This document provides an overview of next generation sequencing (NGS), including its history, key methods, applications and challenges. It discusses that NGS allows for massively parallel sequencing of thousands of DNA molecules simultaneously, providing exact sequences of genes. Some main NGS platforms and their sequencing methods are described, such as Illumina sequencing by synthesis. Applications of NGS discussed include cancer research, pharmacogenetics and preimplantation genetic diagnosis. Challenges associated with NGS like poor quality FFPE samples and large data analysis workflows are also outlined.
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells
The CRISPR/Cas9 system has emerged as one of the leading tools for modifying the genomes of organisms ranging from E. coli to humans. In this presentation, we discuss various methods for generating the crRNA and tracrRNA components that are required for guiding the Cas9 endonuclease to genomic targets. You will also learn how to optimize a new 2-part CRISPR RNA system from IDT that offers multiple benefits over other technologies.
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells
The CRISPR/Cas9 system has emerged as one of the leading tools for modifying the genomes of organisms ranging from E. coli to humans. In this presentation, we discuss various methods for generating the crRNA and tracrRNA components that are required for guiding the Cas9 endonuclease to genomic targets. You will also learn how to optimize a new 2-part CRISPR RNA system from IDT that offers multiple benefits over other technologies.
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
Knowing Your NGS Upstream: Alignment and VariantsGolden Helix Inc
Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output.
This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
Step by Step, from Liquid Biopsy to a Genomic Biomarker: Liquid Biopsy Series...QIAGEN
Liquid biopsies enable us to monitor the evolution of genetic aberrations in primary tumors as they shed the tumor cells into the circulation. The limitation is the ability to detect these low frequency genetic aberrations in a consistent manner to understand short- and long-term implications and how this information will be used in the clinic. This slidedeck will cover the challenges and solutions associated with multiple steps as one starts with liquid biopsy and move towards finding a new biomarker.
Webinar by BIS Research on Precision Oncology BiomarkersBIS Research Inc.
Precision oncology biomarkers are essential tools for tailoring cancer treatment to individual patients, as they provide insights into tumor biology and guide the selection of targeted therapies.
BIS conducted a deep intelligence webinar on the state-of-the-art technologies and emerging strategies used through the precision oncology biomarkers.
DNA Methylation: An Essential Element in Epigenetics Facts and TechnologiesQIAGEN
Check out this slide deck from Dr. Thorsten Singer and Dr. Ralf Peist to learn about DNA methylation in epigenetics, from its significance in cancer to strategies for studying it.
GTC group 8 - Next Generation SequencingYanqi Chan
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. Discuss the application of next generation sequencing in cancer treatment.
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
Knowing Your NGS Upstream: Alignment and VariantsGolden Helix Inc
Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output.
This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
Step by Step, from Liquid Biopsy to a Genomic Biomarker: Liquid Biopsy Series...QIAGEN
Liquid biopsies enable us to monitor the evolution of genetic aberrations in primary tumors as they shed the tumor cells into the circulation. The limitation is the ability to detect these low frequency genetic aberrations in a consistent manner to understand short- and long-term implications and how this information will be used in the clinic. This slidedeck will cover the challenges and solutions associated with multiple steps as one starts with liquid biopsy and move towards finding a new biomarker.
Webinar by BIS Research on Precision Oncology BiomarkersBIS Research Inc.
Precision oncology biomarkers are essential tools for tailoring cancer treatment to individual patients, as they provide insights into tumor biology and guide the selection of targeted therapies.
BIS conducted a deep intelligence webinar on the state-of-the-art technologies and emerging strategies used through the precision oncology biomarkers.
DNA Methylation: An Essential Element in Epigenetics Facts and TechnologiesQIAGEN
Check out this slide deck from Dr. Thorsten Singer and Dr. Ralf Peist to learn about DNA methylation in epigenetics, from its significance in cancer to strategies for studying it.
GTC group 8 - Next Generation SequencingYanqi Chan
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. Discuss the application of next generation sequencing in cancer treatment.
Methods, Challenges and Future Directions of Radiogenomics-Crimson PublishersCrimsonpublishersCancer
Tissue response to the radiation is a complex pathophysiological process and is an inherited polygenic trait. Aim of the Radiogenomics studies is to discover related genetic variants that confer tumor or nontumor tissue radio sensitivity as the target of radio-sensitizing and/or radio-protective agents and to identify specific genetic markers for prognosis or risk prediction. The methods for radiogenomics studies include candidate gene approaches, genome-wide association studies, Next-Generation Sequencing (NGS), epigenetic study, and other methods. The future direction of radiogenomics should be the development of the polygenic risk scores that are incorporated into end point-specific clinical models/nomograms.
Applications of Next generation sequencing in Drug Discoveryvjain38
This presentation gives an overview of the Next generation Sequencing (NGS) technology and what are is current applications in the drug discovery process.
Genetic variability and phylogenetic relationships studies of Aegilops L. usi...Innspub Net
Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.
Proteogenomic analysis of human colon cancer reveals new therapeutic opportun...Gul Muneer
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
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at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
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from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
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Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
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
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Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
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What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
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Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...
Next Generation Sequencing
1. Next Generation
Sequencing
Joshua Lee Voon Kai (0333356)
Tee Zhong Ee (0327975)
Sing (0328048)
Cheong Pui Yi (0326329)
Hsing Lu (0331441)
Julian Tay (0328917)
2. Second
G.S.
Sanger
Sequencing
First G.S.
The Discovery of Next Generation Sequencing (NGS)
“to determine the sequence of a DNA molecule(s) with total size significantly larger than 1 million base
pairs in a single experiment ” (Ploski, 2016).
Third
G.S.
Discovered
- 1977
- Frederick Sanger
- Walter Gilbert
Based on dideoxy
technique
Developed into chain-
termination method, also
known as Sanger
sequencing.
Derived from Sanger
Sequencing
- 1986
dNTP and ddNTP are used
for electrophoresis
technology.
Created by implementing
several new methods into
FQS
Eg.
- Roche/454 platform in
2005
- Solexa/Illumina system in
2006,
Launched
- in 2000
- by Lynx
Therapeutics (USA)
Company.
Launched by Helicos
BioSciences
Achieved due to advances
in automated single
molecule imaging and
fluidics technologies
Lower cost than Sanger
sequencing.
Highly time efficient.
(Barba, Czosnek and Hadidi, 2014)
(Heather and Chain, 2016)
(Ambardar et al., 2016)(Totomoch-Serra, Marquez and Cervantes-Barragán, 2017)
(Ozsolak, 2012)(Kamps et al., 2017)
3. Type of protocols !
Types of Sequencing Method
Pyrosequencing
Sequencing by synthesis
Sequencing by ligation
Ion semiconductor
sequencing
Template Preparation (Amplify)
Emulsion PCR
Bridge PCR
Common steps
1. Template Preparation
2. Sequencing
3. Data Analysis
Goal: Sequence thousands of DNA molecules simultaneously and get the exact sequence of
genes
Example: Roche/454 FLX, Illumina/ Solexa Genome
Analyzer, Applied Biosystems (ABI) SOLiD Analyzer,
Polonator G.007 and Helicos HeliScope
(ABM, n.d.)
4. Illumina Genome Analyzer
● Most widely used system
● Fast approach
● Run multiple sample simultaneously
● Incorporate 1 single nucleotide at a time (1 by 1)
All nucleotide
added. Only 1 will
bind because of the
terminator group
Fluorescence
molecule and
terminator
group cleaved
and washed
away
Repeat until the
sequencing
reaction is
complete
Terminator
group
Fluorescence
dye
Fluorescence
signal is read
at each cluster
and recorded
ACGA…………..
Sequencing by synthesis
(ABM, n.d.)
Model: Illumina Hi Seq 4000
5. Massive parallel
sequencing
Detection of somatic
cells’ genetic changes
High sensitivity &
detection rate
- Allowing million of
sequencing
reactions to happen
at the same time
- Broad spectrum of
mutation detection
(Arsenic et al. 2015)
- The heterogenous of
tumour makes somatic
cell mutation hard to be
detected
- NGS is able to
overcome this
conundrum
(Arsenic et al. 2015)
- Some tumours are
attributed to
mutations at low
variant frequency
alleles
- NGS is able to detect
mutation at low
frequency alleles
(Serrati et al.
Key features of NGS in cancer research
6. Sanger Sequencing (First
Generation Sequencing)
Next Generation Sequencing
Efficacy was limited due to the
inabilities of performing parallel
investigation of multiple genes (Arsenic et al.
2015)
Fast and efficient by performing massive
parallel sequencing (Arsenic et al. 2015)
Somatic cancer mutation can only be
recognized with performing
microdissection (Arsenic et al. 2015)
Both somatic and germline mutation can
be detected (Arsenic et al. 2015)
Low sensitivity to mutation occuring at
an allele frequency lower than 20%
(Arsenic et al. 2015)
High sensitivity and detection rate in
spite of the low frequency allele
(Arsenic et al. 2015)
NGS vs Sanger in cancer research
7. Assist in therapeutic
decision making
Panitumumab treatment
prolonged progression
free survival in KRAS-
WT patients compared to
KRAS-mutant patient
Chemotherapy
applications
Colorectal cancer (CRC)
Affects colon and rectum
Third most common type
of cancer
Great quantity of
activating mutations
CRC
Fast high throughput
and cost effective
technology
Can accurately identify
mutation in known
genes
9 genes from 320
samples
NGS
Detected mutations in KRAS, NRAS , BRAF, PI3KCA, PTEN, TP53, EGFR, AKT, CTNNB1
(Vecchio et al, 2017)
8. ctDNA as a non-invasive
method cancer
biomarker
real time cancer
detection, screen for
diseases, monitoring
therapeutic responses
NGS has high enough
specificity and
sensitivity
Liquid biopsies
Current development
Prevent inherited cancer
syndrome
PGD and IVF used in
combination to detect
aberrations in
blastomere
NGS to detect
chromosomal
aberrations across
entire genome
Preimplantation
genetic diagnosis
Rare variants exerts
detrimental effects drug
metabolising enzymes
NGS is capable of
analysing high number
of genes and identifying
variants
More useful than
analyses single gene
Pharmacogenetics
(Kamps et al, 2017)
(Giannopoulou et al, 2019)
(Kamps et al, 2017)
(Illumina, n.d.)
9. Challenges: Process
● Poor FFPE sample quality:
Preservation Method
● FFPE: Popular in cancer research¹
● ↓ DNA yield & Fragment size -
difficulty in constructing high quality
libraries (important for analysis)
● False positives & artefacts
● Quality variability¹ → ↑ QA,
streamline/automate/optimize²,³→
Improve DV200
(Sample isolation --> library construction)
● Variance of Uncertain Significance
(VUS)
● Normal variation or expected to
cause disease symptoms?
● Correlation of disease to VUS unclear
● Example: BRCA1 has other
associations⁴ → take time to identify
combinations
● Testing healthy patients will be
uninformative, widely-publicized
case of Elisha Cooke-Moore⁵
(Interpretation stage)
¹(Gaffney et al. 2018) ²(Einaga et al. 2017) ³(Fisher et al. 2011) ⁴(Rebbeck et al. 2015) ⁵(Jamie Ducharme 2017)
10. Challenges: Sequence Data Analysis Workflows
(Kulkarni and Frommolt, 2017)
Large Generated Data
Use Centralized
Processing Methods
Scattered Human
Genomics Sequences
International
collaboration efforts
Complex genomic
variation, dynamics and
pathology, VUS
Machine learning
deep neural
networks
11. - NGS helps to conquer the
challenges of low tumour
quality, heterogeneity of
tumour. (Meyerson, Gabriel & Getz 2010)
- In future, smaller samples are
likely to be diagnosed by using
NGS (Meyerson, Gabriel & Getz 2010)
Render remarkable impact in
cancer treatment
Conclusion - NGS
- Able to run multiple
samples at the same time
- High sensitivity and
detection rate
- Cost-effective
- Provide comprehensive
genomic information
(Arsenic et al. 2015)
Effective method to
detect mutation
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<https://www.abmgood.com/marketing/knowledge_base/next_generation_sequencing_introduction.php>
● Ambardar, S., Gupta, R., Trakroo, D., Lal, R. and Vakhlu, J. 2016. ‘High Throughput Sequencing: An Overview of Sequencing
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generation sequencing and Sanger sequencing for the detection of PIK3CA mutations in breast cancer’, BMC clinical
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● Barba, M., Czosnek, H. and Hadidi, A. 2014. ‘Historical Perspective, Development and Applications of Next-Generation
Sequencing in Plant Virology’. Viruses, [online] 6(1), pp.106-136. Available at:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3917434/ [Accessed 27 May 2019].
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p.e0176280. Available from: https://dx.plos.org/10.1371/journal.pone.0176280. [27 May 2019].
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Blumenstiel, B, Cibulskis, K, Friedrich, D, Johnson, R, Juhn, F, Reilly, B, Shammas, R, Stalker, J, Sykes, SM, Thompson, J,
Walsh, J, Zimmer, A, Zwirko, Z, Gabriel, S, Nicol, R & Nusbaum, C 2011, ‘A scalable, fully automated process for construction
of sequence-ready human exome targeted capture libraries’., Genome Biology, vol. 12, no. 1, p.R1. Available from:
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-1-r1. [28 May 2019].
● Gaffney, E, Riegman, P, Grizzle, W & Watson, P 2018, ‘Factors that drive the increasing use of FFPE tissue in basic and
translational cancer research’., Biotechnic & Histochemistry, vol. 93, no. 5, pp.373–386. Available from:
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● Giannapoulou, E, Katsila, T, Mitropoulou, C, Tsermpini, EE & Patrinos, GP 2019, ‘Integrating next generation sequencing in
the clinical pharmacogenomins workflow’, Frontiers in Pharmacology, viewed 27 May 2019,
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● Heather, J. and Chain, B. 2016. ‘The sequence of sequencers: The history of sequencing DNA’. Genomics, [online] 107(1),
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