Abstract 1702: Comprehensive genomic analysis of predictive biomarkers for checkpoint inhibitor therapy from a limited amount of FFPE tissue and cfDNA

PD-L1 expression and MSI status are useful predictive biomarkers for checkpoint inhibitors (CIs) in some tumor types. However, studies have demonstrated that the identification of all potential patients who may benefit from CIs will require the analysis of both tumor cell and tumor microenvironment (TME) biomarkers. For example, recent data suggests that tumor mutation burden (TMB) and tumor mutation signatures as well as inflammatory signatures and T cell clonality in the tumor microenvironment may serve as independent predictive biomarkers of CI response. The need for evaluation of multiple biomarkers using IHC, PCR and/or NGS using limited amounts of tissue poses a challenge in the clinical setting. Here we conduct a study to evaluate whether a panel of tumor and TME biomarkers can be accurately analyzed using low DNA and RNA input from FFPE specimens or using plasma-derived cfDNA. Multiple methods for assessing TMB, MSI status and mutation signatures were compared. The impact of sample quality on biomarker analysis was also evaluated. A set of late stage CRC and matched plasma samples were used in this study. DNA and RNA were co-extracted from FFPE sections using RecoverAll™ kit. cfDNA was extracted from plasma using the MagMAX™ Kit. DNA and RNA yields from FFPE ranged from 855-3875ng and 477-5200ng, respectively. cfDNA yields ranged from 8-38ng. Based on the KAPA DNA QC results, the FFPE samples were determined to be high quality. TMB and mutation signature analysis of FFPE samples were performed using Oncomine Tumor Mutation Load (TML) Assay, the Oncomine Comprehensive Assay v3 (OCAv3) and WES. MSI status in FFPE tissue and cfDNA was determined using the Promega MSI Analysis System. The mutation spectrum in the matched cfDNA samples was determined using the Oncomine PanCancer cfTNA Assay. Inflammatory (IFNG) signatures were assessed using the targeted RNASeq panel, Oncomine Immune Response Research Assay (OIRRA). The clonality of TILs was analyzed using NGS. TMB results generated from the targeted panels using only 20ng DNA input were comparable to WES results. Differences in TMB counts between the NGS assays are likely due to differences in genomic coverage and data filtering. MSI-H status and/or mutations in critical DNA repair or proofreading genes such as MSH6 and POLE correlated with high TMB. Gene expression profiling using OIRRA was successful for all FFPE RNA samples. In summary, this study demonstrates that comprehensive genomic analysis of predictive biomarkers for CI therapy can be performed from limited FFPE samples using co-extraction methods and a combination of targeted NGS and PCR-based assays. DNA and RNA quality have a significant impact on the accuracy of TMB analysis and gene expression profiling. In cases where no tumor tissue is available, the analysis of biomarkers such as MSI and mutation signatures may be possible using cfDNA.

Citation Format: Xiaodong Wang, Zhenyu Yan, Quyen Vu, David Smith, Chad Galderisi, Cynthia S. Spittle, Jin Li. Comprehensive genomic analysis of predictive biomarkers for checkpoint inhibitor therapy from a limited amount of FFPE tissue and cfDNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1702.

An international multicenter study to evaluate reproducibility of automated scoring for assessment of Ki67 in breast cancer

The nuclear proliferation biomarker Ki67 has potential prognostic, predictive, and monitoring roles in breast cancer. Unacceptable between-laboratory variability has limited its clinical value. The International Ki67 in Breast Cancer Working Group investigated whether Ki67 immunohistochemistry can be analytically validated and standardized across laboratories using automated machine-based scoring. Sets of pre-stained core-cut biopsy sections of 30 breast tumors were circulated to 14 laboratories for scanning and automated assessment of the average and maximum percentage of tumor cells positive for Ki67. Seven unique scanners and 10 software platforms were involved in this study. Pre-specified analyses included evaluation of reproducibility between all laboratories (primary) as well as among those using scanners from a single vendor (secondary). The primary reproducibility metric was intraclass correlation coefficient between laboratories, with success considered to be intraclass correlation coefficient >0.80. Intraclass correlation coefficient for automated average scores across 16 operators was 0.83 (95% credible interval: 0.73-0.91) and intraclass correlation coefficient for maximum scores across 10 operators was 0.63 (95% credible interval: 0.44-0.80). For the laboratories using scanners from a single vendor (8 score sets), intraclass correlation coefficient for average automated scores was 0.89 (95% credible interval: 0.81-0.96), which was similar to the intraclass correlation coefficient of 0.87 (95% credible interval: 0.81-0.93) achieved using these same slides in a prior visual-reading reproducibility study. Automated machine assessment of average Ki67 has the potential to achieve between-laboratory reproducibility similar to that for a rigorously standardized pathologist-based visual assessment of Ki67. The observed intraclass correlation coefficient was worse for maximum compared to average scoring methods, suggesting that maximum score methods may be suboptimal for consistent measurement of proliferation. Automated average scoring methods show promise for assessment of Ki67 scoring, but requires further standardization and subsequent clinical validation.

Abstract 4522: An optimized NGS workflow for detection of FLT3 internal tandem duplication (ITD) in AML samples

FLT3 ITD, a prognostic marker and drug target, is present in ~19% of AML patients. FLT3 ITD is a tandem repeat of the entire or partial exon 13-15 region. FLT3 ITDs range in size from 3bp to above 300bp and impact RTK signaling. Recent publications have shown that FLT3 ITD can be detected at single nucleotide resolution by NGS panels. However, detection of large FLT3 ITD and accurate reporting of ITD frequency remain challenging for NGS methods. False negative ITD results or inaccurate mutant/wild type allele ratio measurements could negatively alter treatment decisions for AML patients. The Illumina TruSight Myeloid panel (TMP) is a commercial NGS assay that covers 54 genes involved in myeloid malignancies. Although the TMP assay can detect SBS and small indel, medium to large size FLT3 ITD cannot be detected. Here we present an enhanced workflow to overcome these challenges. Positive controls, dynamic range, accuracy, and inter-run reproducibility were validated for the detection of SBS, indel, and FLT3 ITD using reference standards and DNA extracted from cell lines and AML patient EDTA blood and bone marrow aspirate samples. NGS libraries were prepared following Illumina's standard protocol. 275bp X2 sequencing instead of the standard 150bp X2 was run on MiSeq flowcell v3. Data analysis was performed using a MolecularMD custom pipeline. The analysis of FLT3 ITD was conducted using three methods including two off-the-shelf programs, Pindel and ITDseek, as well as Cigar, a MolecularMD developed ITD detection algorithm. FLT3 ITDs at 126 bp and 21 bp in PL-21 and MOLM-13 cell lines, respectively, were detected by TMP assay using the three algorithms. In contrast to ITDseek which only reports ITD sequence without frequency information, Pindel and Cigar report both ITD sequence and frequency. Compared to Pindel, ITD frequency reported by the custom algorithm is closer to that determined by the fragment analysis. Serial dilution of the 126bp ITD into wild type DNA showed the 0.55% ITD (from fragment analysis) can be reproducibly detected at ~0.6% by the Cigar algorithm. FLT3 ITDs ranging in size from 6bp to 300bp were detected in clinical AML samples using the enhanced TMP workflow and confirmed by a fragment analysis method. Limit of detection, reproducibility and accuracy of SBS and indel detection in other key genes by the TMP assay have also been validated. Low-level mutations, i.e. NRAS G12D at 1.7%, NRAS G13D at 2%, and IDH2 R140Q at 1.4%, were detected by TMP panel from AML samples and further confirmed with an independent assay. A long deletion (52bp) in exon 9 of CALR was also detected by the custom pipeline. In summary, the enhanced TMP workflow allows for accurate detection and reporting of SBS, indel and FLT3 ITDs including large duplications. Optimized detection of FLT3 ITDs will improve AML patient selection for targeted therapy.

Citation Format: Xiaodong Wang, Zhenyu Yan, Peng Fang, Weihua Liu, Scott Glynn, Jennifer Biroschak, Chad Galderisi, Cindy Spittle, Jin Li. An optimized NGS workflow for detection of FLT3 internal tandem duplication (ITD) in AML samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4522.

Surgery versus Interventional Radiology in the Management of Thrombosed Vascular Access for Hemodialysis

Thrombosis is the most frequent complication occurring in vascular access (VA). The two widely used treatment strategies for thrombosed VA are surgical and endovascular. Which is the best and whether different approaches should be used on proximal versus distal VA, is still debated. This is a retrospective study. Over a three years period, we studied among a population of 475 dialysis patients, 54 VA thromboses in 46 patients. Surgical procedure was successful in 14/17 (82%) distal artero-venous fistulas (AVF) while, in 9 proximal AVF, it led to initial success in 6 patients (66%), with a six months primary patency respectively of 93% and 84%. Radiological procedure resolved 6/10 distal AVF (initial success 60%) with primary patency of 66%, and was successful in 16/18 proximal AVF (initial success 89%) with primary patency of 81%. Taking our data all together, no differences are found between two thrombolitic (surgical and endovascular) procedures. But results were different in thrombosed proximal VA (where endovascular treatment should be preferred) versus distal ones (where surgery seems better).

Abstract B072: Liquid biopsy analysis of NSCLC patient plasma using ddPCR and NGS

Introduction: Analysis of cfDNA has potential applications in therapy selection and disease monitoring in the clinical management of NSCLC. Here we use EGFR ddPCR and the Oncomine Lung cfDNA Assay to evaluate the mutation profile and allele burden in a set of plasma samples collected from NSCLC patients. Methods: Plasma samples were collected at Dana-Farber Cancer Institute (DFCI). cfDNA was extracted using the QIAamp DSP circulating NA kit. EGFR ddPCR assays were designed by DFCI. One third of cfDNA extracted from 1 ml plasma was used for each EGFR ddPCR assay (L858R, T790M and ex19del). The L858R and T790M ddPCR assays detect mutations using mutant specific probes. The ex19del assay allows for the detection of a broad range of exon 19 deletions via the loss of wild-type exon 19 signal. Twenty-two plasma samples from patients with EGFR WT tumors were analyzed to assess the background noise (Limit of Blank). The other 32 plasma samples were analyzed in a blinded fashion. ddPCR analysis was performed on the QX200 system and data was analyzed using QuantaSoft software. A subset of 12 plasma samples had sufficient cfDNA for additional analysis using the Oncomine Lung cfDNA Assay on the Ion S5. This NGS panel is designed to detect 150 hotspot mutations in 11 lung cancer-related genes. Torrent Suite Software 5.2 was used for NGS data analysis. The HorizonDx cfDNA Multiplex Reference Standard (AF 5%, 1%, 0.1%, and WT) was also included in the ddPCR and NGS studies. Results: Based on the Limit of Blank data, the positive mutation cut-off for each EGFR ddPCR assay was set at 3 mutant copies with minimum 3000 wild type copies. Studies using the HorizonDx cfDNA standard demonstrated that the analytical sensitivity of the ddPCR assays increases with cfDNA input: the lowest detected allele frequency (AF) is 1%, 0.5%, and 0.25% for 3, 6, and 12ng input, respectively. In plasma samples, EGFR mutations were detected as low as 0.08% AF using ddPCR (4.5 L858R mutant copies/5827 wild type copies). L858R and exon 19 deletions were detected in 13/54 and 21/54 plasma samples, respectively. T790M mutations were detected in 19/54 plasma samples, and coexisted with L858R or ex19del in all cases. The Oncomine™ Lung cfDNA Assay showed 100% concordance with EGFR ddPCR results for the 12 plasma samples analyzed by both methods. Mutations were detected as low as 0.18% AF with 8.5ng plasma cfDNA input in the NGS assay. Using the HorizonDx cfDNA multiplex standard mutations were detected as low as 0.1% AF using 20ng input. In addition, PIK3CA mutations were found to coexist with EGFR ex19 deletions in 3/12 plasma samples using NGS. The AF of PIK3CA mutations and EGFR mutations was comparable in the same samples (TRL23: 24.3% for EGFR del19 and 10.4% T790M vs 20.2% for PIK3CA H1047R; TRL48: 7.8% for EGFR del19 vs 3.4% for PIK3CA E545K; TRL51: 0.85% for EGFR del19 vs 1.02% for PIK3CA E545K). Conclusions: Both ddPCR and NGS were able to detect mutations at 0.1% AF with sufficient cfDNA input. The Oncomine panel confirmed EGFR ddPCR results and detected coexisting PIK3CA mutations. EGFR and PIK3CA mutations were present at a similar AF, suggesting that EGFR and PIK3CA mutations may develop at the same stage of tumorigenesis in these patients. Our study results demonstrate that comprehensive profiling of cfDNA using NGS could be critical for the selection of appropriate therapies for NSCLC patients while ddPCR is an ideal platform for monitoring disease burden during the course of therapy.

Citation Format: WeiHua Liu, Peng Fang, Chad Galderisi, Cindy Spittle, Jin Li. Liquid biopsy analysis of NSCLC patient plasma using ddPCR and NGS [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B072.

Abstract A044: Immunotherapy biomarker assessment in RCC using IHC, gene expression profiling, and mutation burden assessment

The field of immunotherapy includes multiple approaches that harness the power of the immune system to destroy cancer cells. Checkpoint inhibitors have been approved for the treatment of solid tumor and hematologic malignancies. While significant responses have been observed in a subset of patients, outcomes are variable and there is a need to identify additional predictive biomarkers beyond PD-L1 levels as measured by IHC. A more comprehensive assessment of the tumor and its microenvironment can be accomplished through gene expression profiling, mutation burden analysis, and immune repertoire profiling. Exploratory studies such as those presented here using targeted RNA and DNA sequencing will continue to expand our understanding of tumor immune cell interactions and how this information can be used to improve patient selection for checkpoint inhibitors and other immunotherapy. In this study, a set of 30 FFPE tumor samples including CRC, RCC, and NSCLC was analyzed using an IO Biomarker IHC Panel (PD-L1, CD8, CD3, and CD163). PD-L1 staining (% and intensity) was scored for both tumor cells (TC) and immune cells (IC). T-cell and macrophage markers were scored as high, medium, and low. Samples were also analyzed using the ThermoFisher Oncomine™ Immune Response Research Assay. This targeted RNA-sequencing panel measures the expression of 391 genes involved in tumor-immune cell interactions. RNA was extracted using RecoverAll and the quantity and quality was assessed using Qubit and RT-qPCR, respectively. A significant correlation was observed between the RT-qPCR quality score and mapped sequencing reads. A subset of 7 RCC samples with the highest RNA quality and sequencing QC metrics were selected for additional analysis. A trend was observed in the RNA expression level of individual genes such as PD-L1, PD1, CD8A, TNFRSF9, and LAG3 and a composite expression score based on 10 interferon gamma-related genes. Unsupervised clustering was performed using several published gene expression signatures that have been found to correlate with immune response (IR) and/or tumor inflammation. The gene content ranged between 4-13 genes and overlapped between some but not all signatures. The 13-gene signature classified six RCC samples as “high IR” and one sample as “low IR.” Interestingly, similar results were obtained when samples were classified using the other signatures. PD-L1 IHC positive staining patterns varied widely in the “high IR” samples and ranged from 40%TC/30%IC to 0%TC/5%IC. The “low IR” sample was PD-L1 negative in TC and IC. To further understand the relationship between the tumor’s genetic profile and the tumor microenvironment, mutation burden and immune repertoire analysis was performed using NGS-based methods. The results from the two panels will be presented. This exploratory study details how targeted RNA and DNA sequencing can identify patient subsets based on a multiplexed signature rather than a single marker. The use of both molecular and tissue-based assays will lead to a more comprehensive understanding of tumor and immune biology that may uncover new biomarkers for optimal stratification of patients for personalized immunotherapy treatment.

Citation Format: Peng Fang, Zhenyu Yan, Xiaodong Wang, Wes Chang, Chad Galderisi, Cindy Spittle, Jin Li. Immunotherapy biomarker assessment in RCC using IHC, gene expression profiling, and mutation burden assessment [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A044.

Abstract P1-03-01: An international multicenter study to evaluate reproducibility of automated scoring methods for assessment of Ki67 in breast cancer

Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including prognosis-based decisions, but unacceptable between-laboratory variability has limited its clinical value. The International Ki67 Working Group (IKWG) has undertaken a systematic program to determine whether Ki67 immunohistochemistry can be analytically validated and standardized across laboratories. Technological advances and broader availability of devices for automated assessment of stained slides raise the possibility that these machines may improve on reproducibility of traditional pathologist-based visual Ki67 assessment.

Aims: To characterize reproducibility of automated machine-measured Ki67 expression using slides previously analyzed in the IKWG phase 3 study that evaluated reproducibility of visual Ki67 assessment.

Methods: Two sets of 30 previously stained slides containing core-cut biopsy sections of breast tumors were circulated to 14 laboratories for scanning and automated assessment of Ki67 expression. Sites were instructed to return average and maximum percentage of tumor cells positive for Ki67 for each slide, where maximum is designed to reflect “hot spot” analysis. Two laboratories returned scores from 2 operators; not all laboratories reported values for maximum Ki67 scores. Different operators were treated as distinct laboratories in analyses. Sixteen and 10 score sets were available for average and maximum Ki67 analyses, respectively, encompassing 7 unique scanner and 10 software platforms. Pre-specified analyses included evaluation of reproducibility across all laboratories as well as within a subgroup limited to those using Aperio scanners. The primary reproducibility metric was intraclass correlation coefficient between laboratories (ICC), regardless of device platform or software.

Results: Geometric means across 30 cases for 16 operators ranged from 11.06% to 38.11% with overall mean 16.75% (95% CI:14.45-19.42) for average scores. Geometric means for 10 operators ranged from 16.44% to 68.73% with overall mean 25.16% (95% CI: 18.71-33.84) for maximum scores. ICC for automated average scores across 16 operators was 0.83 (95% CI: 0.73-0.91) and ICC for maximum scores across 10 operators was 0.63 (95% CI: 0.44-0.80) although one outlier lab dramatically affected results. For the laboratories using the Aperio platform (8 score sets), ICC for automated average scores was 0.89 (95% CI; 0.81-0.96). These results are similar to ICC of 0.87 (95%CI; 0.81-0.93) reported using these same slides in the Phase 3 visual assessment reproducibility study in which observers counted 500 cells per slide (Leung et al, NPJBrCancer, in press).

Conclusions: Between-laboratory reproducibility for automated machine assessment of average Ki67 is similar to that for pathologist-based visual assessment of Ki67. However, the observed ICC was markedly numerically lower for the maximum score method compared to the average method, suggesting that the maximum score may not be useful as a reproducible measure of proliferation. Automated average scoring methods show promise for standardization of Ki67 scoring, supporting future studies to clinically validate Ki67.

Citation Format: Rimm DL, McShane LM, Leung SCY, Bai Y, Bane AL, Bartlett JMS, Bayani J, Chang MC, Dean M, Denkert C, Enwere E, Galderisi C, Gholap A, Hugh JC, Jadhav A, Kornaga E, Laurinavicius A, Levenson R, Lima J, Miller K, Pantanowitz L, Piper T, Ruan J, Srinivasan M, Virk S, Wu Y, Yang H, Hayes DF, Nielsen TO, Dowsett M. An international multicenter study to evaluate reproducibility of automated scoring methods for assessment of Ki67 in breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-01.

Abstract 1397: Oncomine focus assay: Simultaneous detection of clinically relevant hotspot mutations, CNVs, and gene fusions in 52 oncogenes relevant to solid tumors

Introduction: The Oncomine™ Focus Assay (OFA) is aimed to simultaneously detect and report hotspot mutations, Copy Number Variants (CNVs) and gene fusions in 52 oncogenes clinically relevant to solid tumors. With minimal DNA/RNA input, OFA employs AmpliSeq™ library preparation chemistry to enrich target regions for Ion Torrent™ Next Generation Sequencing. Variants are annotated for actionability by Oncomine® Knowledgebase. Here we report an analytical validation of OFA.

Methods: DNA and RNA, extracted from the FFPE processed GM12878, was used as the negative control to evaluate the specificity of OFA. A RNA sample containing multiple oncogenic gene fusions and a DNA sample containing multiple hotspot SNV and indels were used as the positive controls. Fresh DNA from cancer cell lines (HCC1143 or NCI-H2122) along with DNA from matched normal cell lines, HorizonDx NGS standards TruQ-1, TruQ-2, several engineered FFPE samples with gene fusions or copy number changes, and 43 clinical FFPE samples of a variety of solid tumor types (non-small cell lung cancer, colorectal cancer, gastrointestinal stromal tumor, ovarian cancer, pancreatic cancer, and melanoma) were used to evaluate the OFA performance. The analysis of the sequencing data was primarily performed with the OFA pipeline integrated with the Oncomine® Knowledgebase. Only the genetic alterations with clinical utility were selected as the final output from the data pipeline. The SBS and indels detected by OFA were confirmed by Sanger sequencing. Any CNVs detected were confirmed by FISH, if possible, and detected fusions were confirmed by RT-PCR or FISH.

Results: No clinically relevant genetic alterations were detected from the negative control FFPE-GM12878, indicating the high specificity of the OFA. The LOD for SBS and short indel detection was 5%, as assessed by TruQ-1 and TruQ-2, each containing 9-10 variants. The assay can detect

gene fusion RNA present as 0.1%-1% of the total RNA, and gene amplifications are detected with a minimum of 50% tumor cell content. A known 12X CCND1 amplifications in HCC1143 and a 13X MYC amplification in NCI-H2122 were detected. In addition, a 13X EGFR amplification and 11X CDK4 amplification were detected in a lung cancer FFPE sample and confirmed by FISH. The analytical specificity for detection of SBS and indels was 100% (25/25). The analytical specificity for detection of CNV gain and gene fusions, and the assay sensitivity are currently under assessment.

Conclusions: These results demonstrate the high sensitivity and specificity of OFA. With as little as 10 ng RNA and 10 ng DNA, OFA provides biomarker analysis of patient FFPE tumor specimens focusing on the detection of genetic alterations that have been targeted by oncology drugs or supported by published clinical evidence.

Citation Format: Peng Fang, Zhenyu Yan, Paul Labrousse, Weihua Liu, Jennifer Biroschak, Jennifer Wright, Selby Weeks, Cindy Spittle, Chad Galderisi, Jin Li. Oncomine focus assay: Simultaneous detection of clinically relevant hotspot mutations, CNVs, and gene fusions in 52 oncogenes relevant to solid tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1397.

Abstract 4925: Liquid biopsy using the ion AmpliSeq v2 cancer panel

Introduction:

Plasma cell-free circulating tumor DNA (ctDNA) has the potential to serve as a noninvasive surrogate to determine tumor genotype and monitor treatment response. Here we report the analytical validation of the Ion AmpliSeq v2 Cancer Panel (ACP) in plasma ctDNA samples.

Methods:

Mutations were assessed using the ACP, designed to survey 2800 mutations in 50 cancer-related genes. TruQ reference standards were used to determine LOD. Healthy donor and cancer patient plasma samples were used for other studies. Eight libraries were barcoded and sequenced with PGM sequencing 200 kit v2 on a 318 v2 chip. The sequencing data were analyzed with a combination of Torrent Suite 3.4.2, VarScan, our proprietary analysis pipeline and IGV. The background noise level of hotspot nt positions was calculated from multiple runs of known wild type DNA. In order to increase the sensitivity of the assay to detect low-level mutation, a custom program was developed to detect variants clearly different from background noise (95% confidence) and not reported by the two variant callers. PCR methods were used for concordance testing.

Results:

The performance characteristics of the AmpliSeq v2 Cancer Panel were demonstrated in 1) Minimum DNA input and LOD: With 10 ng DNA input, 43/43 and 42/43 expected mutations were detected at 2.5% or 1%, respectively. With 1 ng DNA input, 42/43 and 40/43 expected mutations were detected at 2.5% and 1%, respectively. 2) Coverage: The mean library coverage for 40 plasma libraries was 2912x with only 5 non-critical regions below 250x coverage. 3) Baseline error rate: 95% of 2290 hot-spots for SBS showed <0.5% background error frequency assessed in 10 healthy control ctDNA samples. The mean background error frequency plus two folds of SD falls below 0.5% for 91% of SBS hot-spots. 4)Precision: All mutations expected for TruQ6 were detected in 4 independent runs at observed allele frequencies with 0.6% mean SD and 0.1% mean deviation from the true value. A 2% TP53 mutation R174W was reproducibly detected in a lung cancer plasma sample in 2 independent runs. 5) Concordance study: Consistent results were observed for 3 positive (Allele Freq 40%, 3% and 0.2%, respectively) and 3 negative melanoma plasma samples previously genotyped by AS-PCR for Braf V600E/K mutations. Additional cancer patient ctDNA samples are being assessed for concordance in the detection of other mutations.

Conclusions:

The ACP offers a useful tool for comprehensive somatic mutation profiling in ctDNA. The limit of detection is 1-2% mutation frequency for most mutations with slight variation across different nucleotide positions. The low concentration of ctDNA obtained from plasma samples can present a challenge. Less than 10 ng DNA input may result in allele drop out for low level mutations due to the inefficient amplification of multiplex PCR compared with PCR methods using a short length single amplicon. Higher DNA input to rescue allele drop-out is under evaluation.

Citation Format: WeiHua Liu, Zhenyu Yan, Candice L. Horn, Fabio Nunes, Steven M. Bray, Philip J. Ebert, Peng Fang, Jennifer Biroschak, Cindy Spittle, Chad Galderisi, Jin Li. Liquid biopsy using the ion AmpliSeq v2 cancer panel. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4925. doi:10.1158/1538-7445.AM2015-4925

Abstract 4261: Oncomine® Cancer Panel: simultaneous detection of clinically relevant hotspot mutations, CNVs, and gene fusions in solid tumors

Introduction: The Oncomine® Cancer Panel (OCP) is designed to simultaneously detect and report hotspot mutations, Copy Number Variants (CNVs) and gene fusions in 143 genes with minimal DNA/RNA sample input. The OCP utilizes the AmpliSeq™ library preparation chemistry for the Ion Torrent™ Next Generation Sequencing (NGS) platform, in combination with data annotations by the Oncomine® Knowledgebase. Here we report analytical validation of OCP.

Methods: DNA and RNA, extracted from the FFPE processed GM12878, was used as the negative control to evaluate the specificity of OCP. A RNA sample containing multiple oncogenic gene fusions, and a DNA sample containing multiple hotspot SNV and indels were used as the positive control. Fresh DNA from cancer cell lines (HCC1143 or NCI-H2122) along with DNA from matched normal cell lines, HorizonDx NGS standards TruQ-1, TruQ-2, several engineered FFPE samples with gene fusions or copy number changes, and 26 clinical FFPE samples of a variety of solid tumor types (lung, breast, colon, ovary, stomach, uterus and larynx) were used to evaluate the OCP performance. The analysis of the sequencing data was primarily performed with the OCP pipeline integrated with Oncomine® Knowledgebase from Life Technologies, supplemented by the MolecularMD proprietary pipeline. Only the genetic alterations with clinical utility were selected as the final output from the data pipeline. Of these detected by OCP, the SBS and indels were confirmed by the Illumina TruSeq, Ion Torrent AmpliSeq commercial cancer panels, or by Sanger sequencing. Any CNVs detected were confirmed by FISH, if possible, and detected fusions were confirmed by RT-PCR or FISH.

Results: No clinically relevant genetic alterations were detected from the negative control FFPE-GM12878, indicating the high specificity of the OCP. High specificity was achieved, in part, using stringent filters, which removed error prone regions from analysis. The LOD for SBS and short indel detection was 5%, as assessed by TruQ-1 and TruQ-2, each containing 15 variants. While the exact LOD for gene fusion detection is currently under evaluation, the 100%, 50% and 20% fusion were detected in the RNA samples from serially diluted EML4-ALK or SL34A2-ROS1 fusion into the FFPE-GM12878 RNA. Four known gene amplifications (MYC, CCND1, MDM2, AKT1) with CNV from 5.4X to 14.5X in HCC1143, and a 15.7X MYC amplification in NCI-H2122 were detected. In addition, an EML4-ALK.E13A20 fusion was detected in a lung cancer FFPE sample, and confirmed by FISH. The analytical sensitivity and the specificity of the OCP are currently assessed with 26 clinical samples and three engineered FFPE samples.

Conclusions: These results demonstrate the high sensitivity and specificity of OCP. With as little as 10 ng RNA and 20 ng DNA, OCP provides comprehensive screening of patient FFPE tumor specimens for the detection of a broad spectrum of clinically relevant genetic alterations.

Citation Format: Peng Fang, Zhenyu Yan, Weihua Liu, Jennifer Biroschak, Paul Labrousse, Jennifer Wright, Cindy Spittle, Chad Galderisi, Li Jin. Oncomine® Cancer Panel: simultaneous detection of clinically relevant hotspot mutations, CNVs, and gene fusions in solid tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4261. doi:10.1158/1538-7445.AM2015-4261

Abstract B297: Clinical assessment of MUC1 protein expression in FFPE tissue: Developent and validation of an immunohistochemistry assay as a predictive assay for response to MUC1 vaccines

Background: Mucin-1 (MUC1, epithelial membrane antigen, EMA) is a transmembrane glycoporotein that is expressed on the apical membrane of epithelial cells of many tissues including breast, prostate, lung, pancreas, stomach, ovaries, intestines, and kidneys. In tumor cells, MUC1 is often overexpressed and aberrantly glycosylated, revealing new epitopes that can trigger a cytotoxic T-cell response. Several approaches are currently being pursued for targeting MUC1 in cancer therapy, mainly focused on vaccines targeting MUC1 antigens. We have developed an immunohistochemistry (IHC) assay to measure MUC1 expression in formalin fixed paraffin-embedded (FFPE) tissues as a potential biomarker assay for MUC1-targeted therapies.

Methods: The IHC assays were developed using the Ventana Benchmark™. The MUC1 antibody was obtained from Ventana. The assay was validated using the recommended protocol supplied by the vendor. The assay was optimized using cell pellets generated from cell lines overexpressing MUC1 cDNA as well as an FFPE breast tumor tissue array which consists of 16 cases of breast cancer paired with adjacent normal tissues. In addition, tissue specimens obtained from remnant material from surgery or autopsy were used for the assay optimization and validation.

Results: Specificity of the staining was demonstrated by positive staining with T47D breast cancer cell line as well as a B16 cell line overexpressing MUC1 and no staining with HMEC human mammary epithelial cells and the control B16 cell line. Thirty-six FFPE tumor tissues from lung, ovary, breast, colon, kidney, liver, thyroid, and prostate were evaluated for MUC1 expression. Tumor positive specimens were scored based on expression in at least 25% of tumor cells. In addition, staining intensities as well as patterns i.e. apical or membrane polarization and cytoplasmic patterns were noted. 29/36 specimens had positive MUC1 staining; negative staining was reported in thyroid, liver, colon, and prostate tumor tissues. In addition, evaluation of the array of paired normal/tumor breast tissues showed specific staining of tumor tissues in 14/16 specimens with no or little staining in the matched normal tissue. Interestingly, one of the tumor tissues exhibited very distinct apical staining pattern that was unique in the set of 16 breast cancer tissues.

Conclusions: We have developed a robust IHC assay for MUC1 that can clearly distinguish MUC1 expression in normal versus tumor tissue as well as demonstrated variable MUC1 expression in a variety of tumor tissues. We are currently exploring the utility of the assay as a biomarker for ONT-10, a novel liposomal cancer vaccine that is currently in clinical trials.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B297.

Citation Format: Sabita Sankar, Jennifer Wright, Kevin Klucher, Scott Peterson, Chad Galderisi. Clinical assessment of MUC1 protein expression in FFPE tissue: Developent and validation of an immunohistochemistry assay as a predictive assay for response to MUC1 vaccines. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B297.

Abstract A42: Evaluation of HGF and MET protein expression in NSCLC tumor specimens from patients previously treated with targeted or chemotherapies

Background: Although epidermal growth factor receptor (EGFR) T790M mutation accounts for majority of the resistance to the first generation EGFR tyrosine kinase inhibitors (TKIs), activation of the MET pathway through increased expression of hepatocyte growth factor (HGF) or amplification of MET (the HGF receptor) has also been identified as a resistance mechanism in patients. Effective treatment of patients that have progressed on first-generation TKIs requires diagnostic assays that detect the major resistance mechanisms and direct therapy selection. We have developed immunohistochemistry (IHC) assays to detect both HGF and MET protein expression in formalin-fixed paraffin-embedded (FFPE) tissues, and evaluated expression levels in patients previously treated with EGFR TKIs or chemotherapy.

Methods: The IHC assays were developed using the Ventana Benchmark automated staining system. The MET antibody (SP44) was obtained from Ventana. Five different HGF antibodies from several vendors were evaluated. The assay was established using cell pellets generated from cell lines overexpressing HGF as well as a FFPE metastatic cancer tissue array. In addition, tissue specimens obtained from remnant material from surgery or autopsy were used for the assay optimization.

Results: The MET (SP44) assay was validated using the recommended protocol supplied by Ventana. Robust staining was observed in multiple FFPE samples, and both cytoplasmic and membranous staining were defined as positive. The expression was scored on the basis of intensity and fraction of positive cells. In contrast, among the 5 HGF antibodies tested for specificity, only the IBL antibody demonstrated HGF-specific staining in cell lines and the metastatic tissue array. The selected MET and HGF antibodies were used to evaluate a set of 25 NSCLC patient FFPE tissues. 19/25 specimens tested showed positive MET expression. Of these, 13 were 3+ whereas 6 were 2+ in terms of staining intensity. Additionally, 2 of the specimens with 2+ score exhibited predominantly cytoplasmic staining. In contrast, HGF expression was more variable with 5/24 with strong, 9/24 with weak and 10/24 with negative staining (one specimen was not evaluable for HGF). There was no clear correlation between MET and HGF staining patterns. In this sample set, there was not a clear correlation between MET or HGF expression and patient status as relapsed versus newly diagnosed.

Conclusions: We have developed robust assays for evaluation of MET and HGF expression in FFPE sections and applied these assays in analyzing 25 NSCLC patient specimens, documenting a higher than expected proportion of the samples as MET or HGF positive. A more expansive dataset, potentially evaluating factors beyond protein expression levels, will be needed to elucidate a relationship between MET pathway activation and response to EGFR TKIs.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A42.

Citation Format: Sabita Sankar, Jennifer Wright, Chad Galderisi. Evaluation of HGF and MET protein expression in NSCLC tumor specimens from patients previously treated with targeted or chemotherapies. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A42.

Abstract A208: Mutation detection in FFPE and plasma circulating DNA with a focused ALK-EGFR-KRAS Next-Generation Sequencing panel

Background: Mutations in ALK, EGFR and KRAS have well-established or anticipated clinical utility in predicting response to targeted therapies either approved or in development for patients with non-small cell lung cancer (NSCLC). Here we report results from a proof-of-concept study using a custom Ion AmpliSeq Next-Generation Sequencing (NGS) panel designed to sequence a range of clinically relevant exons in ALK, EGFR and KRAS genes in formalin fixed paraffin-embedded (FFPE) DNA and plasma circulating DNA.

Methods: The cumulative 2.1kb regions of interest (ROI) include exons 20-25 of ALK, exons 18-22 of EGFR, and exons 2-4 of KRAS, as well as the first 3 bp of the intron at the intron-exon boundaries. The custom panel was designed by Ion AmpliSeq Designer. Sequencing data were analyzed with Torrent Suite 3.4 and MolecularMD's proprietary analysis pipeline.

Results: The study demonstrated the robustness of the custom NGS assay with at least 90% of reads-on-target, an average coverage of above 5000x, and no less than 81% uniformity in the reads. In addition, the minimum coverage for each ROI in all the samples tested was no less than 1000x. The limit of detection (LOD) of the NGS assay, as determined using dilutions of cell line DNA standards, was 0.7% for single base substitution (SBS) mutations, and 1.2% for indels. In addition, the assay was able to quantify mutations with frequencies as low as ∼1% in plasma circulating DNA.

The assay detected 4 KRAS SBS mutations (G12C, G12D, G12V and Q61H), 2 EGFR SBS mutations (G719A, V769M) and 1 EGFR exon 19 deletion (G746-A750del) in 10 FFPE specimens tested from colon and lung cancer patients. These variants were each confirmed using Cancer Panels (Ion Torrent AmpliSeq and Illumina TrueSeq). The assay also detected T790M, L858R, V769M and the exon 19 deletion in EGFR in 7 plasma samples obtained from NSCLC patients. Each of these variants was confirmed by Sanger sequencing, Qiagen RGQ assay, or by MolecularMD's proprietary EGFR droplet digital PCR (ddPCR) assay. A low-frequency EGFR exon 19 deletion identified by the Qiagen RGQ assay was not seen in either the NGS assay or ddPCR assay. No other potential false negatives were identified in the custom NGS assay.

Conclusions: This study demonstrates the feasibility of creating a sensitive and specific ALK-EGFR-KRAS focused NGS assay that covers broader regions of the target genes than the hotspots represented in commercial panels. With a DNA input of merely 20ng of FFPE DNA, or 1-2ng of the plasma circulating DNA, the assay was able to detect both SBS and small indels in the targeted regions. Given the low DNA input requirements and the capability of plasma-based testing, this assay and other custom NGS panels may enable routine monitoring of mutation status for relevant genes in patients with various solid tumors, and may ultimately inform clinical decision-making.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A208.

Citation Format: Peng Fang, Agus Darwanto, Zhenyu Yan, Weihua Liu, Kimberly Pelak, Jessica Kristof, Philip C. Mack, Sabita Sankar, Chad Galderisi, Jin Li. Mutation detection in FFPE and plasma circulating DNA with a focused ALK-EGFR-KRAS Next-Generation Sequencing panel. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A208.

Abstract 3509: Complementary analysis of LKB1/STK11 mutation and protein expression status using next-generation sequencing, Sanger sequencing and immunohistochemistry

Introduction: LKB1 (liver kinase B1)/STK11 (serine-threonine kinase 11) is a tumor suppressor that encodes a serine/threonine kinase which negatively regulates the mTOR (mammalian target of rapamycin) signaling pathway. Somatic mutations in LKB1 occur most notably in lung adenocarcinoma, cervical cancers and melanoma. Inactivation of LKB1 is caused by point mutations, homozygous deletions or promoter methylation. LKB1 mutation status is a predictive marker for responsiveness to both MEK and PI3K inhibitors. We have developed next-generation sequencing (NGS), Sanger sequencing and immunohistochemistry (IHC) assays to assess LKB1 mutation and protein expression status in a set of FFPE patient specimens.

Methods: For NGS, we used the Ion Torrent platform to sequence a 4.4kb region of interest (ROI) around LKB1. A combination of TorrentSuite and in-house tools were used for alignment, variant calling and prioritization of variants. Sanger sequencing was used to validate the presence and absence of variants with a frequency of at least 10% that were identified by NGS. An IHC assay was developed using a commercially available antibody. These assays were validated using a combination of cell lines, a genetically engineered mouse model and FFPE tissue for specificity, sensitivity, reproducibility and concordance.

Results: 35 patient FFPE tissues from a variety of tumors including cervix, endometrium, pancreas, skin and lung were evaluated for LKB1 mutation status using NGS and IHC methods. About 96% of the coding region of LKB1 had sufficient sequencing coverage (read depth >500x) to reliably call low frequency somatic variants. Analytical validation using cell line dilutions demonstrated that our NGS assay is able to detect single base changes with frequencies as low as 2-5%, and small indels with frequencies as low as 5-10%.

We identified 9 coding and splice site variants in our preliminary analysis of 18/35 of the FFPE specimens. We compared the variants in 7 of these FFPE samples to the variants identified in these samples by Sanger sequencing, and found 100% concordance between the variant calls, for NGS variants with frequencies greater than 20%. Sanger sequencing in the remaining FFPE samples is ongoing, and lower frequency NGS variants will be confirmed by other methods. We compared the validated NGS variants with the IHC results to examine the correlation of sequencing results with protein expression analysis. In our preliminary analysis of the first 18 FFPE samples, all of the samples with an IHC score of zero or one (IHC negative) had either a nonsense (n=1) or missense (n=4) variant in STK11.

Conclusions: Our data suggest that accurate assessment of LKB1 status may require complementary methods including NGS and IHC methods.

Citation Format: Kimberly Pelak, Jennifer Wright, Zhenyu Yan, Agus Darwanto, Weihua Liu, Peng Fang, Jin Li, Sabita Sankar, Chad Galderisi. Complementary analysis of LKB1/STK11 mutation and protein expression status using next-generation sequencing, Sanger sequencing and immunohistochemistry. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3509. doi:10.1158/1538-7445.AM2013-3509

Abstract 3490: Highly sensitive detection of EGFR T790M on Ion Torrent PGM

Introduction: EGFR T790M mutation leads to treatment resistance in ∼50% of NSCLC patient undergoing TKI treatment. Early detection of the emergence of this resistance mutation allows for tailoring of the treatment regimen. Detection of EGFR T790M requires higher sensitivity techniques than those needed to detect EGFR activating mutations, and quantitative measurement of T790M may also provide value in monitoring disease progression. Here we demonstrate that our proprietary amplicon next-generation sequencing (NGS) on Ion Torrent PGM provides an attractive solution for T790M detection with the advantage of high sensitivity, specificity, and quantification capability.

Methods: We developed a proprietary library prep method for amplicon sequencing on the Ion Torrent PGM. Ion Torrent barcode sequences were refined in our validation to minimize barcode cross contamination. This optimization of barcodes allows for accurate mutation quantification, especially critical for variants with a frequency below 1%. This also added the benefit of higher throughput and lower cost. We employ this non-enrichment method to quantitatively measure T790M.

DNA from the NCI-H1975 cell line was serially diluted into wild-type NA19240 DNA to determine the limit of detection (LOD), sensitivity, specificity, accuracy and reproducibility of the method. We also used reference FFPE DNA from HorizonDx to validate the accuracy and robustness of the assay. We further validated the test by comparing the performance of our NGS method with ddPCR using the same sample set (serially diluted H1975 into wild-type DNA controls).

Results: Our data demonstrated that the LOD for T790M is 0.2%. And the method could reproducibly identify variants at these frequencies. With an input of 10ng of the HorizonDx FFPE DNA, we measured T790M frequency at 6.7%, which is concordant with the 6.5% mutation frequency reported by HorizonDx. We cross-validated our NGS assay with ddPCR, and the mutation frequencies detected by both platforms are nearly identical, and have a regression coefficient of 0.9995, with comparable LOD of 0.2%. Furthermore, our NGS assay allows us to detect other variants located in this amplicon, e.g. SNP Q787Q, with LOD at 1%. The phasing status of compound mutations can also be determined by this assay.

To further improve the sensitivity, an enrichment method was developed, and the enriched T790M was sequenced by PGM. This method can semi-quantitatively measure T790M frequency with LOD of 0.03%.

Conclusion: Our EGFR T790M NGS assay provides a unique option to reliably quantify T790M down to 0.2% with low DNA input. This highly sensitive and specific detection capability may enable earlier detection of emerging therapeutic resistance, particularly if FFPE results reported here extend to a more accessible specimen type, i.e. plasma circulating DNA, amenable to periodic patient monitoring.

Citation Format: Agus Darwanto, Peng Fang, Zhenyu Yan, Weihua Liu, Kim Pelak, Jessica Kristof, Sabita Sankar, Cynthia Spittle, Chad Galderisi, Jin Li. Highly sensitive detection of EGFR T790M on Ion Torrent PGM. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3490. doi:10.1158/1538-7445.AM2013-3490

Abstract 39: Clinical assessment of PTEN mutation in FFPE tissue: comparison of Sanger sequencing, immunohistochemistry and chromogenic in situ hybridization methods

Background: PTEN is a tumor suppressor that negatively regulates the PI3K signaling pathway by dephosphorylating PIP3, converting it to PIP2. PTEN loss of function results in activation of Akt and downstream signaling pathways, and has been associated with numerous cancers, most commonly endometrial cancer, glioblastoma, melanoma and prostate cancer. PTEN loss can be a result of multiple different aberrations which include mutations in the coding region leading to frame-shift or stop codons, genomic deletions as well as promoter methylation leading to loss of PTEN protein. Determination of PTEN status, both at the DNA and protein levels, may be important for clinical decision-making because loss of PTEN is associated with resistance to various targeted therapies, while inactivating mutations may confer sensitivity to therapeutics targeting PI3K pathway members. We have developed Sanger sequencing, immunohistochemistry (IHC) and chromogenic in situ hybridization (CISH) assays to assess PTEN mutation status in a set of FFPE patient specimens.

Methods: Our Sanger sequencing assay for PTEN was developed to detect known hotspot mutations in exons 5-8, which occur in the majority of PTEN mutations reported in the COSMIC database. The IHC and CISH assays were developed using commercially available reagents. All assays were validated using a combination of plasmids, cell lines and FFPE tissues for specificity, sensitivity, reproducibility and concordance.

Results: 22 patient FFPE tissue specimens from a variety of tumor types including colon, lung, pancreas, uterus and prostate were evaluated for PTEN mutation and expression status by both Sanger sequencing and IHC methods. Sequencing results were: 9 wild-type, 12 heterozygous mutant, and 1 hemizygous mutant. 7 of the 9 specimens reported as wild-type by sequencing exhibited normal protein expression levels by IHC, while 2 were PTEN negative by IHC, suggesting that mechanisms other than mutations in exons 5-8 contributed to the loss of expression of PTEN protein. These 2 specimens were further analyzed by CISH to determine copy number. Of the 13 specimens reported as mutant by sequencing, IHC protein expression results indicated that 6 were PTEN positive and 7 were PTEN negative, underscoring the observation that exon 5-8 mutation status alone is not sufficient to predict PTEN expression levels. Data on CISH analysis of the specimen that was hemizygous mutant by sequencing will be reported to confirm the copy loss.

Conclusion: The data suggest that additional mutations outside the exon 5-8 region as well as promoter methylation may result in loss of PTEN protein, and that accurate clinical assessment of PTEN mutation and protein expression status in FFPE tissues requires complimentary methods including Sanger sequencing, IHC and CISH methodologies.

Citation Format: Kellen Sakrison, Jennifer Wright, Eric Bruening, Stephane Wong, Cynthia Spittle, Sabita Sankar, Chad Galderisi. Clinical assessment of PTEN mutation in FFPE tissue: comparison of Sanger sequencing, immunohistochemistry and chromogenic in situ hybridization methods. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 39. doi:10.1158/1538-7445.AM2013-39

Activity of the fibroblast growth factor receptor inhibitors dovitinib (TKI258) and NVP-BGJ398 in human endometrial cancer cells

The recent identification of activating fibroblast growth factor receptor 2 (FGFR2) mutations in endometrial cancer has generated an opportunity for a novel target-based therapy. Here, we explore the therapeutic potential of 2 FGFR inhibitors, the multikinase inhibitor dovitinib (TKI258) and the more selective FGFR inhibitor NVP-BGJ398 for the treatment of endometrial cancer. We examined the effects of both inhibitors on tumor cell growth, FGFR2 signaling, cell cycle, and apoptosis using a panel of 20 molecularly characterized human endometrial cancer cell lines. Anchorage-independent growth was studied using soft agar assays. In vivo studies were conducted using endometrial cancer xenograft models. Cell lines with activating FGFR2 mutations (S252W, N550K) were more sensitive to dovitinib or NVP-BGJ398 when compared with their FGFR2 wild-type counterparts (P = 0.073 and P = 0.021, respectively). Both agents inhibited FGFR2 signaling, induced cell-cycle arrest, and significantly increased apoptosis in FGFR2-mutant lines. In vitro, dovitinib and NVP-BGJ398 were both potent at inhibiting cell growth of FGFR2-mutant endometrial cancer cells, but the activity of dovitinib was less restricted to FGFR2-mutant lines when compared with NVP-BGJ398. In vivo, dovitinib and NVP-BGJ398 significantly inhibited the growth of FGFR2-mutated endometrial cancer xenograft models. In addition, dovitinib showed significant antitumor activity in FGFR2 wild-type endometrial cancer xenograft models including complete tumor regressions in a long-term in vivo study. Dovitinib and NVP-BGJ398 warrant further clinical evaluation in patients with FGFR2-mutated endometrial cancer. Dovitinib may have antitumor activity in endometrial cancer beyond FGFR2-mutated cases and may permit greater flexibility in patient selection.

Angiosarcoma developing after curative induction chemotherapy and radiotherapy for locally advanced squamous cell carcinoma of the larynx

BACKGROUND

Angiosarcoma arising after radiation is described in breast cancer but occurs elsewhere. Here, we present an angiosarcoma of the neck occurring after curative chemoradiation.

METHODS

This is a case of angiosarcoma developing 5 years after curative therapy for T3N0 squamous cell carcinoma of the supraglottic larynx. Therapy consisted of 3 cycles of induction cisplatin/5-fluorouracil chemotherapy followed by radiotherapy. The patient did well until developing a rapidly progressive lesion of the left neck. Examination showed a 7-cm mass and biopsy revealed angiosarcoma. CT scans assessed the local extent of the tumor and ruled out metastatic disease prior to initiating therapy.

RESULTS

Therapy consisted of 4 cycles of paclitaxel chemotherapy. At completion, examination revealed mild induration of the neck with near-complete resolution of the mass. Imaging confirmed this excellent response.

CONCLUSION

This rare therapy-related second malignancy developed after curative larynx-preserving treatment. Paclitaxel was an effective therapy in this setting.

Effects of fluvastatin treatment on lipid profile, C-reactive protein trend, and renal function in dyslipidemic patients with chronic renal failure

The purpose of this trial was to evaluate the effects of fluvastatin on the lipid pro-file and on renal function, as measured by creatinine clearance, in dyslipidemic patients with chronic renal failure. In this 8-month prospective, open-label, randomized, parallel-group trial, 130 patients (70 men and 60 women), after a 2-month washout period following previous lipid-lowering treatments, were randomly assigned to fluvastatin XL 80 mg given once daily (80 patients) or to standard treatment (50 patients). Mean total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and triglyceride values after 3 and 6 months of treatment with fluvastatin showed statistically significant improvement compared with standard treatment. Improved renal function, as measured by creatinine clearance, was observed at the end of the 6-month treatment period in approximately 65% of patients treated with fluvastatin. The increase in creatinine clearance consistently reached 10% to 15% of baseline values. A statistically significant reduction in C-reactive protein (CRP) over baseline values was observed in approximately 75% of patients treated with fluvastatin. Furthermore, mean values of CRP for the fluvastatin standard treatment groups, respectively, were 6.78 and 10.19 at 3 months and 4.47 and 11 at 6 months. Both treatments were well tolerated. No major adverse events were noted. Results of this study suggest that fluvastatin treatment in patients with chronic renal failure is effective in improving the lipid profile, and it demonstrates good safety and tolerability. Furthermore, fluvastatin may contribute to improved nephroprotection in this patient population.

Inability of L22 ribosomal protein alteration to increase macrolide MICs in the absence of efflux mechanism in Haemophilus influenzae HMC-S

BACKGROUND

Haemophilus influenzae HMC-C with high-level macrolide resistance after multi-step selection by clarithromycin reverted spontaneously and became hypersusceptible to macrolides.

OBJECTIVE

Determination of macrolide resistance mechanism(s) in hypersusceptible and hyperresistant strains.

METHODS

The presence of macrolide efflux in the strains was studied by radioactive erythromycin accumulation. Ribosomal mutations were investigated by sequencing. The possible role of acrAB clusters in macrolide resistance was studied by sequencing and expression analysis.

RESULTS

The parent strain had no ribosomal alteration, but both high-level resistant and hypersusceptible strains had R88P mutations in ribosomal protein L22. Radioactive macrolide accumulation studies pointed to the presence of macrolide efflux in the high-level resistant and parent strains, but not in the hypersusceptible derivative. Transformation of hypersusceptible strains using total DNA from the parent strain restored the macrolide efflux system in the hypersusceptible strain, which was confirmed by MIC levels and radioactive erythromycin accumulation similar to that of the mutant resistant strain. Analysis of sequence and transcription of acrAB gene clusters showed no significant differences between resistant and hypersusceptible derivatives.

CONCLUSION

Mutation in ribosomal protein L22 alone does not confer high-level macrolide resistance unless efflux is present.

Late symptomatic venous stenosis in three hemodialysis patients without previous central venous catheters

It is well known that catheters placed in the subclavian or internal jugular veins may develop stenosis in the vein in which the catheter lies. Because the arteriovenous fistula (AVF) relies on good venous outflow, patients with ipsilateral central venous stenosis are subject to the malfunctioning of AVF. Until now, no data were published on patients showing central vein stenosis (CVS) without a previous central venous catheter (CVC) or a pacemaker. In this article, we report on 3 hemodialysis patients manifesting CVS ipslateral to AVF. None of these patients previously had undergone CVC. The stenosis observed had characteristics and symptoms similar to those observed in stenoses consequent to CVC. We concluded that CVS also may occur in subclavian or axillary veins proximal to a working AVF in hemodialysis patients who have never had a CVC and in the absence of compressive phenomena.

Plasmapheresis in severe forms of myasthenia gravis

In this study we introduce a new combination treatment of plasma exchange (PE) and high daily doses of prednisone for severe forms of myasthenia gravis (MG). The clinical efficacy of the combined therapy has been tested in 18 patients suffering from severe forms of MG. The protocol included 5 sessions of PE, performed in a range of 15 days, 1 session every 3 days, with concurrent administration of oral prednisone (1 mg/kg of body weight), starting at the first session of PE and given daily for at least 3 months. At the end of the entire cycle of PE, almost complete recovery (more than 90% of the initial clinical score) was obtained in 8 of 18 patients while an improvement between 60 and 90% of the initial score was achieved in 9 of 18 patients. An early improvement was noted 24 h after the beginning of plasmapheresis in 11 of 18 patients. No recurrence of symptoms was reported after 36 months of follow-up for 17 patients. The administration of steroid therapy was never followed by an early exacerbation of myasthenic symptoms as reported when it is administered in the absence of concomitant PE. According to our results, we can conclude that high doses of oral prednisone therapy in simultaneous association with PE lead to successful control of severe forms of MG, significantly superior to the therapeutic strategies until now adopted and reported in literature.