry et al (2010) is used to evaluate a broad collection of gene-expression signatures of prognosis and tumor biology. Methods: Eighteen patients with multiple frozen cores (one patient with quadruplicate, twelve with triplicate, and five with doublet samples) were previously identified in the Duke Breast SPORE tissue repository. Cores were assessed for percent invasive cancer cellularity, and tumor size, grade, and ER/PR status. RNA was extracted and hybridized to AffymetrixH133Plus2.0 microarrays. Expression signatures of prognosis and tumor biology were developed or translated to the Affymetrix platform using routines by Prat et al. (2012) and Haibe-Keins et al. (2012). Association between signatures, and precision among replicates are evaluated using Pearson and intraclass correlation. Coefficients are reported with 95% confidence intervals. Results: Among prognostic signatures, an imputed 70-gene signature of MammaPrint had the highest level of precision (ICC = 0.96, 0.91–0.98); strong concordance is seen with Affymetrix-based PAM50 risk-of-relapse (ICC = 0.82, 0.65–0.92); 16 of 18 patients had constant subtype calls. Substantially lower concordance was seen in the GENIUS prognostic model (ICC = 0.62, 0.35–0.82). In ER+ patients (n = 13), two algorithms to impute the 21-gene model of OncotypeDX recurrence score were concordant (r = 0.98, ICC= 0.90 and 0.83) and distinct from the GENIUS ER+ score (average r = 0.74, ICC=0.78). Imputed models for the Rotterdam 76-gene model (+ER status), GGI (+grade), and ROR-T (+tumor size) showed lower levels of correlation (0.47 Conclusions: The number of genomic signatures in breast cancer from archived specimen and cell-line experiments continues to grow, but there are limited resources for validating their prognostic/predictive value in patient populations. Reproducibility across biological replicates is a critical component in establishing clinical utility of a signature that is distinct from using technical replicates for the repeatability of analytes on the array platform. We demonstrate how archived specimen can confirm reproducibility in the ‘Test Validation Phase’ of biomarker development, as advocated by the Institute of Medicine, and inform trial designs to prospectively test clinical utility. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-09-01.

Background: Microarray assessment of breast cancer demonstrates disease subsets among the major breast cancer biologic categories (ER, PR, HER-2) with likely additional prognostic and treatment (predictive) implications. Additional prognostic and predictive biomarkers and optimization of existing genomic platforms are needed to improve personalized breast cancer care. Methods: 76 early-stage ER+ patients with adequate RNA from fresh frozen tumor specimens and a concurrent 21-gene OncotypeDX recurrence score (RS) were identified across independent Duke studies linked to routine prospective breast biospecimen collection. Expression estimates for Affymetrix H133 Plus 2.0 microarrays were reviewed for quality control (Owzar 2008) and normalized across 4 batches with ComBat. Correlations of genomic prognostic signatures to true RS were assessed using Spearman coefficients. Discovery of new gene-level and pathway-level associations to breast cancer prognosis and prediction, based on RS, were corrected for multiple comparisons using the Bonferonni for the family-wise error rate (FWER) or Benjamini-Hochberg methods for the false discovery rate (FDR). Results: A total of 73 samples passed Affymetrix quality control: 32 “low risk”, 32 “intermediate risk”, and 9 “high risk” using standard recurrence score thresholds of 30. Median patient age is 55 (range 35–86). Two published algorithms to impute the RS from the Affymetrix model by Fan and Haibe-Keins were highly concordant (94%) with each other and showed strong correlation to actual RS (rho = 0.62, p = 5e−9). However, when the RS thresholds were applied to the microarray-based scores, lower agreement was observed (misclassification rate of 57%). Strong correlation was also observed with other breast signatures and RS, including an imputed 70-gene signature of MammaPrint (rho = 0.59, p = 3e−8) and the 50-gene PAM50 risk-of-relapse score (rho = 0.54, p = 8e−7), while poor correlation was seen for the GENIUS prognostic model (rho = 0.06, p = 0.6). Discovery of gene-level associations to RS identified 28 genes, including known cancer-associated genes such as BRCA2 (FWER adj p = 0.002), Cyclin E1 (FWER adj p = 0.015), and CDCA5 (FWER adj p = 0.048). Pathway-level association in KEGG and GO Biologic Processes, identified 24 and 104 categories respectively, including Cell Cycle pathways KEGG:04110 (FDR adj p = 0.002) and GO:0000085 (FDR adj p = 0.0007). Among 22 in-vitro derived oncogenic pathway signatures, significant negative correlation is seen with p53 (rho = −0.56, adj p = 4e−6) and positive correlation with beta-catenin (rho = 0.38, adj p = 0.015). A multi-gene model of association to OncotypeDX RS classification is being developed using Prediction Analysis of Microarrays (PAM). Conclusions: Microarray-based prognostic breast cancer signatures are generally concordant. However, their application across platforms is currently sub-optimal. In the context of OncotypeDX RS, additional key cancer-associated genes and pathways are found to be associated with breast cancer prognosis, potentially providing insight into treatment opportunities for ER+ breast cancer. Validation efforts of these findings in an independent patient cohort are underway. Funding: NCI: RC2CA14041-01 and W81XWH-07-1-0394 Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-10-03.

Despite advances in contemporary chemotherapeutic strategies, long-term survival still remains elusive for patients with metastatic colorectal cancer. A better understanding of the molecular markers of drug sensitivity to match therapy with patient is needed to improve clinical outcomes. In this study, we used in vitro drug sensitivity data from the NCI-60 cell lines together with their Affymetrix microarray data to develop a gene expression signature to predict sensitivity to oxaliplatin. To validate our oxaliplatin sensitivity signature, patient-derived colorectal cancer explants (PDCCE) were developed in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice from resected human colorectal tumors. Analysis of gene expression profiles found similarities between the PDCCEs and their parental human tumors, suggesting their utility to study drug sensitivity in vivo. The oxaliplatin sensitivity signature was then validated in vivo with response data from 14 PDCCEs treated with oxaliplatin and was found to have an accuracy of 92.9% (sensitivity = 87.5%; specificity = 100%). Our findings suggest that PDCCEs can be a novel source to study drug sensitivity in colorectal cancer. Furthermore, genomic-based analysis has the potential to be incorporated into future strategies to optimize individual therapy for patients with metastatic colorectal cancer. Mol Cancer Ther; 11(7); 1500–9. ©2012 AACR.

Patients with chronic lymphocytic leukemia (CLL) with deletion or mutation of TP53 have exceedingly poor clinical outcomes. Cenersen, an oligonucleotide targeting TP53, has been shown to abrogate the activity of TP53 gain-of-function mutants and to increase sensitivity of lymphoma cells to cytotoxic chemotherapy in vitro. We combined cenersen with fludarabine, cyclophosphamide and rituximab (FCR) as treatment for patients with high-risk CLL. The purpose of this phase II study was to determine the overall response rate, response duration and toxicity of cenersen administered in combination with FCR. Twenty patients with relapsed or high-risk CLL were evaluated. Nineteen patients were previously treated. The complete response rate was 18%; the overall response rate was 53%. Median progression-free and overall survival was 5.3 and 10.6 months, respectively. The most common serious adverse events were neutropenia and thrombocytopenia. In this single arm phase II study, cenersen combined with FCR yielded clinical responses with acceptable toxicity in patients with high-risk CLL.

We report 10 cases of donor cell leukemia (DCL). All cases except the case of chronic lymphocytic leukemia had anemia, neutropenia, and/or thrombocytopenia when DCL was diagnosed. Eight cases with sex-mismatched hematopoietic stem cell transplant (HCT) showed donor gonosomal complements, suggesting DCL. Clonal cytogenetic abnormalities were detected in 8 cases: 6 were monosomy 7/del(7q). In all 10 cases, engraftment studies confirmed donor cell origin. Retrospective fluorescence in situ hybridization in archived donor cells in 4 cases showed a low level of abnormalities in 2. Of 7 patients with clinical follow-up of 5 months or more, 1 (with acute myeloid leukemia) died of disease; 6 are alive, including 1 with myelodysplastic syndrome with spontaneous remission. Similar to reported cases, we found disproportional sex-mismatched HCTs, suggesting probable underdetection of DCL in sex-matched HCTs. The latency between HCT and DCL ranged from 1 to 193 months (median, 24 months), in keeping with the literature. Analyzing our cases, pooled with reported cases, with survival models showed much shorter latency for malignancy as primary disease, for T-cell large granular lymphocyte leukemia as type of DCL, and for umbilical cord blood as stem cell source.

Donor cell neoplasms are rare complications of treatment regimens that involve stem cell transplantation for hematological malignancies, myelodysplastic processes, or certain genetic or metabolic disorders. We report a case of donor cell leukemia in a pediatric patient with a history of acute myeloid leukemia that manifested as recurrent AML FAB type M5 fourteen months after umbilical cord blood transplantation. Although there was some immunophenotypic drift from the patient's original AML and their posttransplant presentation, the initial pathological impression was of recurrent disease. Bone marrow engraftment analysis by multiplex PCR of short tandem repeat markers performed on the patient's diagnostic specimen showed complete engraftment by donor cells, with a loss of heterozygosity in the donor alleles on chromosome 7. This led to the reinterpretation of this patient's disease as donor-derived leukemia. This interpretation was supported by a routine karyotype and fluorescence in situ hybridization analysis showing loss of chromosome 7 and a male (donor) chromosome complement in this female patient. Also noted was a loss of the patient's presenting chromosomal abnormality, t(11;19)(q23;p13). This case highlights the need for close coordination between all aspects of clinical testing for the transplant patient, including molecular engraftment studies, when distinguishing the very common complication of recurrent disease from the exceedingly rare complication of donor cell leukemia.

e21222Background: Data describing therapeutic outcomes in patients with non-small-cell lung cancers (NSCLC) harboring BRAF alterations remains limited. Methods: A retrospective cohort study was con...

With the emergence of electronic medical records and patient portals, patients are increasingly able to access their health records, including laboratory reports. However, laboratory reports are usually written for clinicians rather than patients, who may not understand much of the information in the report. While several professional guidelines define the content of test reports, there are no guidelines to inform the development of a patient-friendly laboratory report. In this Opinion, we consider patient barriers to comprehension of lab results and suggest several options to reformat the lab report to promote understanding of test results and their significance to patient care, and to reduce patient anxiety and confusion. In particular, patients' health literacy, genetic literacy, e-health literacy and risk perception may influence their overall understanding of lab results and affect patient care. We propose four options to reformat lab reports: 1) inclusion of an interpretive summary section, 2) a summary letter to accompany the lab report, 3) development of a patient user guide to be provided with the report, and 4) a completely revised patient-friendly report. The complexity of genetic and genomic test reports poses a major challenge to patient understanding that warrants the development of a report more appropriate for patients.

The purpose of this study was to analyze laboratory performance on proficiency testing surveys offered jointly by the College of American Pathologists/American College of Medical Genetics and Genomics biannually for the three common Ashkenazi Jewish founder mutations in the BRCA1 and BRCA2 genes.Survey responses were analyzed for accuracy of genotype determination and the associated clinical interpretation. Data on an individual laboratory's participation over time, number of samples tested, turnaround time, and test methodology were also reviewed.Between 2003 and 2012, 23 US laboratories and 39 international laboratories participated. There were six genotyping errors, with a corresponding analytical sensitivity of 99.0% (479/484 challenges; 95% confidence interval: 97.6-99.7%) and an analytic specificity of 99.9% (870/871; 95% confidence interval: 99.4-99.9%). Among the 1,325 clinical interpretations, 92.5% (1,226/1,325; 95% confidence interval: 91.0-93.9%) matched the intended response. Most of the 99 discrepancies-81% (80/99)-incorrectly interpreted the risk for a negative test result as having a lifetime risk of breast cancer "that is the same as that in the general population" instead of "that cannot be determined without BRCA mutation testing of the affected relative."Clinical laboratories demonstrated excellent analytical sensitivity and specificity. The clinical interpretation requires additional education, focusing on the clinical interpretation of negative test results for these three mutations.

MYH9 mutations cause the inherited macro-thrombocytopenic syndromes of May-Hegglin anomaly, Fechtner syndrome, Sebastian syndrome, and Epstein syndrome, collectively referred to as MYH9-related disease. We present the case of a girl with MYH9-related disease whose diagnosis was facilitated by platelet electron microscopy and MYH9 sequencing. We discuss our patient's clinical presentation, now with 12 years of follow-up. We also discuss management and her possible prognosis given her specific MYH9 mutation.

The College of American Pathologists offers biannual proficiency testing for molecular analysis of fragile X syndrome. The purpose of this study was to analyze laboratory performance on the fragile X proficiency surveys from 2001 to 2009.Individual laboratory responses were analyzed for accuracy of genotype determination (normal, gray zone, premutation, or full mutation) and size analysis of the FMR1 trinucleotide repeat region. The analytical sensitivity and specificity of testing for fragile X were calculated, and laboratory performance for trinucleotide repeat sizing was evaluated.Overall, laboratories demonstrated analytical sensitivity of 99% and 96% for detection of full mutations associated with fragile X syndrome in males and females, respectively; analytical sensitivity of 98% for detection of premutations; and analytical specificity of 99.9%. Size measurements of the CGG repeat region were acceptable from most laboratories, with an increase in the range of reported sizes observed for larger repeat expansions.Molecular genetic testing for fragile X syndrome demonstrated excellent sensitivity and specificity by laboratories participating in the College of American Pathologists (CAP) surveys. Allele sizing demonstrated good performance overall with improved accuracy over the study period. Participation in proficiency testing can aid laboratories in assessing individual performance and need for calibration of assays.

While the majority of patients with early-stage mycosis fungoides (MF) have an excellent prognosis, a few cases progress to secondary Sezary syndrome (sSS), which carries a dismal clinical outcome. We retrospectively analyzed 135 cases of MF/SS and correlated molecular detection of T-cell clones in the skin and blood with other clinicopathologic findings. When stratified by the diagnoses, patients with MF demonstrated a 26.5% (31/117) positive rate for a blood T-cell clone, of which 50% (10/20) had an identical T-cell clone in the skin. Follow-up evaluation showed conversion into sSS or leukemic phase in 50% (5/10) of cases with a positive blood T-cell clone (estimated mean interval 41.8 months) in comparison to no cases in the group without a clone (0/31). Interestingly, 4/5 cases of sSS had an identical T-cell clone in the skin, while the remaining case did not have the test performed on skin for clonal comparison. Kaplan-Meier survival analysis demonstrated a poor clinical outcome in the group with a blood T-cell clone, in comparison with the group without, in overall survival (p0.0001) and progression-free survival (p0.0001; HR = 22.6). These findings suggest that molecular detection of a blood T-cell clone may have a role in predicting sSS. Due to amplification of non-neoplastic T-cell expansion in a significant number of cases, comparison of blood T-cell clones with skin may have confirmatory value.

We have observed an increasing number of autopsies on patients with chemotherapy-related complications. One complication is toxic leukoencephalopathy, which is due to a direct toxic effect of chemotherapeutic agents on the central nervous system white matter. Autopsies of four cases of toxic leukoencephalopathy were performed following standard protocols. The brain and spinal cord were examined routinely, and histological sections were taken for evaluation. We report here three patients with hematologic malignancies and one patient with metastatic carcinoma with chemotherapy-induced leukoencephalopathy. The first was a 56-year-old male treated with multiple chemotherapeutics for multiple myeloma. He presented with confusion and focal seizures with a rapid progression to coma and decerebrate posturing. The second was a 36-year-old male who developed mental status changes, ataxia and dysarthria following treatment for lymphoma. The third was a 16-year-old male who developed a profound peripheral and central neuropathy after chemotherapy treatment for T-cell acute lymphoblastic leukemia. The fourth was a 49-year-old female patient who was treated with multiple chemotherapeutics for Stage II breast carcinoma and subsequently developed visual acuity and field defects. The neuropathologic findings in these cases, although similar, varied in severity and distribution. The white matter was affected by severe myelin pallor, edema, and a prominent macrophage infiltrate in each of the cases. The location and extent of the central nervous system pathology correlated with the type and severity of clinical symptoms. These four cases, with their varied presenting symptoms, clinical courses, and degree of pathology, emphasize the importance of considering toxic leukoencephalopathy as an etiology of acute neurologic deterioration following high-dose chemotherapy.

e22149 Background: Although the use of genomic sequencing to guide cancer patients into clinical trials is being developed, much needs to be done before this becomes the standard of care. First, sm...

339 Background: Biomarkers used to identify patients at high risk for recurrence after surgical resection of colorectal cancer (CRC) lack predictive capacity and are applicable only to localized disease. As the use of adjuvant therapy in this setting can be controversial, the development of a biomarker that is prognostic, predictive, and applicable after resection of primary or metastatic disease may dramatically improve patient outcomes. Methods: We compiled microarray data from 850 patients with predominantly primary CRC from four publically available datasets to predict activity of 19 oncogenic pathways to generate patterns of pathway deregulation for each patient tumor. Mixture modeling was applied to the samples using affinity propagation to subgroup tumors bearing unique patterns of pathway deregulation. The model was then applied to a dataset of 133 predominantly metastatic CRC samples from patients undergoing curative surgical resection at the Duke University Medical Center. Results: Mixture modeling resulted in the identification of 6 distinct molecular subgroups of CRC (MSCC) based on pathway deregulation for both primary and metastatic CRC. Kaplan-Meier analysis of the primary data set revealed differences in recurrence free survival among the 6 MSCC (p=0.0004) with patients assigned to MSCC3 having the poorest prognosis and patients assigned to MSCC4 having the best prognosis. A similar result was obtained when the model was applied to the metastatic data set (p

Recurrent genetic abnormalities are important prognostic markers in acute myeloid leukemias (AML). The World Health Organization classification recognizes 7 categories of AML with recurrent cytogenetic abnormalities, all balanced translocations. Additional rare recurrent cytogenetic abnormalities, such as t(8;16)(p11;p13), are described, but their clinicopathologic correlations are not well established. We reviewed the bone marrow morphology, blast immunophenotype, and clinical features …

447 Background: Current biomarkers for colorectal cancer sub-classify tumors based on single mutations, such as KRAS; however, studies of single mutations belie the molecular complexity of colorectal cancer in which an average of 14 key genes per tumor is dysregulated. We hypothesize that colorectal cancer may be molecularly sub-classified based on an oncogenic pathway prediction model in which tumors are grouped based on patterns of oncogenic pathway dysregulation/expression. Methods: Affymetrix microarray data from 850 patients with primary colorectal cancer from publically available datasets were combined using Bayesian factor regression modeling normalization. The activity of 19 separate oncogenic pathways was predicted among tumors to generate patterns of pathway activity for each sample. Mixture modeling was applied to these samples to identify subgroups of tumors with unique patterns of pathway dysregulation. Validation of subclasses was performed on a dataset of 133 primary and metastatic colorectal cancer samples of patients undergoing curative surgical resection at our institution. Tumors were subgrouped according to our previous model and recurrence free survival was calculated. In vivo validation was performed by treating NOD/SCID mice bearing patient derived tumors with everolimus with changes in tumor size calculated between day 0 and day 21. Results: Mixture modeling resulted in 6 individual subgroups of colorectal cancer based on pathway dysregulation. Kaplan Meier curves revealed that patients in subclass 4 had the poorest prognosis while patients in subclass 6 had the best prognosis (p=0.05). Further, tumors in subclass 4 were generally enriched for high mTOR pathway activation and patient derived explants from subclass 4 with high predicted mTOR activity were found to be sensitive to the MTOR pathway inhibitor everolimus. Conclusions: Prediction of oncogenic signaling pathway activity is a powerful tool that may be used to molecularly sub-classify colorectal cancer into biologically relevant subgroups. These subgroups have prognostic and predictive implications for recurrence following surgical resection and responsiveness to targeted therapy.

Abstract 3466 Donor cell leukemia (DCL) in the setting of bone marrow/hematopoietic stem cell transplant (HCT) has not been well characterized. We analyzed 9 cases of DCL and performed a literature review (table). The indications for transplant and subtypes of DCL are shown (table). The 6 myelodysplastic syndrome (MDS) cases included 1 case of refractory cytopenia with multilineage dysplasia (RCMD), 2 cases of refractory anemia and 3 cases which were unclassifiable. Conventional cytogenetic analysis was performed on all 9 cases of DCL (table). All 9 cases had engraftment studies performed either by short tandem repeat analysis (3) or FISH analysis for donor gonosomal complement (6) when DCL was diagnosed. Seven cases had either engraftment studies or cytogenetic analysis performed periodically after HCT to test the donor cell engraftment and engraftment was confirmed in all. FISH analysis for monosomy 7, del(7q) and del(5q) was retrospectively performed on preserved donor cells in 4 cases after DCL was diagnosed. A low level of abnormalities was observed in preserved donor cells for the cases with del(7q) (2.9%) and del(5q) (8.2%). The 2 cases of AML received chemotherapy. Of the MDS cases, 2 received donor cell infusion, 1 received 6 cycles of revlimid, and 3, along with the case of CLL, received either supportive therapy or were simply observed. Six cases have clinical follow up ≥ 5 months and of these, 1 died of disease (AML) while the other 5 are alive, including 4 MDS and the 1 CLL. The disproportionate detection of DCL in sex mismatched HCT suggests a probable under-detection in the sex-matched population. In our analysis, the interval between HCT and diagnosis of DCL (table) falls within the range of currently reported cases. When stratified by type of DCL, the T-LGL group demonstrates presentation significantly earlier than other groups (Fig. A), indicating pathogenesis of T-LGL may involve a distinct pathway. When stratified by types of primary disease, the interval of the neoplastic group is shorter than that of benign group (Fig. B), implying that pre-HCT treatment may play a role in the pathogenesis of DCL. When stratified by stem cell sources, UCB group shows shorter latency than the other sources (Fig. C), suggesting a higher risk of DCL in this cell source. The low level cytogenetic abnormalities of preserved donor cells in our series and the longer latency of the benign group suggest that donor cells with an intrinsic defect may be predisposed to evolve into DCL. Total cases (%) Reported cases (%) Current cases (%) Number of cases 83 74 9 Age (years) Median/range 37.0/3~70 36.0/4~62 53.0/3~70 Gender Male 43 (52.4) 38 (52.0) 5 (55.6) Female 39 (47.6) 35 (48.0) 4 (44.4) Primary disease Neoplasms 76 (91.6) 67 (90.5) 9 (100) Non-neoplasms 7 (8.4) 7 (9.5) 0 (0.0) Donor Related 59 (72.0) 54 (74.0) 5 (55.6) Unrelated 23 (28.0) 19 (26.0) 4 (44.4) Sex-matched 28 (34.6) 27 (37.5) 1 (11.1) Sex-mismatched 53 (65.4) 45 (62.5) 8 (88.9) Donor cell source BM 48 (63.2) 44 (65.7) 4 (44.4) BHSC 16 (21.0) 13 (19.4) 3 (33.3) UCB 12 (15.8) 10 (14.9) 2 (22.2) 2nd neoplasm (DCL) AML 31 (37.4) 29 (39.2) 2 (22.2) MDS/MPN* 27 (32.5) 21 (28.4) 6 (66.7) ALL 20 (24.1) 20 (27.0) 0 (0.0) T-LGL 4 (4.8) 4 (5.4) 0 (0.0) CLL 1 (1.2) 0 (0.0) 1 (11.1) Interval (months) Median/range 24.0/1~312 24.0/2~312 26.0/1~193 Cytogenetics Normal 21 (28.0) 20 (30.3) 1 (11.1) Abnormal 54 (72.0) 46 (69.7) 8 (88.9) -7 or del(7q)** 15 (27.8) 10 (21.7) 5 (62.5) +8** 2 (3.7) 2 (4.4) 0 (0.0) Del(20)** 4 (7.4) 2 (4.4) 2 (25.0) Del(5q)** 2 (3.7) 1 (2.2) 1 (12.5) 11q23** 3 (5.6) 3 (6.5) 0 (0.0) Other abnormalities** 28 (51.9) 28 (60.9) 0 (0.0) Follow up (months) Median/range 8.5/1~108 9.0/1~108 6.0/1~68 Died of disease 28 (46.7) 27 (52.9) 1 (11.1) DCL, donor cell leukemia; BM, bone marrow; BHSC, blood hematopoietic stem cells; UCB, umbilical cord blood; AML, acute myeloid leukemia; MDS, myelodysplastic syndrome; ALL, acute lymphoblastic leukemia (including B-cell and T-cell ALL); T-LGL, T-cell large granular lymphocyte leukemia; CLL, chronic lymphocytic leukemia. All the numbers represent the cases with data available. * One case of myeloproliferative neoplasm is included in this category. ** The percentage is calculated using number of total cytogenetic abnormalities in each column as denominator. Disclosures: No relevant conflicts of interest to declare.

e18003 Background: The incorporation of prognostic and predictive microarray-based biomarker assays in clinical trials or routine clinical practice is challenging. We report the methodology and design of prospective, phase II, gene expression based, directed chemotherapy trials in NSCLC. Methods: Using an Affymetrix platform, we developed genomic signatures of sensitivity to chemotherapy in NSCLC. Retrospective studies validated the sensitivity and specificity of these signatures. We initiated two prospective phase II clinical trials in NSCLC. TOP0703 is an adjuvant study that stratifies between cisplatin + pemetrexed or cisplatin + vinorelbine using genomic predictors of pemetrexed and vinorelbine in non-squamous histology. TOP602 is an advanced stage study stratifying by predicted sensitivity to cisplatin and histology: cisplatin sensitive (cisplatin + pemetrexed for non-squamous or cisplatin + gemcitabine for squamous) and cisplatin resistant (pemetrexed + gemcitabine for non-squamous or docetaxel + ge...

10513 Background: The development of genomic signatures as predictive biomarkers of chemotherapeutics provides the potential to guide therapeutic choice in instances where standard-of-care includes...

TPS102 Background: Genomic assays have been shown to provide the potential for personalized approaches to breast cancer therapy. Full-transcriptome assays using microarrays are challenging, but hav...

Abstract 3430 Poster Board III-318 Background and Significance Chronic lymphocytic leukemia (CLL) is a malignant B cell lymphoproliferative disorder characterized by the clonal expansion and accumulation of CD5+ B cells. CLL is quite heterogeneous in clinical behavior, where some patients remain asymptomatic and require no therapy for many years, whereas other patients follow an aggressive clinical course with early need for therapy and short overall survival. Those patients with somatic deletions and / or mutations of p53, a central mediator of cell cycle control, apoptosis, and a potent tumor suppressor, follow the most aggressive clinical courses of all patients with CLL. Furthermore, these patients tend to be refractory to conventional CLL chemotherapy regimens, and therefore novel therapeutic approaches are needed. Cenersen (Eleos Inc.) is a 20-mer antisense molecule and binds to a coding region of exon 10 in p53 mRNA and has been shown in vitro to increase apoptosis in lymphoma cell lines. We hypothesize that the addition of cenersen to chemo-immunotherapy will enhance leukemic cell apoptosis and thus increase chemotherapy sensitivity in vivo for patients with aggressive CLL. Here we report early clinical responses to cenersen in combination with FCR chemo-immunotherapy at a planned interim analysis for efficacy and safety after enrollment of 17 patients. Methods We have undertaken a clinical trial at Duke University Medical Center of cenersen in combination with chemo-immunotherapy for patients with CLL or SLL (ClinicalTrials.gov identifier: NCT00636155). Patients with relapsed CLL or previously untreated patients with a deletion or mutation of p53 requiring therapy were enrolled. Cenersen was administered at 2.4 mg/kg/day as a continuous infusion over 24 hours starting on day 1 and ending on day 4. Fludarabine was administered daily at 25 mg/m2 on days 2 through 4, cyclophosphamide was administered daily at 250 mg/m2 on days 2 through 4, and rituximab was administered at 375 mg/m2 on day 2. Cycles were repeated every 28 days for a maximum of 6 cycles. The primary outcome measure was the overall response rate (complete and partial responses by iwCLL response criteria), and secondary outcome measures included progression free survival, event free survival and overall survival. All patients received growth factor support as well as prophylaxis with acyclovir and trimethoprim / sulfamethoxazole. Interphase cytogenetics and sequencing analysis for somatic mutations of p53 was performed in all patients. Results To date, 17 patients have been enrolled to a protocol-defined interim analysis of efficacy and safety. Of the enrolled patients, 1 was previously untreated, and the remaining 16 were relapsed (median number of prior therapies 4, range 1 - 8). Among previously treated patients, the mean response duration of the most recent prior regimen was 2 months. 15 of 16 had previously received fludarabine and 14 of 16 patients had previously received rituximab. 10 of 16 patients tested showed 17p deletions by FISH. Among the 14 patients tested to date, 8 showed somatic mutations in p53 by sequence analysis, of these, 6 showed both deletion of 17p as well as somatic mutation of p53. Of the 17 patients enrolled, 14 are evaluable for response: 1 patient has not yet received 3 cycles of therapy and 2 patients voluntarily discontinued trial participation. To date, 5 patients show a partial response by iwCLL criteria, including 2 patients who have concluded all therapy and show a partial response with incomplete hematologic recovery (PRi) with no detectable CLL B cells by flow cytometry analysis of bone marrow aspirate. One of these patients has subsequently undergone allogeneic stem cell transplantation. The remainder of the patients had stable disease (SD), though 3 were removed from study prior to the completion of 3 cycles for inadequate response as determined by the treating physician. There have been 4 episodes of febrile neutropenia, and there have been no toxicities specifically attributed to cenersen. Conclusions We have observed encouraging clinical responses to the combination of cenersen with FCR chemo-immunotherapy among a group of extensively pretreated patients with high risk genetic features. There does not appear to be any excess toxicity associated with the investigational agent. The results to date suggest that there may be therapeutic benefit to p53-targeted therapies in high risk CLL. This study will be continued to full accrual. Disclosures Lanasa: Genentech: Membership on an entity's Board of Directors or advisory committees. Off Label Use: Rituximab, in combination with fludarabine and cyclophosphamide, for the treatment of CLL. Cook:Eleos: Employment. Rizzieri:Eleos: Research Funding.

11057 Background: Personalized approaches to breast cancer therapy depend on genomic assays. While assays based on fixed tissues offer greater convenience, the spectrum of biology interrogated is limited. Full-transcriptome assays using microarrays are more challenging, but have the advantage of providing multiple prognostic and predictive signatures in one assay. We have created a clinical infrastructure with the objective of obtaining full genome expression data on breast cancer samples as a clinical assay for use in a prospective trial. Methods: “Performance of Genomic Expression Profiles to Direct the Use of Preoperative Chemotherapy for Early Stage Breast Cancer” is a prospective trial validating genomic signatures for predicting response to doxorubicin (A) or docetaxel (T) treatment in HER2 negative cancers. Fresh-frozen cores are reviewed by the study pathologist for tumor content. RNA is then extracted and probe generated to hybrize to an Affymetrix U133Plus2.0 microarray. Microarray data quality is determined using summary metrics for U133Plus2.0 arrays and principal component analysis (PCA) plots. The data is then used for predicting A or T sensitivity. Results: Thirteen cancers have been analyzed in the context of the above trial. Histologic type was lobular for 1, and predominantly ductal for 12 (10 ER positive, 3 ER negative). Median tumor size was 3.4 cm (range, 1.8–5.7). Microarray analysis was successful on 11 tumors (84%), providing data of sufficient quality to make predictions of A and T sensitivity. One sample hybridization failed QC as detected by PCA analysis, and one sample had insufficient RNA. The median “tissue to array data” time and “study consent to initiation of treatment” time were 5 days (range, 3–8) and 14 days (range, 11–36), respectively. Conclusions: Our initial experience shows that full-genome expression analysis on frozen tumor using an Affymetrix platform is feasible as a clinical assay for breast cancer. The resulting data is being used in a prospective marker validation protocol for predicting chemosensitivity. The data can also be analyzed for a variety of other potential prognostic and predictive signatures for guiding therapy. No significant financial relationships to disclose.

8108 Background: Platinum-based combination chemotherapy is the standard of care for advanced NSCLC despite response rates in Phase III trials of 18%. We designed a novel phase II study evaluating ...

11068 Background: Genome-wide expression profiling has now been extensively used for research on breast cancer biology and led to many new insights regarding disease heterogeneity. However, clinical applications require an understanding of various technical considerations, including the extent to which a random sample provides a representative measure of the patient’s tumor. Using genome- scale expression data derived from cancer cell lines and tumor biopsies, we have developed signatures for predicting response to specific cytotoxic chemotherapies. Our objective in this study is to assess the concordance of chemosensitivity predictions and of microarray-based classifiers of ER and HER2 status in a series of multiple samples from individual breast cancer biopsies. Methods: Patients with multiple frozen cores were identified in the Duke Breast SPORE tissue repository. Cores were assessed for percent invasive cancer cellularity, primary tumor size, and standard biomarker assessments. RNA was hybridized to A...