FAIRSpectra - Enabling the FAIRification of Analytical Science
Next generation sequencing in cancer treatment
1. The Application of Next
Generation Sequencing
in Cancer Treatment
Chintu Ngulube
0331975
Chobna Geneshwaren 0328532
Dikshita Ramkhalawon 0332052
Lee Jia Jing
0331140
Marlia Abdul Ghanie 0331520
2. Introduction
What is DNA sequencing?
Process of determining the sequence of nucleotides in a section of
DNA.
2
(Kulski, 2016)
History of sequencing
1869 - Discovery of DNA
1909 - Chemical characterisation
1953 - Structure of DNA
1977 - Sanger sequence invented (First Genome)
1986 - Automated sequencing machine first invented
1990 - Human Genome Project started
1992 - TIGR first sequencing factory
1995 - First bacterial genome (H. influenzae)
1998 - First animal genome (C. elagans)
2003 - Completion of Human Genome Project
2005 - First next generation sequencing instrument
2013 - More than 10,000 genome sequences in NCBI database
3. 3
● In 1977, Fredrick Sanger
developed DNA sequencing
technology based on chain
termination method.
● Also known as Sanger
sequencing/Dideoxy nucleotide
chain termination sequencing.
● Adopted as primary technology
in first generation laboratory
and commercial sequencing
application because of its high
efficiency and low radioactivity.
(Behjati and Tarpey, 2016)
First generation sequencing
4. What is Next Generation
Sequencing (NGS)?
● Multiple technological and
practical advances, high-
throughput sequencing.
● Each of the three billion
bases in the human
genome sequenced
multiple times.
● An effective way to capture
large amount of genomic
information about cancer.
(Gagan and Van Allen, 2016)
5. What is Next Generation Sequencing (NGS)?
● Collective technologies developed by:
Roche 454 sequencing
Platform : FLX genome sequencer
Method : Pyrosequencing detection
of
pyrophosphate release
Illumina sequencing
Platform : HiSeq 2005, MiSeq
Method : Reverse terminator
sequencing by
synthesis
PGM Sequencing
Platform : IonPGM/IonProton
Method : Sequencing by Synthesis
SOLiD sequencing
Platform : 5500 SOLiD W System
Method : Sequencing by ligation
(Buermans and den Dunnen, 2014)
7. “
● NGS can predict progression of premalignant into
malignant lesions and classify tumors after surgery.
● Utility of NGS analyses to identify drug targets and
drug-resistance mutations for several cancer types.
● In hematologic tumours, NGS uses locus-specific primer
to detect persistence of minimal residual disease during
therapy.
● NGS allow improvement of classification and
identification of actionable mutations in neurological
tumours and paediatric oncology.
( Kalps et al.2017)
8. “
● ChIP- seq is used to characterise cistrome of of
oestrogen receptor in hormone dependent breast
cancer.
● NGS is used in detecting cancer somatic mutation
thus large number of cancer were explored using this
method . ( one example is illustrated in table below)
( Chun 2017)
11. Advantages
NGS has a more compressive
analysis of variation type
Massively Parallel
(less time consuming)
Less DNA is required to produce massive
sequencing data.
Higher sensitivity to detect low
frequency
Decreased sequencing cost
(Serrati S. et al 2016)
12. Disadvantages
Less cost effective when using a low
number of samples.
It can be time consuming for sequencing
of low number of targets
(Highly complex)
(Serrati S. et al 2016)
13. Limitations
The confounding
factor of human
heterogeneity
Tissue for NGS has to be obtained
from relevant sites as well as at a
relevant time point in the
treatment course. This can result
in repeated biopsies.
High complexity of
workflow and results
NGS have posed a challenge for
analysis of vast genomic data,
gene interactions, annotations
and expression studies.
14. Selection of suitable target
capture approach and
sequencing platforms
Support for sequencing from
short read lengths is one of
the major shortcoming which
limit its application.
The difficulties in
identification of driver
mutations
The driver mutations can
evolve during the course of
cancer. As tumors are treated
or as they grow, a variety of
acquired genomic alterations
may emerge .
15. Familial Genetic Testing
❏ Genetic testing for
high penetrance
familial cancer genes.
❏ Patients that don’t
meet current criteria
for recommended
genetic testing
become eligible for
screening.
Current developments
Identification of Somatic
Mutations in Cancers
❏ Future treatments rely on
therapies directed to multiple
targets to prevent relapses
common to these treatment
modalities.
❏ Somatic mutations may
contribute as a mechanism for
disease relapse.
15
(Cliff et al.2011)
16. CMS extends Health Plan Coverage for NGS Testing
❏ Cover NGS testing for patients with advanced cancer in
its insurance plan.
❏ To identify patients with certain genetic mutation that
may benefit from U.S. Food and Drug Administration-
approved treatments.
❏ If known cancer cannot be matched with approved
treatment, it can help determine patient’s candidacy for
cancer clinical trial.
16
(10 Developments Ready to Advance Next
Generation Sequencing in 2019 | Twist
Bioscience2019)
17. Conclusion
17
● Four main sequencing methods :
- Pyrosequencing (454)
- Reversible terminator sequencing (Illumina)
- Sequencing by ligation (SOLiD)
- Semiconductor sequencing (Ion Torrent)
● NGS is cost effective, screen more samples and also detect multiple variants across
targeted areas of the genome.
● Next generation sequencing is used for a range application including :
- Sequencing whole genomes
- Sequencing specific genes or genomic regions
- Gene expression analysis
- Study of epigenetics
18. References
● 10 Developments Ready to Advance Next Generation Sequencing in 2019 | Twist Bioscience 2019
Twistbiosciencecom. viewed 28 May 2019,
<https://twistbioscience.com/company/blog/10DevelopmentsReadytoAdvanceNextGenerationSequencing
2019>.
● Behjati, S. and Tarpey, P. (2013). What is next generation sequencing?. Archives of disease in childhood
- Education & practice edition, 98(6), pp.236-238.
● Buermans, H. and den Dunnen, J. (2014). Next generation sequencing technology: Advances and
applications. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1842(10), pp.1932-1941.
● Chun x 2017, Journal of medical and clinical genomics, viewed 25 may 2019, <
https://www.omicsonline.org/open-access/applications-of-nextgeneration-sequencing-in-cancer-research-
and-moleculardiagnosis-2472-128X-1000147.php?aid=87612>
● Gagan, J. and Van Allen, E. (2015). Next-generation sequencing to guide cancer therapy. Genome
Medicine, 7(1).
● Kamps,R, Brandão,D Bianca J., van den Bosch,Aimee D. C. Paulussen,Sofia Xanthoulea,Marinus J.
Blok, 2017,‘Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer
Classification’,international journal of molecular science,18 (2), pp 308-312, Viewed 25 May 2019,
<<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343844/>
19. References
● Luthra, Rajyalakshmi et al. “Next-Generation Sequencing in Clinical
Molecular Diagnostics of Cancer: Advantages and Challenges.” Cancers vol.
7,4 2023-36. 14 Oct. 2015, doi:10.3390/cancers7040874
● Meldrum, Cliff et al. “Next-generation sequencing for cancer diagnostics: a
practical perspective.” The Clinical biochemist. Reviews vol. 32,4 (2011):
177-95.
