Ministry of Higher Education and Scientific Research

Duhok Polytechnic University

Shekhan Technical College of Health
Higher Education Committee

Nadwa Hussen Ali

Supervised by

Dr. Meqdad Saleh Ahmed

(2023 - 2024)
Table of Contents
1. Introduction.............................................................................................. 1

2. Techniques and Methods ......................................................................... 2

2.1. Sanger Sequencing ............................................................................ 3

2.2. Next-Generation Sequencing............................................................. 4

2.3. Third-Generation Sequencing ........................................................... 5

3. Applications of DNA Sequencing ........................................................... 6

3.1. Genetic Research ............................................................................... 8

3.2. Clinical Diagnostics........................................................................... 9

3.3. Forensic Analysis .............................................................................. 9

4. Challenges in DNA Sequencing ............................................................ 10

4.1. Data Analysis and Interpretation ..................................................... 11

4.2. Error Rates and Accuracy................................................................ 12

4.3. Cost and Scalability ......................................................................... 13

5. Future Directions in DNA Sequencing.................................................. 14

5.1. Nanopore Sequencing ...................................................................... 15

5.2. Single-Molecule Sequencing ........................................................... 15

5.3. Synthetic DNA Sequencing ............................................................. 16

6. Conclusion ................................................................................................ 17

7. References ................................................................................................. 18
1. Introduction
The plummeting costs of DNA sequencing render it possible to approach
such a grand goal. Yet, the current state-of-the-art clinical research toolkit
contains blunt instruments. The gold-standard clinical studies - randomized
controlled trials - seldom make use of molecular data, and even more rarely
make use of the blooming availability of vast new categories of "omic" data.
The RCT has been a bedrock of clinical research in the quest to establish the
safety and efficacy of drugs and protocols. Many lessons have been learned,
usually through hard experience. But the RCT has had limitations that have
led to years of delays in drug development and, remarkably, questions about
its power. Randomizing patients to one of two treatments enables the
estimator of the average effect of treatment to pick up the difference
between the average treatment value of outcomes under the true treatment
and any other treatment. (Eichler et al.2021)

The cost of determining a human DNA sequence has fallen drastically, from
about $3 billion for the first sequence in 2003 to less than $1000 in 2015.
The race to sequence much larger numbers of human genomes is now on.
Vast amounts of patient genomic information will soon be available, and
vast amounts of treatment and outcome information will also be released
under the aegis of precision or personalized medicine. In an ideal clinical
research world, massive data on patient genomic and treatment outcomes
could be rapidly combined to advance our understanding of human biology,
so that the path to better cures and therapeutics could be quickly mapped.
Health maintenance or decreasing the time to the cure all rely on
understanding biology. (Tyson et al.2020)

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2. Techniques and Methods
Usually, helical single molecule sequencing is faster. New techniques use
polymerase to rapidly identify DNA bases in a small chamber. Many
machines sequence one DNA fragment at a time, as it is typically faster. 454
grows a lawn of DNA in a large device with a few beads. Ultrasonic
vibrations distribute the beads evenly in the chamber. (Chakrawarti et al.)

Some new methods are based on structures. For example, 454 sequencing
machines grow identical DNA molecules on beads. DNA polymerase copies
the bases using mononucleotide triphosphates. Correct polymerization
releases inorganic pyrophosphate, generating enough phosphate ions to form
a light disc detected by sensitive detectors. The location of the disc matches
the primer position. After polymerase is done, DNA fragments are released,
allowing the next round of base copying to start. (Piccaluga, 2023)

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2.1. Sanger Sequencing

Figure 1: Sanger sequencing

The Sanger sequencing method, developed in 1977, involves the synthesis of

DNA molecules using chain-elongating deoxynucleotides and chain-
terminating dideoxynucleotides. PCR is performed with a DNA primer,
DNA template, and a mixture of normal and dideoxynucleotides. Chain-
elongation stops at the incorporation of the dideoxynucleotides. The
products are then heat-denatured and analyzed by capillary gel
electrophoresis. This method is highly accurate with an error rate of one base
per 1000 bases sequenced. (Cheng et al.2023)

DNA sequencing is the process of determining the precise order of the

nucleotides within a DNA molecule. It includes any method or technology

3
that is used to determine the order of the four bases: adenine, guanine,
cytosine, and thymine. The advent of rapid DNA sequencing methods has
greatly accelerated biological and medical research and discovery. DNA
sequencing has become the basis for essential science, medicine, and
forensics and is a key tool in many applications of biotechnology. Given
this, the process of sequencing DNA becomes cheaper, faster, and easier
over time. There are two major strategies used to sequence DNA: Maxam-
Gilbert (chemical) sequencing and Sanger (chain-termination) sequencing.
And now Illumina sequencing seems to have pushed back on these two
competitors, becoming the dominant technology as seen.

Figure 2: Illumina Sequencing

2.2. Next-Generation Sequencing

The Genome Analyzer, introduced by Illumina in 2006, was the first
successful massively parallel sequencer. It used sequencing-by-synthesis
with reversible dye-terminator chemistry. The method incorporated each of
the four dNTPs enzymatically with 10-12 cycles to resolve each base. A key
feature was the use of dTTPαS to generate reversible steps. The Genome
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Analyzer II can produce up to 10 gigabases of data in single-end read format
or 20 gigabases in pair-end format in 12 days. The Genome Analyzer IIx
system can generate 40-80 gigabases of data over the same period. (Gorden
et al.2021)

In the 1990s, the NHGRI aimed to reduce the cost of genome sequencing
significantly. They developed methods to directly interpret DNA sequence
information and achieved this through parallel sequencing and optical
imaging. The NHGRI has now reached their goal, known as the "$1000
Genome" program. (Schloss et al.2020)

2.3. Third-Generation Sequencing

The time constants observed in the DNA polymerase DRP experiments also
give an important clue for the polymerase errors. SYBR Green II
experiments revealed the stoppable kinesin which was stalling on
undetectable DNA duplexes with the high GC content in the split headpiece
(M237V/S237V) kinesin constructs. Hence, the acidic helix-loop-helix
subdomain seems sensitive not only to the pH but also to the centrifugal
force generated during the ATP hydrolysis. These results suggest that the
helix-loop-helix subdomain maintains an optimal pH and force condition
where the duplex DNAs do not accumulate ahead of the catalytic site of the
DNA polymerase. (Kumar et al.2022)

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Figure 3: PacBio SMRT technology and Oxford Nanopore can use unaltered
DNA to detect methylation.

Recent third-generation sequencing technology produces single molecule

real-time (SMRT) sequencing using nanometer-sized zero-mode waveguide
arrays. SMRT sequencing can detect polymerase activity from single DNA
polymerase molecules due to the reduced background noise. It reveals
complex DNA template structures, including repeated elements, hairpins, G-
quadruplexes, and other non-B-DNA helices compatible with T7, along with
duplex DNAs. Demonstrations for SNP detection and full-length mRNA
analyses have been reported as applications. Consensus sequencing using
shorter reads from the same long molecule can achieve higher accuracy
compared to individual long reads with a 10% error rate. (Yoo et al.2022)

3. Applications of DNA Sequencing

Disease risk diseases are influenced by both genetic (e.g., DNA) and non-
genetic (e.g., diet, exercise, smoking, and environmental) factors. The study
of the genetic basis for these diseases is called complex trait analysis. SNPs
are used to identify genetic variations that mark the probability of an

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individual developing a disease. Once genetic tests are developed that reflect
these genetic variations, they could be used to personalize treatment for an
individual. Current knowledge of DNA variation has significantly advanced
our understanding of the genetic variation which plays a role in neurological
and psychiatric problems as well as phenotype variability. Understanding the
genetic basis for undesirable medical traits may help people to understand
that the trait is not what they want, and that they are at risk for the problem.

DNA sequencing is used in a wide variety of biological and medical fields.

Here are a few examples presented: Completion of the human genome
project provided a complete sequence of the over three billion DNA base
pairs in a human genome. This work has had major applications in medicine,
including: One makes use of specific DNA variations to determine how a
patient will respond to a therapeutic protocol. This is called
pharmacogenomics. For example, some women with breast cancer respond
to the drug Herceptin if their tumor cells have a mutation in the HER2 gene.
Researchers are working on determining the pharmacogenomic response to,
and the correct dose of drugs for, however, a large number of other
medications that are used in the treatment of numerous medical conditions.
A very large number of genes determine anatomical and physiological
characteristics. SNPs are being used to identify the genetic variation that
underlies non-disease traits including hair and skin color, immune function,
response to infection, and athletic performance. (Nurk et al.2022)

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3.1. Genetic Research

Figure 4: genetic research

Many scientific goals rely on DNA sequencing of diverse biological systems

stored in JGI systems. HPC4EI's computational efforts assist in translating
DNA sequences into knowledge for biology and biotechnology. The
challenge lies in efficiently turning raw sequences into biological insights
due to the waste heat generated by high-speed sequencing instruments. Data
storage, software applications, analysis, and visualization pose further
problems. The large quantities of DNA sequence data are challenging for
researchers and biologists trying to solve real-world problems.

Recent scientific advances simplify DNA collection and minimize

environmental damage. This, coupled with advanced DNA sequencing
technology, has resulted in a wealth of genetic data. The DOE's HPC4EI
program at JGI ensures that this valuable genetic knowledge is preserved.
Using high-performance computing, they analyze complex biological data to
advance understanding of the environment, harness microorganisms for
clean energy, and explore unknown ecosystems.

Today's genetic research relies on DNA sequencing to understand genetic

code, evolutionary changes, and body composition. It also helps identify

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disease causes and pathogens. Next-gen DNA sequencing has made it a vital
tool in biological research. (Molla et al., 2021)

3.2. Clinical Diagnostics

The first human genome took 13 years and $3 billion. Cheaper DNA
sequencing emerged during the third and fourth human genomes. Lee Hood
called it the "middle-out strategy." Colding asked Roche to fund 454 Life
Sciences. By 2005, DNA sequencing was much cheaper, suggesting the
$10,000 genome was possible.

Just under a third of DNA sequencing platforms sequenced a human genome

as one of their initial products, with many more following in their footsteps
in the years since. The first was 454 Life Sciences, a company acquired by
Roche. The second was Solexa, a company acquired by Illumina, whose
platform has probably sequenced more human genomes than any other
platform to date. Having single-handedly launched the modern era of
genomics, Illumina completely dominates sequencing market share as of this
writing. For this reason, Chapter 3 covers next-generation sequencing
technologies in descending order of Illumina market share. A related
outcome of the 454 and Solexa launches was rapid gains in DNA sequencing
throughput, a trend that continues to the present day. (Jeon et al.2021)

3.3. Forensic Analysis

The work of Arvind Narayanan and his team has been of special interest.
This team was able to detect individuals from their DNA sequence data
using the HapMap dataset. Their approach was to run through a list of likely
suspects and compare his or her SNP list to the anonymized list of SNPs.
Even though this approach had a low success rate, it is important to address

9
privacy concerns and to find an acceptable format for collecting and storing
DNA sequence data. Their results also indicated that even individuals not
sharing any DNA data have a 12% general chance of matching. This might
well be far too high given the sensitive nature of the data. Their estimate
grows even higher for individuals who are either European or both European
and Asian descent. Their stance is that it is possible to threaten the identity
of semi-anonymous individuals by going through these SNP catalogs, cross-
referencing and tasks along those lines. This is a large cause for concern and
potential target for insurance companies and employers.

In forensic analysis, DNA sequence data has been added to other kinds of
biological evidence in the identification of cold cases and also in the
exoneration of some innocent defendants. Despite the fact that DNA
sequence information is often the most discriminating measure among
individuals, the fact that individuals share DNA sequence data with their
close relatives or with strangers from certain countries needs to be taken into
account. There are existing methods for predicting some of these attributes
from just the DNA sequence data of that person. (Mittelman, 2021)

4. Challenges in DNA Sequencing

In addition, we aim to predict per base error probabilities of sequences to
facilitate sequencing error correction to a given reference species. We
achieve these two tasks in the context of whole human genome sequencing
by using a technique called nanopolish. The procedure seeks to learn the
signal of re-squiggling relevant sequences of the same base from the lower
quality vanilla signal. This procedure is repeated, followed by an EM
algorithm for a fixed amount of time, so that at the end we have a model that

10
gives us the likelihood of the higher quality signal and a pair of optimal
matched state path and hidden path for every signal-sequence pair. Our
prediction of sequencing error probabilities is thus directly related to the
state from which the given base would emanate. The decoding described in
this dissertation corresponds to fixing, beforehand, the known local
alignment of the signal and DNA sequences to be computed.

In this dissertation, we are interested in finding a reliable mapping from the

optical signal to DNA sequences. First, among two signals of high and low
quality, we aim to classify the higher quality signal in terms of allelic or
non-allelic deletion, insertion, or homo/heterozygous single nucleotide
polymorphism.

Optical sequencing techniques, like the ones developed by Oxford Nanopore

Technologies, have the potential to greatly reduce the cost of sequencing at
the expense of lower accuracy. However, long reads, which make the
techniques appealing for biological applications, allow an optical error
model imposed by nature to accumulate numerous sequencing mistakes. The
vast majority of sequencing output is thus inaccessible because of the low
accuracy, as algorithms cannot be developed for analysis purposes. (Hu et
al., 2021)

4.1. Data Analysis and Interpretation

The randomized or athermal shear distribution of the breakpoint of a DNA
fragment is uniform along the piece of DNA. Thus, the breakpoint is equally
likely anywhere within a given piece of DNA. This alignment of any given
fragment with a piece of DNA is a random process. When fragments entirely
arise from DNA molecules, their alignment is decadent. Given a typical

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fragment yields alignments like those in Figure 2. We follow the current
practice of calling each DNA fragment a read. A read that was reversed
before binding to the sequenced sample DNA molecule is said to read in
reverse or revcomp. A typical read originates at an unknown position in an
unknown DNA molecule. Its actual origin depends on both the sample DNA
and the shearing procedure. The randomness and uniformity of the shear and
source distributions make the alignment and orientation of sequenced reads
random when the reads originate at unique sites in a single copy of a
genome.

A typical DNA sample contains DNA molecules of many different lengths.

The two DNA strands in a molecular sample of length n sequences with a
fixed offset of the molecule from one of the ends of average length n.
Frequently, the sample DNA is fragmented randomly by shearing its strands.
The resulting fragments are of many different lengths. The length
distribution of the fragments depends on the sample and the shearing
procedure. The end of each fragment samples one of the two ends of the
original sample DNA molecule. Biological and mechanical effects of
shearing break many of the sampled fragments at unknown places within the
original DNA molecules. (Faust et al.2024)(Maghini et al., 2021)

4.2. Error Rates and Accuracy

The second issue is the decision on sequencing strategy and technique. High
accuracy sequence data is crucial for various purposes, including SNP
detection, assembly, mapping, and haplotype determination. Sequence
quality affects k-mer frequency computations and characterization of low
coverage data. Error rates vary between centers and instruments. The

12
number of bases sequenced and instrument noise may be contributing
factors.

DNA sequencing technology has improved, but errors still occur at a rate of
one per 10,000 base pairs. More funding is needed to complete sequencing
of eukaryotic genomes. Base data is used to find genes and proteins.
Genomes contain all genetic information, but not all is necessarily active.
Researchers must first define scientific questions before beginning a
sequencing project. (Delahaye & Nicolas, 2021)

4.3. Cost and Scalability

The key role that cloud platforms will play in enabling scientists to mine the
data is apparent in RNA-sequencing (RNA-seq), also known as
transcriptome analysis. This technique assesses the expressed portion of the
genome by sequencing pre-messenger RNA, mRNA, tRNA, and other small
RNAs to establish the start and stop sites of the corresponding genes, the
level of expression, and how genes are spliced and assembled. RNA-
sequenced reads generally range from 25 to a hundred nucleotides in length
of which one or both of the sequence ends must map to the genome of
reference. RNA-seq requires billions of sequence bases per sample and that
data is analyzed, batch by batch, in the cloud. RNA-seq yields high-level
estimates of the complexity of the tissue measured, including the
development and extent of perturbation, which is critical for diagnostics
required for clinical trials underway to develop disease modifying treatments
for dementia.

Cost of human genome sequencing was over $1 billion. Frighteningly, the

raw materials to perform the work on complex genomes are similarly high:

13
sequencing the human genome required 3 liters of capillary buffer to do one
single read per individual base pair. Technology by Illumina has improved
upon individual health in the 15 years since the first human genome was
sequenced but the cost per genome is still approximately $1,500. Other
whole-light technologies such as Oxford Nanopore and Pacific Biosciences
have not yet reached the same throughput as cloud platforms. (Wonkam,
2021)

5. Future Directions in DNA Sequencing

The advantages of string-based DNA sequencing tech improve current
approaches. NGS tech is optimized for high-throughput sequencing and uses
the same detection principle. However, sequencing DNA strands by
synthesis is different. The order of nucleotides depends on the reaction step,
resulting in a more robust sequence and low-cost error correction.
Amplification of DNA is not needed, preventing GC-bias and increasing
read length. Technological hurdles need to be overcome for accurate use.

Several improvements to DNA sequencing technology can be envisioned,

with a focus on scaling up parallel sequencing. The Roche/454 Life Sciences
system, the first NGS technology, used picotiter plates with over 1 million
wells and paved the way for human genome sequencing. Other systems like
ION Torrent, Illumina/Solexa, Applied Biosystems/SOLiD, and Helicos also
aimed to achieve high-throughput sequencing and reduce per-base
sequencing costs by using different chip designs. This eliminated the need
for the costly Sanger technology. (Menon2021)

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5.1. Nanopore Sequencing
The DNA block's biological way of translating information into the ionic
current varies with nature and the type of DNA. Resistance is lower for
single strands passing through a narrowed pore, transmitting signals on a
shorter timescale. To sequence living matter, single bases must be firmly
held in the pore to generate interactions between the polymeric filament and
the bases. The forces that hold the base stationary and the absence of
interactions from neighboring bases are not yet understood. Materials and
engineering can help provide sensitivity and force for the obstructing base to
approach the pore's mouth.

The idea of sequencing DNA using a polymer and a nanopore dates back to
the 1990s. David D. Deamer and Daniel Branton proposed that it should be
possible to determine the DNA sequence as it passes through a membrane
with a nanopore. The key is to drive the DNA through the pore so that each
nucleotide base blocks the flow of ions in a characteristic way.
Distinguishing all four bases requires a synthetic polymer with 20^4
combinations. Initially, there were doubts about achieving this resolution,
but recent developments in synthetic pore manufacturing and
nanofabrication have renewed interest in the concept. (MacKenzie &
Argyropoulos, 2023)

5.2. Single-Molecule Sequencing

In more recent work, the integration of nanopores from a family of proteins,
α-hemolysin (αHL), was realized. In this architecture, DNA motor proteins
are usedto pull double-stranded DNA (dsDNA) through the pore.
Transmembrane protein pores have been used in combination with tunneling
currents to make single molecule conductance measurements. It is now
15
possible to send DNA markers through a potential nanopore. Biomolecules
of self-organizing alkanethiols allow attachment of a nanopore to favor αHL
for macro molecules. This experiment is a step towards further describing
sequencing of DNA by the αHL protein, as it requires the incorporation of
the ligand αHL at the end of the nanopore. Prospects for direct reading of an
extended sequence of single-stranded DNA through nanopores have recently
been published. Similarly, for some RNA sequencing methods, single
molecule RNA may be an attractive feature of nanopores.

DNA sequencing. 6.2. Single-molecule sequencing. A third generation of

sequencing technologies. Single-molecule or next generation sequencing
(NGS) methods are developing rapidly. The world's market value of NGS in
2016 was $7.2 billion. Unlike Sanger sequencing, which used the chain
termination method for the amplification of DNA fragments or copies in an
immobilized manner, NGS sequencing is parallel sequencing. NGS is a
sensitive way that data can be detected and works for a broad range of
applications. Single-molecule sequencing of DNA markers called bi-related
DNA conductive nano electrical lines has been achieved. (Exworthy et
al.2024)

5.3. Synthetic DNA Sequencing

DNA Synthesis, DNA Sequencing, DNA Directed RNA Synthesis, and
DNA Directed Protein Synthesis were designed and analyzed in 1984 but
never carried out or confirmed in practice. An iconographic representation of
optimal RNA synthesis would include a DNA metaphoric copy of the DNA
sequence currently being synthesized and a tight but still open RNA
polymerase that synthesizes RNA product in the correct direction. An
iconographic representation of optimal DNA synthesis would include a

16
DNA metaphoric copy of the DNA sequence currently being synthesized
and a tight but still open DNA polymerase that synthesizes DNA product in
the correct direction.

So far, we have successfully assembled short pilot and development scale

synthetic DNAs. We have used DNA sequences from isolated and cloned
DNA fragments or natural plasmids as starting material. Our long-term goal
is to build very long but simple repetitive DNA sequences. This will help us
conduct larger scale biological research projects using P. syringae colonies.
Additionally, synthetic DNA synthesis has potential applications in non-
biological areas, such as polymer technology and laboratory processes. It
requires difficult direct synthesis of short DNA sequences without using a
template or encrypted information. (Baum et al.2024)(Jiang et al.2021)

6. Conclusion
In conclusion, we believe that the Paracel platform is a good, efficient
candidate for solving many problems in computational biology, including
sequence error detection. Interested readers can build their own distributed
software for solving complex biological problems using Paracel as a
foundation. The source code of ParMBD can be downloaded for installation,
and more information about ParMBD is also available on the following
website. The future research will focus on RNA-seq data analysis and
multiple sequence alignment.

In this work, Paracel Sequence was used to solve the most compute-
intensive part of sequence error detection, and we achieved a 2x speedup.
Furthermore, ParMBD was proposed to take Paracel's advantage in solving
sequence error detection problems. We analyzed the performance of

17
ParMBD and showed that it scaled well with the sequence length and the
sequence numbers. The publicly available tools were compared based on
time consumption, space usage, and memory usage. Both real and simulated
data were considered in our comparative analysis.

7. References
Eichler, H. G., Pignatti, F., Schwarzer‐Daum, B., Hidalgo‐Simon, A.,
Eichler, I., Arlett, P., ... & Rasi, G. (2021). Randomized controlled trials
versus real world evidence: neither magic nor myth. Clinical Pharmacology
& Therapeutics, 109(5), 1212-1218.

Tyson, J. R., James, P., Stoddart, D., Sparks, N., Wickenhagen, A., Hall, G.,
... & Quick, J. (2020). Improvements to the ARTIC multiplex PCR method
for SARS-CoV-2 genome sequencing using nanopore. BioRxiv.

Chakrawarti, N., Deo, I., & Verma, R. (). Next-generation sequencing-

revolutionizing genomic research. degruyter.com.

Piccaluga, P. P. (2023). Editorial on the 20th Anniversary of the Genome

Project Realization. The History of DNA Sequencing. Digital Medicine and
Healthcare Technology.

Cheng, C., Fei, Z., & Xiao, P. (2023). Methods to improve the accuracy of
next-generation sequencing. Frontiers in bioengineering and biotechnology,
11, 982111.

Gorden, E. M., Sturk-Andreaggi, K., & Marshall, C. (2021). Capture

enrichment and massively parallel sequencing for human identification.
Forensic Science International: Genetics, 53, 102496.

18
Schloss, J. A., Gibbs, R. A., Makhijani, V. B., & Marziali, A. (2020).
Cultivating DNA sequencing technology after the human genome project.
Annual review of genomics and human genetics, 21, 117-138.

Kumar, A., Reed, A. J., Zahurancik, W. J., Daskalova, S. M., Hecht, S. M.,
& Suo, Z. (2022). Interlocking activities of DNA polymerase β in the base
excision repair pathway. Proceedings of the National Academy of Sciences,
119(10), e2118940119.

Yoo, K. W., Yadav, M. K., Song, Q., Atala, A., & Lu, B. (2022). Targeting
DNA polymerase to DNA double-strand breaks reduces DNA deletion size
and increases templated insertions generated by CRISPR/Cas9. Nucleic
Acids Research, 50(7), 3944-3957.

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko,
A., ... & Phillippy, A. M. (2022). The complete sequence of a human
genome. Science, 376(6588), 44-53.

Molla, K. A., Sretenovic, S., Bansal, K. C., & Qi, Y. (2021). Precise plant
genome editing using base editors and prime editors. Nature Plants.

Jeon, S. A., Park, J. L., Park, S. J., Kim, J. H., Goh, S. H., Han, J. Y., &
Kim, S. Y. (2021). Comparison between MGI and Illumina sequencing
platforms for whole genome sequencing. Genes & Genomics, 43, 713-724.

Mittelman, D. (2021). Heating up cold cases: an interview with Bruce

Budowle on human identification. Forensic Genomics.

Hu, T., Chitnis, N., Monos, D., & Dinh, A. (2021). Next-generation
sequencing technologies: An overview. Human Immunology.

19
Faust, H., Duffek, P., Hentschel, J., & Popp, D. (2024). Evaluation of
Automated Magnetic Bead–Based DNA Extraction for Detection of Short
Tandem Repeat Expansions With Nanopore Sequencing. Journal of Clinical
Laboratory Analysis, 38(6), e25029.

Maghini, D. G., Moss, E. L., Vance, S. E., & Bhatt, A. S. (2021). Improved
high-molecular-weight DNA extraction, nanopore sequencing and
metagenomic assembly from the human gut microbiome. Nature Protocols.

Delahaye, C. & Nicolas, J. (2021). Sequencing DNA with nanopores:

Troubles and biases. PloS one.

Wonkam, A. (2021). Sequence three million genomes across Africa.

Menon, S. (2021). Comparison of High-Throughput Next generation

sequencing data processing pipelines. International Research Journal of
Modernization in Engineering Technology and Science (IRJMETS), 3(8),
125-136.

MacKenzie, M. & Argyropoulos, C. (2023). An introduction to nanopore

sequencing: past, present, and future considerations. Micromachines.

Exworthy, M., Lunt, N., Tuck, P., & Mistry, R. (2024). From
commodification to entrepreneurialism: how commercial income is
transforming the English NHS. Public Money & Management, 44(4), 308-
316.

Baum, C., Berlips, J., Chen, W., Cui, H., Damgard, I., Dong, J., ... & Zhang,
H. (2024). A system capable of verifiably and privately screening global
DNA synthesis. arXiv preprint arXiv:2403.14023.

20
Jiang, C., Zhang, Y., Wang, F., & Liu, H. (2021). Toward Smart Information
Processing with Synthetic DNA Molecules. Macromolecular Rapid
Communications, 42(11), 2100084.

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