Documento que presenta la cartera de servicios y el equipamiento del Servicio Científico Técnico de Secuenciación y Genómica Funcional de la Universidad de Zaragoza y el Instituto Aragonés de Ciencias de la Salud.
Microbiome research is undergoing a crisis due to issues like the correlation-causation fallacy in studies and poor experimental design. The document discusses challenges with studying the microbiome, including biases and errors introduced from DNA extraction methods, sample storage conditions, and contamination from extraction kits. It emphasizes that every step in microbiome research, from sample collection to analysis, needs careful consideration to draw accurate conclusions.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
This document discusses food authenticity testing and the issues with current testing methods. It introduces next generation sequencing (NGS) as a new method for food authenticity testing. NGS allows for the simultaneous detection of thousands of potential food contaminants in a single test, overcoming limitations of current polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) methods. NGS involves amplifying DNA from all species in a mixed sample, sequencing the amplified products, and comparing the sequences to a reference database to identify contaminants. While a major improvement, NGS also has limitations, such as an inability to currently quantify contamination levels.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
DNA sequencing determines the order of nucleotides in a DNA molecule. Next-generation sequencing (NGS) methods like pyrosequencing have accelerated research by allowing high-throughput, low-cost sequencing. Pyrosequencing works by detecting pyrophosphate release during DNA synthesis. It has applications in genetics, epigenetics, forensics, medicine, and more. NGS continues to advance sequencing capabilities and make whole genome analysis increasingly accessible.
The document discusses using structured phenotype data to improve the interpretation and prioritization of candidate genes from exome sequencing data, particularly for undiagnosed diseases. It outlines current challenges in candidate gene prioritization based on phenotypes alone. It then describes how ontologies can be used to semantically represent and compare phenotypes across species to leverage knowledge from model organisms. The document presents results showing that combining phenotype data with variant data using a tool called PhenIX improves the ability to correctly prioritize candidate genes from exome data compared to using variant data alone. This demonstrates the utility of structured phenotype data for computational analysis of exomes to diagnose rare diseases.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
This document summarizes techniques for rapid diagnostic testing by copying nature. It discusses how current culture-based detection of bacteria from clinical samples can take 2-3 days. New molecular detection methods directly detect bacteria in 1-2 hours but sample preparation is the limiting step. The document presents new sample preparation techniques inspired by nature, such as magnetic particle-based extraction of DNA from bacteria and a pelleting method to separate bacteria from blood similar to how horseshoe crabs capture bacteria. Faster sample preparation methods could enable more rapid identification of bacteria using downstream techniques like PCR, sequencing, or mass spectrometry.
Microbiome research is undergoing a crisis due to issues like the correlation-causation fallacy in studies and poor experimental design. The document discusses challenges with studying the microbiome, including biases and errors introduced from DNA extraction methods, sample storage conditions, and contamination from extraction kits. It emphasizes that every step in microbiome research, from sample collection to analysis, needs careful consideration to draw accurate conclusions.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
This document discusses food authenticity testing and the issues with current testing methods. It introduces next generation sequencing (NGS) as a new method for food authenticity testing. NGS allows for the simultaneous detection of thousands of potential food contaminants in a single test, overcoming limitations of current polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) methods. NGS involves amplifying DNA from all species in a mixed sample, sequencing the amplified products, and comparing the sequences to a reference database to identify contaminants. While a major improvement, NGS also has limitations, such as an inability to currently quantify contamination levels.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
DNA sequencing determines the order of nucleotides in a DNA molecule. Next-generation sequencing (NGS) methods like pyrosequencing have accelerated research by allowing high-throughput, low-cost sequencing. Pyrosequencing works by detecting pyrophosphate release during DNA synthesis. It has applications in genetics, epigenetics, forensics, medicine, and more. NGS continues to advance sequencing capabilities and make whole genome analysis increasingly accessible.
The document discusses using structured phenotype data to improve the interpretation and prioritization of candidate genes from exome sequencing data, particularly for undiagnosed diseases. It outlines current challenges in candidate gene prioritization based on phenotypes alone. It then describes how ontologies can be used to semantically represent and compare phenotypes across species to leverage knowledge from model organisms. The document presents results showing that combining phenotype data with variant data using a tool called PhenIX improves the ability to correctly prioritize candidate genes from exome data compared to using variant data alone. This demonstrates the utility of structured phenotype data for computational analysis of exomes to diagnose rare diseases.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
This document summarizes techniques for rapid diagnostic testing by copying nature. It discusses how current culture-based detection of bacteria from clinical samples can take 2-3 days. New molecular detection methods directly detect bacteria in 1-2 hours but sample preparation is the limiting step. The document presents new sample preparation techniques inspired by nature, such as magnetic particle-based extraction of DNA from bacteria and a pelleting method to separate bacteria from blood similar to how horseshoe crabs capture bacteria. Faster sample preparation methods could enable more rapid identification of bacteria using downstream techniques like PCR, sequencing, or mass spectrometry.
Polymerase Chain Reaction (PCR)-Based Sex Determination Using Unembalmed Huma...IOSR Journals
The strategy developed for sex determination in skeletal remains is to amplify the highly degraded DNA, by use of primers that span short DNA fragments. To determine sex of unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, using Polymerase Chain Reaction (PCR). A single blind study of Polymerase Chain Reaction (PCR)-based sex determination using amelogenin gene and alphoid repeats primers on unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, was undertaken. With amelogenin gene, genetic sex identification was achieved in four samples only. PCR Sensitivity = 40%, Specificity = 100%, Predictive value of positive test = 100%, Predictive value of negative test = 25%, False positive rate = 0%, False negative rate = 150%, Efficiency of test = 50%. Fisher’s exact probability test P = 1. Z-test: z-value = -1.0955, p>0.05; not statistically significant. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. PCR Sensitivity = 100%, Specificity = 0%, Predictive value of positive test = 100%, Predictive value of negative test = 0%, False positive rate = 0%, False negative rate = 0%, Efficiency of test = 100%. Fisher’s exact probability test P = 1. Z-test: z- and p values were invalid. The study, has demonstrated the applicability of PCR method of sex determination in unembalmed human skeletal fragments from Sokoto, Northwestern Nigeria. With amelogenin gene primers, correct genetic sex identification was achieved in four samples only. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. Therefore, alphoid repeats is more efficient and more reliable than amelogenin gene, in sex determination from unembalmed human skeletal fragments. This is the first known study determining the sex of unembalmed human skeletal fragments by means of PCR in Nigeria. There is need for further studies in Nigeria to complement the findings of this study.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Detection of Wuchereria bancrofti DNA in paired serum and urine samples using...dewisetiyana52
This study aimed to standardize PCR-based systems for the diagnosis of lymphatic filariasis using serum and urine samples. Paired biological samples were collected from 20 individuals known to be infected with Wuchereria bancrofti. Conventional and semi-nested PCR assays were optimized to detect W. bancrofti DNA. The internal PCR system was able to detect as little as 10 fg of W. bancrofti DNA and detected infection in all 20 patients using both serum and urine samples. In contrast, the semi-nested PCR only detected infection in 2 of the 20 patients. This study demonstrates the potential of using a simple internal PCR system and urine samples for the diagnosis of W. b
NGS for Infectious Disease Diagnostics: An Opportunity for Growth Alira Health
Infectious diseases are a major public health concern causing over 3.5 million deaths worldwide. Diagnosing patients as quickly and effectively as possible is crucial for managing disease outbreaks. Next-generation sequencing (NGS) provides unique capabilities to understand the genetic profile of infectious disease patients that no other technology can match.
Whole-genome metagenomics allows clinicians to take a deeper dive into pathogens by generating big-data about their characteristics. This data can be rapidly analyzed using complex bioinformatics software algorithms to achieve clinical-grade diagnostic accuracy. In a healthcare system shifting towards personalized medicine, NGS can provide clinicians the tools that they need to prescribe individualized treatments to save patients who were previously untreatable. The result is improved quality of care, better treatment regimes, and cost-saving healthcare.
The document discusses the rise of big data in microbiology due to decreasing costs of DNA sequencing and computational resources. It describes how high-throughput sequencing is generating vast amounts of microbial genomic and metagenomic data. However, analyzing these large, complex datasets presents numerous technical and social challenges for microbiologists, including handling data volume, integrating diverse data types, accessing resources, and incentivizing data sharing. Overcoming these bottlenecks will be key to unlocking the scientific insights contained within the microbial "big data" tidal wave.
1. Whole genome sequencing is becoming more affordable and widespread, allowing for large datasets and personalized medicine applications.
2. However, genomic data is extremely sensitive and can be used to identify individuals and their relatives, even when anonymized. Once a genome is leaked, it cannot be revoked.
3. Computer scientists are exploring techniques to protect genomic privacy, such as differential privacy and secure computation, but enabling privacy-preserving genomic research remains a challenge.
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field was referred to as environmental genomics, ecogenomics or community genomics. Recent studies use "shotgun" Sanger sequencing or next generation sequencing (NGS) to get largely unbiased samples of all genes from all the members of the sampled communities.
The ASR Zebrafish facility provides several services including fish housing, embryo production, gene manipulation, and phenotypic analysis. Gene expression can be manipulated through RNA, DNA, and morpholino microinjections. Phenotypic analysis includes visualization of morphology, histology, fluorescence, and apoptosis. The facility also supports toxicity and drug screening in zebrafish using 96 or 384 well formats with wildtype or transgenic lines. Shared resources are partially supported by Georgetown and Howard University.
This document discusses analytical validation needs for next-generation sequencing, including somatic variants. It notes that targeted sequencing and whole genome sequencing have similar analytical validation requirements but reference data needs to cover all genomic regions. There is limited utility in benchmarking or reference pipelines as custom assay development often uses custom informatics. Increased transparency is needed on exact intervals tested and validation metrics based on variant type and allelic fraction.
overview on Next generation sequencing in breast csncerSeham Al-Shehri
Next-generation sequencing (NGS) and its application to breast cancer research is discussed. NGS allows for comprehensive profiling of microRNA (miRNA) expression, which can provide insights into tumorigenesis pathways. The document outlines the NGS process, including template preparation, sequencing/imaging, and complex data analysis using statistical methods and software. Key applications are identifying miRNA involvement in cancer driver genes and exploring miRNA expression patterns to discover potential diagnostic or prognostic biomarkers for breast cancer subtypes.
1) Researchers studied a novel method for quantifying and tracking macrophage homing into atherosclerotic plaques using superparamagnetic iron oxide nanoparticles (SPIO).
2) They injected SPIO into ApoE-deficient mice with and without proinflammatory cytokines and found higher iron content and more macrophages in plaques of cytokine-treated mice using histology and mass spectrometry.
3) This demonstrates that SPIO allows both quantitative and qualitative assessment of macrophage infiltration and shows infiltration is enhanced by cytokines, suggesting SPIO-enhanced MRI could noninvasively monitor monocyte recruitment dynamics into plaques over time.
1) Researchers studied a novel method for quantifying and tracking macrophage homing into atherosclerotic plaques using superparamagnetic iron oxide nanoparticles (SPIO).
2) They injected SPIO into ApoE-deficient mice, some of which also received proinflammatory cytokines, and tracked iron uptake in plaques over time.
3) Both quantitative iron assays and staining showed greater iron and macrophage presence in plaques of cytokine-treated mice, demonstrating SPIO can monitor macrophage recruitment influenced by inflammation. This noninvasive MRI-based method may help study monocyte involvement in atherosclerosis.
Dr. Sascha Ott (University of Warwick) - Data-driven systems medicinemntbs1
The summary of Dr. Sascha Ott's presentation from the Jun 11-12th 2019 event Data-driven systems medicine at Cardiff University Brain Research Imaging Centre.
Dr. Douglas Marthaler - Use of Next Generation Sequencing for Whole Genome An...John Blue
Use of Next Generation Sequencing for Whole Genome Analysis of Pathogens - Dr. Douglas Marthaler, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
Errors and Limitaions of Next Generation SequencingNixon Mendez
This document discusses some key errors and limitations of next-generation sequencing (NGS). It notes that while NGS has significantly reduced costs and improved throughput, it also has some drawbacks compared to previous sequencing technologies. Specifically, it outlines issues related to low quality bases, PCR errors during amplification, and high error rates that can make rare mutations difficult to detect. Limitations include short read lengths that hamper assembly of repetitive regions, contamination risks, incomplete representation of repeats, difficulties assembling segmental duplications and genes fragmented across scaffolds. The document emphasizes the need for validation of genome assemblies and development of hybrid approaches combining long and short reads to overcome these challenges.
PerkinElmer is a global leader focused on improving human and environmental health through discovery research. They provide technologies and expertise to scientists in areas like environmental monitoring, food quality, pharmaceutical development, life sciences, and diagnostics. The document provides an overview of PerkinElmer's technologies and applications in areas like high content screening, plate readers, in vivo imaging systems, and target discovery which help researchers gain insights across drug discovery, disease research, and genomics. It also includes key statistics about PerkinElmer's history, locations, patents, and the scale of samples and data they have helped analyze.
This document describes a study that uses next-generation re-sequencing and bioinformatics to analyze presence/absence variation of accessory chromosomes across isolates of the wheat pathogen Zymoseptoria tritici. The genome of the reference isolate IPO323 contains 21 chromosomes including 8 accessory chromosomes. Low-cost next-generation sequencing of 13 novel Z. tritici isolates is performed and the reads are aligned to the IPO323 reference genome to determine if accessory chromosomes present in IPO323 are also present in the novel isolates based on read coverage. De novo assembly of reads from the novel isolates is also conducted and compared to IPO323 to identify any additional accessory chromosomes or sequences not present in IPO323. This
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...eventi-ITBbari
Bioinformatica e genomica comparata: nuove strategie sperimentali e computazionali per la produzione e analisi di dati NGS finalizzati a sviluppare processi e prodotti innovativi per la salute dell’uomo, l’ambiente e l’agroalimentare.
This document discusses Wnt signaling and provides an overview of research tools that can be used to study the pathway. It describes the discovery of Wnt proteins and their roles in canonical and noncanonical signaling. The document also reviews the functions of Wnt signaling in development, tissue homeostasis, and various pathological conditions. It proposes using PCR arrays, siRNA, methylation arrays, and reporter assays to develop a Wnt gene signature and measure pathway activity through changes in gene expression and protein levels.
Polymerase Chain Reaction (PCR)-Based Sex Determination Using Unembalmed Huma...IOSR Journals
The strategy developed for sex determination in skeletal remains is to amplify the highly degraded DNA, by use of primers that span short DNA fragments. To determine sex of unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, using Polymerase Chain Reaction (PCR). A single blind study of Polymerase Chain Reaction (PCR)-based sex determination using amelogenin gene and alphoid repeats primers on unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, was undertaken. With amelogenin gene, genetic sex identification was achieved in four samples only. PCR Sensitivity = 40%, Specificity = 100%, Predictive value of positive test = 100%, Predictive value of negative test = 25%, False positive rate = 0%, False negative rate = 150%, Efficiency of test = 50%. Fisher’s exact probability test P = 1. Z-test: z-value = -1.0955, p>0.05; not statistically significant. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. PCR Sensitivity = 100%, Specificity = 0%, Predictive value of positive test = 100%, Predictive value of negative test = 0%, False positive rate = 0%, False negative rate = 0%, Efficiency of test = 100%. Fisher’s exact probability test P = 1. Z-test: z- and p values were invalid. The study, has demonstrated the applicability of PCR method of sex determination in unembalmed human skeletal fragments from Sokoto, Northwestern Nigeria. With amelogenin gene primers, correct genetic sex identification was achieved in four samples only. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. Therefore, alphoid repeats is more efficient and more reliable than amelogenin gene, in sex determination from unembalmed human skeletal fragments. This is the first known study determining the sex of unembalmed human skeletal fragments by means of PCR in Nigeria. There is need for further studies in Nigeria to complement the findings of this study.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Detection of Wuchereria bancrofti DNA in paired serum and urine samples using...dewisetiyana52
This study aimed to standardize PCR-based systems for the diagnosis of lymphatic filariasis using serum and urine samples. Paired biological samples were collected from 20 individuals known to be infected with Wuchereria bancrofti. Conventional and semi-nested PCR assays were optimized to detect W. bancrofti DNA. The internal PCR system was able to detect as little as 10 fg of W. bancrofti DNA and detected infection in all 20 patients using both serum and urine samples. In contrast, the semi-nested PCR only detected infection in 2 of the 20 patients. This study demonstrates the potential of using a simple internal PCR system and urine samples for the diagnosis of W. b
NGS for Infectious Disease Diagnostics: An Opportunity for Growth Alira Health
Infectious diseases are a major public health concern causing over 3.5 million deaths worldwide. Diagnosing patients as quickly and effectively as possible is crucial for managing disease outbreaks. Next-generation sequencing (NGS) provides unique capabilities to understand the genetic profile of infectious disease patients that no other technology can match.
Whole-genome metagenomics allows clinicians to take a deeper dive into pathogens by generating big-data about their characteristics. This data can be rapidly analyzed using complex bioinformatics software algorithms to achieve clinical-grade diagnostic accuracy. In a healthcare system shifting towards personalized medicine, NGS can provide clinicians the tools that they need to prescribe individualized treatments to save patients who were previously untreatable. The result is improved quality of care, better treatment regimes, and cost-saving healthcare.
The document discusses the rise of big data in microbiology due to decreasing costs of DNA sequencing and computational resources. It describes how high-throughput sequencing is generating vast amounts of microbial genomic and metagenomic data. However, analyzing these large, complex datasets presents numerous technical and social challenges for microbiologists, including handling data volume, integrating diverse data types, accessing resources, and incentivizing data sharing. Overcoming these bottlenecks will be key to unlocking the scientific insights contained within the microbial "big data" tidal wave.
1. Whole genome sequencing is becoming more affordable and widespread, allowing for large datasets and personalized medicine applications.
2. However, genomic data is extremely sensitive and can be used to identify individuals and their relatives, even when anonymized. Once a genome is leaked, it cannot be revoked.
3. Computer scientists are exploring techniques to protect genomic privacy, such as differential privacy and secure computation, but enabling privacy-preserving genomic research remains a challenge.
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field was referred to as environmental genomics, ecogenomics or community genomics. Recent studies use "shotgun" Sanger sequencing or next generation sequencing (NGS) to get largely unbiased samples of all genes from all the members of the sampled communities.
The ASR Zebrafish facility provides several services including fish housing, embryo production, gene manipulation, and phenotypic analysis. Gene expression can be manipulated through RNA, DNA, and morpholino microinjections. Phenotypic analysis includes visualization of morphology, histology, fluorescence, and apoptosis. The facility also supports toxicity and drug screening in zebrafish using 96 or 384 well formats with wildtype or transgenic lines. Shared resources are partially supported by Georgetown and Howard University.
This document discusses analytical validation needs for next-generation sequencing, including somatic variants. It notes that targeted sequencing and whole genome sequencing have similar analytical validation requirements but reference data needs to cover all genomic regions. There is limited utility in benchmarking or reference pipelines as custom assay development often uses custom informatics. Increased transparency is needed on exact intervals tested and validation metrics based on variant type and allelic fraction.
overview on Next generation sequencing in breast csncerSeham Al-Shehri
Next-generation sequencing (NGS) and its application to breast cancer research is discussed. NGS allows for comprehensive profiling of microRNA (miRNA) expression, which can provide insights into tumorigenesis pathways. The document outlines the NGS process, including template preparation, sequencing/imaging, and complex data analysis using statistical methods and software. Key applications are identifying miRNA involvement in cancer driver genes and exploring miRNA expression patterns to discover potential diagnostic or prognostic biomarkers for breast cancer subtypes.
1) Researchers studied a novel method for quantifying and tracking macrophage homing into atherosclerotic plaques using superparamagnetic iron oxide nanoparticles (SPIO).
2) They injected SPIO into ApoE-deficient mice with and without proinflammatory cytokines and found higher iron content and more macrophages in plaques of cytokine-treated mice using histology and mass spectrometry.
3) This demonstrates that SPIO allows both quantitative and qualitative assessment of macrophage infiltration and shows infiltration is enhanced by cytokines, suggesting SPIO-enhanced MRI could noninvasively monitor monocyte recruitment dynamics into plaques over time.
1) Researchers studied a novel method for quantifying and tracking macrophage homing into atherosclerotic plaques using superparamagnetic iron oxide nanoparticles (SPIO).
2) They injected SPIO into ApoE-deficient mice, some of which also received proinflammatory cytokines, and tracked iron uptake in plaques over time.
3) Both quantitative iron assays and staining showed greater iron and macrophage presence in plaques of cytokine-treated mice, demonstrating SPIO can monitor macrophage recruitment influenced by inflammation. This noninvasive MRI-based method may help study monocyte involvement in atherosclerosis.
Dr. Sascha Ott (University of Warwick) - Data-driven systems medicinemntbs1
The summary of Dr. Sascha Ott's presentation from the Jun 11-12th 2019 event Data-driven systems medicine at Cardiff University Brain Research Imaging Centre.
Dr. Douglas Marthaler - Use of Next Generation Sequencing for Whole Genome An...John Blue
Use of Next Generation Sequencing for Whole Genome Analysis of Pathogens - Dr. Douglas Marthaler, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
Errors and Limitaions of Next Generation SequencingNixon Mendez
This document discusses some key errors and limitations of next-generation sequencing (NGS). It notes that while NGS has significantly reduced costs and improved throughput, it also has some drawbacks compared to previous sequencing technologies. Specifically, it outlines issues related to low quality bases, PCR errors during amplification, and high error rates that can make rare mutations difficult to detect. Limitations include short read lengths that hamper assembly of repetitive regions, contamination risks, incomplete representation of repeats, difficulties assembling segmental duplications and genes fragmented across scaffolds. The document emphasizes the need for validation of genome assemblies and development of hybrid approaches combining long and short reads to overcome these challenges.
PerkinElmer is a global leader focused on improving human and environmental health through discovery research. They provide technologies and expertise to scientists in areas like environmental monitoring, food quality, pharmaceutical development, life sciences, and diagnostics. The document provides an overview of PerkinElmer's technologies and applications in areas like high content screening, plate readers, in vivo imaging systems, and target discovery which help researchers gain insights across drug discovery, disease research, and genomics. It also includes key statistics about PerkinElmer's history, locations, patents, and the scale of samples and data they have helped analyze.
This document describes a study that uses next-generation re-sequencing and bioinformatics to analyze presence/absence variation of accessory chromosomes across isolates of the wheat pathogen Zymoseptoria tritici. The genome of the reference isolate IPO323 contains 21 chromosomes including 8 accessory chromosomes. Low-cost next-generation sequencing of 13 novel Z. tritici isolates is performed and the reads are aligned to the IPO323 reference genome to determine if accessory chromosomes present in IPO323 are also present in the novel isolates based on read coverage. De novo assembly of reads from the novel isolates is also conducted and compared to IPO323 to identify any additional accessory chromosomes or sequences not present in IPO323. This
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...eventi-ITBbari
Bioinformatica e genomica comparata: nuove strategie sperimentali e computazionali per la produzione e analisi di dati NGS finalizzati a sviluppare processi e prodotti innovativi per la salute dell’uomo, l’ambiente e l’agroalimentare.
This document discusses Wnt signaling and provides an overview of research tools that can be used to study the pathway. It describes the discovery of Wnt proteins and their roles in canonical and noncanonical signaling. The document also reviews the functions of Wnt signaling in development, tissue homeostasis, and various pathological conditions. It proposes using PCR arrays, siRNA, methylation arrays, and reporter assays to develop a Wnt gene signature and measure pathway activity through changes in gene expression and protein levels.
This document summarizes a presentation on using micro and nanotechnologies for cancer diagnostics and therapy. It discusses using various technologies like microarrays, comparative genomic hybridization, and integration of genome and transcriptome data to analyze cancer at multiple levels. In particular, it focuses on using these techniques to study neuroblastoma and identify genetic signatures that can predict patient outcomes and survival. Signatures identified include miRNA profiles and their interactions with mRNA that are associated with poor survival in neuroblastoma patients.
Microarrays allow researchers to examine gene expression patterns across thousands of genes simultaneously. A microarray contains probes for known genes that are used to detect complementary mRNA in a biological sample. Microarrays can be used to study gene expression differences between normal and diseased tissues, classify tumor subtypes, and diagnose cancers. They also show promise for personalized cancer treatment by predicting patient prognosis and response to therapy.
Next generation sequencing & microarray-- Genotypic TechnologyGenotypic Technology
Greetings from Genotypic Technology, Bangalore (www.genotypic.co.in). We are a 13 year old genomics and bioinformatics company ( 65+ employees, Service. Products and R & D) based in Bangalore, India, primarily working on applications of Microarrays and Next Generation Sequencing in Human Health and Disease, including in Molecular Diagnostics, Prognosis, Therapeutics, Vaccine Research, Basic Science Research, Veterinary Science, Agriculture, Industrial Biotechnology, Microbial Genetics and more.
Our major strength is in customized genomics solutions, particularly in your field, we can develop panel of markers for specific diseases, optimize, validate and help commercialize on open platforms or specific instrument platforms- in microarrays and sequencing based methods/ assays. We can also use genomic markers to aid in treatment of specific disease using personalized medicine approaches. All this can be done on a comprehensive end-to-end manner in our company as we have a very good blend of molecular biology and bioinformatics with totally 6 Ph.Ds. We work closely with Agilent's R &D as their partner.
The document discusses various applications and techniques of DNA microarrays, including summarizing key points about Affymetrix GeneChips, spotted microarrays, experimental design, data analysis, and several case studies on various topics like ovarian cancer, Sjogren's syndrome, wine yeast genomics, and norovirus genotyping. Microarrays allow analysis of gene expression patterns and copy number variations across genomes through comparative hybridization experiments. The document provides an overview of microarray technology and applications in genomic and biomedical research.
A microarray is a laboratory tool used to detect the expression of thousands of genes at the same time. DNA microarrays are microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene.
New Generation Sequencing Technologies: an overviewPaolo Dametto
The document provides a history of DNA sequencing technologies. It begins with the discovery of DNA's structure in 1953 and the development of recombinant DNA technology in the 1970s. First generation Sanger sequencing produced short reads over 1,000 years to sequence the human genome. Next generation sequencing (NGS) platforms since 2005 have dramatically reduced costs while increasing throughput. NGS methods like Roche/454 pyrosequencing, Illumina/Solexa sequencing by synthesis, SOLiD ligation sequencing, and single-molecule real-time sequencing by Pacific Biosciences now enable large-scale genome and transcriptome analysis.
The document discusses using PCR arrays to profile gene expression and epigenetics. PCR arrays allow researchers to analyze expression of up to 84 genes related to a pathway or disease using real-time PCR. They include controls to check for genomic DNA contamination and assay performance. As an example, the document describes how a researcher could use a PCR array to compare gene expression between metastatic and non-metastatic breast tumor samples.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.1- Next Generation Sequencing. Technologies and Applications. Part I: NGS Introduction and Technology Overview.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
1. The document describes a study analyzing serum protein profiles from 15 individual samples using online two-dimensional low-flow liquid chromatography-tandem mass spectrometry (LC-MS/MS).
2. Over 400 proteins were quantified across the samples, with 237 proteins showing at least a two-fold change in abundance between samples.
3. Principal component analysis separated the samples obtained from one source, indicating the impact sample preparation can have on protein profiles. Deeper profiling of individual samples is needed for precision medicine applications like biomarker discovery.
This document provides an overview of Wnt signaling and research tools for studying the pathway. It begins with an introduction to Wnt proteins and receptors, and describes the canonical and noncanonical Wnt signaling pathways. The document then discusses the function of Wnt signaling in development, tissue homeostasis, and various pathological conditions. Various research tools for investigating Wnt signaling are presented, including whole genome expression profiling, siRNA inhibition of β-catenin, Wnt target gene PCR arrays, and EpiTech methylation arrays. The document proposes a workflow for developing a Wnt gene expression signature and demonstrates using custom PCR arrays and methylation analysis to understand differential Wnt responses between cell lines. It concludes by describing a combined Wnt signaling PCR
Alzheimer’s disease (AD) is a devastating neurodegenerative disease that is genetically complex. Although great progress has been made in identifying fully penetrant mutations in genes that cause early-onset AD, these still represent a very small percentage of AD cases. Large-scale, genome-wide association studies (GWAS) have identified at least 20 additional genetic risk loci for the more common form: late-onset AD. However, the identified SNPs are typically not the actual risk variants, but are in linkage disequilibrium with the presumed causative variants [1].
To help identify causative genetic variants, we have combined highly accurate, long-read sequencing with hybrid-capture technology. In this collaborative webinar*, we present this method and show how combining IDT xGen® Lockdown® Probes with PacBio SMRT® Sequencing allows targeting and sequencing of candidate genes from genomic DNA and corresponding transcripts from cDNA. Using a panel of target capture probes for 35 AD candidate genes, we demonstrate the power of this approach by looking at data for two individuals with AD. Some additional benefits of this method include the ability to leverage long reads, phase heterozygous variants, and link corresponding transcript isoforms to their respective alleles.
Reference: 1. Van Cauwenberghe C, Van Broeckhoven C, Sleegers K. (2016) The genetic landscape of Alzheimer disease: clinical implications and perspectives. Genet Med, 18(5):421–430.
* This presentation represents a collaboration between Pacific Biosciences and Integrated DNA Technologies. The individual opinions expressed may not reflect shared opinions of Pacific Biosciences and Integrated DNA Technologies.
This document summarizes the sequencing and analysis of the Monascus pilosus genome. Key points include:
- The genome was sequenced using a whole genome shotgun strategy combining EST, BAC/fosmid, and plasmid libraries. The draft assembly resulted in 15.2 Mb arranged in 5 scaffolds.
- A total of 8,887 ESTs were generated and assembled into 4,168 contigs and 2,719 singletons, representing 4,015 tentative unigenes. Highly expressed genes included heat shock proteins and elongation factors.
- Genome analysis identified 9,997 predicted genes, 513 genes undergoing alternative splicing, and gene clusters involved in lovastatin and polyketide biosynthesis. The genome provides
Please note: This presentation accompanies a recorded webinar at:
https://www1.gotomeeting.com/register/347794241
Biomarkers for studying gene regulation and cell function can be efficiently analyzed by multiplexed methods. Dr. Jim Lazar from OriGene Technologies will provide an overview of four different but related detection technologies that can be used to analyze genetic variants, microRNA expression, transcription factor binding, and protein expression on the Luminex xMAP platform. OriGene’s broad panel of assays and tools for discovery, analysis and validation of multiple classes of important biomarkers will allow researcher to develop more accurate descriptions of biologically complex systems.
The document discusses data sharing and analysis platforms for rare diseases like RD-Connect and MatchMaker Exchange, describing RD-Connect's genome-phenome analysis platform that enables variant identification and diagnosis. It also summarizes RD-Connect's role in facilitating data integration and sharing across resources to overcome bottlenecks in rare disease research like lack of data and samples.
Two-Tailed PCR - New Ultrasensitive and Ultraspecific Technique for the Quant...Kate Barlow
This document discusses methods for quantifying and analyzing microRNAs (miRNAs) using quantitative PCR (qPCR). It presents a new two-tailed RT-qPCR method that provides high sensitivity and specificity for detecting miRNAs, including discrimination of miRNA isoforms. The method allows unlimited multiplexing in the reverse transcription step followed by singleplex qPCR. The document benchmarks the two-tailed RT-qPCR method on biological samples, showing it can sensitively detect less than 10 molecules and maintain specificity across the entire miRNA sequence. It also demonstrates two-tube multiplexing of the method to profile expression levels of several miRNAs in different tissues.
This document discusses next generation molecular profiling technologies. It begins with an overview of first generation molecular profiling techniques like gene sequencing, microarrays, and fluorescence in situ hybridization (FISH). It then describes some key advantages of next generation sequencing technologies like their ability to generate more sequence data at lower cost. Examples of second generation DNA and RNA profiling methods are provided, including exome sequencing and RNA-sequencing. The document also briefly discusses emerging areas like third generation sequencing and next generation protein profiling using mass spectrometry. Epigenetic profiling using techniques like methyl-binding domain sequencing is summarized in the section on next generation epigenetic profiling.
The document provides an overview of genomics and molecular profiling techniques. It discusses:
- The lab for bioinformatics and computational genomics which has 10 "genome hackers" and 42 scientists.
- An introduction to personalized medicine and biomarkers.
- First generation molecular profiling techniques like gene sequencing, microarrays, PCR.
- Next generation sequencing techniques like Roche 454, Illumina, SOLID which allow high throughput sequencing.
- Next generation applications like RNA sequencing, exome sequencing, epigenetic profiling.
- The role of bioinformatics in analyzing large genomic and molecular profiling data.
Similar to Sequencing and functional genomics Unit_Biomedical Research Center of Aragon_Zaragoza (20)
Skybuffer SAM4U tool for SAP license adoptionTatiana Kojar
Manage and optimize your license adoption and consumption with SAM4U, an SAP free customer software asset management tool.
SAM4U, an SAP complimentary software asset management tool for customers, delivers a detailed and well-structured overview of license inventory and usage with a user-friendly interface. We offer a hosted, cost-effective, and performance-optimized SAM4U setup in the Skybuffer Cloud environment. You retain ownership of the system and data, while we manage the ABAP 7.58 infrastructure, ensuring fixed Total Cost of Ownership (TCO) and exceptional services through the SAP Fiori interface.
Fueling AI with Great Data with Airbyte WebinarZilliz
This talk will focus on how to collect data from a variety of sources, leveraging this data for RAG and other GenAI use cases, and finally charting your course to productionalization.
In the realm of cybersecurity, offensive security practices act as a critical shield. By simulating real-world attacks in a controlled environment, these techniques expose vulnerabilities before malicious actors can exploit them. This proactive approach allows manufacturers to identify and fix weaknesses, significantly enhancing system security.
This presentation delves into the development of a system designed to mimic Galileo's Open Service signal using software-defined radio (SDR) technology. We'll begin with a foundational overview of both Global Navigation Satellite Systems (GNSS) and the intricacies of digital signal processing.
The presentation culminates in a live demonstration. We'll showcase the manipulation of Galileo's Open Service pilot signal, simulating an attack on various software and hardware systems. This practical demonstration serves to highlight the potential consequences of unaddressed vulnerabilities, emphasizing the importance of offensive security practices in safeguarding critical infrastructure.
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
Programming Foundation Models with DSPy - Meetup SlidesZilliz
Prompting language models is hard, while programming language models is easy. In this talk, I will discuss the state-of-the-art framework DSPy for programming foundation models with its powerful optimizers and runtime constraint system.
Monitoring and Managing Anomaly Detection on OpenShift.pdfTosin Akinosho
Monitoring and Managing Anomaly Detection on OpenShift
Overview
Dive into the world of anomaly detection on edge devices with our comprehensive hands-on tutorial. This SlideShare presentation will guide you through the entire process, from data collection and model training to edge deployment and real-time monitoring. Perfect for those looking to implement robust anomaly detection systems on resource-constrained IoT/edge devices.
Key Topics Covered
1. Introduction to Anomaly Detection
- Understand the fundamentals of anomaly detection and its importance in identifying unusual behavior or failures in systems.
2. Understanding Edge (IoT)
- Learn about edge computing and IoT, and how they enable real-time data processing and decision-making at the source.
3. What is ArgoCD?
- Discover ArgoCD, a declarative, GitOps continuous delivery tool for Kubernetes, and its role in deploying applications on edge devices.
4. Deployment Using ArgoCD for Edge Devices
- Step-by-step guide on deploying anomaly detection models on edge devices using ArgoCD.
5. Introduction to Apache Kafka and S3
- Explore Apache Kafka for real-time data streaming and Amazon S3 for scalable storage solutions.
6. Viewing Kafka Messages in the Data Lake
- Learn how to view and analyze Kafka messages stored in a data lake for better insights.
7. What is Prometheus?
- Get to know Prometheus, an open-source monitoring and alerting toolkit, and its application in monitoring edge devices.
8. Monitoring Application Metrics with Prometheus
- Detailed instructions on setting up Prometheus to monitor the performance and health of your anomaly detection system.
9. What is Camel K?
- Introduction to Camel K, a lightweight integration framework built on Apache Camel, designed for Kubernetes.
10. Configuring Camel K Integrations for Data Pipelines
- Learn how to configure Camel K for seamless data pipeline integrations in your anomaly detection workflow.
11. What is a Jupyter Notebook?
- Overview of Jupyter Notebooks, an open-source web application for creating and sharing documents with live code, equations, visualizations, and narrative text.
12. Jupyter Notebooks with Code Examples
- Hands-on examples and code snippets in Jupyter Notebooks to help you implement and test anomaly detection models.
Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.
Salesforce Integration for Bonterra Impact Management (fka Social Solutions A...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on integration of Salesforce with Bonterra Impact Management.
Interested in deploying an integration with Salesforce for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
This presentation provides valuable insights into effective cost-saving techniques on AWS. Learn how to optimize your AWS resources by rightsizing, increasing elasticity, picking the right storage class, and choosing the best pricing model. Additionally, discover essential governance mechanisms to ensure continuous cost efficiency. Whether you are new to AWS or an experienced user, this presentation provides clear and practical tips to help you reduce your cloud costs and get the most out of your budget.
GraphRAG for Life Science to increase LLM accuracyTomaz Bratanic
GraphRAG for life science domain, where you retriever information from biomedical knowledge graphs using LLMs to increase the accuracy and performance of generated answers
How to Interpret Trends in the Kalyan Rajdhani Mix Chart.pdfChart Kalyan
A Mix Chart displays historical data of numbers in a graphical or tabular form. The Kalyan Rajdhani Mix Chart specifically shows the results of a sequence of numbers over different periods.
Dandelion Hashtable: beyond billion requests per second on a commodity serverAntonios Katsarakis
This slide deck presents DLHT, a concurrent in-memory hashtable. Despite efforts to optimize hashtables, that go as far as sacrificing core functionality, state-of-the-art designs still incur multiple memory accesses per request and block request processing in three cases. First, most hashtables block while waiting for data to be retrieved from memory. Second, open-addressing designs, which represent the current state-of-the-art, either cannot free index slots on deletes or must block all requests to do so. Third, index resizes block every request until all objects are copied to the new index. Defying folklore wisdom, DLHT forgoes open-addressing and adopts a fully-featured and memory-aware closed-addressing design based on bounded cache-line-chaining. This design offers lock-free index operations and deletes that free slots instantly, (2) completes most requests with a single memory access, (3) utilizes software prefetching to hide memory latencies, and (4) employs a novel non-blocking and parallel resizing. In a commodity server and a memory-resident workload, DLHT surpasses 1.6B requests per second and provides 3.5x (12x) the throughput of the state-of-the-art closed-addressing (open-addressing) resizable hashtable on Gets (Deletes).
Taking AI to the Next Level in Manufacturing.pdfssuserfac0301
Read Taking AI to the Next Level in Manufacturing to gain insights on AI adoption in the manufacturing industry, such as:
1. How quickly AI is being implemented in manufacturing.
2. Which barriers stand in the way of AI adoption.
3. How data quality and governance form the backbone of AI.
4. Organizational processes and structures that may inhibit effective AI adoption.
6. Ideas and approaches to help build your organization's AI strategy.
Skybuffer AI: Advanced Conversational and Generative AI Solution on SAP Busin...Tatiana Kojar
Skybuffer AI, built on the robust SAP Business Technology Platform (SAP BTP), is the latest and most advanced version of our AI development, reaffirming our commitment to delivering top-tier AI solutions. Skybuffer AI harnesses all the innovative capabilities of the SAP BTP in the AI domain, from Conversational AI to cutting-edge Generative AI and Retrieval-Augmented Generation (RAG). It also helps SAP customers safeguard their investments into SAP Conversational AI and ensure a seamless, one-click transition to SAP Business AI.
With Skybuffer AI, various AI models can be integrated into a single communication channel such as Microsoft Teams. This integration empowers business users with insights drawn from SAP backend systems, enterprise documents, and the expansive knowledge of Generative AI. And the best part of it is that it is all managed through our intuitive no-code Action Server interface, requiring no extensive coding knowledge and making the advanced AI accessible to more users.
2. SAI UZ
Nucleic Acids
Analysis
UATI IACS
Genomics
Main Services: Real Time-PCR, Sequencing and Genotyping
Study of micro-organisms, plants, animals and humans
Sequencing and Functional Genomics Unit
4. SERVICE EQUIPMENT
DNA extraction
-Manual
-Automated
AutoGenFlex3000 System (Autogen)
Large volume DNA extraction (5 ml)
Whole blood, tissue samples, cultured cells and
saliva
40 samples per batch
KingFisher DuoPrime (ThermoScientific)
Small volume (10-50 µL) or large volume (300-
500 µL)
Interchangeable magnetic rod
6/12/24 samples per run
Analysis of amount and
integrity of Nucleic Acids
Nanodrop-1000 (ThermoScientific)
Qubit 3.0 (ThermoScientific)
Experion Automated Electrophoresis
System (Bio-Rad)
TapeStation 2200 (Agilent)
Projects
Biobank Aragón
Gastrointestinal Pathology (Program to prevent colorectal cancer)
Primary Dyslipidemia
Service Portfolio
5. SERVICE EQUIPMENT
Oligonucleotids design Oligo 7
PyroMark Assay Design
Amplification of DNA by PCR Verity thermocyclers
(Applied Biosystems)
Service Portfolio
6. SERVICE EQUIPMENT
Real Time-PCR:
-Gene Expression analysis
-Genetic Variation analysis:
*SNP genotyping
(allelic discrimination)
*Copy Number Variation (CNV)
-Presence/Absence studies
Real Time PCR instrument:
Viia7 (Applied Biosystems)
Up to 6 fluorophores simultaneously
Medium to high throughput
Interchangeable blocks
- Fast 96-well plates
- 384-well plates
- TaqMan Array Microfluidic Cards
Projects
MicroRNA study in rare diseases
CNV study in pharmagenetics
Service Portfolio
7. SERVICE EQUIPMENT
DNA Sequencing:
-De novo sequencing
-Resequencing
Sequencing instrument:
3500XL Genetic Analyzer (Applied
Biosystems)
Fragment Analysis:
-Microsatellites
-AFLPs
-MLPA
-LOH
SNP genotyping
Service Portfolio
8. Projects
Mutation screening for University Hospitals:
-Hereditary breast and ovary cancer
-Colon cancer
-MODY diabetes
Resequencing to establish the molecular
basis of human hereditary diseases:
-Research on genes related to primary dyslipidemia and
atherosclerosis
-Rare diseases of plasma high-density lipoproteins
-Investigation of the genetics of coronary heart disease risk in
subjects with familial hypercholesterolaemia
-Relationship between chitotriosidase genotype and immune
response to oxidized LDL in subjects with familial
hypercholesterolemia and beta-thalassemia
Service Portfolio
9. Projects
Microsatellite Analysis:
-Characterization of grape vine cultivars by molecular
markers
-Microsatellite fragments size determination for individual
identification and parentage testing, mutation search in
veterinary pathology, mutations involved in ovine prolificacy
species, identification by DNA-barcoding, mitochondrial DNA
biodiversity.
SNaPshot:
-Classification of Tuberculosis Strains.
-Genetic variability in genes related to bone metabolism in
Gaucher Disease patients
Service Portfolio
11. PGM ION S5XL
ION CHEF ION ONE TOUCH 2 ION ONE TOUCH ES
Ion Torrent Platform
ION REPORTER
12. Scalability
Chip 314 316 318 510 520 530 540 550
Reads 0,5 M 3 M 5 M 2-3 M 3-5 M 15-20 M 60-80 M 100-130 M
Output 20 MG 200 MG 1-2 GB 200 MG 1-2 GB 3-5 GB 10-15 GB 25 GB
Ion S5XL Ion GeneStudio S5
Ion GeneStudio S5 Plus / S5 Prime
PGM
13. Projects
WGS
−Whole genome sequencing of samples of Micobacterium Tuberculosis to
compare with the reference genome H37Rv (Ion Xpress™ Plus Fragment
Library Kit, Ion PGM, Ion S5XL).
−Whole genome sequencing of samples of Neisseria GonorNrhoeae to
compare strains.
Resequencing
−Resequencing of samples of Micobacterium Tuberculosis to compare SNPs
with the reference genome H37Rv by ampliseq panel. (Ion Chef, Ion PGM,
chip 316).
−Identification of the Human Endogenous Retroviruses (HERV-K) over-
expressed in multiple sclerosis by massive sequencing of PCR product (Ion
Xpress Plus Fragment Library kit, Ion S5XL).
Metagenomics
−Sequencing of the microbiome present in the digestive system of calves (16S
Metagenomics Kit, Ion S5XL, Ion Reporter software).
−Sequencing of the microbiome present in samples of runoff ponds potentially
contaminated with lindane and its isomers. The main interest was the
cyanobacteria and the sphingomonadaceas.
RNAseq
−Measurement of the expression of genes related to the expansion capacity of
subcutaneous adipose tissue (TAS) by RNAseq in biopsies of TAS (Ion
AmpliSeq™ Transcriptome Human Gene Expression Panel, Ion Chef, Ion
S5XL, chip 540).
Service Portfolio
14. SERVICE EQUIPMENT
Pyrosequencing:
-DNA Methylation studies
-SNP analysis
Pyrosequencer PSQ
96MA (Biotage)
96 samples simultaneously
Projects
SNP genotyping:
- Photobiology and Dermatology
- Digestive Diseases
DNA methylation:
- Neurosurgery (MGMT promoter methylation in
malignant gliomas)
Service Portfolio
15. SERVICE EQUIPMENT
Mouse Genotyping PCR
Projects
Neurodegeneration:
-Alzheimer
-Amyotrophic lateral sclerosis (ALS)
Service Portfolio
SERVICE EQUIPMENT
Human Cell Line Authentication
by STR profiling
PCR, Sequencer
Projects
Authentication of Diffuse and Intrinsic Glioma of the brainstem protuberance (DIPG) cell lines
16. Service Activity
Solicitudes Importe %
Electroforesis DNA 0 0,00 € 0,00
Extracción DNA 45 8.100,71 € 15,57
Extracción RNA 1 256,50 € 0,49
Cuantificación AN (Nanodrop) 5 13,04 € 0,03
Cuantificación AN (Qubit) 1 17,25 € 0,03
Análisis Integridad RNA (Experion) 4 228,25 € 0,44
Análisis Integridad RNA (TapeStation) 1 14,82 € 0,03
Amplificación AN 0 0,00 € 0,00
Purificación de material PCR 14 78,30 € 0,15
PCR a Tiempo Real (ViiA7) 109 1.914,60 € 3,68
Secuenciación. Análisis completo (3500XL) 79 14.818,96 € 28,48
Secuenciación. Autoanálisis (3500XL) 77 13.826,39 € 26,57
Análisis de Fragmentos ( 3500XL) 18 1.568,85 € 3,02
Pirosecuenciación 13 468,90 € 0,90
NGS 8 10.354,61 € 19,90
Extracción DNA ratones 0 0,00 € 0,00
Genotipado ratones 0 0,00 € 0,00
Otros 25 373,08 € 0,72
TOTAL 400 52.034,26 € 100,00
2018 (Oct 2017-Sept 2018)