Final year project presentation.2
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The document describes experiments to generate adenovirus vectors for cancer gene therapy using aqueous two-phase systems (ATPS). The methods section details growing adenovirus in HEK293T cells and purifying and quantifying the adenovirus. Results show cell densities for HEK293T, HeLa and HepG2 cells and infection percentages for different ATPS phases. The conclusions note unsuccessful virus quantification but identifies PEG600-ammonium sulfate as a promising ATPS that is time-effective, cost-effective and yields high virus amounts.
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Design of an Intelligent System for Improving Classification of Cancer Diseases
The methodologies that depend on gene expression profile have been able to detect cancer since its inception. The previous works have spent great efforts to reach the best results. Some researchers have achieved excellent results in the classification process of cancer based on the gene expression profile using different gene selection approaches and different classifiers
Early detection of cancer increases the probability of recovery. This thesis presents an intelligent decision support system (IDSS) for early diagnosis of cancer-based on the microarray of gene expression profiles. The problem of this dataset is the little number of examples (not exceed hundreds) comparing to a large number of genes (in thousands). So, it became necessary to find out a method for reducing the features (genes) that are not relevant to the investigated disease to avoid overfitting. The proposed methodology used information gain (IG) for selecting the most important features from the input patterns. Then, the selected features (genes) are reduced by applying the Gray Wolf Optimization algorithm (GWO). Finally, the methodology exercises support vector machine (SVM) for cancer type classification. The proposed methodology was applied to three data sets (breast, colon, and CNS) and was evaluated by the classification accuracy performance measurement, which is most important in the diagnosis of diseases. The best results were gotten when integrating IG with GWO and SVM rating accuracy improved to 96.67% and the number of features was reduced to 32 feature of the CNS dataset.
This thesis investigates several classification algorithms and their suitability to the biological domain. For applications that suffer from high dimensionality, different feature selection methods are considered for illustration and analysis. Moreover, an effective system is proposed. In addition, Experiments were conducted on three benchmark gene expression datasets. The proposed system is assessed and compared with related work performance.
Plenary presentation saturday 11 7_dr. lucie bruijn
This document discusses opportunities and challenges for developing therapies for ALS. It summarizes that over 25 genes have been linked to ALS risk and describes some of the major genes involved like SOD1, TDP43, FUS and C9orf72. Model systems and pathways identified from genes are providing new treatment targets. There are many drugs and approaches in clinical trials. The document outlines the ALS Association's research strategies like establishing a translational program and consortium initiatives to accelerate drug development. Biomarkers, stem cell models and automated microscopy are providing new tools to study mechanisms and do preclinical testing.
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...Thermo Fisher Scientific
Accurate detection of low-frequency somatic mutations as well as low level structural variants such as copy number variation (CNV) in circulating cell-free DNA (cfDNA) using blood samples from subjects previously diagnosed with cancer provides a potential non-invasive approach to monitor cancer status and evaluate cancer evolution in the future. We have previously reported the Oncomine™ Breast cfDNA Assay enables detection of somatic mutations in plasma down to a level of 0.1% variant allelic frequency in breast cancer relevant genes. Here we extend this technology to simultaneously detect single nucleotide variants (SNVs) as well as copy number variation (CNV) from a single cfDNA sample.KshivetsWSCTS2023_Brazil.pdf
OBJECTIVE: 5-survival (5YS) and life span after radical surgery for esophageal cancer (EC) pa¬tients (ECP) (T1-4N0-2M0) was analyzed. The importance must be stressed of using complex system analysis, artificial intelligence (neural networks computing), simulation modeling and statistical methods in combination, because the different approaches yield complementary pieces of prognostic information.
METHODS: We analyzed data of 557 consecutive ECP (age=56.6±8.9 years; tumor size=6±3.5 cm) radically operated (R0) and monitored in 1975-2023 (m=415, f=142; esophagogastrectomies (EG) Garlock=288, EG Lewis=269, combined EG with resection of pancreas, liver, diaphragm, aorta, VCS, colon transversum, lung, trachea, pericardium, splenectomy=168; adenocarcinoma=319, squamous=228, mix=10; T1=130, T2=115, T3=184, T4=128; N0=282, N1=70, N2=205; G1=157, G2=142, G3=258; early EC=111, invasive=446; only surgery=425, adjuvant chemoimmunoradiotherapy-AT=132: 5-FU+thymalin/taktivin+radiotherapy 45-50Gy). Multivariate Cox modeling, clustering, SEPATH, Monte Carlo, bootstrap and neural networks computing were used to determine any significant dependence.
RESULTS: Overall life span (LS) was 1876.9±2219.8 days and cumulative 5-year survival (5YS) reached 52%, 10 years – 45.5%, 20 years – 33.4%, 30 years – 26.9%. 187 ECP lived more than 5 years (LS=4271±2411.9 days), 99 ECP – more than 10 years (LS=5883±2296.6 days). 228 ECP died because of EC (LS=629.8±324.1 days). AT significantly improved 5YS (67.8% vs. 48.7%) (P=0.00084 by log-rank test). Cox modeling displayed that 5YS of ECP significantly depended on: phase transition (PT) N0—N12 in terms of synergetics, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), T, G, histology, age, AT, localization, prothrombin index, hemorrhage time, residual nitrogen, protein (P=0.000-0.019). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and
healthy cells/CC (rank=1), PT early-invasive EC (2); PT N0—N12 (3), erythrocytes/CC (4), thrombocytes/CC (5); stick neutrophils/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), eosinophils/CC (9), leucocytes/CC (10); monocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5-year survival of ECP after radical procedures significantly depended on: 1) PT “early-invasive cancer”; 2) PT N0--N12; 3) Cell Ratio Factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) EC characteristics; 9) EC cell dynamics; 10) tumor localization; 11) anthropometric data; 12) surgery type. Optimal diagnosis and treatment strategies for EC are: 1) screening and early detection of EC; 2) availability of experienced thoracoabdominal surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant ch
KshivetsWSCTS2023_Brazil.pdf
OBJECTIVE: 5-survival (5YS) and life span after radical surgery for esophageal cancer (EC) pa¬tients (ECP) (T1-4N0-2M0) was analyzed. The importance must be stressed of using complex system analysis, artificial intelligence (neural networks computing), simulation modeling and statistical methods in combination, because the different approaches yield complementary pieces of prognostic information.
METHODS: We analyzed data of 557 consecutive ECP (age=56.6±8.9 years; tumor size=6±3.5 cm) radically operated (R0) and monitored in 1975-2023 (m=415, f=142; esophagogastrectomies (EG) Garlock=288, EG Lewis=269, combined EG with resection of pancreas, liver, diaphragm, aorta, VCS, colon transversum, lung, trachea, pericardium, splenectomy=168; adenocarcinoma=319, squamous=228, mix=10; T1=130, T2=115, T3=184, T4=128; N0=282, N1=70, N2=205; G1=157, G2=142, G3=258; early EC=111, invasive=446; only surgery=425, adjuvant chemoimmunoradiotherapy-AT=132: 5-FU+thymalin/taktivin+radiotherapy 45-50Gy). Multivariate Cox modeling, clustering, SEPATH, Monte Carlo, bootstrap and neural networks computing were used to determine any significant dependence.
RESULTS: Overall life span (LS) was 1876.9±2219.8 days and cumulative 5-year survival (5YS) reached 52%, 10 years – 45.5%, 20 years – 33.4%, 30 years – 26.9%. 187 ECP lived more than 5 years (LS=4271±2411.9 days), 99 ECP – more than 10 years (LS=5883±2296.6 days). 228 ECP died because of EC (LS=629.8±324.1 days). AT significantly improved 5YS (67.8% vs. 48.7%) (P=0.00084 by log-rank test). Cox modeling displayed that 5YS of ECP significantly depended on: phase transition (PT) N0—N12 in terms of synergetics, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), T, G, histology, age, AT, localization, prothrombin index, hemorrhage time, residual nitrogen, protein (P=0.000-0.019). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and
healthy cells/CC (rank=1), PT early-invasive EC (2); PT N0—N12 (3), erythrocytes/CC (4), thrombocytes/CC (5); stick neutrophils/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), eosinophils/CC (9), leucocytes/CC (10); monocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5-year survival of ECP after radical procedures significantly depended on: 1) PT “early-invasive cancer”; 2) PT N0--N12; 3) Cell Ratio Factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) EC characteristics; 9) EC cell dynamics; 10) tumor localization; 11) anthropometric data; 12) surgery type. Optimal diagnosis and treatment strategies for EC are: 1) screening and early detection of EC; 2) availability of experienced thoracoabdominal surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5)AT
KshivetsWSCTS2023_Brazil.pdf
5-year survival of ECP after radical procedures significantly depended on: 1) PT “early-invasive cancer”; 2) PT N0--N12; 3) Cell Ratio Factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) EC characteristics; 9) EC cell dynamics; 10) tumor localization; 11) anthropometric data; 12) surgery type. Optimal diagnosis and treatment strategies for EC are: 1) screening and early detection of EC; 2) availability of experienced thoracoabdominal surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant chemoimmunoradiotherapy for ECP with unfavorable prognosis.
Stephanie Allen-Diagnóstico prenatal no invasivo y diagnóstico genético repro...
Stephanie Allen-Diagnóstico prenatal no invasivo y diagnóstico genético repro...Fundación Ramón Areces
This document provides an overview of non-invasive prenatal diagnosis (NIPD) for single gene disorders using cell-free fetal DNA. It summarizes the development and validation of two NIPD approaches through the NIPSIGEN study: 1) Bespoke assays for specific mutations and 2) Relative haplotype dosage analysis using SNPs to track inheritance of mutated genes. It reports on the clinical implementation of these approaches in the West Midlands Regional Genetics Lab for conditions like DMD/BMD, SMA, CF, and CAH. Results from over 50 NIPD tests conducted to date show 100% accuracy compared to invasive testing. The document concludes by outlining the clinical service and pathways that are now availableRadiomics and Deep Learning for Lung Cancer Screening
The document summarizes research on using radiomics and deep learning approaches for lung cancer screening. It describes:
1) Using radiomic features like shape, texture, and intensity from lung nodules on CT scans and an SVM-LASSO model to classify nodules with 87.9% sensitivity and 78.2% specificity, outperforming the Lung-RADS system.
2) A deep learning model developed for a Kaggle competition that achieved 67.4% accuracy on nodule classification but only ranked 99th due to overfitting issues without enough data.
3) Future work could integrate quantification of nodule characteristics like spiculation with plasma biomarkers to improve diagnostic accuracy.
Flow Cytometry Training : Introduction day 1 session 1
Flow Cytometry Training talks - part 1
This forms the first session of the Garvan Flow , Flow Cytometry Training course. this is a 1 1/2 day training course aimed at giving new and experienced researchers a better understanding of cytometry in medical and biological research.
Development of Quality Control Materials for Characterization of Comprehensiv...
Development of Quality Control Materials for Characterization of Comprehensiv...Thermo Fisher Scientific
Targeted next-generation sequencing (NGS) panels can detect hundreds of mutations in key genes using amplification based and hybrid-capture based NGS technologies. Although NGS technology is a powerful tool, optimizing and characterizing test performance on hundreds of variants is extremely challenging, time consuming, and expensive. Samples must be sourced, variants identified and orthogonally confirmed, then quantified and diluted. This effort is then multiplied across dozens of samples, and then samples must be run over many runs and days to assess assay reproducibility, precision, sensitivity, etc. In this study, we developed a novel reference material, experimental design, and analysis pipeline that allows for highly streamlined NGS assay characterization, enabling thorough test characterization across 500+ variants within only 6 runs.PHSC 620 Presentation Final
This document outlines a study examining the effects of different cell culture plate coatings on Alpha Mouse Liver 12 (AML12) cells. The coatings tested were collagen, matrigel, and non-coated plates. The study aimed to characterize cell morphology, growth rates, mRNA and protein expression, and sensitivity to acetaminophen toxicity when cultured on different coatings. Results found no significant differences in growth rates, morphology, or toxicity responses between plate coatings. mRNA expression analysis found only actin and albumin expression from cells on collagen plates, and all targets from matrigel plates but not at levels above non-coated plates. Overall, the coatings did not produce the expected enhanced characterization of the AML12
Predictive Analytics of Cell Types Using Single Cell Gene Expression Profiles
Conducted domain independent predictive analysis pipeline using R for cell type predictions. Applied many predictive analytics models, and machine learning techniques.
Assessment of TP53 Mutation Status in Breast Tumor Tissue using the "Ion Ampl...
Assessment of TP53 Mutation Status in Breast Tumor Tissue using the "Ion Ampl...Thermo Fisher Scientific
TP53 mutations are found in 30% of breast tumors and are associated with poor prognosis in distinct subtypes of breast cancer. Direct sequencing is commonly used to obtain TP53 mutation status in tumor tissue, but has limitations in detection level and is time-consuming. Methods targeting hotspots is insufficient for TP53 analysis since the mutations are widely spread along the gene1. Here we describe the development of the Ion TorrentTM next-generation semiconductor sequencing and Ion AmpliSeqTM technology (Life TechnologiesTM).Aug2013 Heidi Rehm integrating large scale sequencing into clinical practice
This document discusses integrating large scale genomic sequencing into clinical practice. It describes how the Laboratory for Molecular Medicine at Partners Healthcare has transitioned from testing a few genes to now offering over 150 tests using next generation sequencing technologies. It also discusses the evolution of testing panels, moving from targeted panels to exome and genome sequencing. Validation of sequencing methods and challenges of variant interpretation are discussed.
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NK-cell therapy for Hematologic Malignancies. Prof. Akihiro Shimosaka
NK-cell therapy for Hematologic Malignancies. Prof. Akihiro Shimosaka
High Quality DNA Isolation Suitable for Ultra Rapid Sequencing
High Quality DNA Isolation Suitable for Ultra Rapid Sequencing
Maldi tof-ms analysis in identification of prostate cancer
Maldi tof-ms analysis in identification of prostate cancer
High Throughput Screening for ARV Drugs in HIV Prevention Studies
High Throughput Screening for ARV Drugs in HIV Prevention Studies
Design of an Intelligent System for Improving Classification of Cancer Diseases
Design of an Intelligent System for Improving Classification of Cancer Diseases
Plenary presentation saturday 11 7_dr. lucie bruijn
Plenary presentation saturday 11 7_dr. lucie bruijn
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
Ion Torrent™ Next Generation Sequencing – Detect 0.1% Low Frequency Somatic V...
Stephanie Allen-Diagnóstico prenatal no invasivo y diagnóstico genético repro...
Stephanie Allen-Diagnóstico prenatal no invasivo y diagnóstico genético repro...
Radiomics and Deep Learning for Lung Cancer Screening
Radiomics and Deep Learning for Lung Cancer Screening
Flow Cytometry Training : Introduction day 1 session 1
Flow Cytometry Training : Introduction day 1 session 1
Development of Quality Control Materials for Characterization of Comprehensiv...
Development of Quality Control Materials for Characterization of Comprehensiv...
Predictive Analytics of Cell Types Using Single Cell Gene Expression Profiles
Predictive Analytics of Cell Types Using Single Cell Gene Expression Profiles
Assessment of TP53 Mutation Status in Breast Tumor Tissue using the "Ion Ampl...
Assessment of TP53 Mutation Status in Breast Tumor Tissue using the "Ion Ampl...
Aug2013 Heidi Rehm integrating large scale sequencing into clinical practice
Aug2013 Heidi Rehm integrating large scale sequencing into clinical practice
Final year project presentation.2
- 1. The Generation of Adenovirus Vectors by ATPS Intended for Gene Therapy of Cancer SAQLAIN SULEMAN
- 2. Introduction • Background information Experiments • Method • Results Discussion • Conclusions • Future work
- 4. Genome
- 5. ATPS
- 6. Method Growing adenovirus Purifying adenovirus Quantification
- 7. HEK293T cell density Estimated cell density of subsequent plates 2.0 x 106 1.0 x 106 9.875 x 106 2.46875 x 106 Results HeLa cell density Estimated cell density on subsequent plates 8.125 x 106 2.03125 x 106 6.975 x 106 2.325 x 106 4.2625 x 106 1.065625 x 106 HepG2 cell density Estimated cell density on subsequent plates 7.0 x 104 1.75 x 104
- 8. Results ATPS 1 ATPS 2 ATPS 3 Phase system Phase ratio Phase one: PEG1000 – potassium phosphate 1: 1.17 Phase two: PEG8000 – potassium phosphate 1: 1.38 Phase three: PEG400 – ammonium sulphate 1: 2.57 Phase four: UCON970 – sodium citrate 1: 3.25 Phase five: PEG600 – ammonium sulphate 1: 1.67
- 9. Results
- 10. Results 0 10 20 30 40 50 60 70 80 90 100 Phase 1 Phase 2 Phase 3 Phase 4 PercentageofInfectedCells Upper Lower
- 11. Results 0 10 20 30 40 50 60 70 Phase 1 Phase 2 Phase 3 Percentageofinfectedcells Upper Phase Lower Phase
- 12. Conclusions Unsuccessful quantification of adenovirus vectors PEG600- ammonium sulphate ATPS: - Time effective - Cost effective - High yields
- 13. Acknowledgments Dr M. Themis Dr P. Hewitson & Dr S. Ignatova Hassan Khonsari Dr E. Makarov Ataun Bhatti
Editor's Notes
- The quantification of AdLacZ stained cells in ach phase can be seen in this graph. So as you can see, this indicates the majority of adenovirus vectors were purified into the upper PEG rich phase. This was with the exception of phase 4, which did not use PEG but UCON970 and sodium citrate. You can also see that phase 3 (PEG600/ammonium sulphate), though phase 2 (PEG8000-potasium phosphate) also purified the majority of adenovirus vectors into the upper PEG rich phase.