next generation sequencing (recent collection2018)

NEXTGENERATION SEQUENCING TECHNIQUES
by Dr. Amir Abdelazim2018
RECENT ADVANCEMENT IN NEXT GENERATION
SEQUENCING TECHNIQUES
I will try to summarize:
 basic background of NGS technologies
 possible applications
 computational approaches and tools involved in NGS data analysis
 future opportunities and challenges in the area.
Introduction:
Next Generation Sequencing (NGS), a recently evolved technology, this novel approach is a newbie and
has critical advantages over the traditional Capillary Electrophoresis (CE) based Sanger Sequencing.
The advancement of NGS has led to numerous important discoveries, which could have been costlier and
time taking in case of traditional CE based Sanger sequencing.
NGS methods are highly parallelized enabling to sequence thousands to millions of molecules
simultaneously. This technology results into huge amount of data, which need to be analysed to conclude
valuable information. Specific data analysis algorithms are written for specific task to be performed. The
algorithms in group, act as a tool in analysing the NGS data. Analysis of NGS data unravels important clues
in quest for the treatment of various life-threatening diseases; improved crop varieties and other related
scientific problems related to human welfare.
DNA sequencing is a method to obtain the exact order of occurrence of nucleotides in a DNA. With the help
of DNA sequence, researchers can illuminate genetic information from a biological system.

The first-generation sequencing method, called Sanger sequencing, was developed by Edward Sanger in
1975. Since its inception, Sanger sequencing was considered as the gold standard for DNA sequencing for
around three decades.
The first major breakthrough of first-generation sequencing was the Human Genome Project (HGP), 13-
years long, $3 million project, completed in 2003. Due to inherent limitations in throughput, speed, scalability
and resolution of first-generation Sanger sequencing approach, second-generation of sequencing method,
or Next- Generation Sequencing (NGS) has been developed to cater high demand for cheaper as well as
faster sequencing technology.
The NGS is fundamentally different approach to sequencing that lead to several ground-breaking discoveries
and brought a new revolution in genomic research by revealing limitless insight related to genome,
transcriptome and epigenome.
Principally, basic idea behind NGS is similar to capillary electrophoresis (CE)based Sanger sequencing,
but NGS extends the idea to perform massive parallel sequencing, where millions of fragments of DNA from
a single sample are accurately sequenced.
The NGS enables sequencing of large stretch of DNA base pairs, producing hundreds of gigabases of data
in a single sequential run.
The NGS, also known as Massive Parallel Sequencing, allows the complete genome (of human) to be
sequenced in less than a day.

More recently, third generation sequencing (TGS) has evolved, however, it is still in its infancy. Because of
its maturity and understanding, among all the three sequencing generations, the NGS is more widely
accepted.
Fig. 1 Overview of sequencing generations
What does NGS offer?
The NGS is a powerful, flexibly, indispensable and universal biological tool that infused
several areas of biological study. Some of the promises and capabilities of NGS are as
follows:
1. It provides us a much cheaper and faster alternative to traditional Sanger sequencing. Researchers
can now sequence whole small genome in a day. More than five human genomes can be sequenced
in a single run, generating data in less than a week, costing less than $5000 per genome (Illumina).
Overview of NGS:
 What does NGS offer?
 Evolution of NGS
 NGS versus Sanger sequencing
 NGS versus Microarray technology
 Challenges in data interpretation
 Limitations of NGS and promises of TGS

2. High-throughput sequencing (HTS) of the human genome lets us discover genes and regulatory
pathways associated with disease.

3. Targeted sequencing of specific genes or genomic region helps in the identification of disease-
causing mutations. It helps in the faster diagnosis, and outcome of disease-targeted sequencing may
help in better therapeutic decision-making for several genetic diseases.
4. RNA-Seq (NGS of RNA) provides entire transcriptomic information of a sample without any need of
previous knowledge related to genetic sequence of an organism. RNA-Seq provides a strong
alternative approach to Microarrays for gene expression studies, and let the researchers visualize
RNA expression in the form of sequence.
5. Variant study is common in medical genetic, where DNA sequence and data are compared with a
reference sequence to catalogue the differences. These differences may range from single nucleotide
polymorphisms (SNPs) to complex chromosomal rearrangement .
Evolution of NGS
 The root of the development of NGS goes back to the discovery of double helix structure of DNA by
James Watson and Francis Crick in 1953.
 Robert Holley was the first who sequenced nucleic acid during 1964-1965.
 In 1977, Frederick Sanger and Walter Gilbert developed sequencing methods for long length of DNA.
The development of NGS took place in late 20th and early 21st century.
The first NGS technology, known as Massively Parallel Signature Sequencing (MPSS), was launched by a
USA based Lynx Therapeutics Company in 2000. This company was latertaken over by Illumina – one of the big players in
sequencing market.
After MPSS, 454 Life Sciences launched a similar kind of sequencing technology in 2004 that gained 6-
fold cost reduction compared to traditional Sanger sequencing. Later, Life Sciences was acquired by Roche Company.
During 2005-2006, the 454 GS 20 Roche platform was launched that could produce 20 Mbp;
For these three pioneer works, the Nobel Prize was given to Watson and Crick in 1962,
Holley in 1968 and Sanger and Gilbert in 1980.

In 2007, this model was replaced by GS FLX capable of producing 100 Mbp, which was further enhanced
to 400 Mbp in 2008.
The Roche 454 GS-FLX was upgraded to 454 GS-FLX + Titanium sequencing platform that
can produce over 600 Mbp and read length of up to 1000 bp. Roche also produced ‘GS Junior’ platform
which handy and can be placed on a bench 2014.
In 2006, Genome Analyzer was released by Solexa, which was acquired by Illumina
in 2007. Solexa sequencer was capable to sequence 1 Gbp in single run (Illumina).
During the last five years, Illumina has developed Mi-Seq and Hi-Seq platforms. The Mi- Seq platform can
sequence up to 15 Gbp, while Hi-Seq systems achieves up to 600 Gbp.
Hi-Seq 2500 system can sequence a human genome in a day.
The first SOLiD sequencing system was launched in 2007, followed by SOLiD 5500w and 5500 lw in 2010.
The recent SOLiD4 platform can sequence between 35-50 Gbp with a maximum read length between 35-
50 bases.
Life Technologies Ion Torrent sequencer was released in 2011 that uses sequencingby-
synthesis and emulsion PCR. It does not use florescence, like other sequencing methods. This technology
measures H+ ion release during base incorporation (Ion Torrent). Some of its models are PGM 314, PGM
316, PGM 318, PI and PII. The PII is launched in early 2015 with average reading length of 100 bases and
sequencing capacity of up to 64 Gbp.
The NGS market which focus is on human whole-genome resequencing. Currently, they do not offer any
other applications such as exome, RNASeq, ChIP-Seq, etc. Complete Genomics platform can achieve a
sequencing rate of 3000 Gbp per run with maximum reading length of 70 bases.
Complete Genomics is going to launch its first commercial product, the Revelocity system, which have been
designed to provide total end-to-end genomic solution (Complete Genomics).

NGS versus Sanger sequencing
The traditional automated Sanger sequencing method, also called first generation sequencing, had led to
several most important accomplishments that include completion of the HGP. However, due to its heavy
cost and time intensive task, in the late 20th and early 21st century, new methods (NGS) have been
developed to replace the automated Sanger method.
The major advancement offered by NGS is:
i) capability to generate massive volume of data
ii) read more than one billion short reads in single run
iii) a fast and inexpensive method to get accurate genomic information.
Preparation of sample for NGS are faster and straight forward in comparison to capillary electrophoresis
(CE)-based Sanger sequencing.
In NGS, it may be started directly from a gDNA or cDNA library. The DNA fragments are then ligated to
platform specific oligonucleotide adapters and needs less than 1.5 hours to complete.
On the other hand, CE-based Sanger sequencing needs genomic DNA that are fragmented and cloned into
either bacterial or yeast artificial chromosomes (BACs/YACs). Further, each
BAC/YAC are subcloned into a sequencing vector and transformed to appropriate microbial host. Before
sequencing, template DNA is purified from individual colonies. These processes may consume days or even
weeks, depending on genomic size.
Table 1.Sample preparation in CE-based Sanger sequencing and NGS methods

NGS versus Microarray technology
The measurement of mRNA expression under different experimental conditions has been of interest to the
biologist. In the past decade, microarray technology has been extensively applied to simultaneously monitor
gene expression on a genome-wide scale.
In microarray technology, cDNA is hybridized on an array of complementary oligonucleotide probes
corresponding to gene sunder study, and the abundance of mRNA is completed from its hybridization
intensity.
Microarray technology has been widely used for the study of cancer genomes and transcriptome but some
of its promises have not materialized due to limitations of microarray data. For instance, microarray based
gene expression profiles only give a semi-quantitative assessment of gene expression due to nature of the
probes included in the platform. Also, microarray technology is unable to give any information related to
structural genomic aberrations and bases pair mutations.
The NGS has replaced the limitation of microarrays to detect poorly expressed genes.
In 2008, Nature News published an article “The death of microarrays?’ stating that “High-throughput gene
sequencing seems to be stealing a march on microarrays” and “Sequencing does put microarrays at risk in
some areas of the life-sciences research market”
NGS is used as a tool for the identification and analysis of DNA regions which interact with regulatory
proteins in functional regulation of gene expression. It offers novel, and rapid means for genome-wide
characterisation and profiling of mRNAs, small RNAs, transcription factor regions, chromatin structure and
DNA methylation patterns.

Challenges in data interpretation
The ‘Big Data Problem’ is a pressing issue originated with social networking, life sciences and bioinformatics
research. The real difficulty with biomedical research is lack of appropriate computational tool and
infrastructure to carry out analysis and interpretation of modern vast datasets.
The major issues with analysis, interpretation, reproducibility and accessibility of NGS data have
been pointed out by Nekrutenko and Taylor (2012). Described as follows:
 Adoption of existing analysis practices: There must be some well-defined and accepted data
analysis practices so that it can be adopted as common analysis practice. For instance, 1000 Genome
Project and HapMap are highly coordinated effort that defines series of accepted practices for ‘variant
discovery’. Despite of well documented analytical procedure developed by 1000 Genome Project, the
research communities are still using a mix of heterogeneous approaches for various studies.
 Difficulty of reproducibility: Research publications would be influential, if it maintains complete
detail on how to repeat the reported analysis so that other researchers can adopt similar approaches
 Adoption of existing analysis practices
 Difficulty of reproducibility
 Potential of integrative resources
 Making HPC infrastructure useful
 Improving long-term archiving

in their own research studies. But today’s publications reporting computational analysis lack to provide
sufficient information, such as input data sets, program source code or scripts, all parameter settings
so that computational reproducibility may be achieved. Similarly, NGS data analysis results cannot
be accurately verified, reproduced, adopted or used, that creates a shocking reproducibility crisis .
 Potential of integrative resources: most of researchers face difficulties in computationally complex
analysis on large datasets, and also computation analysis steps are not well documented. In this
direction, a number of integrative frameworks have been developed which bring diverse tools together
under the aegis of unified interface.
Examples of these frameworks are :
 BioExtract (Lushbough, 2010)
 Galaxy (Goecks et al., 2010)
 GenePattern (Reichet al., 2006)
 GeneProf (Halbritter et al., 2011)
 Mobyle (Néron, et al., 2009)
These potential integrative resources empower bioinformaticians and biomedical researchers to make use
of powerful computing infrastructure, required for NGS data analysis.
 Making HPC infrastructure useful: Analysing NGS data is computation extensive. There are several
powerful high performance computing (HPC) resources that may be applied for NGS computation.
The HPC resources may include computing clusters that can be distributed over different
geographical regions. With the popularity of Cloud Computing.
There are many ‘softwares available as a service’ analysis solution for sequence data:
1. DNAnexusa
2. GenomeQuestb.
3. Free and open-source software (FOSS) (e.g) Crossbow used for variant discovery, Myrna for RNA-
Seq analysis and CloVR for metagenomic annotations.
 Improving long-term archiving: One of the major concerns for analysis services is its longevity, i.e.,
an online analysis tool is not guaranteed to be online forever. One promising solution is to archive the
snapshots of a particular analysis.

Limitations of NGS and promises of TGS
 Although, NGS is cheaper and faster in comparison to traditional Sanger sequencing but still it is too
expensive to be affordable by small labs or an individual.
 NGS data analysis is time-consuming and needs sufficient knowledge of bioinformatics to harvest
accurate information from these sequence data.
The National Human Genome Research Institute (NHGRI) posed an open goal to minimize the cost of human genome sequencing
to $1000 to fuel further development in NGS technologies so that routine sequencing of human genomes can be used as a tool
to diagnose various diseases.
 NGS supports read lengths of small size, which results into highly repetitive sequences. Support for
sequencing from short read lengths is one of the major shortcoming which limit its application,
especially in de novo sequencing.
 Data processing steps is another major bottleneck for the implementation and capitalization of NGS
technology.
Third generation sequencing (TGS) takes advantage of the above gaps of NGS technologies and allows direct sequencing of
single molecules. Single molecule sequencing (SMS) technologies have the ability to sequence with longer read lengths keep the
cost and time both lower without compromising the quality of the genome assembly.
Methodology of Next Generation Sequencing
 How the stuff works
 Major platforms in NGS

How the stuff works
Basic principle on which NGS works is similar to traditional Sanger sequencing methods involving capillary
electrophoresis. Mostly, different NGS platforms adopt their own specific protocol in the sequencing
methods. NGS starts with template preparation, and generally, the double-stranded DNA is considered as
the starting material. However, the source from which this material is derived may vary. Sources can be
either genomic DNA, immuno-precipitated DNA, reverse-transcribed RNA or cDNA.
The next step involves library preparation. If genomic DNA was considered in the previous step, it should be
fragmented into linear DNA molecules. If RNA was considered in the previous step by the means of reverse
transcription, cDNA is obtained for preparation of linear DNA molecules. Moreover, the fragmentation of
these DNA molecules into smaller fragments is involved, which along with specific size selection steps serve
to break the considered DNA template into smaller, but sequence-able fragments depending upon requisite
platform. Moreover, adapter ligation is also involved in this process, which adds platform specific, synthetic
DNAs at the end of the DNA fragments present in this library to facilitate the sequencing reactions. Thus,
sequence library preparation involves some common steps of fragmentation, size selection and adapter
ligation.
Next step involves library amplification, to produce significant signal for nucleotide addition. This step
involves either by the attachment of DNA fragment to microbead or attachment of the same to glass slide,
when some PCR techniques are followed. Library amplification eventually leads into the sequencing reaction
and imaging process.
Ultimate destiny of NGS is to analyse the data produced through this sequencing process. NGS data analysis
is complex and crucial task. It involves assessment of some important and vital genes or regulatory elements
in the given genome. There are several tools available which can be either downloaded to local machine or
used on the Web for NGS data analysis.

Fig. 2 How stuff works: NGS an overview
Major platforms in NGS
Illumina Sequencing is one of the major platforms used in NGS. In this sequencing technology reads of
100-150bp are considered. Comparatively longer fragments are considered from the template library for
ligation using generic adaptors. Further, these ligated fragments are attached to a glass slide. In the next
stage, Polymerase Chain Reaction (PCR) is carried out, in order to amplify and make several copies of a
read. Later, amplified copies of reads are separated into single strands, which is to be sequenced. Next,
the slide is flooded with fluorescently labelled nucleotides (A, G, C & T) and DNA polymerase. Each
nucleotide has a unique colour to identify itself. Terminator ensures that only one base is added at a time.
The fluorescent signal in form of image is recorded, which indicates the base added. At this stage, glass slide is
reprepared for next cycle. Terminators are removed, which allows the next base to add in this process. At the same time, fluorescent signal is
also removed in order to prevent future contaminations of the signals. The process is repeated by addition of a nucleotide at a time and imaging
process in between. Using the computers, the bases are detected at each site in each image, which in turn help in construction of a sequence.

454 sequencing technology has the ability to sequence much longer reads as compared to Illumina. The
basic principle is similar to Illumina, where the optical signals are read on the addition of the bases. Though
454 sequencing involves fragmentation of DNA or RNA too, in this case, the fragmentation results into 1kb
long reads. In the process of library amplification, the fragments are attached to the microbeads. Using
PCR, the fragments are amplified. Here, the wells also contain DNA polymerase and sequencing buffers.
In the next stage, the slide is flooded with any one of the four nucleotide species (A, G, C, or T). Addition
of each nucleotide releases an optic signal.
The locations of signals are spotted to identify the bead where the nucleotides are added
to. The process recycles after washing the mix. 454 sequencing generates graphs for each sequence read,
which reflects the signal density for each nucleotide wash. Using computational approach, the density of
signals in each wash facilitates the retrieval of the sequence.
Ion Torrent PGM (Personal Genome Machine) sequencing is different from Illumina and 454 sequencing
platforms. This sequencing platform does not uses optic signals.
They utilize the concept that the addition of a dNTP to a DNA polymer releases an H+ ion. Here template
DNA or RNA is fragmented into size of ~200bp. Using emulsion PCR, the amplification takes place. Just as
in case 454 sequencing, the slide is flooded with single types of dNTP, along with buffers and polymerase.
H+ ion released on addition of dNTP to a DNA polymer decreases the pH. The pH changes are detected
and recorded from each well, which allows determining the bases type and its concentration in that well.
Helicos (HeliScope Genetic Analysis System) is the first commercial NGS platform which used the
concept of single molecule fluorescent sequencing.

Single molecule sequencing strategy process:
 simplifies the DNA sample preparation process
 avoids PCR induced errors.
In this process, DNA is simply trimmed into smaller fragments, tailed with poly A, and hybridized to a flow
cell surface containing oligo-dT for sequencing-by-synthesis of billions of molecules in parallel. Requirement
for less material adds a plus to this sequencing technique as compared to other technologies.
Pacific Biosciences’s SMRT is single molecule real-time sequencing technologies which is popular from
the last few years due to its higher accuracy, suitability for small genome, and study of facile closure bacterial
genome without any additional experiment. It provides considerably longer and highly accurate DNA
sequence from single molecule and deciphers where methylated bases occur, which is usually not produced
by other sequencing platforms. The average reads of current Pacific Biosciences’s instrument is 10 Kbp or
longer, which is almost 100 times longer than other NGS platforms, 100 times smaller amount of gaps
compared to NGS. In several studies it has been revealed that SMRT-based assemblies facilitate a more
comprehensive gene annotation than NGS-based assemblies where lots of genes are generally missed or
fragmented.
The SMRT sequencing technologies are considered as third generation sequencing (TGS). Some of the
applications of SMRT are de nova assembly of novel genomes, DNA methyltransferase, etc.
Table 2.A comparative reviews of various NGS and TGS platforms

Application Areas
The NGS has served in several aspects of medical and biochemical researches worldwide. Below we
discuss some widely used applications of NGS.
Whole genome sequencing (WGS)
The WGS involves sequencing of entire genome, for instance HGP is a good example of whole genome
sequence which was completed in 2013. HGP was based on traditional capillary electrophoresis-base
Sanger sequencing method that cost ~3 billion USD and was completed in more than ten years.
In contrast, NGS performs massively parallel sequencing which facilitates the HTS and thereby responsible
for entire genome sequencing in less than a day at minimum cost. Human genome sequencing helps in
identifying the specific genes and their regulatory partners involved in the pathological processes. The WGS
provides deeper understanding for genetic variations (impacting the normal function of a body), drug
response on a gene set, and many other complex/simple biological processes. In the coming days, there
will be more favourable applications of WGS for human welfare.
Exome sequencing
It helps in investigating the protein coding regions within the genome. Exome shares only
small portion of the whole genome. Exomes are gene-coding region and therefore important site of concern
for clinicians and researchers. Mutations, i.e., alterations in this part of genome results are possible causes
of a disease or other abnormal conditions. In case of human genome, exome represents less than 2% of the
total genome, but contains nearly 85% of disease-causing variants. Therefore, sequencing this part of
genome inspite of WGS results in the cost-effective sequencing. Important applications of exome
sequencing involve variant association studies, discovering relevant mutations in exome region,
identification of disease-related variations and so on.
 Whole genome sequencing (WGS)
 Exome sequencing
 Targeted resequencing
 Chromatin immunoprecipitation sequencing (ChIP-Seq)
 RNA sequencing (RNA-Seq)

Targeted resequencing
It involves in the sequencing of genomic regions of interest. This region is generally a small subset of the
genome, such as exome, a set of genes, a particular chromosome or a region of particular interest. This
enables in reduced cost sequencing approach.
Moreover, narrowing down the search region enables one to get closer variation analysis which could have
been impossible, when considering genome analysis on broader terms.
Targeted resequencing has been found useful in discovering the point mutations, insertion or deletions, gene
rearrangements and variations occurring in copy number.
Chromatin immunoprecipitation sequencing (ChIP-Seq)
It is used to analyse the interactions of proteins with DNA and RNA. ChIP-Seq combines the ChIP technique
and NGS technique to identify the binding sites of the DNA associated proteins. This enables in interpreting
the regulation events which may be causative to many biological processes such as gene regulation, DNA
repair, and DNA synthesis. ChIP-Seq also serves important role in classifying the disease situations resulting
from abnormal functioning of the genomic contents and their expression levels.
Important applications of ChIP-Seq include analysis of epigenetic modifications, mapping of epigenetically
modified DNA sequences, interactions of viral protein with human genome resulting in complex disease
situations.
RNA sequencing (RNA-Seq)
RNA sequencing (RNA-Seq) is a transcriptome sequencing approach and involves a wide variety of
applications, ranging from simple mRNA profiling to discovery of the entire transcriptome. RNA-Seq is being
popular nowadays because they are found uncovering information which may have been missed by array-
based platforms regardless of prior knowledge of the transcript sequence.
Key features of RNA-Seq include:
 detection of transcripts with low expression levels
 transcript analysis with or without reference sequence.
 a powerful tool for accurate quantification of expression levels.
The previous list of applications of NGS is not exhaustive. There are several other applications directly or
indirectly attached with HTS. Moreover, as stated before, NGS is
a newbie, but with the passage of time there will be several improvements and additions
to this technology which shall help for quality researches for human welfare.

Database Archives
NGS platforms are producing unprecedented amount of sequence data. Some of the
popular and commonly used NGS database archives are as follows:
Sequence Read Archive
To archive large volumes of NGS data, National Centre for Biotechnology Information (NCBI) designed an
archive to accommodate these data sets.
The three partners of International Nucleotides Sequencing Database Collaboration (INSDC)
1. National Centre for Biotechnology Information (NCBI)
2. European Bioinformatics Institute (EBI)
3. DNA Data Bank of Japan (DDBJ)
They established an archive, named as Sequence Read Archive (SRA), to facilitate the
scientific community an archive for NGS data sets. The SRA enhance the reproducibility and facilitate the
researchers for new discoveries by comparing data sets. The SRA stores raw NGS data and alignment
information from different platforms that includes Roche 454, Illumina Genome Anlayzer, SOLiD system by
Applied Biosystems, Heliscope by Helicos, IonTorrent by Life Technologies and Complete Genomics. The
SRA database is accessible from three different collaborating organizations
http://www.ncbi.nlm.nih.gov/Traces/sra/- http://www.ebi.ac.uk/ena - http://trace.ddbj.nig.ac.jp/dra/index_e.html-
 Sequence Read Archive
 RNA-Seq Atlas
 NGS Catalog
 LANL HIV-DB Next Generation Sequence Archive
 Gene Expression Omnibus

Fig. 3 Year-wise growth of number of bases and its data size for SRA database
RNA-Seq Atlas
RNA-Seq Atlas is a database repository of RNA-Seq gene expression profiles and query tools. It provides
free, easy and user-friendly access to RNA-Seq gene expression profiles and several tools to compare
tissues as well as genes having specific expression patterns. To enhance its scope, RNA-Seq Atlas data
are linked to functional and genetic databases that provides information related to corresponding genes
using NCBI nucleotide database, gene signalling and pathway analysis using Kyoto Encyclopedia of Genes
and Genomes (KEGG), and evaluation of gene functions using Gene Ontology (GO) database.
NGS Catalog
Another database, called NGS Catalog, has been developed by Xia and collaborators, that collects, curates
and manages NGS data taken from published articles.
This Catalog stores publication information related to NGS studies, their mutation characteristics, and
mutated genes and gene fusion detected. The NGS Catalog is accessible through
http://bioinfo.mc.vanderbilt.edu/NGS/. Also, this database gives a comprehensive and updated software list
widely applied by NGS community, and general pipeline for the analysis of Exom-Seq, WGS and RNA-Seq
data. This catalog contains over 295 records – 47 RNA-Seq datasets, 194 Exome sequencing and 54 whole
genome sequencing.
LANL HIV-DB Next Generation Sequence Archive
It is a repository for next-generation lenti-virus sequence data sets containing HIV, SIV
and anti-HIV/SIV antibody ultra-deep sequences. It can be accessed through
http://www.hiv.lanl.gov/content/sequence/HIV/NextGenArchive/
Gene Expression Omnibus
Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, NGS,
and other forms of high-throughput functional genomics data submitted by the research community. It
supports MIAME-compliant Array as well as sequence-based data submissions. Now GEO contains over
2,000 HTS platform entries, out of total ~14,500 platforms.

Computational Analysis
Various platforms of NGS technologies have made it possible to sequence huge amount of high throughput
data in less time and cost. In today’s era of NGS, single laboratory is able to sequence the entire human
genome within a week for a few thousand dollars only. Production of NGS data is followed by its analysis.
Careful analysis of NGS data results in important knowledge discovery and conclusions. With the
advancement of time, there are uncountable efforts from researchers in developing algorithm and tool for
analysis of the NGS data. Different platform need different steps and protocol in their analysis portion.
To name some applications are CisGenome, MACS, PeakSeq, QUEST, SISSRs, CNV-Seq.

Fig. 4. The computational workflow for drug discovery starting from raw image data obtained from NGS sequencing is divided
into three broad steps namely NGS data processing, Network construction and analysis, and Drug discovery.
BOX 1 representing NGS data processing. The raw image data are processed into sequences by base-calling algorithms. Then
reads are mapped with reference genomes/transcripts with available databases (GOLD/ MirWalk, Rfam). As a result uniquely
mapped reads, multiple mapped reads and unmapped reads can be identified. Mapped reads then undergo for read quantification
with help of peak-calling algorithms which enable to identify alternative splicing event, protein binding site, differentially expressed
genes, noncoding RNA, small variants in sequences and can also give insight to allele specific expression.
BOX 2 depicts Network reconstruction and analysis of DEGs and ncRNA. In this step, co-expression network is constructed by
WGCNA method and results into some coexpressed gene modules. Then we go for enrichment analysis of modules to identify
module hub genes by Guilt-By-Association method involving GO annotations, Reactome and KEGG pathways. Then go for
regression modelling to identify key hub genes from module. Then validate them by model reconstruction. Through this step we
are able to get key genes for the disease.
BOX 3 represents steps of Drug discovery. The identified genes can be subjected for respective protein identification (Expasy
tools, etc). This protein will act as drug target having drug binding sites. Then we move towards lead identification which would
give us enormous library of potent ligands that could bind protein. Then we go for virtual screening which involves selection of few
potent leads based on binding affinity, etc. The most potent lead candidates are then subjected for optimization in order to
maximize its druggability. Thus at last we get drug that can be further subjected to experimental and clinical trials.
Computation analysis:
5.1. ChIP-Seq analysis
Chromatin immunoprecipitation (ChIP) is commonly used in determining the Protein- DNA interactions. As
discussed before, these interactions are vital in identifying the gene-expression profiles during cellular
development and differentiation. ChIP-Seq is a combination of ChIP and NGS which has been widely
 ChIP-Seq analysis
 RNA-Seq analysis
 Non-coding RNA (ncRNA) Analysis
 HiChIP Analysis
 ChIP-chip versus ChIP-seq

accepted nowadays for protein- DNA interactions on a genome-wide scale. There are series of steps
involved in ChIP and it is a tedious and complicated process. Eventually, after PCR amplification, there is
application of massively parallel sequencing. Increasing demand and adaptation for ChIP-seq to reveal
transcriptional and epigenetic regulatory mechanism in experimental laboratories round the globe has
become comprehensive and sophisticated. For example, we discuss simple approach of analysing the
Illumina ChIP-Seq data, which helps in retrieval of useful information from the raw sequence reads. In the
first step, the sequenced data undergoes through the Image Analysis phase and Base Calling phase. The
Genome Analyzer facilitates the generation of actual sequence data from the images acquired during the
sequencing of this data via synthesis chemistry.
In the next step, there is use of ELAND, an alignment algorithm, which aligns a set of short sequence tags
against a genome. The output of this algorithm lists all the reads of the given sequence with respect to their
genomic coordinates.
For alignment of larger genomes (>1Mb), alignment program ‘Eland_extended’ is used.
For alignment of smaller genomes (<1Mb), alignment program ‘PhagAlign’ is used.
Researchers view their ChIP-seq data as a peak on a genome browser. Most of them use the University of California Santa Cruz (UCSC)
genome browser available over www (http://genome.ucsc.edu). UCSC genome browser has several functions. This browser is not only a web
based application with standard browsing capabilities, but it also has several built features/tools to provide genomic information, evolutionary
conservation, and relevant data from NIH funded genomic groups like Encyclopedia of DNA elements, commonly known as ENCODE. Using
UCSC genome browser, the read data which are specifically aligned to a given genome are viewed as a custom track. This track can be
submitted in either BED format or Wiggle (WIG) format. BED format is a text file, which contains chromosomal start and end positions. The WIG
format allows the visual examination for GC percent, probability scores and transcriptome data. Although, BED format provides better visual
presentation of the data compared to the WIG format, there are limitation issues for file size, which can be uploaded on UCSC genome browser.
The plus point in WIG format is its compactness, as compared to the BED format, which enables to examine larger dataset.
Software requirement for ChIP-Seq analysis includes the installation of Illumina Genome Analyser Pipeline suite, which comprises of the Image
analysis script, Base calling script and alignment script (GERALD), to align the reads with the reference genome.
RNA-Seq analysis
RNA-Seq basically counts the number of reads that align to one of thousands of different cDNAs, producing
results similar to gene expression of microarrays. Reads are aligned to an annotated reference genome,
and those aligning to exon, genes and splicing junctions are counted. Similarity, variants (CSNPs, indel)
may be counted for variant analysis. The final steps are data visualization and interpretation, calculating
gene- and transcript expression and reporting differential expression. The workflow of RNA-Seq data
analysis is shown in next Fig. In the first step, the sequencing output files are produced in compressed
FASTQ format, and serve as input for next stage of the analysis. In the next stage, reads are aligned to the

reference genome. The reads aligning to the exons, genes and splice junctions are counted and normalized
resulting in generation of data of approximately 1.3Mb. Moreover, if desired, the cSNPs, indels can also be
counted. Final stage involves the data visualization, data interpretation for the Gene- and transcript-level
expression and differential expression levels.
RNA-Seq can be used for(Beyond gene expression analysis, ):
i) identifying alternative splicing events,
ii) allele-specific expression
iii) rate and novel transcripts, and so on.
Fig. 5. Workflow of RNA-Seq data generation and analysis
RNA-Seq is found to be vital tool for RNA profiling, discovering, and quantifying the rare, novel RNA
transcripts. This sequencing technology has results similar to the gene expressions of the microarray
data, but the informatics challenges and methods of analysis is different than microarray data analysis.
There are two broad ways, in which the RNA-Seq analysis is different from microarray.
 In the case of RNA-Seq, the sequences obtained via RNA-Seq methods are generally mapped to the
libraries of known exons from known transcripts.
 Moreover, RNA-Seq measures the number of distinct sequence reads using differential statistical
tests.
All these factors facilitate the RNA-Seq method in following unbiased step in analysis, which could have
been possible from previous assumptions about the nature of transcriptome. This technology provides an

advantage in investigating the species which have poor or missing genomic annotation. In case of
microarray, the step involved in library mapping is absent and the continuous probe intensities are measured.
Galaxy project is an academic initiative that allows RNASeq alignment, counting process, producing and
uploading FASTQ files, selecting from a limited number of alignments and counting parameters.
There are several tools available for transcriptome data analysis too. Specifically,
 the free, open-source Tuxedo Suite comprising of Bowtie,
 TopHat,
 Cufflinks has been widely used.
Some of the commercial software providers for the analysing the RNA-Seq data are
 CLC Bio,
 GeoSpiza,
 GenomeQuest,
 Strand Scientific Intelligence.
I will try also to discuss the analysis protocol for Illumina based RNA-Seq data.Complex transcript data
demands for highest sensitive algorithms and tools for measuring and detecting the changes in abundance
and structure. The demand for improved throughput and costs requirement has enabled in development of
better and sophisticated tools for RNA-Seq analysis.
Non-coding RNA (ncRNA) Analysis
It is known that most of the genes in human genome are transcribed but only a fraction of them encode for
proteins. The remaining transcriptome is considered as non-coding RNA (ncRNA). Regulatory ncRNAs
affect the expression and function of protein coding genes. Various studies related to cancer and ncRNA
have been carried out whose goal was to discover molecular signatures and cancer biomarkers. The
discovery of cancer biomarkers may reveal parameters for the early detection of cancer, its diagnosis,
prognosis and prediction of response to anticancer drugs, prediction of recurrence, and identification of
putative drug targets.
Computational analysis of ncRNA can be comprised of three essential tasks:
i) post-sequencing data analysis pipeline for ncRNa detection, classification and expression
analysis;
ii) a data module providing annotation information and storage for the analysis results;
iii) a visualization and query system to depict and perform the functional analysis of raw data, and
present results.

The ncRNAs can be grouped in to various classes, each one having their own 3-dimentional folding and its
own specific function, which are described in next table. Among all the ncRNA classes, microRNA (miRNA),
long ncRNA (lncRNA) and PIWI interacting RNA (piRNA) are the most studied in cancer research
Table 3. Different classes of ncRNA with their functions
The miRNAs consist of on average 22 nucleotides in length and mediate gene silencing by paring with
specific region of mRNA to prevent its translation. The target genes of miRNA are mostly concerned with
the fundamental cellular processes and aberrations in the expression of miRNAs have been rigorously
studied in various cancers as they act as oncogenes (tumor suppressor genes). Also, miRNA may directly
regulate transcription by interaction with the promoter region of divergently transcribed genes.
In a study by Lui et al. (2011), they compared the expression of miRNAs having gastric cancer against
normal samples. Among the 20 cancerous samples, 19 were detected as over expressed and the miR-1,
miR-20a, miR-27a, miR-34, and miR-423-5p were identified as potential biomarkers for the gastric cancer
diagnosis.
In study by , Wu et al., (2012) analysed samples of 42 breast cancer patients and detected over 800
circulating miRNAs. One of the earliest software tools for large-scale RNA-Seq data analysis is miRDeep
(Fridlander et al., 2008), which is a stand-alone tool that can detect both known and novel miRNAs. Later,
miRDeep was enhanced to miRDeep* (An et al., 2013) which has been proved to output-perform its earlier
versions.
Tools for the prediction and analysis of various classes of small ncRNAs on RNA-Seq data DARIO , CPSS
,ncPRO-seq, RNA-CODE .

There are several database resources for ncRNA, but the most widely used database for cancer studies are:
 human genome hg18 assembly .
 miRBase .
 Rfam .
 microRNA.org .
 RNA Hybrid
 miRDB
 DIANA-microT
 TarBase
 miR2Disease miRecords
 miRWalk2.0
The lncRNAs have more than 200 nucleotides in length and most of them are still not fully characterized.
Several studies reported alternations in different lncRNAs in different types of cancers .The lncRNAs, along
with ncRNAs, have been identified as possible suspects in the involvement with several neurodeneration-
related processes and proteins .
One of the software pipelines for the detection of novel lncRNAs is called lncRScan.
A comprehensive database for lncRNA, known as Noncode, became available very recently
Unlike miRNAs and siRNAs which are broadly expressed in most of the cells and tissue types, the expression
and functions of piRNAs are confined to germ cells and gonadal somantic cells . The piRNAs, like other
ncRNAs, has been found to play possible role in the biogenesis of cancer. It interacts with PIWI proteins to
promote silencing of transposable elements and maintain the integrity of DNA.
The circular RNAs (circRNAs), forming a covalently closed continuous loop, are untranslated, very stable
and conserved RNA molecules in animals.Few circRNAs have been found as potential gene regulators, but
biological functions of most of them are still unclear. a computational method for the detection of circRNAs
in humans, mouse and C. elegans, and their finding suggests that circRNAs are often expressed in tissue
or develop mental stage specific manner. identified and quantified human circRNAs from ENCODE
Robozero RNA-Seq data and found that most of the circRNAs are expressed only in few cell types. A very
recent tool, called CIRI , has been proved to outperform other precedent approach for the detection of
circRNAs from NGS data. CIRI is an annotation independent approach deploying a de nova algorithm for

the detection of novel circRNAs based on paired chiastic clipping signals combined with a filtering system to
eliminate false positives.
HiChIP Analysis
Recently, a highly integrative pipeline, HiChIP has been developed for processing and systemic analysis of
large amounts of ChIP-seq data. The work flow of this pipeline provides solutions to several challenges
which has been reported for computational analysis of Chip-Seq/NGS data.
Main functions of HiChIP are
i) read quality checking;
ii) read mapping and filtering;
iii) peak calling and peak consistency analysis;
iv) result visualizations.
Moreover, this pipeline is inclusive of important modules for creating binding profiles over selected genomic
features, de novo motif finding from transcription factor binding sites and functional annotation of peak
associated genes.
HiChIP is optimized to include options for filtering out less reliable mapped reads to reduce noise in the given
experimental setup. For instance, difficulties in defining the boundaries of diffuse binding sites at high
resolution; identifying the direct target genes of transcriptional factor binding sites and histone modifications.
It is expected that improvement in existing design and addition of new, better modular design of HiChIP will
enable smooth integration of existing pipeline.
ChIP-chip versus ChIP-seq
ChIP followed by microarray hybridization is known as ChIP-chip, is similar in several aspects from recently
evolved ChIP-seq. Both of these provide valuable insight to the protein-DNA interactions such as
transcriptions factor bindings and histone
modifications. Both ChIP-chip and ChIP-seq are widely used approaches for genomewide identification and
characterization of in vivo protein-DNA interactions and have led to several important discoveries. Though
having some basic similarity, the ChIP-chip had several limitations, which was overwhelmed by ChIP-seq.
Biases present in each of these platforms that can arise from both the technology and analysis methods has
been experimentally reported (Ho et. al., 2011). This research reflecting the practical advantages,

emphasizes the ChIP-seq to be an alternate for ChIP-chip. The Table 4 highlights the difference between
these two platforms.
Table 4. Difference between ChIP-chip and ChIP-seq
Software Tools
Analysis of NGS data set is a challenging task that requires a systematic and intelligent approach to process
it efficiently. The workflow to analyze large-scale NGS should include the processes: data quality
assessment, comprehensive analysis, interpretation of results, and presentation of results in meaningful
formats. There are several free as well as commercial software tools available for the analysis and
visualization of NGS data sets. A list of most commonly used software tools under different task group is
shown in next table
List of NGS data analysis tools
Integrated Tools
 BaseSpace http://www.illumina.com/informatics/research/sequencing-dataanalysis-management/basespace.html
 CLC Genomics Workbench http://www.clcbio.com/products/clc-genomics-workbench/
 ERGO http://www.igenbio.com/ergo
 Galaxy https://wiki.galaxyproject.org/
 Genomatix Genome Analyzer http://www.genomatix.de/solutions/genomatix genomeanalyzer. html
 Golden Helix http://goldenhelix.com/
 JMP Genomics http://www.jmp.com/en_us/software/jmp-genomics.html
 Lasergene Genomics Suite http://www.dnastar.com/t-products-dnastar-lasergenegenomics. aspx
 NextGENe http://softgenetics.com/NextGENe.html
 OmicsOffice for NGS (SeqSolve) https://www.integromics.com/omicsoffice-for-ngs/
 Partek Flow http://www.partek.com/partekflow
 SHORE http://1001genomes.org/software/shore.html
Alignment
 Bowtie http://bowtie-bio.sourceforge.net/
 BFAST http://sourceforge.net/projects/bfast/
 BWA http://bio-bwa.sourceforge.net/
 SAMStat http://samstat.sourceforge.net/
 Exonerate http://www.ebi.ac.uk/~guy/exonerate/
 GenomeMapper http://1001genomes.org/
 GMAP http://www.gene.com/share/gmap/

 GNUMAP http://dna.cs.byu.edu/gnumap/
 MAQ http://maq.sourceforge.net/
 MOSAIK https://github.com/wanpinglee/MOSAIK
 MUMmer http://mummer.sourceforge.net/
 Novoalign & NovoalignCS http://www.novocraft.com/
 PASS http://pass.cribi.unipd.it/cgi-bin/pass.pl
 SSAHA http://www.sanger.ac.uk/Software/analysis/SSAHA/
 SOAP http://soap.genomics.org.cn/
 SWIFT http://bibiserv.techfak.uni-bielefeld.de/swift
 Vmatch http://www.vmatch.de/
 ZOOM http://www.bioinfor.com/zoom/general/overview.html
De Nova Assembly
 AbySS http://www.bcgsc.ca/platform/bioinfo/software/abyss
 ALLPATHS-LG ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/
 Edena http://www.genomic.ch/edena.php
 MIRA4 http://chevreux.org/projects_mira.html
 SOAPdenovo2 http://soap.genomics.org.cn/soapdenovo.html
 SSAKE http://www.bcgsc.ca/platform/bioinfo/software/ssake
 VCAKE http://sourceforge.net/projects/vcake/
 Velvet http://www.ebi.ac.uk/~zerbino/velvet/
SNP/Indel Discovery
 GATK https://www.broadinstitute.org/gatk/
 SAM Tools http://samtools.sourceforge.net/
 SOAPsnp http://soap.genomics.org.cn/soapsnp.html
 ssahaSNP http://www.sanger.ac.uk/resources/software/ssahasnp/
 PolyBayes http://clavius.bc.edu/~marth/PolyBayes/
 PyroBayes http://bioinformatics.bc.edu/marthlab/wiki/index.php/PyroBayes
Genome Annotation Browser/Viewer
 Anno-J http://www.annoj.org/
 EagleView http://www.niehs.nih.gov/research/resources/software/biostatistics/e agleview/
 Integrative Genomics
 Viewer http://www.broadinstitute.org/igv/
 LookSeq http://www.sanger.ac.uk/resources/software/lookseq/
 Sequence Assembly Manager http://www.bcgsc.ca/platform/bioinfo/software/sam
 Staden http://staden.sourceforge.net/
 UCSC Genome Browser http://genome.ucsc.edu/
 XmatchView http://www.bcgsc.ca/platform/bioinfo/software/xmatchview
ChIP-Seq & HITS-CLIP Applications
 CisGenome http://www.biostat.jhsph.edu/~hji/cisgenome/
 CNV-Seq http://tiger.dbs.nus.edu.sg/cnv-seq/
 MACS http://liulab.dfci.harvard.edu/MACS/
 PeakSeq http://info.gersteinlab.org/PeakSeq
 QUEST http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html
 SISSRs http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/
Transcriptom e Analysis
 E-RANGE http://woldlab.caltech.edu/rnaseq/
 G-Mo.R-Se http://www.genoscope.cns.fr/externe/gmorse/
 MapNext http://evolution.sysu.edu.cn/english/software/mapnext.htm
 Partek Genomic Suite http://www.partek.com/
 RNA-Star https://github.com/alexdobin/STAR/releases
 TopHat http://ccb.jhu.edu/software/tophat
Metageno mics Analysis
 MEGAN5 http://ab.inf.uni-tuebingen.de/software/megan5/
 MOCAT http://vm-lux.embl.de/~kultima/MOCAT/
 Parallel-META http://www.computationalbioenergy.org/parallel-meta.html
 QIIME http://qiime.org/
 WebMGA http://weizhonglab.ucsd.edu/metagenomic-analysis
Utilit ies and FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Picard http://broadinstitute.github.io/picard/

Computational Opportunities and Challenges
NGS has dynamically enhanced the way the researchers approached in studying the DNA/RNA
expressions. The technological advancements like automation, parallel processing, multiplexing has
enabled production of low cost, high throughput data. Moreover, the NGS has tremendously helped in
Clinical/Medical research. It is expected that proper understanding of the genomic variations and
expressions will help in development of personalized medicines specific for individuals.
Specific strategies (as in RNA-Seq) have helped in understanding the change in expression without the need
of reference genome, which was not possible in microarray data analysis.
Identification of vital DNA or RNA protein interaction have been made possible using ChIP-Seq technology
which have been thought to improve our epigenetic studies. It is expected, that in the coming years, ChIP-
Seq would facilitate the epigenome-wide association studies, to identify the disease mechanisms in a given
population.
Utilization of NGS techniques have been found useful in diagnosing clinically important genetic disorders.
Sequencing of cancerous genome shall be exposing the altered/activated pathways, networks and other
relevant information.
NGS technologies not only enhanced our ability to detect genetic variations in non-coding region, but also
helped us in development of enhanced statistical analysis methods in order to distinguish the true
variations from sequencing errors.
NGS has made it efficient for understanding the genomics, but at the same time there are several challenges
in the way. Efficient data analysis pipelines are needed to address the robustness of the NGS. Moreover,
with the passage of time, more high-throughput assays on gene expression and DNA binding activities are
becoming available. This in turn, raise the requirement for systems biology approaches for identifying and
inferring associative or causal relationships between genes or proteins.
NGS is a powerful tool and seems to have various applications in clinical diagnostics, but this technology
stands in complex state and its successful adoption into clinical laboratory would need expertise from
molecular biology and bioinformatics.
There is a need for computational power (Data processing) as well as computational management. Storage
space for huge data generated is also considered one of the challenges of NGS.

Security of personal genomic data and ethical and political concern (for personalized genome data) have
been addressed as possible challenges in the days nearby). In addition, the cost of initial installation of NGS
platforms is very much. Estimated start-up cost may rise over $100,000. Individual sequencing can cost over
$1,000 per genome.
NGS do have false-positive and false-negative rates, because of sequencing errors and amplification
biases, which necessitates the requirement of improved and optimized library construction methods;
enhanced sequencing technologies and better filtering algorithms.
The information challenge with NGS is because of its short read lengths which makes it difficult to assemble
complete genome. Most of the limitations are expected to be handled by third generation sequencing
(TGS) technologies such as SMRT and nano-pore technologies. However, TGS will also have modeling,
data management and processing challenges leading to big data problems, demanding for HPC such as
supercomputers and computer clusters. It is expected that due to availability of cloud computing based
services by various companies including Amazon, Google, IBM, Joyent and Microsoft, the need for HPC and
storage can be solved. Further, advancement in distributed computing and availability of distributed
computing architecture such as Hadoop and Aneka, it has become possible to handle petabyte-scale
datasets distributed over a massive parallel architecture.
Today, there are several companies offering cloud computing based resources for NGS and TGS data
management and enable processing of large-scale raw sequence data. In comparison to NGS, there are
more challenges for TGS due to scales and diversity of data it generates. Currently, petabyte scale of raw
data is available from 1000 genome projects. The availability of HPC through cloud computing services,
TGS is expected to allow scanning of entire genomes, microbiomes and transcriptome within minutes with
affordable cost. Scanning and mining such large-scale datasets poses several challenges for storage,
processing, analysis, data transfer, access control, integration of data, and standardization of data formats.
At the end Summary of what you must know about NGS
The advancement of NGS technologies aided in generating genome-wide sequence data in a couple of
days, and this huge amount of data led to numerous important discoveries. However, this technology needs
specific data analysis algorithms which are written for specific task to be performed. The algorithms in group,
act as a tool in analyzing the NGS data. Analysis of NGS data unravels important clues in quest for the
treatment of various life-threatening diseases; improved crop varieties and other related scientific problems
related to human welfare. After reading you must understand applications and computational approaches
for analysis of various types of NGS data, including ChIP-Seq analysis, RNA-Seq analysis, Non-coding

RNAs identification and HiChIP analysis. Importance of ChIP-Seq over ChIP-chip. Moreover, you must know
about available database archives for NGS data and also exhaustive list of algorithms/software to perform
various tasks during NGS data analysis. It is expected to covers computational opportunities and also the
challenges in the analysis and interpretation of NGS data.
List of Abbreviations
1. Capillary Electrophoreses (CE)
2. Chromatin Immunoprecipitation Sequencing (ChIPSeq)
3. Free and Open Source Software (FOSS)
4. Gene Expression Omnibus (GEO)
5. Gene Ontology (GO)
6. High Performance Computing (HPC)
7. High-throughput sequencing
8. (HTS); Human Genome Project (HGP)
9. Kyoto Encyclopedia of Genes and Genomes (KEGG)
10.Massively Parallel Signature Sequencing (MPSS); Mega base pair (Mbp)
11.National Institute of Health (NIH)
12.Next-Generation Sequencing (NGS)
13.Non-coding RNA (ncRNA)
14.Personal Genome Machine (PGM)
15.Polymerase Chain Reaction (PCR)
16.Sequence Read Archive (SRA)
17.Single Molecule Real-Time (SMRT)
18.Single Molecule Sequencing (SMS)
19.Single Nucleotide Polymorphisms (SNPs)
20.Third Generation Sequencing (TGS)
21.Whole Genome Sequencing (WGS)

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