Programme d’analyse globale et intégrative du
micro-environnement tumoral - Vassili SOUMELIS, MD, PhD
Laboratoire d’Immunologie Clinique et Inserm U932
Circulating Tumor Cells (CTC) and pathological Complete Response (pCR) are strong independent prognostic factors in Inflammatory Breast Cancer (IBC) in a pooled analysis of two multicentre phase II trials (BEVERLY 1 & 2) of neoadjuvant chemotherapy combined with bevacizumab
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...Lawrence Greenfield
The OncoScan microarray offers high-quality copy number, genotype, and somatic mutation data with whole-genome coverage and high resolution in cancer genes for use with challenging FFPE samples.
The Molecular Analysis on Circulating Tumor Cells to Determine Prognostic and...QIAGEN
Circulating tumor cells (CTCs) is an emerging source used molecular cancer diagnostics. Through expression profiling of CTCs, it allows a deeper understanding about which metabolic pathways enable tumor cells to survive in the circulation, how they become resistant to a drug regimen, how they transform and adapt and, finally, which cellular markers should targeted for future therapies.
This webinar will introduce the AdnaTest CTC detection platform which has been proven in several clinical trials to provide prognostic and predictive information in breast, ovarian and prostate cancer. The platform by itself is still open for research and allows access to any potential target of interest. Join us to learn more about this novel platform, its technology and applications in liquid biopsy.
The document summarizes key information from a conference on gene profiling in clinical oncology, including:
1) New markers such as EGFR, KRAS, ALK, HER2, and PI3K mutations are defining subsets of non-small cell lung cancer and informing targeted therapy approaches.
2) Drugs like erlotinib, gefitinib, and crizotinib, which target EGFR, ALK, and c-MET mutations respectively, have shown efficacy in molecularly selected patient populations.
3) Comprehensive genomic profiling of lung tumors is needed to discover new targets, as around a third of cases still have unknown driver mutations.
Newer diagnostic tools in oncology such as liquid biopsies provide non-invasive approaches to diagnosing and monitoring cancer. Liquid biopsies analyze biomarkers found in bodily fluids and can detect circulating tumor cells, circulating tumor DNA, RNA, and exosomes shed by tumors into the bloodstream. These liquid biomarkers offer advantages over traditional tissue biopsies by being less invasive, able to capture the heterogeneity of tumors, and allow for real-time monitoring of treatment response and disease progression. Emerging technologies now allow liquid biopsies to provide genomic information that can help classify and treat cancers based on their molecular profiles rather than the organ or tissue of origin.
Circulating Tumor Cells (CTC) and pathological Complete Response (pCR) are strong independent prognostic factors in Inflammatory Breast Cancer (IBC) in a pooled analysis of two multicentre phase II trials (BEVERLY 1 & 2) of neoadjuvant chemotherapy combined with bevacizumab
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...Lawrence Greenfield
The OncoScan microarray offers high-quality copy number, genotype, and somatic mutation data with whole-genome coverage and high resolution in cancer genes for use with challenging FFPE samples.
The Molecular Analysis on Circulating Tumor Cells to Determine Prognostic and...QIAGEN
Circulating tumor cells (CTCs) is an emerging source used molecular cancer diagnostics. Through expression profiling of CTCs, it allows a deeper understanding about which metabolic pathways enable tumor cells to survive in the circulation, how they become resistant to a drug regimen, how they transform and adapt and, finally, which cellular markers should targeted for future therapies.
This webinar will introduce the AdnaTest CTC detection platform which has been proven in several clinical trials to provide prognostic and predictive information in breast, ovarian and prostate cancer. The platform by itself is still open for research and allows access to any potential target of interest. Join us to learn more about this novel platform, its technology and applications in liquid biopsy.
The document summarizes key information from a conference on gene profiling in clinical oncology, including:
1) New markers such as EGFR, KRAS, ALK, HER2, and PI3K mutations are defining subsets of non-small cell lung cancer and informing targeted therapy approaches.
2) Drugs like erlotinib, gefitinib, and crizotinib, which target EGFR, ALK, and c-MET mutations respectively, have shown efficacy in molecularly selected patient populations.
3) Comprehensive genomic profiling of lung tumors is needed to discover new targets, as around a third of cases still have unknown driver mutations.
Newer diagnostic tools in oncology such as liquid biopsies provide non-invasive approaches to diagnosing and monitoring cancer. Liquid biopsies analyze biomarkers found in bodily fluids and can detect circulating tumor cells, circulating tumor DNA, RNA, and exosomes shed by tumors into the bloodstream. These liquid biomarkers offer advantages over traditional tissue biopsies by being less invasive, able to capture the heterogeneity of tumors, and allow for real-time monitoring of treatment response and disease progression. Emerging technologies now allow liquid biopsies to provide genomic information that can help classify and treat cancers based on their molecular profiles rather than the organ or tissue of origin.
The document discusses circulating tumor cells (CTCs) and their clinical applications. It summarizes the work of Brian Kirby's research group, which works at the interface of microfluidics, microtechnology, and cellular analysis. The group has developed a technique called GEDI (Geometrically Enhanced Differential Immunocapture) to isolate CTCs from blood samples. GEDI leverages fluid mechanical design and size-dependent interactions to maximize capture of rare CTCs while eliminating leukocytes. The group has used captured CTCs from castrate-resistant prostate cancer patients to functionally evaluate drug responses by examining markers like tubulin bundling and nuclear accumulation of the androgen receptor. They are currently conducting the
The Presence and Persistence of Resistant and Stem Cell-Like Tumor Cells as a...QIAGEN
Epithelial ovarian cancer is the fifth leading cause of cancer-related deaths of women in the United States and Europe and ranks as the second most common type of gynecological malignancy. Most cases are diagnosed in advanced stages and although the response rates to platinum-based chemotherapy are high, the majority of patients nevertheless have poor survival rates. Although the reasons for these poor outcomes are likely to be multifactorial, one particular area of interest has recently focused on hematogenous tumor cell dissemination that has been shown to originate from disseminated tumor cells (DTCs) in the bone marrow (BM) and circulating tumor cells (CTCs) in the blood. Here, we demonstrate that the negative prognostic impact of CTCs and DTCs arise from specific cellular phenotypes and are associated with platinum-resistance and stem cell-associated proteins.
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...QIAGEN
A liquid biopsy is often described as a sensitive and specific blood test to detect circulating tumor cells (CTCs). CTCs, shed by both the primary and metastasized tumors, carry specific information about their origins and markers that will enable us to discover new diagnosis, prognosis and therapeutic targets. This slidedeck gives an overview of the recent progress in exploring the predictive potential of circulating biomarkers, including circulating tumor cells, circulating tumor DNA, microRNAs, long non-coding RNAs (lncRNAs) and exosomes. Addressing both biological and technical aspects, we detail the isolation and characterization of circulating biomarkers. Challenges and solutions are also featured.
1) High grade gliomas include grade III anaplastic astrocytomas, anaplastic oligodendrogliomas, and grade IV glioblastomas.
2) The standard of care for glioblastoma is maximal safe surgical resection followed by radiotherapy with concurrent and adjuvant temozolomide chemotherapy. Molecular markers like MGMT promoter methylation and IDH1 mutation provide prognostic information.
3) For anaplastic gliomas, the treatment involves surgical resection followed by radiotherapy. For anaplastic gliomas with 1p/19q codeletion, PCV chemotherapy is given before or after radiotherapy based on trials showing improved outcomes.
Maintrac liquid biopsy allows quantitative detection of circulating tumor cells without fixation, isolation, or enrichment. It uses fluorochrome-labeled antibody targeting EpCAM antigen on circulating tumor cells. In contrast, Cellsearch uses fixation and enrichment procedures that lead to loss of cells and antigenicity, resulting in dead cells. Comparison of the two methods using the same blood sample from a patient showed Maintrac detected more total events and circulating tumor cells than Cellsearch. Other CTC detection technologies have limitations such as relying too heavily on EpCAM expression or assuming CTCs are larger than blood cells. Cell-free tumor DNA analysis has problems like representing destroyed cells and additional mutations from DNA degradation.
CTC Detection and Molecular Characterization – Challenges and SolutionsQIAGEN
Circulating Tumor Cells (CTCs) have been extensively explored as circulating biomarkers in various cancers. Due to their rarity, heterogeneity and stem cell-like properties, detecting and profiling CTCs from blood samples is very challenging. In this webinar, Dr. Siegfried Hauch will introduce the well-known AdnaTests, which uses the Combination of Combinations Principle (COCP) to enable enriching and detecting CTCs in whole blood with high specificity and sensitivity, and how to overcome challenges in CTC enrichment and detection. The AdnaTests combine an immunomagnetic capturing method that increases purity, and is followed by molecular profiling of the captured CTCs. In addition, leukocyte contamination is another issue in CTCs detection and may lead to false positive results due to illegitimate expression of target genes or false interpretation. The AdnaWash is developed to reduce leukocyte contamination to such a level that whole gene panels can be analyzed while maintaining the required specificity and sensitivity.
This document describes a case of a 73-year-old man who presented with neurological symptoms and was found to have a brain lesion that was determined to be a solitary cerebral metastasis. Further investigation did not reveal the primary site. The patient underwent resection of the brain lesion, which was determined to be metastatic prostate cancer based on histopathology. Subsequent multiparametric MRI of the prostate revealed a lesion highly suggestive of prostate cancer. The document argues that multiparametric MRI of the prostate should be included in the diagnostic workup for patients presenting with cerebral metastases of unknown primary, as it may help identify occult prostate primary cancers earlier and guide more targeted treatment.
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathologyCirdan
Personalised / Precision Medicine has revolutionized cancer treatment and, in parallel, is also deeply transforming the way we practice tissue pathology. The aim of this talk is to briefly review the status of molecular diagnostic tests applicable to tissues and cells, as well as the main technical and conceptual areas that, in my opinion, will be dictating the evolution of tissue pathology and its integration with the molecular era. These areas are, among others – a) digital pathology in the pipeline of therapeutic pathology; b) tissue-based NGS and its integration in routine diagnostics; c) the promise of liquid biopsy diagnostics and its necessary “partnership” with tissue molecular testing; d) Pathology IT, databases and bioinformatics; and e) the training of future tissue pathologists. In the process of this review, it may be apparent that a solid, integrated, morpho-molecular approach to pathology may serve our patients better.
The document summarizes a study that aimed to predict clinical failure in patients with metastatic prostate cancer by identifying genes related to prostate cancer. Researchers analyzed gene expression levels of androgen receptor, estrogen receptor, and stem cell markers in cancer and stromal cells collected via laser capture microdissection from biopsy samples of 76 patients. Logistic regression analysis showed that expression of Sox2, Her2, and CRP in cancer cells and AR and ER in stromal cells highly predicted prostate-specific antigen recurrence. Ten factors were identified as prognostic for cancer-specific survival, including expression of Oct1, TRIM36, Sox2, c-Myc, AR, Klf4, ER, and clinical parameters. Patients were divided into risk
The document discusses criteria for evaluating genomic tests, including whether the test is clinically meaningful, how it was validated, reliability, practicality, and cost-effectiveness. It emphasizes that tests must provide value beyond traditional measures and require multiple studies as evidence. Genomic tests are developed through a process similar to drug development, starting with initial studies to develop relevant profiles which are then validated in additional studies with prospective design. Sources of variability must be rigorously controlled and clinical context is important.
Clinical Genomics for Personalized Cancer Medicine: Recent Advances, Challeng...Yoon Sup Choi
I reviewed recent advances, challenges, and opportunities to implement clinical cancer genomics. Case studies of advanced systems, such as Foundation Medicine, MI-ONCOSEQ are introduced for benchmark. A few fundamental limitations to establish personalized oncology are also discussed.
This document discusses genomic oncology and personalized medicine, using lung cancers as a model. It summarizes several key technologies that enable genomic oncology like cDNA microarrays, array CGH, and next generation sequencing. It provides examples of how these technologies have been used to classify cancers like diffuse large B-cell lymphoma and myelodysplastic syndrome, and identify genetic mutations that can guide targeted therapies for cancers like EGFR-mutated lung cancer.
The document discusses circulating tumor cells (CTCs) in lung cancer and summarizes some key challenges and applications. It notes that CTCs can be detected and enumerated using the FDA-approved CellSearch system, but this only captures EpCAM+ CTCs. Emerging technologies like ISET aim to detect a broader range of CTC subtypes. Studies show CTC counts correlate with stage and prognosis in lung cancer and may serve as pharmacodynamic biomarkers of treatment response. Characterizing CTC phenotypes like epithelial-mesenchymal transition could provide insights into metastasis. Circulating tumor microemboli are also detected in some patients and may help tumor cells survive in circulation.
Kshivets O. Esophageal and Cardioesophageal Cancer SurgeryOleg Kshivets
1) The 5-year survival of esophageal/cardioesophageal cancer patients after radical surgery significantly depended on the phase transition from "early-invasive cancer" and lymph node metastases.
2) The study analyzed data from 407 patients and found that 5-year survival was influenced by factors like the ratio of cancer cells to blood cells.
3) Neural network modeling correctly predicted 5-year survival based on phase transitions and cell ratio factors, with an accuracy of 100%.
Circulating cell free DNA is a potential tumor marker in a non-invasive blood test for the treatment and evaluation of cancer and recurrence monitoring. As circulating tumor DNA is often present at low frequencies within circulating cell free DNA, targeted sequencing on the Ion Torrent™ platform is an optimal tool or mutation detection with very little sample input required. Here, we demonstrate a complete workflow from isolation through molecular characterization of circulating tumor DNA. We have optimized a protocol using magnetic beads to isolate circulating cell free DNA. This protocol is easily automated to process up to 192 samples a day. It is also easily scalable for any input volume and can elute in volumes down to 15 μL resulting in no loss of low frequency alleles. We demonstrate comparable performance between this bead based isolation and column based isolation. We have completed molecular characterization of circulating cell free DNA using the multiplexing capabilities of AmpliSeq™ and the Ion PGM™. With the Ion AmpliSeq™ Cancer Hotspot Panel v2, we performed targeted sequencing of 50 genes of interest, covering 2800 COSMIC mutations. We demonstrate good reproducibility of amplicon representation as well as allelic frequencies. Through saturation studies and subsampling, we have determined the limit of detection of hotspots circulating cell free DNA on the Ion PGM™ to be below 1%. We further demonstrate proof of principle of this workflow on circulating cell free DNA and matched FFPE samples. Our results verify the accuracy and ease of our workflow. This protocol, from isolation through targeted sequencing, will not only result in a simple sample preparation for circulating cell free DNA but also facilitate rapid mutation detection to advance cancer research.
This document discusses biomarkers for lung cancer diagnosis, prognosis, and prediction of treatment response. It emphasizes the importance of tumor tissue samples for biomarker analysis but also explores opportunities for using liquid biopsies of blood and other body fluids. A variety of biomarker types are considered, including mutations, gene fusions, protein expression, and microRNAs. The need for standardized biomarker testing methodologies and validation is stressed, along with organizing reference laboratories through country networks.
Kshivets O. Lung Cancer: Optimal Treatment StrategiesOleg Kshivets
This document describes a study examining optimal treatment strategies for non-small cell lung cancer (NSCLC) patients. The study reviewed data from 535 NSCLC patients who underwent complete surgical resection between 1985-2008. Patients received one of three treatments: surgery alone (316 patients), surgery plus postoperative radiotherapy (102 patients), or surgery plus adjuvant chemoimmunoradiotherapy (117 patients). The study found that adjuvant chemoimmunoradiotherapy resulted in significantly higher 5-year survival rates compared to radiotherapy or surgery alone, especially for patients with lymph node involvement. Overall 5-year survival for the entire group was 63.6%, demonstrating the benefit of aggressive surgical resection and adjuvant therapies.
Types of immunotherapy
Oncology
cancer vaccines
adoptive T cell transfer
oncolytic viruses
monoclonal antibodies
cytokine
treatment of cancer with immunotherapy
Using liquid biopsies to study cancer dynamics and drug resistanceSpeck&Tech
Liquid biopsies, which analyze cell-free DNA in blood, can be used to study cancer evolution and drug resistance over time. By tracking genetic mutations in plasma samples taken at different time points, researchers can create a temporal map of how a tumor changes with and without treatment. This approach has identified biomarkers of drug resistance and shown that tumors with higher levels of circulating tumor DNA have worse outcomes and are less responsive to some therapies. While liquid biopsies hold promise for early cancer detection and precision medicine, more large clinical studies are still needed to validate their clinical utility.
1. Lung neuroendocrine tumors (NETs) have been increasing in incidence and include typical carcinoid (TC), atypical carcinoid (AC), large-cell neuroendocrine carcinoma (LCNEC), and small-cell lung cancer (SCLC).
2. Diagnosis of lung NETs can be difficult due to non-specific symptoms and frequently involves histopathological examination. Treatment depends on tumor grade and stage.
3. For localized disease, surgery is the primary treatment. For advanced or metastatic NETs, options include somatostatin analogues, targeted therapies like everolimus, chemotherapy, and peptide receptor radionuclide therapy.
This document summarizes a book about the creation and growth of Google. It describes how Larry Page and Sergey Brin founded Google based on their PhD research at Stanford. They created the PageRank algorithm to better rank search results and founded Google as their own search business in 1998. The document then discusses Google's culture of prioritizing the customer experience. It recommends the book for those interested in business, marketing, or learning more about one of the most influential technology companies.
This document is a curriculum vitae for Robert Dolman that summarizes his personal and employment details. It lists his name, address, contact information, date of birth, education history, and qualifications. It then outlines his work experience at four companies from 1997 to the present, describing his roles and responsibilities at each job. These roles involved color matching, formulation, customer service, production, and technical support within the polymer and printing industries. The CV also lists some of his skills, hobbies including music and sports, and his ambition to succeed in his career.
The document discusses circulating tumor cells (CTCs) and their clinical applications. It summarizes the work of Brian Kirby's research group, which works at the interface of microfluidics, microtechnology, and cellular analysis. The group has developed a technique called GEDI (Geometrically Enhanced Differential Immunocapture) to isolate CTCs from blood samples. GEDI leverages fluid mechanical design and size-dependent interactions to maximize capture of rare CTCs while eliminating leukocytes. The group has used captured CTCs from castrate-resistant prostate cancer patients to functionally evaluate drug responses by examining markers like tubulin bundling and nuclear accumulation of the androgen receptor. They are currently conducting the
The Presence and Persistence of Resistant and Stem Cell-Like Tumor Cells as a...QIAGEN
Epithelial ovarian cancer is the fifth leading cause of cancer-related deaths of women in the United States and Europe and ranks as the second most common type of gynecological malignancy. Most cases are diagnosed in advanced stages and although the response rates to platinum-based chemotherapy are high, the majority of patients nevertheless have poor survival rates. Although the reasons for these poor outcomes are likely to be multifactorial, one particular area of interest has recently focused on hematogenous tumor cell dissemination that has been shown to originate from disseminated tumor cells (DTCs) in the bone marrow (BM) and circulating tumor cells (CTCs) in the blood. Here, we demonstrate that the negative prognostic impact of CTCs and DTCs arise from specific cellular phenotypes and are associated with platinum-resistance and stem cell-associated proteins.
Liquid Biopsy Overview, Challenges and New Solutions: Liquid Biopsy Series Pa...QIAGEN
A liquid biopsy is often described as a sensitive and specific blood test to detect circulating tumor cells (CTCs). CTCs, shed by both the primary and metastasized tumors, carry specific information about their origins and markers that will enable us to discover new diagnosis, prognosis and therapeutic targets. This slidedeck gives an overview of the recent progress in exploring the predictive potential of circulating biomarkers, including circulating tumor cells, circulating tumor DNA, microRNAs, long non-coding RNAs (lncRNAs) and exosomes. Addressing both biological and technical aspects, we detail the isolation and characterization of circulating biomarkers. Challenges and solutions are also featured.
1) High grade gliomas include grade III anaplastic astrocytomas, anaplastic oligodendrogliomas, and grade IV glioblastomas.
2) The standard of care for glioblastoma is maximal safe surgical resection followed by radiotherapy with concurrent and adjuvant temozolomide chemotherapy. Molecular markers like MGMT promoter methylation and IDH1 mutation provide prognostic information.
3) For anaplastic gliomas, the treatment involves surgical resection followed by radiotherapy. For anaplastic gliomas with 1p/19q codeletion, PCV chemotherapy is given before or after radiotherapy based on trials showing improved outcomes.
Maintrac liquid biopsy allows quantitative detection of circulating tumor cells without fixation, isolation, or enrichment. It uses fluorochrome-labeled antibody targeting EpCAM antigen on circulating tumor cells. In contrast, Cellsearch uses fixation and enrichment procedures that lead to loss of cells and antigenicity, resulting in dead cells. Comparison of the two methods using the same blood sample from a patient showed Maintrac detected more total events and circulating tumor cells than Cellsearch. Other CTC detection technologies have limitations such as relying too heavily on EpCAM expression or assuming CTCs are larger than blood cells. Cell-free tumor DNA analysis has problems like representing destroyed cells and additional mutations from DNA degradation.
CTC Detection and Molecular Characterization – Challenges and SolutionsQIAGEN
Circulating Tumor Cells (CTCs) have been extensively explored as circulating biomarkers in various cancers. Due to their rarity, heterogeneity and stem cell-like properties, detecting and profiling CTCs from blood samples is very challenging. In this webinar, Dr. Siegfried Hauch will introduce the well-known AdnaTests, which uses the Combination of Combinations Principle (COCP) to enable enriching and detecting CTCs in whole blood with high specificity and sensitivity, and how to overcome challenges in CTC enrichment and detection. The AdnaTests combine an immunomagnetic capturing method that increases purity, and is followed by molecular profiling of the captured CTCs. In addition, leukocyte contamination is another issue in CTCs detection and may lead to false positive results due to illegitimate expression of target genes or false interpretation. The AdnaWash is developed to reduce leukocyte contamination to such a level that whole gene panels can be analyzed while maintaining the required specificity and sensitivity.
This document describes a case of a 73-year-old man who presented with neurological symptoms and was found to have a brain lesion that was determined to be a solitary cerebral metastasis. Further investigation did not reveal the primary site. The patient underwent resection of the brain lesion, which was determined to be metastatic prostate cancer based on histopathology. Subsequent multiparametric MRI of the prostate revealed a lesion highly suggestive of prostate cancer. The document argues that multiparametric MRI of the prostate should be included in the diagnostic workup for patients presenting with cerebral metastases of unknown primary, as it may help identify occult prostate primary cancers earlier and guide more targeted treatment.
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathologyCirdan
Personalised / Precision Medicine has revolutionized cancer treatment and, in parallel, is also deeply transforming the way we practice tissue pathology. The aim of this talk is to briefly review the status of molecular diagnostic tests applicable to tissues and cells, as well as the main technical and conceptual areas that, in my opinion, will be dictating the evolution of tissue pathology and its integration with the molecular era. These areas are, among others – a) digital pathology in the pipeline of therapeutic pathology; b) tissue-based NGS and its integration in routine diagnostics; c) the promise of liquid biopsy diagnostics and its necessary “partnership” with tissue molecular testing; d) Pathology IT, databases and bioinformatics; and e) the training of future tissue pathologists. In the process of this review, it may be apparent that a solid, integrated, morpho-molecular approach to pathology may serve our patients better.
The document summarizes a study that aimed to predict clinical failure in patients with metastatic prostate cancer by identifying genes related to prostate cancer. Researchers analyzed gene expression levels of androgen receptor, estrogen receptor, and stem cell markers in cancer and stromal cells collected via laser capture microdissection from biopsy samples of 76 patients. Logistic regression analysis showed that expression of Sox2, Her2, and CRP in cancer cells and AR and ER in stromal cells highly predicted prostate-specific antigen recurrence. Ten factors were identified as prognostic for cancer-specific survival, including expression of Oct1, TRIM36, Sox2, c-Myc, AR, Klf4, ER, and clinical parameters. Patients were divided into risk
The document discusses criteria for evaluating genomic tests, including whether the test is clinically meaningful, how it was validated, reliability, practicality, and cost-effectiveness. It emphasizes that tests must provide value beyond traditional measures and require multiple studies as evidence. Genomic tests are developed through a process similar to drug development, starting with initial studies to develop relevant profiles which are then validated in additional studies with prospective design. Sources of variability must be rigorously controlled and clinical context is important.
Clinical Genomics for Personalized Cancer Medicine: Recent Advances, Challeng...Yoon Sup Choi
I reviewed recent advances, challenges, and opportunities to implement clinical cancer genomics. Case studies of advanced systems, such as Foundation Medicine, MI-ONCOSEQ are introduced for benchmark. A few fundamental limitations to establish personalized oncology are also discussed.
This document discusses genomic oncology and personalized medicine, using lung cancers as a model. It summarizes several key technologies that enable genomic oncology like cDNA microarrays, array CGH, and next generation sequencing. It provides examples of how these technologies have been used to classify cancers like diffuse large B-cell lymphoma and myelodysplastic syndrome, and identify genetic mutations that can guide targeted therapies for cancers like EGFR-mutated lung cancer.
The document discusses circulating tumor cells (CTCs) in lung cancer and summarizes some key challenges and applications. It notes that CTCs can be detected and enumerated using the FDA-approved CellSearch system, but this only captures EpCAM+ CTCs. Emerging technologies like ISET aim to detect a broader range of CTC subtypes. Studies show CTC counts correlate with stage and prognosis in lung cancer and may serve as pharmacodynamic biomarkers of treatment response. Characterizing CTC phenotypes like epithelial-mesenchymal transition could provide insights into metastasis. Circulating tumor microemboli are also detected in some patients and may help tumor cells survive in circulation.
Kshivets O. Esophageal and Cardioesophageal Cancer SurgeryOleg Kshivets
1) The 5-year survival of esophageal/cardioesophageal cancer patients after radical surgery significantly depended on the phase transition from "early-invasive cancer" and lymph node metastases.
2) The study analyzed data from 407 patients and found that 5-year survival was influenced by factors like the ratio of cancer cells to blood cells.
3) Neural network modeling correctly predicted 5-year survival based on phase transitions and cell ratio factors, with an accuracy of 100%.
Circulating cell free DNA is a potential tumor marker in a non-invasive blood test for the treatment and evaluation of cancer and recurrence monitoring. As circulating tumor DNA is often present at low frequencies within circulating cell free DNA, targeted sequencing on the Ion Torrent™ platform is an optimal tool or mutation detection with very little sample input required. Here, we demonstrate a complete workflow from isolation through molecular characterization of circulating tumor DNA. We have optimized a protocol using magnetic beads to isolate circulating cell free DNA. This protocol is easily automated to process up to 192 samples a day. It is also easily scalable for any input volume and can elute in volumes down to 15 μL resulting in no loss of low frequency alleles. We demonstrate comparable performance between this bead based isolation and column based isolation. We have completed molecular characterization of circulating cell free DNA using the multiplexing capabilities of AmpliSeq™ and the Ion PGM™. With the Ion AmpliSeq™ Cancer Hotspot Panel v2, we performed targeted sequencing of 50 genes of interest, covering 2800 COSMIC mutations. We demonstrate good reproducibility of amplicon representation as well as allelic frequencies. Through saturation studies and subsampling, we have determined the limit of detection of hotspots circulating cell free DNA on the Ion PGM™ to be below 1%. We further demonstrate proof of principle of this workflow on circulating cell free DNA and matched FFPE samples. Our results verify the accuracy and ease of our workflow. This protocol, from isolation through targeted sequencing, will not only result in a simple sample preparation for circulating cell free DNA but also facilitate rapid mutation detection to advance cancer research.
This document discusses biomarkers for lung cancer diagnosis, prognosis, and prediction of treatment response. It emphasizes the importance of tumor tissue samples for biomarker analysis but also explores opportunities for using liquid biopsies of blood and other body fluids. A variety of biomarker types are considered, including mutations, gene fusions, protein expression, and microRNAs. The need for standardized biomarker testing methodologies and validation is stressed, along with organizing reference laboratories through country networks.
Kshivets O. Lung Cancer: Optimal Treatment StrategiesOleg Kshivets
This document describes a study examining optimal treatment strategies for non-small cell lung cancer (NSCLC) patients. The study reviewed data from 535 NSCLC patients who underwent complete surgical resection between 1985-2008. Patients received one of three treatments: surgery alone (316 patients), surgery plus postoperative radiotherapy (102 patients), or surgery plus adjuvant chemoimmunoradiotherapy (117 patients). The study found that adjuvant chemoimmunoradiotherapy resulted in significantly higher 5-year survival rates compared to radiotherapy or surgery alone, especially for patients with lymph node involvement. Overall 5-year survival for the entire group was 63.6%, demonstrating the benefit of aggressive surgical resection and adjuvant therapies.
Types of immunotherapy
Oncology
cancer vaccines
adoptive T cell transfer
oncolytic viruses
monoclonal antibodies
cytokine
treatment of cancer with immunotherapy
Using liquid biopsies to study cancer dynamics and drug resistanceSpeck&Tech
Liquid biopsies, which analyze cell-free DNA in blood, can be used to study cancer evolution and drug resistance over time. By tracking genetic mutations in plasma samples taken at different time points, researchers can create a temporal map of how a tumor changes with and without treatment. This approach has identified biomarkers of drug resistance and shown that tumors with higher levels of circulating tumor DNA have worse outcomes and are less responsive to some therapies. While liquid biopsies hold promise for early cancer detection and precision medicine, more large clinical studies are still needed to validate their clinical utility.
1. Lung neuroendocrine tumors (NETs) have been increasing in incidence and include typical carcinoid (TC), atypical carcinoid (AC), large-cell neuroendocrine carcinoma (LCNEC), and small-cell lung cancer (SCLC).
2. Diagnosis of lung NETs can be difficult due to non-specific symptoms and frequently involves histopathological examination. Treatment depends on tumor grade and stage.
3. For localized disease, surgery is the primary treatment. For advanced or metastatic NETs, options include somatostatin analogues, targeted therapies like everolimus, chemotherapy, and peptide receptor radionuclide therapy.
This document summarizes a book about the creation and growth of Google. It describes how Larry Page and Sergey Brin founded Google based on their PhD research at Stanford. They created the PageRank algorithm to better rank search results and founded Google as their own search business in 1998. The document then discusses Google's culture of prioritizing the customer experience. It recommends the book for those interested in business, marketing, or learning more about one of the most influential technology companies.
This document is a curriculum vitae for Robert Dolman that summarizes his personal and employment details. It lists his name, address, contact information, date of birth, education history, and qualifications. It then outlines his work experience at four companies from 1997 to the present, describing his roles and responsibilities at each job. These roles involved color matching, formulation, customer service, production, and technical support within the polymer and printing industries. The CV also lists some of his skills, hobbies including music and sports, and his ambition to succeed in his career.
2010 06 sq-03_lakdawalla_transcriptome_sequencingElsa von Licy
This document discusses RNA sequencing (RNA-Seq) and related techniques. It introduces total RNA sequencing which allows sequencing of all RNA molecules from a sample, including non-coding RNA, using less than 100ng of input RNA. Double-strand specific nuclease (DSN) normalization is described as a method to normalize total RNA sequencing libraries. The document also discusses applying RNA sequencing to analyze formalin-fixed paraffin-embedded (FFPE) samples.
This document summarizes a presentation on next generation epigenetic profiling. It introduces epigenetics and how epigenetic changes like DNA methylation are important in causing cancer in addition to genetic changes. It discusses using methyl-binding domain sequencing to discover genome-wide methylation patterns and biomarkers. Examples are given of specific genes like MGMT and BRCA1 that show methylation changes in cancer. Integrating deep sequencing data with other assays is described to better understand methylation patterns and their effects on gene expression and cancer. Developing targeted panels of cancer-related genes with known epigenetic alterations is discussed for clinical applications.
The document describes a study that used bisulfite sequencing and the Bismark alignment program to determine cytosine methylation rates in the chloroplast and whole genomes of Zea mays (maize). False-positive methylation rates were determined using the unmethylated chloroplast genome. Whole genome methylation rates in CpG, CHG and CHH contexts were found to be 87.0-87.8%, 73.4-74.9% and 2.9% respectively, consistent with previous studies. The proposed workflow for bisulfite sequencing included quality control with Trim Galore and FastQC followed by alignment with Bismark.
This document summarizes epigenetics quality control (EpiQC) efforts for several reference epigenome samples, including various epigenetic assays and datasets that have been or will be generated. It discusses completed whole-genome bisulfite sequencing, methylation array, and single molecule real-time sequencing data for several samples, as well as planned additional assays including oxidative bisulfite sequencing and single-cell reduced representation bisulfite sequencing. The goal is to establish high-quality reference epigenomes for use in assay development and validation through a collaborative consortium.
The APIC Enterprise Module provides a single point of control to simplify the operation of your enterprise network. The heart of the controller is a rich policy engine that translates higher order business intent into network configuration. The controller exposes a rich REST based API to allow other applications to take advantage capabilities of the controller and unlock the power of the underlying network infrastructure. This session will present the basic constructs of the controller such as the policy engine, and the capabilities of the REST API. There will be examples of how these capabilities can be integrated into other applications to simplify operations, improve security and enhance user experience.
The document discusses epigenetics and DNA methylation in oncology. It provides an introduction to epigenetics and how epigenetic modifications can regulate gene expression without changing DNA sequence. It then discusses using DNA methylation as an epigenetic biomarker for cancer, including prostate and bladder cancers. Specific methylated genes are highlighted as biomarkers for bladder cancer detection in urine samples from patients with hematuria. Validation study results show the biomarkers can accurately detect bladder cancer with high sensitivity and negative predictive value, reducing unnecessary cystoscopies.
Long-lasting alterations to DNA methylation and ncRNAs could underlie the eff...Ben Laufer
Fetal alcohol spectrum disorders (FASDs) are characterized by life-long changes in gene expression, neurodevelopment and behavior. What mechanisms initiate and maintain these changes are not known, but current research suggests a role for alcohol-induced epigenetic changes. We assessed alterations to adult mouse brain tissue by assaying DNA cytosine methylation and small noncoding RNA (ncRNA) expression, specifically the microRNA (miRNA) and small nucleolar RNA (snoRNA) subtypes. We found long-lasting alterations in DNA methylation as a result of fetal alcohol exposure, specifically in the imprinted regions of the genome harboring ncRNAs and sequences interacting with regulatory proteins. The findings of this study help to expand on the mechanisms behind the long-lasting changes in the brain transcriptome of FASD individuals.
Webinar Link: http://www.youtube.com/watch?v=fzdc0GIdCnA
Short intro epigenetics & nutrigenomics& the early impact of nutrition Norwich Research Park
Our “genes” are not fixed: “Plasticity” of the genotype by epigenetic mechanisms => important for the phenotypic impact of nutrition.
• Histone and DNA modifications have impact on gene transcription efficiency. Methylation (more stable) and acetylation (more flexible) have impact on chromatin
structures.
• Epigenetic modifications have impact on offspring, embryo development, ageing and disease development or prevention => example: Dutch Hunger Winter.
Health status of future parents are very important for the future health of children.
Early healthy nutrition & lifestyle essential for successful healthy life & “ageing”.
This document discusses epigenetics and provides an overview of key concepts. It begins with a brief history of epigenetics research from the 1940s to present day. It then defines epigenetics as the study of heritable alterations in gene expression that do not involve changes to DNA sequence. Several epigenetic mechanisms are identified, including DNA methylation, histone modification, and non-coding RNA. The document notes that epigenetic changes are involved in various diseases and disorders. It also discusses how environmental, behavioral, dietary, and psychological factors can influence epigenetics.
1. Plants first evolved from green algae around 475 million years ago and transitioned to land, developing vascular systems to transport water and nutrients and reproducing via spores protected in structures.
2. Around 400 million years ago, early vascular plants diversified and seedless plants like ferns came to dominate. Later, the evolution of heterospory led to the development of seeds around 360-280 million years ago.
3. Angiosperms evolved flowers and fruit around 130 million years ago, allowing dispersal by animals. This was a key factor in the immense diversification of angiosperms to over 235,000 species today.
This document contains a global grocery list including milk, white rice, and water. It then lists the prices of these items in Mexico and the US in pesos and dollars. While the prices are higher in Mexico, the author argues that it is not expensive or hard to buy groceries there because pesos are relatively easy to obtain, such as through working for or selling items to locals.
Prepaing for an Electronic Plan Review Solution 9_18_2014Randall Scheideman
This document discusses considerations for implementing an electronic plan review system. It notes that paper plans are expensive and risky due to costs of printing, shipping, storage and potential for loss or errors. An electronic system allows for immediate communication, consolidated comments, reduced processing and travel times, and real-time status updates. The document outlines key topics to address, including distinguishing an electronic plan review system from a permitting system, ensuring both markup tools and workflow capabilities are included, and conducting workflow analysis and configuration to improve efficiency.
This document outlines a lesson plan for a Year 3 English class. The lesson focuses on the topic "My Best Friend, Claire" and is divided into four sections: Listening and Speaking, Reading, Writing, and Language Arts. Each section lists learning outcomes, teaching standards, learning activities for both the teacher and pupils, and any teaching aids used. The listening and speaking section involves pupils describing a picture puzzle and reciting a poem. The reading section has pupils identifying words containing the phoneme /eƏ/. The writing section has pupils rearranging words to form sentences and filling in blanks. Finally, the language arts section involves pupils performing a jazz chant and creating a poster about Claire.
The passage describes a sermon given by a Yale Divinity School student about the Christian tradition of Advent and waiting for Christmas. The student explained how she grew up viewing Advent as a time to wait in wonder for the birth of Jesus, but later felt pressure to "forget" about Jesus each year so she could experience fresh surprise on Christmas Eve. The passage then discusses T.S. Eliot's poem "The Four Quarters" and how it offers a different perspective on waiting - to wait without hope or expectations, as those could be hopes for the "wrong thing." It argues this does not mean sinking into despair but rather opening oneself up to whatever unexpected good news God may bring, without tightly holding onto preconceived narratives
This document discusses Moffitt Cancer Center's Total Cancer Care program which aims to transform cancer care through a personalized approach. It involves collecting extensive clinical, molecular, and biospecimen data from patients over their lifetime to power research. The goals are to improve outcomes through early detection, personalized treatment, and clinical trials matching. Moffitt has established an extensive biorepository and informatics platform to integrate data from over 78,000 consented patients to enable precision oncology research.
- The document discusses the Total Cancer Care (TCC) approach at Moffitt Cancer Center, which aims to provide personalized cancer care through comprehensive data collection and analysis.
- TCC collects extensive clinical, genomic, treatment and outcomes data from over 78,000 consented patients to power research studies and clinical trials matching. Molecular profiling has been conducted on over 14,000 tumor samples.
- The TCC data is housed in a large integrated database and used by researchers for studies in areas like radiochemotherapy response, exome sequencing, immunology biomarkers, and cancer epidemiology.
- The database also helps clinicians identify eligible patients for clinical trials and develop evidence-based treatment pathways. The goal is to transform cancer
Enabling Translational Medicine with e-ScienceOla Spjuth
This document discusses how e-science can enable translational medicine and support cancer research. It highlights several projects using e-science approaches:
1) The SAIL method integrates data across biobanks to enable cross-archive research.
2) eCPC uses imaging analysis, biomarkers, and microsimulation modeling on high-performance computing to develop more accurate risk prediction and screening strategies.
3) The ClinSeq project applies clinical sequencing, machine learning, and data integration to develop individualized cancer diagnostics and define clinically relevant biomarkers.
An integrated approach to analyzing breast cancer at the proteomic and genomic level is presented using a cytometric readout. The approach analyzes fine needle aspirates to assess proteins, mRNA expression of HER2, and genomic integrity. Feasibility testing used a model system of mixed cell lines and analyzed 40 breast tumors and 10 normal tissues fixed in two solutions. The clinical performance relates to the model system and the cell-based assay could apply to xenograft models and circulating tumor cells.
This document discusses innovation in clinical laboratory medicine in France and immunology. It notes that historically, university hospital professors were expected to excel in teaching, medical duties, and research to quickly transfer innovations from research to patient care. However, recent regulations and cost-cutting have made this triple mission difficult by increasing administrative burdens and prioritizing reducing healthcare costs over quality. This threatens clinical research initiatives by medical laboratory scientists and reduces training opportunities for future professionals. Nonetheless, there is hope in increasing public awareness of the importance of laboratory medicine and engaging in networking and knowledge-sharing to support innovation.
Sk microfluidics and lab on-a-chip-ch6stanislas547
This document discusses cancer diagnostics and monitoring using microfluidic lab-on-a-chip technologies. It describes how integrating DNA/protein separation, detection, and analysis into microfluidic chips could allow for frequent, non-invasive testing of cancer biomarkers in blood or other bodily fluids. This would enable more precise monitoring of cancer treatment effectiveness and earlier detection of recurrence compared to standard techniques. The document outlines approaches involving microfluidic separation channels coupled to molecular detection and proposes a credit card-sized disposable chip sensor integrated with a small control unit for point-of-care cancer screening and monitoring.
This document discusses proteomics and its application in cancer research. Proteomics is the large-scale study of the structure and function of proteins, and it has been used to identify biomarkers for cancer diagnosis, prognosis, and treatment prediction. By analyzing differentially expressed proteins in cancer tissues and bodily fluids, proteomics can provide insights into cancer development and new targets for therapeutic development. The document outlines several areas of focus in cancer proteomics research, including bioinformatics tools for integrated genomic and proteomic analysis, the need for high-quality biospecimens and reagents, and applications of radiolabeled monoclonal antibodies in cancer detection and therapy.
Genomics is the study of an organism's entire genome, which is the complete set of genetic material present in its DNA. This includes all the genes, non-coding regions, and regulatory sequences. Genomics involves sequencing and analyzing the DNA to identify genes, variations (such as single nucleotide polymorphisms or SNPs), and other structural features of the genome.
Lab-on-a-Chip for cancer diagnostics and monitoringstanislas547
This document discusses lab-on-a-chip technology for cancer diagnostics and monitoring. It describes how lab-on-a-chip allows miniaturization of diagnostic tools to fit on a small chip. Examples are given of chips that can detect cancer markers from small samples of blood or other bodily fluids. The document outlines how lab-on-a-chip could provide frequent, non-invasive monitoring of cancer markers to guide treatment and detect recurrence. However, challenges remain in developing control units and integrating all necessary functions like fluid handling and molecular analysis onto a single chip.
Maldi tof-ms analysis in identification of prostate cancerMoustafa Rezk
MALDI-TOF-MS analysis was used to generate proteomic profiles from plasma samples to identify biomarkers for prostate cancer. Samples were prepared using magnetic beads to separate proteins, then analyzed using MALDI-TOF-MS. Bioinformatics tools were used to generate classification models to distinguish prostate cancer patients from healthy controls based on differences in peak intensities. A 5-peak model achieved 87.5% sensitivity and 92.9% specificity. The study demonstrated the potential of MALDI-TOF proteomic profiling for early prostate cancer screening and diagnosis in Egypt. Proteomic biomarkers may help reduce unnecessary biopsies and stratify patients in the future.
This document provides an overview of the November 2000 issue of JALA (Journal of Analytical Laboratories Automation). It describes the development of a novel robotic system for the New York Cancer Project biorepository in collaboration with the Medical Automation Research Center. The biorepository receives 50-100 blood samples per day which are processed robotically to extract, quantify, aliquot and store DNA, plasma and RNA to be accessible to investigators. The robotic system aims to provide rapid random access to the hundreds of thousands of DNA samples stored for high-throughput analysis in studies of gene-environment interactions and cancer risk.
The Center of Excellence in Cancer Research (CECR) was established in June 2013 at Tanta University Educational Hospital in Egypt. It is directed by Dr. Mohamed L. Salem and focuses on correlating immunologic and clinical data from genomic, transcriptomic, and proteomic profiling of circulating and primary tumor cells. The CECR has facilities for flow cytometry, cell sorting, microarrays, and Luminex technology. Its research team studies cancer immunology and diagnosis.
This document discusses the application of data science in genome studies. It begins with a brief history of genome research, including major projects like the Human Genome Project. It then discusses large genome studies and biological databases, such as the HapMap Project, ENCODE Project, TCGA, and 1KGP. Finally, it discusses future trends in genome research, including biobanks, multi-omics studies, clinical applications, single-cell genomics, and data science learning resources.
Achieving High Yields in Scalable Xeno Free Culture Formats with Mesenchymal ...Merck Life Sciences
Watch the presentation of this webinar here: https://bit.ly/3ryE5ST
Optimize your mesenchymal stem cell growth. Join our webinar to learn more about our GMP-compliant xeno free media formulation that supports high performance expansions and compatibility with scalable xeno free manufacturing conditions.
Optimizing ex vivo cell expansion processes in preparation for clinical use is a critical step in cell therapy manufacturing. Given the curative and lifesaving impacts these therapies can have on patients, overcoming roadblocks with scalability and supply chain, using high quality raw materials are essential for therapeutic access.
The GMP-compliant Stemline® XF MSC Medium and cocktail promotes expansion of human mesenchymal stromal/stem cells (hMSCs) to high densities while maintaining cell identity and quality. This product was designed for derivation and expansion of MSCs using xeno free conditions in planar and microcarrier-based culture platforms, easing the transfer between research, clinical, and manufacturing scale cultures.
In this webinar, you will:
• Explore the current landscape and future trends of cell culture media for adult mesenchymal stem cells
• Discover ways to derive MSC's from Bone Marrow in Xeno Free conditions from static to microcarrier-based suspension culture platforms.
• Learn how Stemline® XF MSC Media provides robust performance and reduces scalability roadblocks
Presented by: Kathleen Ongena, Ph.D., Head of Customer Applications and Mark Ventresco, Cell Therapy Product Manager
Achieving High Yields in Scalable Xeno Free Culture Formats with Mesenchymal ...MilliporeSigma
Watch the presentation of this webinar here: https://bit.ly/3ryE5ST
Optimize your mesenchymal stem cell growth. Join our webinar to learn more about our GMP-compliant xeno free media formulation that supports high performance expansions and compatibility with scalable xeno free manufacturing conditions.
Optimizing ex vivo cell expansion processes in preparation for clinical use is a critical step in cell therapy manufacturing. Given the curative and lifesaving impacts these therapies can have on patients, overcoming roadblocks with scalability and supply chain, using high quality raw materials are essential for therapeutic access.
The GMP-compliant Stemline® XF MSC Medium and cocktail promotes expansion of human mesenchymal stromal/stem cells (hMSCs) to high densities while maintaining cell identity and quality. This product was designed for derivation and expansion of MSCs using xeno free conditions in planar and microcarrier-based culture platforms, easing the transfer between research, clinical, and manufacturing scale cultures.
In this webinar, you will:
• Explore the current landscape and future trends of cell culture media for adult mesenchymal stem cells
• Discover ways to derive MSC's from Bone Marrow in Xeno Free conditions from static to microcarrier-based suspension culture platforms.
• Learn how Stemline® XF MSC Media provides robust performance and reduces scalability roadblocks
Presented by: Kathleen Ongena, Ph.D., Head of Customer Applications and Mark Ventresco, Cell Therapy Product Manager
Kshivets O. Cancer, Computer Sciences and Alive SupersystemsOleg Kshivets
1. The document presents research on 12,162 cancer patients analyzing blood, biochemical and immune system parameters to establish relationships between these factors and cancer progression.
2. Statistical analysis revealed complex networks between patient homeostasis and tumor characteristics that determine tumor behavior and patient prognosis. Higher ratios of healthy to cancer cells correlated to better prognosis.
3. The cancer-patient system is found to pass through three phase transitions from normal to invasive cancer that qualitatively change tumor aggressiveness and patient survival chances.
INBIOMEDvision Workshop at MIE 2011. Victoria LópezINBIOMEDvision
1) Personalized medicine currently faces challenges in processing large-scale genomic data, interpreting the functional effects of genomic variations, integrating systems-level data, and translating discoveries into medical practice.
2) Bioinformatics can help address these challenges through algorithms for mapping and aligning sequencing data, predicting functional effects, prioritizing genes, integrating multi-omics data into networks, and disseminating discoveries through databases to inform medical practice.
3) Fully realizing personalized medicine will require overcoming limitations of current approaches, validating computational predictions, and updating medical practice and education to routinely incorporate genomic information.
SNOMED CT concept model for molecular pathology_final.pptxHariHaran685388
This document discusses the need for standardized terminology to represent observational data in molecular genetics and precision medicine. It outlines challenges in representing genetic and molecular pathology findings in existing clinical terminologies like SNOMED CT and LOINC. The document proposes a harmonized concept model between SNOMED CT and LOINC for observable entities to address these challenges. It describes work at UNMC to apply this model to structured encoding of cancer pathology reports, incorporating genetic and molecular data. The goal is to develop terminology that enables clinical decision support and research by integrating genetic and molecular research findings with clinical concept models.
L'Institut national du cancer, la Fondation Arc et la Ligue contre le cancer ont organisé le séminaire de préparation à l'appel à projet "Programme d'Actions Intégrées de Recherche (PAIR) sur les cancers de l'enfant" qui s'est tenu le 13 avril 2016 à Paris.
Similar to Vassili Soumelis - Programme d’analyse globale et intégrative du micro-environnement tumoral (20)
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdfSelcen Ozturkcan
Ozturkcan, S., Berndt, A., & Angelakis, A. (2024). Mending clothing to support sustainable fashion. Presented at the 31st Annual Conference by the Consortium for International Marketing Research (CIMaR), 10-13 Jun 2024, University of Gävle, Sweden.
2. Programme d’analyse globale et intégrative du
micro-environnement tumoral
Vassili SOUMELIS, MD, PhD
Laboratoire d’Immunologie Clinique
et
Inserm U932
7. Oncogene Tumor supressor geneNormal Tumor
Influence du micro-environnement sur l’évolution du cancer
8. Le micro-environnement: nouvelle cible thérapeutique?
1/ Rôle dans la progression tumorale
2/ Implication dans la résistance à la chimiothérapie
3/ Eficacité de nouvelles thérapies ciblant le micro-environnement
(exemple: immunothérapie)
15. De l’échantillon clinique aux données biologiques: approche
modulaire
Clinical sample
Cellular TME:
- ImmunoHistoChemistry
- FACS, 3 Ab panels
Soluble TME:
- Multiple Analyte Profiling
- Tumor infiltrating lymphocyte
secretion profiles
- Functional effect of tumor-derived
supernatants
Clinical data
Diagnosis / Follow-up
Extracellular Matrix
composition :
ImmunoHistoChemistry
Glucose
Metabolism
Oxidative stress
Transcriptomic:
Epithelial and Stromal
compartments
Human breast or ovarian cancer
450 patients included to date
16. Caractérisation de la diversité du microenvironnement
cellulaire
DC
CD4+ T cells, CD8+ T cells, B cells, NK cells
Joyce et al. Nat Rev Cancer 2009
+ T
BMDC
Macrophage
Neutrophil
Mast cell
MDSC
MSC Fibroblast
Lymphocyte
TEM Endothelial cell
Pericyte
Blood vessel
LyLymphocyLy
Normal epithelial cell
Tumor epithelial cell
Lymphatic endothelial cell
17. De l’échantillon clinique aux données biologiques: approche
modulaire
Clinical sample
Cellular TME:
- ImmunoHistoChemistry
- FACS, 3 Ab panels
Soluble TME:
- Multiple Analyte Profiling
- Tumor infiltrating lymphocyte
secretion profiles
- Functional effect of tumor-derived
supernatants
Clinical data
Diagnosis / Follow-up
Extracellular Matrix
composition :
ImmunoHistoChemistry
Glucose
Metabolism
Oxidative stress
Transcriptomic:
Epithelial and Stromal
compartments
Human breast or ovarian cancer
450 patients included to date
18. INTEGRATIVE ANALYSIS
DATA INTEGRATION
1
2
3
5
4
55
DATA QUERY
Sam ple Type
+
Pathology
+
Biotechnology
+
Gene A
Scientist / Clinician
KDI core
system
Detection of new target
6
DATAPRE-PROCESSING
Web applications
m odules
Sam ple
Patient
Clinical data
Low throughput
biotechnological
platform
High-throughput
biotechnological
platform
Low-throughput
biotechnological
platform
Analysis pipelines
SaSS m ple TyTT pe
+
PaPP thology
+
Biotechnology
+
Gene A
KDDDI core
syyyyysssssttttteeeeemmmmm
Detection of new
66
Anal
WEBSERVICES(SOAP)
Clinical data
Alteration data
- DNA copy number
- mutations
Expression data
- gene expression
« ClinicalDB »
« BIRD »
« Bioinfo-Portal »
Biological data
- Histological Analyzis
- Cellular phenotyping
- Supernatant Analysis
- Functional Experiments
«Algebra»
«Gersimi»
De l’échantillon tumoral à l’intégration des données:
un circuit “haute fidélité”
19. Apply T-MEGA datasetTheoritical modeling
Antonio Cappucio
2/ Modeling
Today
1/ Biostatistical analysis
Prognostic/Predictive
Biomarkers
3/ Biomarkers and therapeutic targets
T-MEGA: état d’avancement des analyses de données
LE.*RE LE.*RS
LS.*RE
LS.*RS
SE
Co-segregation of biological parameters
Yann Kieffer, Marine Jeanmougin
21. Importance du soutien financier: dynamiser et péréniser
Ø Personnel: la plupart en CDD financé par des contrats de recherche de
durée limitée
Ø Analyses biologiques modulaires: financer des modules déjà
plannifiés ou ajouter de nouveaux modules
Ø Etendre le programme à d’autres tumeurs: cancer du sein, ovaire
Ø Permettre la pérénisation pour répondre à des questions cliniques sur
l’évolution des cancers
Ø Initier le développement de nouvelles thérapeutiques ciblant le micro-
environnement
Clinical sample
Cellular TME:
- ImmunoHistoChemistry
- FACS, 3 Ab panels
Soluble TME:
- Multiple Analyte Profiling
- Tumor infiltrating
lymphocyte secretion profiles
- Functional effect of tumor-
derived supernatants
Clinical data
Diagnosis / Follow-up
Extracellular Matrix
composition :
ImmunoHistoChemistry
Glucose
Metabolism
Oxidative
stresssupernatants
Transcriptomic:
Epithelial and Stromal
compartments