Abstract
Colorectal cancer (CRC), a common malignancy, is a biologically heterogeneous disease. Next-generation sequencing (NGS) has enabled CRC characterization by identifying somatically mutated ...genes which now allow us to better define colorectal tumor subtypes (e.g. by mutated pathways). However, the relationship of such CRC subtypes to patient survival and genetic and lifestyle risk factors has not been comprehensively studied.
To identify somatic mutations in CRC cases, we designed a targeted AmpliSeq panel of CRC related genes and genomic regions informed by whole exome sequencing data from ~1,200 CRC cases. The sequencing was conducted on Illumina HiSeq 2500 with a mean coverage of 740x and 240x for DNA extracted from FFPE tumor tissues and matched normal samples, respectively. Strelka, MuTect, VarDict, and Varscan2 were used to identify somatic single nucleotide variants and indels. Sanger sequencing was performed to validate a subset of variants. To date, we have sequenced ~2,400 CRC tumors and matched control tissues from four studies participating in the Colon Cancer Family Registry (CCFR) and Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). In most tumors, we identified non-silent mutations in genes belonging to the WNT (77%), p53 (44%), IGF2/PI3K (22%), RTK-RAS (47%), and TGF-beta (26%) signaling pathways. Among the 15% of tumors that could be classified as hypermutated, based on the number of mutations, 39% exhibited non-silent mutations in MLH1, MLH3, MSH2, MSH6, and PMS2 and 41% exhibited non-silent mutations in POLE and POLD1.
In a subset of studies with available survival data, we used Cox regression to assess the association of hypermutation status and the presence of non-silencing mutations in key signaling pathways with overall (OS) and disease-specific (DSS) survival. OS and DSS were significantly more favorable in cases with hypermutated vs. non-hypermutated CRC (HR=0.77, 95% CI: 0.60-0.98, p=0.04 and HR=0.35, 95% CI: 0.22-0.57, p=2x10-5, respectively); these associations were most pronounced for POLE/POLD1 mutated hypermutated CRC (HR=0.69, 95% CI: 0.46-1.02, p=0.06, HR=0.21, 95% CI: 0.08-0.56, p=2x10-3, respectively). There was no significant association of mutations in WNT, p53, IGF2/PI3K, RTK-RAS, or TGF-beta pathways with survival (p>0.05).
The comprehensive molecular characterization of this large panel of CRC cases will support further studies of molecular subtypes of CRC with clinical, lifestyle, and environmental factors. A better understanding of molecular mechanisms of CRC will be valuable in developing strategies for prevention, diagnosis, and treatment of this life-threatening disease.
Citation Format: Syed Zaidi, Amanda Phipps, Tabitha Harrison, Catherine Grasso, Robert Steinfelder, Quang Trinh, Charles Connolly, Barbara Banbury, Adilya Rafikova, Philipp Hofer, Stefanie Brezina, Marios Giannakis, Xinmeng Jasmine Mu, Michael Quist, Charles Fuchs, Levi Garraway, Li Hsu, Lincoln Stein, Andrea Gsur, Shuji Ogino, Steven Gallinger, Polly Newcomb, Peter Campbell, Wei Sun, Thomas Hudson, Ulrike Peters. Deep targeted tumor sequencing of colorectal cancer cases to study associations of molecular subtypes with clinical, genetic, and lifestyle risk factors 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 1224.
Considering the high prevalence of colorectal cancer (CRC) and relatively high mortality there is strong interest in identification of clinically relevant biomarkers. Telomere shortening is supposed ...to contribute to genomic instability and crucially involved in process of carcinogenesis. Peripheral blood leukocyte (PBL) telomere length was previously investigated in several studies as potential biomarker for CRC but with controversial results. This prompted us to investigate relative PBL telomere length in association with different histological findings throughout the continuum of colorectal carcinogenesis in order to reflect the whole spectrum of putative CRC development in a large study involving 2011 individuals. The study based on the Colorectal Cancer Study of Austria (CORSA), including 384 CRC cases as well as age- and gender-matched 544 high-risk adenomas, 537 low-risk adenoma patients and 546 colonoscopy-negative controls. Relative expression of telomeric repeats and the single copy reference gene, albumin (T/S ratio) was determined using monochrome multiplex quantitative PCR (MMQPCR). Telomeres were found to be significantly longer in CRC patients compared to control subjects (
= 3.61x10
). Yet, no significant differences in telomere length could be detected for high-risk (
= 0.05956) and low-risk colorectal adenoma patients (
= 0.05224). In addition, results presented in this manuscript highlight the impact of various epidemiological factors on PBL telomere length and its involvement in CRC. However, further large studies also including colorectal adenomas are necessary to confirm these results.
Abstract Background In CF infants, normonatremic Na+ depletion (NNaD), identified by fractional Na+ excretion (FENa ) values < 0.5%, was recently linked to impaired growth. Our paper investigates the ...relationship between FENa and growth in CF children > 2 years. Methods FENa values were calculated in 35 CF and 24 control children, and tested for correlations with z -scores for weight, height and BMI. Results All CF children and controls had normal plasma Na+ concentrations. A total of 25 of 35 (71.4%) CF patients had decreased FENa values < 0.5% (group I). FENa results of 10 CF patients (group II) and 23/24 controls (group III) were normal. In Na+ -depleted CF children, compared to normal controls, mean z -scores for weight (− 0.18 ± 0.87 vs + 1.03 ± 0.57, p < 0.001), height (− 0.06 ± 0.89 vs + 0.53 ± 0.72, p = 0.009) and BMI (− 0.22 ± 0.87 vs + 1.00 ± 1.06, p < 0.001) were significantly reduced. Also, we found positive correlations between FENa values and z -scores for weight ( r = 0.521), height ( r = 0.292) and BMI ( r = 0.468), respectively. Conclusion NNaD may contribute to poor growth in CF.
Summary
Background and objectives
Indirect bonding (IDB) proved to be an effective method for appropriate bracket positioning in patients. Different methods and materials are available for ...fabricating transfer trays. This in vitro study was designed to measure and compare the transfer accuracy of two common IDB methods.
Materials and methods
Sixty stone models were fabricated and separated in two groups of 30 models each (15 working models, 15 patient models). After placing brackets on the working models, 30 IDB trays were made: 15 silicone (method I) and 15 double-vacuum forms (method II). With these trays, the brackets were transferred to the patient models. The bracket positions were scanned before and after the IDB procedure with an intraoral scanner. The linear and angular discrepancies were then determined digitally by measuring six different dimensions: occluso-cervical, mesio-distal, bucco-lingual, tip, rotation, and torque.
Results
The silicone trays showed fewer transfer discrepancies, on average, in all measured dimensions. There were significant differences between the methods in the occluso-cervical (P < 0.001), mesio-distal (P = 0.001), and torque (P = 0.044) dimensions. With both methods, 100 per cent of the horizontal and transversal measurements of both methods were within the clinically acceptable range of 0.25 mm. With method I, 98.5 per cent of the vertical and 95.9 per cent of the angular measurements were within the range of 0.25 mm and 1°, respectively. With method II, 94 per cent of the vertical and 84.8 per cent of the angular measurements were within the clinically acceptable range.
Conclusions
Although both transfer methods showed a high precision, silicone trays scored better in terms of accuracy than double-vacuum forms.
e20584
Background: During multimodal cancer therapy an acute lymphocytopenia occurs, which is associated with poor survival in inoperable stage III NSCLC patients. A prospective analysis of ...peripheral blood mononuclear cells (PBMCs) during multimodal treatment was performed to assess dynamic changes of leukocyte subpopulations after concurrent chemo-radioimmunotherapy (cCRT) in order to extract biomarkers to predict progression free survival (PFS). Methods: 20 patients (17 male, 3 female), at median age of 65.5 years (range 34 to 79), 11 suffering from adenocarcinoma, 8 squamous cell carcinoma, and 1 undifferentiated NSCLC, were enrolled in the study. They received thoracic radiotherapy (TRT, 2/20, 10%), cCRT (11/20, 55%), or cCRT with checkpoint inhibition (cCRT-ICI, 7/20, 35%), one patient (1/20, 5%) withdrew consent and was excluded from analysis. Patients were grouped into poor ( < 6months), intermediate (≥6 < 12 months), or favorable (≥12 months) PFS. Blood was analyzed via flow cytometry for leukocyte sub-populations at 9 time points. Here, we report on NK cells and focus on the time period starting after end of TRT until 6 months thereafter. The area under curve (AUC) of absolute cell counts for this period was calculated to provide an aggregate measure for the time-course dynamics. Results: NK cell counts were consistently low in all patients at the end of TRT. Patient-individual recovery of cell counts 6 months after RTend (expressed as the AUC) was observed, which was beneficially affected by consolidation ICI (one-tailed t-test, p = 0.031). Retrospective assignment of the AUC values to the PFS groups revealed a positive association of high AUC values with PFS. Patients with longest PFS (≥12 months; 9/19) had higher AUC values compared to patients with intermediate PFS (≥6 < 12 months; 5/19; t-test p = 0.043) or poor PFS ( < 6months; 5/19; p = 0.0018). The difference between AUC values of intermediate and poor PFS groups was also significant (p = 0.039). Conclusions: Patients who responded with early NK cell expansion after TRT, cCRT, or cCRT-ICI had significantly longer PFS compared to those without increase. Longitudinal monitoring of NK cells and calculating the AUC (RTend and 6 months thereafter), which reflects absolute cell counts, is a promising biomarker to predict PFS.
The quality of samples stored within a biobank relies on the specimen collection, the transportation, the pre-analytical processing and the long-term storage. Standard Operating Procedures (SOPs) are ...essential tools to guarantee the quality of samples.
The aim of this paper is to present an IT-supported tool (Pre-An Evaluation Tool) that allows assessing the compliance of current pre-analytical procedures (defined in SOPs) of a biobank with international guidelines. The Pre-An Evaluation Tool was implemented based on CEN technical specifications for pre-analytical procedures using REDCap.
The data collection instrument of the Pre-An Evaluation tool consists of more than 250 items related to the CEN technical specifications. In order to create a dynamic questionnaire, items following a branching logic were implemented.
The Pre-An Evaluation tool is a user-friendly tool that facilitates the assessment of the coverage of the CEN technical specifications by specific SOPs. This tool can help to identify gaps within SOPs and therefore contribute to the overall quality of biological samples stored within a biobank.
Abstract Background : X-ray repair cross complementation group 1 (XRCC1) plays a key role in base excision repair. The purpose of this study was to examine the association of two genetic ...polymorphisms in XRCC1 (rs1799782 and rs25487) with risk of colorectal polyps and colorectal cancer (CRC). Methods : In the ongoing colorectal cancer study of Austria (CORSA), a total of 3091 Caucasian participants was genotyped using 5′-nuclease TaqMan assays. Multiple logistic regression was applied to compare individuals of the control group against three different case groups namely CRC cases, high-risk and low-risk polyps. Results : The two investigated SNPs in XRCC1 were not found to be associated with neither CRC risk nor polyp risk. Comparing the CRC cases versus the controls the OR was 0.60 (95%CI 0.27–1.31) for the heterozygous polymorphic genotype of SNP rs1799782 and 1.47 (95%CI 0.81–2.65) for the homozygous polymorphic genotype of SNP rs25487. Comparing the high-risk polyp group versus the controls the OR was 2.64 (95%CI 0.61–11.42) for the homozygous polymorphic genotype of SNP rs1799782 and 0.89 (95%CI 0.60–1.33) for SNP rs25487, respectively. In an haplotype analysis also no statistically significant association was found. Conclusion : Our finding that none of the two investigated SNPs of XRCC1 were significantly associated with risk of CRC or polyps is consistent with the results of a recently published meta-analysis.
e20590
Background: There are no blood-based biomarkers for survival prediction in inoperable stage III NSCLC patients. We propose a method for calculation of novel area under curve (AUC) biomarkers ...of the dynamic change of multiple leukocyte subpopulations before, during, and after thoracic irradiation (TRT), chemoradiotherapy (CRT), and chemo-radio-immunotherapy (CRT-ICI) in this patient cohort. The extracted biomarkers identify patients with early progression after TRT. Methods: 20 patients (17 male, 3 female), at median age of 65.5 years (range 34 to 79) were enrolled in the study. The median follow-up time was 60 weeks. Eleven patients suffered from adenocarcinoma, 8 squamous cell carcinoma, and 1 undifferentiated NSCLC. They received TRT (2/20, 10%), CRT (11/20, 55%), or CRT-ICI (7/20, 35%). One patient (1/20, 5%) withdrew consent and was excluded from analysis. Primary endpoints were progression free survival (PFS) at 6 and 12 months. Patient blood was analyzed via flow cytometry for 7 circulating leukocyte populations at baseline, twice during radiotherapy, at the end of radiotherapy (RTend), and 10, 20, 35, 48, and 60 weeks after enrollment. We analyzed CD3
+
total T cells, CD4
+
T cells, CD8
+
T cells, CD19+/CD20
+
B cells, CD3
-
CD56
+
NK cells, CD56 bright NK cells, and CD56 dim NK cells. Here, we report on CD4
+
and CD8
+
T cells. The AUC from RTend to zenith of absolute cell counts provided aggregate measures for the time-course data. We performed hierarchical clustering and cluster characterization. Relevant features were selected by stepwise drop-out. Results: Clustering of the AUC between RTend and zenith for CD4
+
T cells and CD8
+
T cells delineated two prognostic groups. The favorable group was characterized by higher AUC values for CD4
+
and CD8
+
T cells compared to the unfavorable group. All patients (9/9, 100%) in the favorable group versus 36.4% (4/11) patients in the unfavorable group were progression-free at 6 months (Fisher´s exact test, two-tailed: p-value = 0.00472). This effect was observed as a trend with PFS at 12 months. Here 66.6% (6/9) of patients had PFS at 12 months in the favorable group versus 27.3% (3/11) in the unfavorable group (Fisher´s exact test, two-tailed: p-value = 0.175). There is a directly proportional relationship of the reported AUC values to PFS at 6 months and 12 months. Conclusions: Patients who responded with T cell expansion after immunogenic cell death by TRT, CRT, or CRT-ICI had significantly longer PFS compared to those without increase. Longitudinal monitoring of CD4
+
and CD8
+
T cells and the AUC from RTend to zenith is a promising biomarker for detecting early progression in the present study which is the subject of validation in an ongoing prospective study (PRECISION, NCT05027165).
Biosample collections and biobank information systems have become a key enabler for medical research. Therefore it is important to identify potentially relevant ontologies to semantically enrich ...information related to the biobanking domain.
We present a three-stage semi-automated evaluation approach which allows identifying relevant ontologies for the biobanking domain based on competency questions.
After identifying candidate biobanking ontologies (Stage 1) and competency questions (Stage 2), a six-step lexical evaluation approach, which assesses the coverage of concepts, properties or instances defined by competency questions is suggested and described (Stage 3).
We were able to perform a proof-of-concept evaluation of the OMIABIS ontology using our proposed three-stage approach together with a sample competency question.
Our evaluation approach allows a swift evaluation of candidate ontology entities based on a search for higher hierarchy key terms that exist in comprehensive medical vocabularies in order to state the usability of specific ontologies for the biobanking domain.
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