bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of a large NGS panel to hot-spot testing and small panels for the ability to accurately stratify advanced colorectal cancer patients to appropriate treatment pathways.
Authors: Lyle Stephen , Powers Winslow , Xu Jia , Huettner Claudia S. , Russell Meaghan , Protopopov Alexei 
Published: February 2017

510 Background: It is well established that KRAS mutations confer resistance to anti-EGFR therapy for colorectal cancer patients. More recently, other RAS mutations (NRAS and BRAF) have been determined to cause similar resistance and treatment guidelines are changing to incorporate testing of these genes as well. In addition, evidence suggests that mutations outside of hot-spot regions (Codons 12 & 13 of KRAS and NRAS; BRAF V600E) can also mediate therapeutic response. Recent data also suggest that other genes are relevant for treatment planning. We evaluated the ability of a 415 gene panel, CancerPlex, to accurately stratify colorectal cancer patients to appropriate treatment pathways compared to single gene “hot-spot” testing and small gene panels ( ≤ 50 genes). Methods: 70 colorectal cancer samples were analyzed by a large NGS panel of 415 genes that includes full-gene sequencing for SNPs, short insertions and deletions, and CNVs. All actionable mutations for each patient were recorded. We calculated relative frequencies of variants present in key oncogenic drivers to compare the effectiveness of current single gene testing with data obtained using a large panel. Testing was performed in a CLIA-certified laboratory (KEW Group Inc, Cambridge, MA). Results: 40% of samples contained a KRAS hot-spot mutation. When expanded to NRAS and BRAF hot-spots, an additional 8% of patients were identified as resistant to anti-EGFR therapy. An additional 15% of clinically significant variants were captured by full-gene sequencing of these 3 genes. Thus, > 25% of mutations lie outside traditional hot-spot regions. The majority of BRAF mutations were not V600E. The 415 gene panel identified clinically significant driver mutations in 99% of patients, while in smaller panels missed a significant number of actionable changes. In very few patients were actionable changes limited to KRAS, NRAS and BRAF hot-spots. Conclusions: Hot-spot testing and small gene panels can miss clinically significant genomic alterations. The detection of mutations outside of small panels and hot-spots may lead to more appropriate and successful treatment of colorectal cancers.
The quality of CT surveillance in resected colorectal cancer survivors at Veterans Health Administration facilities.
Authors: Sehdev Amikar , Sherer Eric A , Hui Sui , Wu Jingwei , Haggstrom David Andrew 
Published: February 2017

525 Background: Annual CT scan for three years is the current standard for post-treatment surveillance of colorectal cancer (CRC) survivors following curative treatment. We conducted a retrospective study with the primary aim to assess the patient, physician & organizational characteristics associated with quality of CT surveillance at Veterans Administration (VA) facilities. Methods: The Department of Veterans Affairs Central Cancer Registry was used to identify patients with stage I-III CRC between 2001 & 2009. Patient (age, race, marital status, income, priority status, year of diagnosis, stage, comorbidity), provider (primary care, specialist, other) & facility (region & organizational survey) characteristics were measured. In the primary analysis, we analyzed the impact of the 2005 ASCO update in CRC surveillance guidelines. In the secondary analysis, we included only patients diagnosed after 2005 to avoid any bias due to change in guidelines. Overuse (OU) was defined as > 1 CT/12 months, whereas underuse (UU) was defined as < 1 CT/12 months. The Wald test was used for univariate analysis & logistic regression models, for multivariate analysis. Results: The primary analysis demonstrated no change in the receipt of CT scans before & after the 2005 guideline update, as there was an increasing trend favoring more CT scans in general.In the secondary analysis, there were a total of 2,263 patients. Overall, UU (19.44% patients) occurred more often than OU (15% patients). In univariate analyses, age, stage, insurance status, provider type & facility region were significant in both OU & UU analyses (p <.001). Comorbidity was associated with OU only (p =.02). Different organizational characteristics were significant for OU & UU cohorts. Multivariate analyses showed younger age [AOR = 2.17 (1.65 - 2.86)] & higher stage [AOR =.71 (.59 -.85)] were associated with OU at p <.001. Older age [AOR = 1.89 (1.54 - 3.10)], lower stage [AOR =.63 (.49 -.81)] at p <.001 & facility region [AOR = 1.84 (1.01 - 3.35)] at p =.04 were associated with UU. Conclusions: While present, there did not appear to be substantial rates of UU or OU among CRC survivors in the VA. Age & cancer stage were associated with the quality of CT surveillance.
Sensitive, specific, and modular KRAS, NRAS, and BRAF assays for simultaneous detection of 30 important point mutations in colorectal cancer specimens.
Authors: Madanahally Divakar Kiran , Concepcion Alvin , Shea Jessica , Gupta Smriti , Kong Lilly 
Published: February 2017

547 Background: Point mutations in KRAS, NRAS, and BRAF are implicated in the oncogenic RAS/RAF/MEK/ERK pathway and are prognostic and predictive markers in treating metastatic colorectal cancer patients. Here, we report the performance of three single tube highly multiplex and modular KRAS/NRAS/BRAF Assays capable of detecting 30 point mutations from FFPE-extracted DNA on the fully automated Modaplex System. Methods: Primers for multiplex KRAS/NRAS/BRAF Assays to detect 13, 13, and 4 point mutations for KRAS, NRAS, and BRAF genes, respectively, were designed using proprietary technology. Analytical sensitivity of each mutation was assessed using mutation specific ultramer oligos or Horizon Dx Mockblock specimens. Analytical specificity was determined on known wild-type FFPE DNAs. The assays were tested on DNA extracted from clinical FFPE specimens that were characterized by pyrosequencing. Modaplex data on these specimens were compared to pyrosequencing for concordance. Results: The modular Modaplex KRAS/NRAS/BRAF point mutation panels detect and differentiate 30 mutations in the KRAS, NRAS, and BRAF genes in three wells. Each assay requires just 5 µL of clinical sample extract (10-50ng DNA per assay) with a setup time of 15-30 minutes. The total run time including data analysis and setup is 4 hours. The kit includes an internal control to determine mutation status; and calibration controls to determine amplicon size. Analytical studies demonstrate the assays are sensitive (number of copies detected in one reaction), selective (mutant to wild-type ratio), and specific (relative to wild-type genomic DNA background). Nearly 110 clinical FFPE samples were tested, and the assays showed more than 95% concordance with pyrosequencing method (98% for BRAF, 97% for KRAS, and 100% for NRAS). Conclusions: Modaplex KRAS/NRAS/BRAF assays provide an accurate and sensitive method of mutation detection. These automated multiplexed assays to detect key mutations in three genes can be performed on a single platform facilitating clinical or translational research. *Modaplex KRAS/NRAS/BRAF Assays are for Research Use Only. Not for clinical diagnostic use.
Demographic, tumor characteristics, and outcomes associated with SMAD4 mutation in colorectal cancer.
Authors: Mehrvarz Sarshekeh Amir , Overman Michael J. , Kee Bryan K. , Fogelman David R. , Dasari Arvind , Raghav Kanwal Pratap Singh , Vilar Sanchez Eduardo , Manuel Shanequa , Shureiqui Imad , Wolff Robert A. , Patel Keyur , Luthra Rajyalakshmi , Shaw Kenna Rael , Eng Cathy , Maru Dipen M. , Routbort Mark , Meric-Bernstam Funda , Kopetz Scott 
Published: February 2017

565 Background: SMAD4 regulates signaling in TGF-β pathway as inactivation of SMAD4 renders resistance of cells to TGF-β1-induced growth inhibition. Sporadic mutation of SMAD4 has been reported to be present in 8.6-25% of colorectal cancers (CRC), but the clinicopathologic features and outcomes associated with this mutation have not been described. Methods: Data for patients (pts) with metastatic or locally advanced unresectable CRC who received treatment at MD Anderson Cancer Center whose tumors underwent genotyping for SMAD4 mutation were reviewed and clinicopathologic characteristics, and survival outcomes were evaluated. Tumors were sequenced using a hotspot panel (Ion Torrent, Life Technology) predicted to cover 80% of the reported mutations in SMAD4, and further targeted resequencing that included full-length SMAD4 was performed on mutated ones by HiSeq (Illumina) with full exome coverage to an average depth of 800. Results: Among 616 pts (47.4% females) with CRC, 11.2% of pts (n = 69) had SMAD4 mutation by hotspot testing. SMAD4 mutation was associated with colon cancer versus rectal cancer (OR = 2.1, p = 0.01) and female gender (15% vs 8%, OR = 2.12, p = 0.004). There was no association between the presence of SMAD4 mutation and age, stage at the presentation, tobacco history, colonic location, presence of distant metastasis, histology, nor tumor grade. When compared to pts with wild-type SMAD4, those with SMAD4 mutation had shorter survival from date of testing (median survival of 20.2 months versus 14 months, respectively; log-rank, HR = 1.4, p = 0.014). Full-length sequencing was performed on mutated tumors and it confirmed that missense mutations in R361 and P356 in the MH2 domain were the most common, which are predictive of disruption of both homo- and hetero-oligomerization required for activation. Conclusions: This study is the largest retrospective study to date characterizing SMAD4 mutation in metastatic CRC, and demonstrates a prognostic role for this subgroup of CRC. The prevalence and spectrum of SMAD4 mutations is consistent with previous studies and data from TCGA. Further studies are required to evaluate the implication of the dysregulated TGF- β pathway on response to therapy.
Micro-RNAs in stage II colorectal cancer: Is there any role?
Authors: Mohamed Salem Eid , Allahloubi Nasr Mohamed Ali , Bahnassy Abeer Ahmed , Khorshid Ola , Gadelmola Mohamed Elsayed 
Published: February 2017

566 Background: Patients with stage II CRC have a varying survival outcome. Therefore, it is critical to identify new prognostic biomarkers that can help to identify more aggressive forms of the disease. The aim of this study was to identify the potential prognostic value of miRNAs in patients with stage II CRC. Methods: The study included 124 patients with stage II CRC who attended the NCI - Medical Oncology clinics, received treatment and followed-up during the period from January 2004 to December 2014. The expression levels of the five studied miRNAs were examined by qRT-PCR analysis. Additionally, blood samples were drawn from 41 patients recruited in the study in the last 3 years of recruitment to assess the level of miRNAs in blood. Results: In tumor tissues of 124 patients, miR-137, miR-145 and miR-320 were significantly under-expressed in 39.5%, 38.4% and 52.4% of cases, respectively while miR-21 and miR-498 were significantly over-expressed in 48.4% and 40.3%, respectively. On the other hand, assessment of these miRNAs in the blood of 41 cases revealed that miR-137, miR-145 and miR-320 were significantly under-expressed in 46.3%, 46.3% and 51.2% of cases, respectively while miR-21 and miR-498 were significantly over-expressed in 46.3% and 43.9%, respectively. The concordance between tissue and blood was weak with miR-320 and miR-145 (kappa 40-65%), intermediate with miR-498 and miR-137 (kappa 65-75%) while strong concordance has been achieved with miR-21 (kappa 75-85%). Performance status, over-expression of miR-21 and miR-498 and under-expression of miR-137, miR-145, and miR-320 were associated with significantly inferior DFS and OS in univariate analysis. In a multivariate analysis, deregulated miR-498 and miR-320 were independent prognostic factors for worse DFS, while over-expressed miR-498 and miR-21 were found to be independent prognostic factors for inferior OS. Conclusions: MiRNAs play an important role as prognostic markers in stage II CRC patients. Large-scale collaborative efforts are still absolutely essential to aid in determining the clinical potential of miRNAs as diagnostic, prognostic, and predictive biomarkers in CRC in order to achieve better survival outcomes.
Clinical and molecular assessment of response to regorafenib.
Authors: Kakizawa Nao , Suzuki Koichi , Takayama Yuji , Ichida Kosuke , Fukui Taro , Watanabe Fumiaki 
Published: February 2017

568 Background: Regorafenib provides anti-tumor effects in 3rd or 4th line for metastatic colorectal cancer patients (pts), but some of pts show severe adverse effects (AE). It is, therefore, crucial to select patients more likely benefit from regorafenib. Methods: Twenty pts were treated with regorafenib for metastatic colorectal cancer and 91 plasma samples from 16 pts were available for monitoring of circulating tumor DNA (ctDNA) in blood. The treatment response, adverse effects, progression-free survival (PFS), overall survival (OS) and morphologic response in CT image were evaluated. KRAS mutant ctDNA (MctDNA) was determined by digital PCR. Results: According to Response Evaluation Criteria in the Solid tumors (RECIST), 6 patients (30%) showed SD, and 8 pts (40%) exhibited PD. Median PFS was 1.2 months (range; 0.2-14.2 months), and median OS was10.6 months (range; 0.7-15.6 months). Treatments are continued for 4 pts but discontinued for others. The reasons of discontinuation were PD for 8 pts and AE for 7 pts. Seven pts showing AE include 3 pts with liver function disorder, 3 pts with severe fatigue and one pt with Grade 3 skin toxicity. Three pts with liver function disorder showed extensive multiple liver tumors. PS 2 was seen in 2 pts with severe fatigue. PFS in pts showing treatment discontinuation due to AE was 0.6 month but PFS in pts with other reasons rather than AE was 3.3 months. According to morphologic response criteria, 3 among 6 pts harboring SD in RECIST, showed optimal response in early period of the treatment. These 3 pts with morphological response showed better PFS such as 3.5, 5.3, and 14.2 months, respectively. Six pts displayed KRAS mutant ctDNA (MctDNA) in blood. Among them, 2 pts showed MctDNA during treatment and then exhibited tumor progression. Emergence of MctDNA was observed in one pt without KRAS mutation in tumor tissues. MctDNA was detectable in the blood of these 2 pts prior to radiographic detection of disease progression. Conclusions: Pts with extensive multiple liver tumor or poor PS unlikely benefit from Regorafenib. Pts with optimal morphologic response likely benefit from Regorafenib by adequate management of other AEs. In addition, monitoring of KRAS mutation in ctDNA could be predictive biomarker for treatment response.
Interaction of KRAS somatic mutation and colorectal carcinoma and its association with differential DNA methylation.
Authors: Jasmine Farzana , Kamal Mohammed , Roy Shantanu , Rahman Mustafizur , Raza Maruf , Paul Rupash , Hasan Kamrul , Haq Zahidul , Ahsan Habibul , Kibriya Muhammad Ghulam 
Published: February 2017

577 Background: We examined if KRAS somatic mutation in colorectal carcinoma (CRC) is associated with differential tumor DNA methylation. Methods: We did a genome-wide methylation assay (450K) for a total of 250 paired samples from 125 CRC patients (m = 72, f = 53) at different stages (stage 1: 25, stage II: 33 and stage III: 67). Of them 101 had left-sided CRC (descending colon to rectum); 30 had MSI, and 34 had somatic mutation in KRAS (rs112445441). Results: Frequency of KRAS mutation was not different between right and left-sided CRC (29% vs. 27%). But, like other series, MSI was more frequent in the right-sided tumor (54% vs. 17%, p = 0.003). In patients with wild type KRAS tumor (n = 91), paired comparison between tumor and corresponding normal tissue identified a total of 1244 tumor-specific differential methylation loci (DML) covering 532 genes that were significant at FDR 0.001 and magnitude of difference ≥ 20%; But similar analysis in patients with KRAS mutation (n = 34) revealed 7612 tumor-specific DML covering 2357 genes - suggesting an association of KRAS mutation and DNA methylation. We also found that MSI in tumor tissue was associated with DNA methylation change too. Next, we identified 726 genes that are markedly differentially methylated in tumor compared to corresponding normal tissue only in presence of KRAS mutation, irrespective of MSI status, staging, and location of tumor (KRAS mutation associated tumor-specific genes – list enriched in GO ontology “developmental process”, “biological regulation”). We also identified 241 genes that are differentially methylated in tumor compared to normal tissue irrespective of KRAS mutation, MSI status, staging, and location of tumor. (common tumor-specific genes) Conclusions: KRAS somatic mutation is independently associated with methylation changes in a number of genes related to carcinogenesis in CRC.
Alteration of ADCC-related genes as a novel predictor of efficacy of cetuximab (cet)-based chemotherapy in patients (pts) with metastatic colorectal cancer (mCRC) (JACCRO CC-05/06 AR).
Authors: Sunakawa Yu , Yang Dongyun , Cao Shu , Roberts Chris , Wang Eva , Moran Miriana , Astrow Stephanie H. , Thompson Debrah , Hsiang Jack , Zhang Wu , Tsuji Akihito , Takahashi Takehiro , Denda Tadamichi , Kochi Mitsugu , Shimada Ken , Takeuchi Masahiro , Fujii Masashi , Nakajima Toshifusa , Ichikawa Wataru , Lenz Heinz-Josef 
Published: February 2017

589 Background: Cet exerts its therapeutic effects not only through EGFR-signal blockade but also through antibody-dependent cell-mediated cytotoxicity (ADCC), mainly driven by natural killer (NK) cells. NK cells play a key role by releasing granzyme B (GZMB) via perforin (PRF1)-formed pores, leading to tumor cell apoptosis. CD137 (TNFRSF9) is expressed on NK cells, which regulates activation and proliferation of T cells. We hypothesized that genetic alteration in NK cell-mediated ADCC may serve as a predictor of cet in mCRC pts. Methods: Genomic DNA and RNA were isolated from tumor tissues of 77 KRAS exon2 wild-type (wt) pts enrolled in 2 Japanese phase II trials of cet plus oxaliplatin-based chemotherapy as 1st-line therapy, FOLFOX (n= 28/57, UMIN000004197) and SOX (n= 49/67, UMIN000007022). We evaluated associations between functional polymorphisms and gene expression of TNFRSF9, GZMB, and PRF1, and clinical outcome using PCR-based direct sequencing and molecular profiling panel (HTG EdgeSeq Oncology Biomarker Panel) based on next generation sequencing. Recursive partitioning (RP) method was also used to explore the associations. Results: In the population with median age of 63 years and follow-up time of 31.4 months (m), response rate (RR), median progression-free survival (PFS), and overall survival (OS) were 73 %, 10.0 m, and 33.9 m, respectively. TNFRSF9 rs161826 (A > G) was associated with PFS but not RR or OS in both univariate (any G vs A/A: 9.2 m vs 13.8 m, HR 1.75, P= 0.030) and multivariate analyses (P= 0.050). No association of rs161826 with gene expression was observed. PRF1 polymorphisms were not associated with outcome, while high PRF1 mRNA expression had association with shorter PFS (9.7 m vs 18.0 m, HR 2.60, P= 0.028), and it remained significant in multivariate analysis (P= 0.002). In RP analysis, PRF1 mRNA expression also showed significant association with PFS. Conclusions: TNFRSF9 rs161826 and PRF1 gene expression are significantly associated with PFS in pts with KRAS wt mCRC treated with cet-based chemotherapy. Gene expression and variation in NK cell-mediated ADCC may predict efficacy of cet (UMIN000010635). Clinical trial information: UMIN000010635.
The lymphocyte-to-monocyte ratio as a predictor of overall survival in comparison to established systemic markers of inflammation in resectable colorectal cancer.
Authors: Chan Joseph , Diakos Connie Irene , Chan David , Gill Anthony J , Engel Alexander , Clarke Stephen John 
Published: February 2017

593 Background: The prognostic significance of systemic inflammatory markers in colorectal cancer (CRC) such as the neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR) and modified Glasgow prognostic score (mGPS) have been well defined in literature. In addition, commonly utilized genetic markers such as combined BRAF-MMR status have also been found to be prognostic. Recent evidence suggests that the lymphocyte-to-monocyte ratio (LMR) may hold prognostic utility in CRC. However the LMR has still not been clearly defined in either its clinical utility or in comparsion to other established biomarkers. Methods: Consecutive patients from the Northern Sydney Local Health District undergoing curative surgical resection for colorectal cancer from January 1998 to December 2012 were collated. Of the 3281 patients identified, 1623 patients with complete pre-operative blood counts, BRAF-MMR IHC and clinicopathologic data were further analysed. Variables were analysed in univariate and then a multivariate cox regression model using forwards conditional method looking for association with overall survival (OS). Results: In multivariate analysis of 1623 patients, elevated LMR was associated with better overall survival (OS) (HR 0.565, 95% CI: 0.475-0.672, P < 0.001) independent of age (P < 0.001), T stage (P < 0.001), N stage (P < 0.001) and grade (P = 0.049). Other biomarkers such as NLR, PLR and combined BRAF-MMR status were not significantly associated with OS. In multivariate subgroup analysis of 389 patients with available mGPS data, LMR remained the only independently prognostic biomarker (HR 0.620, 95% CI: 0.437-0.880, p = 0.007). Conclusions: The LMR is an independent predictor of OS in CRC patients undergoing curative resection. Furthermore, the LMR appears to be superior to previously established biomarkers.
Histological tumor regression after preoperative chemotherapy for colorectal liver metastases: Correlations with radiological response and prognosis.
Authors: Inada Ryo , Iwamoto Shigeyoshi , Kaibori Masaki , Ishizaki Morihiko , Iida Hiroya , Matsui Kosuke , Oishi Masaharu , Matsumoto Tomoko , Michiura Taku , Inoue Kentaro , Kon Masanori , Hamada Madoka 
Published: February 2017

609 Background: The purpose of this study was to characterize histological tumor regression grade (TRG) to colorectal liver metastases (CLM) treated with preoperative chemotherapy followed by liver surgery, and to evaluate whether TRG correlates with radiological response and prognosis. Methods: This study included 30 patients with CLM treated by surgical resection after preoperative chemotherapy with oxaliplatin- or irrinotecan-based regimens with or without molecular target agents. TRG was determined by the amount of fibrosis and necrosis replaced from tumor cells, ranging TRG 0 (0%), 1 (1-24%), 2 (25-50%), 3 (51-99%), and 4 (100%). Results: TRG 0, 1, 2, 3, and 4 were observed in 0%, 6.7%, 10.0%, 66.7%, and 16.6% of the patients, respectively. There were no relations between TRG and regimen, including molecular target agents. As shown in the table, radiological response was not significantly correlated with TRG. Patients with histological major response (TRG 3+4) had better prognosis (MST; TRG 1+2 vs. 3+4: 20.0 vs. 50 months, P= 0.007), and a multivariate analysis identified histological major response as an independent good prognostic factor. Conclusions: In this analysis, histological TRG predicted survival after preoperative chemotherapy and resection for CLM. Preoperative radiological response could not evaluate TRG. [Table: see text]