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  • American Association for Cancer Research (AACR)  (7)
  • April, Craig  (7)
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  • American Association for Cancer Research (AACR)  (7)
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  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 72, No. 8_Supplement ( 2012-04-15), p. 3179-3179
    Abstract: High throughput sequencing technologies open up a new dimension in cancer genomics by enabling the characterization of cancer genomes at base-pair resolution. To date, the majority of large-scale genomics projects rely on fresh-frozen biospecimens in their studies, which are difficult to obtain and often lack long-term clinical data. Unlike fresh-frozen samples, archived formalin-fixed paraffin-embedded (FFPE) tissues are more readily accessible, and are often associated with known clinical outcomes and more complete clinical annotations. However, sequencing library preparation methods need to be further optimized with regard to applicability to FFPE samples. To test whether next-generation sequencing technologies could overcome previously reported artifacts associated with formalin fixation and report accurate sequencing results, we compared whole-genome and targeted enrichment DNA sequencing data obtained from five FFPE tumor samples for which matching frozen tissues were available. We successfully generated sequencing libraries using 1 µg of genomic DNA as input material and a modified TruSeq™ sample preparation protocol. We designed a custom enrichment pool targeting exons from 215 cancer-related genes and utilized this pool to pull-down and sequence approximately 1.3 Mb region of the genome with an average 400x coverage depth to test if deep sequencing would improve validation of tumor-specific somatic mutations. We used the Illumina sequence analysis pipeline and the Windows-based second generation DNA sequencing software NextGENe® to analyze the data and identify sequence variations that are different from the human reference genome. CNV detection was overall higher among FFPE samples compared with fresh-frozen samples, demonstrating that tissue processing impacts sequencing data quality. We obtained good concordance in variant calls between matched FFPE and fresh-frozen samples. Discordant variant calls were mainly due to low depth of coverage in the regions where variant calls were made. Improvements to DNA sequencing methods for archived samples will significantly enhance cancer research and will result in more reliable prediction of individual cancer therapies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Res earch; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3179. doi:1538-7445.AM2012-3179
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2012
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 70, No. 8_Supplement ( 2010-04-15), p. 1144-1144
    Abstract: We are developing novel sample preparation technologies for genomic analysis of circulating tumor cells (CTCs): a new cell-sorting device for purification of single CTCs from a tube of blood; and highly sensitive and quantitative genomic technologies for single cell analysis using Illumina's microarray and next-generation sequencing platforms. We have prototyped a new ultra-rare cell enrichment device that produces cell samples compatible with Illumina's nucleic-acid analysis platforms. Sorting is performed on whole blood samples with no pre-fractionation, to minimize the genetic alteration of CTCs. To validate the performance of our cell sorting device, we have monitored the recovery of LNCaP prostate cancer cells spiked into 7.5ml normal blood samples at concentration of 10 cells/7.5ml. For ease of analysis, the cancer cells were labeled with cell tracker dye and leukocyte nuclei in blood were labeled with Hoechst 33342 dye. Cancer cells were immunomagnetically labeled in blood with EpCAM beads and then isolated by our cell sorter. We found that the capturing efficiency of our platform was 60% ± 24% for 10 cells/7.5ml samples. The purity of cancer cells among contaminating white blood cells was 91% ± 6%, after a second round of extraction of individual cancer cells. The entire purification protocol of CTCs from 7.5ml blood samples takes 2 hours. This platform has been earlier validated for CTC isolation from blood samples of breast cancer patients and is currently under evaluation for prostate and ovarian cancer patients. We are also developing new genomic technologies for whole-genome expression profiling, somatic mutation analysis, and transcriptome sequencing of purified CTCs: a) using a Multiple Displacement Amplification (MDA)-based protocol and a 300K-SNP chip readout, we were able to obtain 88.3% and 93.9% call rate, and 97.4% and 99.9% call accuracy with direct cell lysis from 1 and 5 LNCaP cells, respectively. We also detected the chromosomal amplification and loss-of-heterozygosity; b) with our current RNA amplification protocol, we were able to generate reproducible expression profiles, R2 = 0.37 and 0.75, from 1 and 10 cell inputs, respectively. In addition, the expression profiles correlated well with those obtained with standard 100 ng total RNA input, R2 = 0.36 and 0.72, respectively; c) we have also developed next-generation sequencing protocols to profile single-cell transciptomes. We have introduced a new platform for isolation of small numbers of CTCs from patient blood samples that are compatible with Illumina genomic assays. Our gDNA and RNA amplification protocols work with direct cell lysates; no need to extract DNA or RNA from single cells. The protocols are compatible with Illumina microarray and next-gen sequencing platforms. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1144.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2010
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  • 3
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2010
    In:  Cancer Research Vol. 70, No. 8_Supplement ( 2010-04-15), p. 1149-1149
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 70, No. 8_Supplement ( 2010-04-15), p. 1149-1149
    Abstract: We are developing highly sensitive and quantitative genomic technologies for genetic and expression analysis of single cells or trace amount of DNA/RNA materials, using microarray and next-generation sequencing platforms. We have tested various Multiple Displacement Amplification (MDA)-based protocols under a variety of reaction conditions. With our current protocol and a 300K-SNP chip readout, we were able to obtain 88.3% and 93.9% call rate, and 97.4% and 99.9% call accuracy with direct cell lysis from 1 cell and 5 cells, respectively. We are also developing RNA amplification methods for high-throughput expression profiling of single cells. With our current protocol, we were able to generate reproducible expression profiles, R2 = 0.73 and 0.77, using 10 pg and 50 pg total RNA input, respectively. In addition, the profiles correlated well with those obtained with standard 100 ng total RNA input, R2 = 0.61 and 0.77, respectively. Our data show that sequencing of single-cell transcriptomes can clearly distinguish embryonic stem cells from embryonic fibroblasts and tumor cells. We are currently using these technologies to study medical specimens such as circulating tumor cells and cancer stem cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1149.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2010
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  • 4
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2011
    In:  Cancer Research Vol. 71, No. 8_Supplement ( 2011-04-15), p. LB-268-LB-268
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 71, No. 8_Supplement ( 2011-04-15), p. LB-268-LB-268
    Abstract: Formalin-fixed archival tissues represent an invaluable resource for cancer research, since they are widely available and afford correlations of historical clinical data with gene expression signatures thereby facilitating better disease classification and prediction. While FFPE tissue is commonly available in block form, it is also standard practice to archive sectioned slices (AS-FFPE), often at room temperature, which further degrades genetic material due to oxidation. Because of these limitations, gene expression studies using FFPE material are usually performed on material derived from freshly cut blocks and not AS-FFPE samples. Previous mRNA data generated on freshly cut FFPE blocks for two independent liver cancer sample sets yielded gene expression signatures which classified hepatocellular carcinoma (HCC) samples into three subclasses (Cancer Res 2009, 69: 7385) and cirrhotic liver (CL) samples into two (good and poor survival) groups (N Engl J Med 2008, 359:1995). Here, using the WG-DASL HT assay (29K probes), we report on our efforts to use RNA derived from 5-year old AS-FFPE samples that were obtained from a subset of the previously assayed liver cancer sample sets, to generate clinically informative gene expression profiles. With a passing quality control filter of & gt;80% probes detected (p & lt; 0.01) we were able to obtain good quality data for 64/83 (77%) and 37/48 (77%) of the HCC and CL samples, respectively. On average, for the two sample sets, the sample reproducibility across all 29K probe intensities was R2 ∼ 0.85. We next performed prediction analysis using a nearest template prediction method and compared the results with that originally predicted for each of the two sample set. With a confidence threshold of p & lt; 0.05, 38/64 (59%) of the passing HCC samples yielded a prediction with an accuracy of 95% and an error rate of 5%. At the same confidence threshold (p & lt; 0.05), 13/37 (35%) of the passing LC samples yielded a prediction with an accuracy of 69% and an error rate of 31%. Together our results suggest that, despite degradative events such as oxidation and hydrolysis that further fragment archived FFPE sections, gene expression signatures derived from AS-FFPE samples can accurately classify disease states and provide clinically relevant prognoses. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-268. doi:10.1158/1538-7445.AM2011-LB-268
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2011
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 24 ( 2013-12-15), p. 7222-7231
    Abstract: Ovarian cancer is a clinically and molecularly heterogeneous disease. The driving forces behind this variability are unknown. Here, we report wide variation in the expression of the DNA cytosine deaminase APOBEC3B, with elevated expression in the majority of ovarian cancer cell lines (three SDs above the mean of normal ovarian surface epithelial cells) and high-grade primary ovarian cancers. APOBEC3B is active in the nucleus of several ovarian cancer cell lines and elicits a biochemical preference for deamination of cytosines in 5′-TC dinucleotides. Importantly, examination of whole-genome sequence from 16 ovarian cancers reveals that APOBEC3B expression correlates with total mutation load as well as elevated levels of transversion mutations. In particular, high APOBEC3B expression correlates with C-to-A and C-to-G transversion mutations within 5′-TC dinucleotide motifs in early-stage high-grade serous ovarian cancer genomes, suggesting that APOBEC3B-catalyzed genomic uracil lesions are further processed by downstream DNA "repair" enzymes including error-prone translesion polymerases. These data identify a potential role for APOBEC3B in serous ovarian cancer genomic instability. Cancer Res; 73(24); 7222–31. ©2013 AACR.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 6
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 23, No. 14 ( 2017-07-15), p. 3794-3801
    Abstract: Purpose: Recent progress in understanding the molecular biology of epithelial ovarian cancer has not yet translated into individualized treatment for these women or improvements in their disease outcome. Gene expression has been utilized to identify distinct molecular subtypes, but there have been no reports investigating whether or not molecular subtyping is predictive of response to bevacizumab in ovarian cancer. Experimental Design: DASL gene expression arrays were performed on FFPE tissue from patients enrolled on the ICON7 trial. Patients were stratified into four TCGA molecular subtypes. Associations between molecular subtype and the efficacy of randomly assigned therapy with bevacizumab were assessed. Results: Molecular subtypes were assigned as follows: 122 immunoreactive (34%), 96 proliferative (27%), 73 differentiated (20%), and 68 mesenchymal (19%). In univariate analysis patients with tumors of proliferative subtype obtained the greatest benefit from bevacizumab with a median PFS improvement of 10.1 months [HR, 0.55 (95% CI, 0.34–0.90), P = 0.016]. For the mesenchymal subtype, bevacizumab conferred a nonsignificant improvement in PFS of 8.2 months [HR 0.78 (95% CI, 0.44–1.40), P = 0.41] . Bevacizumab conferred modest improvements in PFS for patients with immunoreactive subtype (3.8 months; P = 0.08) or differentiated subtype (3.7 months; P = 0.61). Multivariate analysis demonstrated significant PFS improvement in proliferative subtype patients only [HR, 0.45 (95% CI, 0.27–0.74), P = 0.0015]. Conclusions: Ovarian carcinoma molecular subtypes with the poorest survival (proliferative and mesenchymal) derive a comparably greater benefit from treatment that includes bevacizumab. Validation of our findings in an independent cohort could enable the use of bevacizumab for those patients most likely to benefit, thereby reducing side effects and healthcare cost. Clin Cancer Res; 23(14); 3794–801. ©2017 AACR.
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 4957-4957
    Abstract: Background: Prostate cancer (PCa) is a leading cause of cancer-related mortality worldwide. Many men treated for clinically localized PCa will be cured, however, 20 to 30% of men will relapse and some will experience metastatic-lethal (ML) progression. Gleason score (GS) is one of the best predictors of PCa aggressiveness, but additional tumor biomarkers may improve its prognostic accuracy. We developed a gene expression signature of GS to enhance prediction of PCa outcomes. Methods: Elastic Net regularization was used to construct a gene expression signature by contrasting tumors with GS 8-10 (high) vs. ≤6 (low) in The Cancer Genome Atlas (TCGA). Tumor tissue samples obtained at radical prostatectomy for a Fred Hutchinson (FH) patient cohort of men with localized PCa were used to generate genome-wide gene expression data. The gene expression signature was then evaluated for its ability to predict recurrence and ML progression in the FH patient cohort (N=503; NRecurrence=106; NML progression=27; mean follow-up for recurrence=8 years). Results: The expression signature includes transcripts representing 49 genes. In the FH cohort, the signature was associated with recurrence and ML progression with hazard ratios (HRs) for a 25% increase in the signature of 1.51 (95% CI: 1.24-1.82; P=2.7×10-5) and 2.41 (95% CI: 1.51-3.85; P=0.0002), respectively. Among patients with GS 7 tumors, the signature was also significantly associated with PCa recurrence (HR=1.38, 95% CI: 1.09-1.76; P=0.008) and ML progression (HR=2.42, 95% CI: 1.30-4.52; P=0.006). The signature’s area under the curve (AUC) for predicting recurrence and ML progression was 0.68 and 0.76, respectively. Compared to a model with pathological stage and GS only, the gene expression signature significantly improved the AUC for overall recurrence (3%, P=0.0003) and ML progression (7%, P=0.0004), particularly among patients with GS 7 tumors (recurrence: 5%, P=0.01; ML progression: 13%, P=0.009). Higher levels of the signature were associated with increased expression of genes in cell cycle-related pathways including G2M checkpoint, epithelial mesenchymal transition, and E2F targets pathways, and decreased expression of genes in several pathways including androgen response, estrogen response, oxidative phosphorylation, and apoptosis. Conclusion: The gene expression signature based on GS may improve the prediction of overall recurrence as well as ML progression in PCa patients after radical prostatectomy, in particular among men with GS 7 tumors. Citation Format: Min A Jhun, Milan S. Geybels, Jonathan L. Wright, Suzanne Kolb, Craig April, Marina Bibikova, Elaine A. Ostrander, Jian-Bing Fan, Ziding Feng, Janet L. Stanford. Gene expression signature of Gleason score is associated with prostate cancer outcomes in a radical prostatectomy cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4957. doi:10.1158/1538-7445.AM2017-4957
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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