Sequencing genes and genomes in biology. The most important technique available to the molecular biologist is DNA sequencing, by which the precise order of nucleotides in a piece of DNA can be determined
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
Transcriptomics is the study of RNA, single-stranded nucleic acid, which was not separated from the DNA world until the central dogma was formulated by Francis Crick in 1958, i.e., the idea that genetic information is transcribed from DNA to RNA and then translated from RNA into protein.
The human genome is pervasively transcribed, giving rise to an increasing number of long non-coding RNA genes. Most of these genes are novel or poorly characterized, and their relevance in human health and disease remains elusive. In our lab, we have developed various tools to study lncRNAs, amongst others to assess their role in cancer. As such, we are looking for novel biomarkers and therapeutic targets. I will describe various tools and ongoing research programs, including a comprehensive annotated catalog of human lncRNAs (LNCipedia), a targeted screen for focal lncRNA copy number alterations, a web tool for antisense oligonucleotide design, Zipper plot to visualize the transcriptional activity of lncRNAs in their genomic context, decodeRNA functional context mapping, and probe based lncRNA capture sequencing in body fluids.
Transcriptomics is the study of RNA, single-stranded nucleic acid, which was not separated from the DNA world until the central dogma was formulated by Francis Crick in 1958, i.e., the idea that genetic information is transcribed from DNA to RNA and then translated from RNA into protein.
The human genome is pervasively transcribed, giving rise to an increasing number of long non-coding RNA genes. Most of these genes are novel or poorly characterized, and their relevance in human health and disease remains elusive. In our lab, we have developed various tools to study lncRNAs, amongst others to assess their role in cancer. As such, we are looking for novel biomarkers and therapeutic targets. I will describe various tools and ongoing research programs, including a comprehensive annotated catalog of human lncRNAs (LNCipedia), a targeted screen for focal lncRNA copy number alterations, a web tool for antisense oligonucleotide design, Zipper plot to visualize the transcriptional activity of lncRNAs in their genomic context, decodeRNA functional context mapping, and probe based lncRNA capture sequencing in body fluids.
DNA Sequencing - DNA sequencing is like reading the instructions inside a cellAmitSamadhiya1
DNA sequencing is like reading the instructions inside a cell. It's figuring out the exact order of the building blocks that make up our DNA, represented by the letters A, T, C, and G. This order is like a code that tells our bodies how to function and grow.
By reading this code, scientists can understand genes, diagnose diseases, and even trace our ancestry. There are different ways to sequence DNA, kind of like having a few different ways to read a book. These techniques are constantly improving, making it faster and easier to unlock the secrets hidden in our DNA.
sequencing presentation. providing deep and insightful points about Sanger sequencing, Maxam-gilbert sequencing, Illumina sequencing, and single molecule sequencing.
whole genome analysis
history
needs
steps involved
human genome data
NGS
pyrosequencing
illumina
SOLiD
Ion torrent
PacBio
applications
problems
benefits
SLIDE CONTAIN BREIF NOTE ON PCR. IT CONTAINS 21 SLIDES INCLUDING, WHAT IS PCR? COMPONENTS, WORKING MECHANISM, APPLICATIONS, CONCLUSION, AND SOME REFRENCES, HISTORY ALSO
Original Next Gen Seq Methods set of slides prepared for Technorazz Vibes 2016. There is also a shorter version.
This starts with an introduction to qPCR followed by an introduction to Library Complexity. Microarrays are discussed as well along with a very short introduction to FISH. Finally discussion of Next gen seq methods is done where generation of sequencers are discussed and a short discussion of the ILLUMINA protocol. Finally comparison of ILLUMINA amongst other 3rd gen sequencer, description of the standard pipeline and the omics technologies that have risen from this seq data.
mRNA stability and localization.RNA is critical at many stages of gene expression. How frequently it will be translated, how long it is likely to survive, and where in the cell it will be translated. RNA cis-elements & associated proteins
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
2. • The most important technique available to the molecular biologist is
DNA sequencing, by which the precise order of nucleotides in a piece of
DNA can be determined.
• The techniques in use today can be divided into two categories:
1. Chain-termination method
2. Next-generation sequencing
2
4. 10.1.1. Chain termination DNA sequencing in outline
Chain termination DNA sequencing is based on the principle that single-
stranded DNA molecules that differ in length by just a single nucleotide
can be separated from one another by polyacrylamide gel electrophoresis.
. short oligonucleotide + template = primer
. deoxyribonucleotide triphosphates (dNTPs—dATP, dCTP, dGTP, and
dTTP)
. dideoxynucleotides (ddNTPs—ddATP, ddCTP, ddGTP, and ddTTP)
4
6. 10.1.2. Not all DNA polymerases can be used for sequencing
• Many DNA polymerases have a mixed enzymatic activity, being able to
degrade as well as synthesize DNA.
• Degradation can occur in either the 5′→3′ or 3′→5′ direction.
• The 3′→5′ activity could have the same effect, but more importantly will
remove a dideoxynucleotide that has just been added at the 3′ end,
preventing chain termination from occurring.
• In the original method Klenow polymerase = (5′→3′ ) ,
processivity
• Taq polymerase processivity , exonuclease
6
7. 10.1.3. Chain-termination sequencing with
Taq polymerase
• thermal cycle sequencing
• similar to PCR
• four dideoxynucleotides chain termination
10.1.4. Limitations of chain-termination sequencing
• It is necessary to sequence each region of a genome multiple times, in order to identify errors present in individual sequence reads
• One of the goals of personalized medicine is to use individual genome sequences to make accurate diagnoses of a person’s risk of
developing a disease, and to use that person’s genetic characteristics to plan effective therapies and treatment regimes.
From Sanger sequencing to genome databases and beyond
• personalized medicine has huge potential with both diagnoses and treatment options being driven by different factors associated with
an individual
• Ultimately, it is the advancements in the abovementioned NGS technologies that enable the construction of large open access
databases. The availability of these databases will allow patients to gain access to more sophisticated tests that provide important
genetic information, allowing for more targeted medical care.
7
8. . A large library made up of thousands or millions of DNA fragments is
sequenced in a single experiment
10.2. Next-generation sequencing
The difference between chain-
termination and next-generation
sequencing
8
9. 10.2.1 Preparation of a next-generation
sequencing library
• Breakage of DNA
• Immobilization
• Amplification
DNA fragmentation
Sonication random positions
Immobilization of the library
Glass slide / small metallic beads
Amplification of the library
The final step in library preparation
9
10. Immobilization of the DNA fragments in a
sequencing library by base pairing to metallic
beads. (a) Each DNA fragment is attached to a
single bead via a streptavidin–biotin linkage.
(b) Individual beads, with their attached DNA
fragments, are placed within water droplets in
an oil–water emulsion.
Immobilization of the DNA fragments in a sequencing
library by base pairing to oligonucleotides on a glass side
10
11. 10.2.2. Next-generation sequencing methods
There is no electrophoresis or any other fragment separation step.
1. Reversible terminator sequencing
Modified nucleotides / The termination step is reversible / Maximum length of 300 bp / Illumina
sequencing
2. Pyrosequencing
Does not require electrophoresis / More rapid / Detection of pulses of chemiluminescence /
Pyrophosphate / Sulfurylase
In the reaction mixture so that if a deoxynucleotide is not incorporated into the polynucleotide
then it is rapidly degraded before the next one is added = apyrase
Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments
11
12. Pyrosequencing
Illumina sequencing. The fragments are attached to
primers immobilized on a solid surface, performing
a bridge-amplification and generating clusters of
DNA with identical molecules.
12
13. 10.2.3. Third-generation sequencing
. Real-time sequencing also enables read lengths to be longer
. Best methods = single molecule real-time sequencing (SMRT)
. Read lengths of up to 20 000 bp
Real-time DNA sequencing with each
nucleotide addition detected with a zero-mode
waveguide
13
14. 10.2.4. Directing next-generation sequencing at
specific sets of genes
• All parts of the genome are sequenced at the same time
• Target enrichment method
Target enrichment. (a) Baits are used to capture DNA
fragments representing genes of interest. (b) Only the
captured DNA fragments are sequenced
14
15. 10.3 How to sequence a genome
• Bacteriophage ϕX174 , SV40 virus, pBR322.
• The first chromosome sequence, for chromosome III of the yeast
Saccharomyces cerevisiae, was published in 1992, and the entire yeast
genome was completed in 1996
• The main challenge lies with sequence assembly
• The simplest way of doing this is the shotgun approach
15
16. 10.3.1 Shotgun sequencing of prokaryotic genomes
Shotgun sequencing of the Haemophilus influenzae genome
• Sonicate / cloned in plasmid and M13 vectors / two chain-termination DNA sequences
• After cloning, 28,643 chain termination sequencing experiments were carried out with 19,687 of the
clones.
• A few of these sequences—4339 in all—were rejected because they were less than 400 bp in length.
• The remaining 24 304 sequences were entered into a computer, which then spent 30 hours searching
for overlaps among the sequences.
• The result was 140 contiguous sequences or contigs, each made up of a series of overlapping
sequence reads.
• It might have been possible to continue sequencing more of the sonicated fragments in order
eventually to close the gaps between the individual contigs.
• The most successful involving hybridization analysis of a clone library prepared in a λ vector
16
17. A schematic of the key steps in the H.
influenza genome sequencing project
Using oligonucleotide
hybridization to close gaps in
the H. influenzae genome
sequence. Oligonucleotides 2
and 5 both hybridize to the
same λ clone, indicating that
contigs I and III are adjacent.
The gap between them can be
closed by sequencing the
appropriate part of the λ clone.
17
18. 10.3.2. Sequencing of eukaryotic genomes
One problem with the shotgun approach. An incorrect
overlap is made between two sequence reads that both
terminate within a repeated element. The result is that
a segment of the DNA molecule is absent from the
DNA sequence
18
19. The hierarchical shotgun approach
• Pre-sequencing phase
• These fragments then cloned into a high-capacity vector such as a BAC
• Massive task
• Chromosome walking
• The weakness of chromosome walking is that it begins at a fixed starting point and
builds up the clone contig step by step, and hence slowly, from that fixed point.
• The more rapid techniques for clone contig assembly do not use a fixed starting point
and instead aim to identify pairs of overlapping clones.
• The various techniques that can be used to identify overlaps are collectively known
as clone fingerprinting. Clone fingerprinting is based on the identification of
sequence features that are shared by a pair of clones.
19
20. Hierarchical shotgun sequencing can avoid problems
with repeat sequences. Sequence assembly of the reads
from clone 2 could result in the segment between the two
repeats being lost. However, the sequence of clone 3
enables the mistake to be recognized and corrected
Building up a series of overlapping clones using a
clone fingerprinting technique
20
21. Shotgun sequencing of eukaryotic genomes
• The most successful strategy is to use two or more sequencing libraries,
with one of the libraries containing fragments that are longer than the
longest repeat sequences in the genome being studied.
• Drosophila melanogaster
The strategy used to ensure that repetitive DNA
regions were assembled correctly when the
Drosophila melanogaster genome was sequenced.
Two identical 8-kb repeats are adjacent in the
genome. The end-sequences of the 10-kb fragment
that spans one of these repeats can be checked
against the master sequence to ensure that the
segment between the two repeats has not been lost. 21
22. What do we mean by ‘genome sequence’?
• It is important to recognize that a ‘complete’ genome sequence is currently an
impossibility for a eukaryotic genome.
• The standard being that at least 95% of the euchromatin should be sequenced and all
except the most refractory gaps filled.
• N50 size = the total length of all the contigs added together
22
24. Channels used by the Oxford Nanopore
platform to sequence DNA.
Polymerase fixed to the bottom of an individual
well. In the Pacific Bioscience platform, the
DNA moves generate signals because of the
incorporation of phosphate-labeled nucleotides.
24
25. In the Ion Torrent platform, the chip is the
sequencer. Each well of the chip acts as a pH meter
that is able to detect changes in the concentration
of H+ produced in DNA polymerization.
25
26. DNA Sequencing Sensors
Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass
sequencing sensors, or new generation sequencing (NGS) meant a quantitative leap both in the volume of genetic material that
was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies,
already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each
run. All of this would be impossible without sensors and detection systems becoming smaller and more precise.
Massively parallel sequencing techniques for forensics
DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing
(NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as
biotechnology, virology, and medical diagnostics. these techniques have also gained attention in the forensic field. Relevance to
the forensic analysis is that besides generation of standard STR-profiles, DNA repeats can also be sequenced to look for
polymorphisms. Furthermore, additional SNPs can be sequenced to acquire information on ancestry, paternity or phenotype. The
current MPS systems are also very helpful in cases where only a limited amount of DNA or highly degraded DNA has been
secured from a crime scene. If enough autosomal DNA is not present, mitochondrial DNA can be sequenced for maternal lineage
analysis.
26
27. Comparison of the different sequencing platforms. The data
shown refer to the most favorable conditions for each platform
27
28. The Third Revolution in Sequencing Technology
Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered
for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome
sequencing much cheaper and faster. However, NGS methods have several drawbacks and pitfalls, most notably their short reads.
Recently, third-generation/long-read methods appeared, which can produce genome assemblies of unprecedented quality.
Moreover, these technologies can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing
without the need for assembly.
Overview of Next Generation Sequencing Technologies
Sequencing platforms that are smaller, require less power, less reagents and maintenance will be utilized in medical, agricultural,
ecological and other settings. At the front end, advances in robotics, liquid handling, sample processing (nucleic acid
preparation) will contribute to these advancements. Equally important will be advances in faster and more accurate bioinformatic
data analysis as well as data transfer and storage.
Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species
However, so far, there are still controversies about the source of the virus and its intermediate host. Here, we found the novel
coronavirus was closely related to coronaviruses derived from five wild animals. However, genome and ORF1a homology show
that the virus is not the same coronavirus as the coronavirus derived from these five animals, whereas the virus has the highest
homology with Bat coronavirus isolate RaTG13.
28
29. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of
emergence as a result of a recent recombination event
Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome
(sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. The levels of genetic
similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak
in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely.
Characterization and Clinical Significance of Natural Variability in Hepatitis B Virus Reverse
Transcriptase in Treatment-Naive Chinese Patients by Sanger Sequencing and Next-Generation
Sequencing
HBV RT sequences were analyzed in 427 patients by Sanger sequencing and in 66 patients by next-generation sequencing.
Primary or secondary NA resistance (NAr) mutations were not found, except A181T in RT (rtA181T) by Sanger sequencing, but
they were detected by next-generation sequencing. Mutations were found in 56 RT amino acid (aa) sites by Sanger sequencing, 36
of which had mutations that could lead to changes in B or T cell epitopes in the RT or S protein. The present study demonstrates
that next-generation sequencing (NGS) was more suitable than Sanger sequencing to monitor NAr mutations at a low rate in the
treatment-naive patients, and that mutations in the RT region might be involved in the progression to ALD.
Simple protocol for population (Sanger) sequencing for Zika virus
genomic regions
The present study provided a simple and low-cost Sanger protocol to sequence relevant genes of the ZIKVgenome. The identity of
Sanger generated sequences with published consensus NGS support the use of Sanger method for ZIKV population studies. Primer
sets were designed in order to conduct a nested RT-PCR and a Sanger sequencing protocols.
29
30. Next-Generation Sequencing Technologies and their Application to the Study and Control of
Bacterial Infections
It is a challenge that the comparability of the sequence data generated on different platforms with different error profiles using
different library preparation methods has still not been comprehensively assessed and validated. On the positive side, the cost
of sequencing, data transfer and analysis will continue to decrease and the DNA purification including library preparation and
the actual sequencing will become faster and more efficient. The Achilles heel of the current long read technologies, the high
error rates, will continue to improve until they become as precise as the short-read technologies at which time the latter will
become obsolete.
30
31. • 1. DNA Sequencing Sensors: An Overview
Jose Antonio Garrido-Cardenas 1, Federico Garcia-Maroto 2, Jose Antonio Alvarez-Bermejo 3, Francisco Manzano-Agugliaro 4
PMID: 28335417 PMCID: PMC5375874 DOI: 10.3390/s17030588
• 2. Massively parallel sequencing techniques for forensics: A review
Brigitte Bruijns 1 2, Roald Tiggelaar 1 3, Han Gardeniers 1 PMID: 30101986 PMCID: PMC6282972 DOI: 10.1002/elps.201800082
• 3. From Sanger sequencing to genome databases and beyond
Jenny Straiton, Tristan Free, Abigail Sawyer, Joseph Martin PMID: 30744413 DOI: 10.2144/btn-2019-0011
• 4. Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments
Andrea Arias 1, Pablo López 2, Raphael Sánchez 3, Yasuhiro Yamamura 4, Vanessa Rivera-Amill 5 PMID: 30096879 PMCID: PMC6122037 DOI:
10.3390/ijerph15081697
• 5. Detection of Rare Mutations in EGFR-ARMS-PCR-Negative Lung Adenocarcinoma by Sanger Sequencing
Chaoyue Liang # 1, Zhuolin Wu # 2, Xiaohong Gan 3, Yuanbin Liu 4 5, You You 4 5, Chenxian Liu 1, Chengzhi Zhou 4 5, Ying Liang 4, Haiyun Mo 6, Allen M
Chen 3 7, Jiexia Zhang 4 8 PMID: 29214771 PMCID: PMC5725350 DOI: 10.3349/ymj.2018.59.1.13
• 6. Simple protocol for population (Sanger) sequencing for Zika virus genomic regions
Gabriela Bastos Cabral 1, João Leandro de Paula Ferreira 1, Renato Pereira de Souza 2, Mariana Sequetin Cunha 2, Adriana Luchs 3, Cristina Adelaide
Figueiredo 4, Luís Fernando de Macedo Brígido 1 PMID: 29185594 PMCID: PMC5719533 DOI: 10.1590/0074-02760170248
• 7. Characterization and Clinical Significance of Natural Variability in Hepatitis B Virus Reverse Transcriptase in Treatment-Naive Chinese Patients by Sanger
Sequencing and Next-Generation Sequencing
Ya Fu 1 2, Yongbin Zeng 1 2, Tianbin Chen 1 2, Huijuan Chen 1 2, Ni Lin 1 2, Jinpiao Lin 1 2, Xiaofeng Liu 1 2, Er Huang 1 2, Songhang Wu 1 2, Shu Wu 1 2,
Siyi Xu 1 2, Long Wang 1 2, Qishui Ou 3 2 PMID: 31189581 PMCID: PMC6663897 DOI: 10.1128/JCM.00119-19
• 8. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event
D Paraskevis 1, E G Kostaki 2, G Magiorkinis 2, G Panayiotakopoulos 3, G Sourvinos 4, S Tsiodras 5 PMID: 32004758 PMCID: PMC7106301 DOI:
10.1016/j.meegid.2020.104212
• 9. Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species
Chun Li 1, Yanling Yang 2, Linzhu Ren 3 PMID: 32169673 PMCID: PMC7270525 DOI: 10.1016/j.meegid.2020.104285
31
32. • 10. The Third Revolution in Sequencing Technology
Erwin L van Dijk 1, Yan Jaszczyszyn 2, Delphine Naquin 2, Claude Thermes 2 PMID: 29941292 DOI: 10.1016/j.tig.2018.05.008
• 11. Overview of Next Generation Sequencing Technologies
Barton E Slatko 1, Andrew F Gardner 1, Frederick M Ausubel 2 PMID: 29851291 PMCID: PMC6020069 DOI: 10.1002/cpmb.59 2019
• 12. . Next-generation sequencing technologies and their application to the study and control of bacterial infections
J Besser 1, H A Carleton 1, P Gerner-Smidt 2, R L Lindsey 1, E Trees 1 PMID: 29074157 PMCID: PMC5857210 DOI: 10.1016/j.cmi.2017.10.013
• 13. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
R D Fleischmann 1, M D Adams, O White, R A Clayton, E F Kirkness, A R Kerlavage, C J Bult, J F Tomb, B A Dougherty, J M Merrick, et al.
PMID: 7542800 DOI: 10.1126/science.7542800
• 14. Visual mapping by high resolution FISH M Heiskanen 1, L Peltonen, A Palotif PMID: 8909124 DOI: 10.1016/0168-9525(96)30083-8
• 15. Genome sequencing in microfabricated high-density picolitre reactors
Marcel Margulies 1, Michael Egholm, William E Altman, Said Attiya, Joel S Bader, Lisa A Bemben, Jan Berka, Michael S Braverman, Yi-Ju Chen,
Zhoutao Chen, Scott B Dewell, Lei Du, Joseph M Fierro, PMID: 16056220 PMCID: PMC1464427 DOI: 10.1038/nature03959
Nature. 2006 May 4;441(7089):120. Ho, Chun He [corrected to Ho, Chun Heen]
• 16. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides
J M Prober 1, G L Trainor, R J Dam, F W Hobbs, C W Robertson, R J Zagursky, A J Cocuzza, M A Jensen, K Baumeister PMID: 2443975 DOI:
10.1126/science.2443975
33. • 17. A sequencing method based on real-time pyrophosphate
M Ronaghi 1, M Uhlén, P Nyrén PMID: 9705713 DOI: 10.1126/science.281.5375.363
• 18. CircumVent thermal cycle sequencing and alternative manual and automated DNA sequencing protocols using the highly thermostable VentR
(exo-) DNA polymerase
L E Sears 1, L S Moran, C Kissinger, T Creasey, H Perry-O'Keefe, M Roskey, E Sutherland, B E Slatko PMID: 1476733
• 19. A method for constructing radiation hybrid maps of whole genomes
M A Walter 1, D J Spillett, P Thomas, J Weissenbach, P N Goodfellow PMID: 8075634 DOI: 10.1038/ng0594-22