This document provides an agenda for a lecture on copy number variations (CNV) and their role in cancer development and pharmacogenetics. It begins with an introduction to CNVs, including definitions and mechanisms for their creation. It then discusses how CNVs can contribute to disease susceptibility and notes their role in directly influencing cancer cell genomes. The document outlines how common and rare CNVs may serve as "first hits" to the tumor genome or influence cancer risk. It provides some examples of specific cancers associated with CNVs and discusses how pharmacogenetics focuses on CNV effects in cancer treatment for drugs like tamoxifen and irinotecan. The document concludes by noting the promising potential for further discovery regarding C

1. Presented by: Narjes Khatoon Shabani Sadr
Provided for : Cancer Genetics - Dr. Galedari

3. Agenda for this Lecture
• Introduction of Copy number variations (CNV)
• types of CNV :bi-allelic and multi-allelic CNVs.
• Mechanism for the creation CNV
• Role in disease
• Define Cancer
• CNV role in cancer development
• Copy-number changes and cancer
• CNVs and cancer predisposition:
first hits to the tumor genome
• Common cancer CNVs
• Rare cancer CNVs
• Examples of cancer associated with CNVs
• CVN and Pharmacogenetics in oncology
• Conclusions

4. • The gene copy number (also "copy number variants" or CNVs) is the number
of copies of a particular gene in the genotype of an individual.
• Recent evidence shows that the can be elevated in
.
Introduction Copy number variations (CNV)

5. Introduction Copy number variations (CNV) :
A brief history of CNVs
• The first CNV in humans – discovered in the early – was found
to be widespread throughout all populations, with a range of striking
but largely benign phenotypic consequences.
• However, the first large, systematic structural comparisons of the
genomes of healthy humans were only carried out in and used
to identify large numbers of CNVs that are present at
significant frequency.
• Further studies have revealed well over a thousand CNVs, which at
one time were believed to account for of the human
genome, a figure inflated somewhat by the limited spatial resolution
of the methods used and consequent overestimation of the sizes of
the genomic regions involved.

6. • Copy-number variations (CNVs)—a form of structural
variation—are alterations of the DNA of a genome
that results in the cell having an abnormal or, for
certain genes, a normal variation in the number of
copies of one or more sections of the DNA.
• CNVs correspond to relatively large regions of the
genome that have been deleted (fewer than the
normal number) or duplicated (more than the normal
number) on certain chromosomes.

7. • For example, the chromosome that normally has
sections in order as A-B-C-D might instead have
sections A-B-C-C-D (a duplication of "C") or A-B-D (a
deletion of "C").
• This variation accounts for roughly 13% of human
genomic DNA and each variation may range from
about one kilo base (1,000 nucleotide bases) to
several megabases in size.
Introduction Copy number variations
(CNV)

8. Introduction Copy number variations
(CNV)
• DNA copy number variations (CNVs) are an important component of genetic
variation, affecting a greater fraction of the genome than single nucleotide
polymorphisms (SNPs).

9. • CNVs correspond to relatively large regions of
the genome that have been deleted or
duplicated on certain chromosomes.
• This variation accounts for roughly 13% of
human genomic DNA and each variation may
range from about 1 kb to several megabases
in size.
• CNVs contrast with SNPs, which affect only
one single nucleotide base.

10. What is a copy number variant?
• Human DNA has one copy of autosomal regions on each
chromosome.
• However, as discovered by the Human Genome Project,
many genetic regions display a variation in the number of
copies (more or less than two copies).
• Alleles containing 0 –13 gene copies have been reported
across the human population.

11. What is a copy number variant?
• These genetic variants are termed and are defined as
DNA segments ranging in size from to
among individuals owing to , ,
, , or .
• Although the contribution of CNVs to the of
common diseases is questionable, CNVs in some
genes play a clear role in drug efficacy
and toxicity.(especially in cancer)

12. Copy Number Variations in the Human
Genome
Chromosome Position
Person 1
Person 2
SignalSignal
Extra DNA
Missing DNA

13. bi-allelic and multi-allelic CNVs.

14. Mechanism for the creation CNV
• Most CNVs are stable and , so CNV between
individuals is largely a product of genetic heritage,
however, arise through diverse mechanisms
at various stages of development.
• Multiple homologous recombination reactions on each
chromosome are required for the meiotic cell divisions
that give rise to gametes, and although these events are of
very high fidelity, occasional mistakes are inevitable.
• Therefore, most CNV in the human genome likely arises
through non-allelic homologous recombination events in
which unmatched regions of chromosomes are mistakenly
recombined during meiosis.

15. • However, two lines of evidence suggest that this is not
the whole story.
• Firstly, various studies have revealed extensive CNV
between different cells in the same individuals; these
CNVs must have arisen post-fertilization.
• Secondly, some complex genetic rearrangements cannot
be readily reconciled with a non-allelic homologous
recombination mechanism; these have been proposed to
arise through rare replication defects resulting from
broken DNA at one replication fork invading another fork,
resulting in a template switch.
• This was subsequently superseded by a more general
micro homology-mediated break-induced replication
(MMBIR) model.
Mechanism for the creation CNV

16. Non-allelic homologous recombination (NAHR)

17. Non-homologous end joining (NHEJ) can result in a
genomic rearrangement that immediately or eventually
results in the or of genetic material after multiple
double-strand DNA breaks occur and are repaired.

18. Non-homologous end joining (NHEJ) can result in a
genomic rearrangement that immediately or eventually
results in the gain or loss of genetic material after multiple
double-strand DNA breaks occur and are repaired.

19. Role in disease
• Like other types of genetic variation, some CNVs have been
associated with or to disease.
• Gene copy number can be in cancer cells. For instance,
the copy number can be than normal in
.
• In addition, a higher copy number of CCL3L1 has been associated
with lower susceptibility to HIV infection, and a low copy number
of FCGR3B (the CD16 cell surface immunoglobulin receptor) can
increase susceptibility to systemic lupus erythematosus and similar
inflammatory autoimmune disorders. Copy number variation has also
been associated with autism, schizophrenia, and idiopathic learning
disability.

20. Define Cancer
is a term used to describe a large group
of diseases that are characterized by a cellular
malfunction.
• Healthy cells are programmed to “
”.
• Cancerous cells do not have this programming
and therefore and out of
control.
• They also serve no physiological function.
These cells are now termed a neoplasm.
• This neoplasmic mass often forms a clumping
of cells known as a tumor.

21. • Although the exact pathogenic mechanisms leading to
many cancers are unclear, the consensus view is that
cancer results from dysregulation of the activity or
expression of genes that control cell growth and
differentiation, leading to abnormal cell proliferation.
have been reported in ,
and presumably contribute to this dysregulation.
Define Cancer

22. Copy-number changes and cancer
• CNVs have clearly been shown to have the potential to indirectly
influence a healthy individual’s susceptibility to , for example
by the or .
• A more direct and immediate role of copy-number change is seen in
cancerous cells themselves, which frequently display CNVs that are
absent in the patient’s normal cells in characteristic (although cancer-
type specific) parts of the genome.
• Arguably, such copy-number changes in cancer cells should not be
called ‘variants’ because they do not fall within the spectrum of
normal human variation.

23. • Aneuploidy, double-minutes and nonreciprocal
translocations have long been recognized in many cancers
and are one form of CNV.
• But cancers have also been shown to gain additional copies
of certain smaller genomic regions.
• Such gains are of particular interest when they are found in
many patients with a given cancer type or in the early
stages of cancer because they can then be inferred to
harbor so-called ‘driver genes’ that favor the growth of
abnormal cells.
Copy-number changes and cancer

24. • By contrast, in the later stages of many cancers, ‘genomic
chaos’ often ensues, which makes it difficult to determine
which copy-number changes are significant or causative
and which are purely incidental or of minor importance.
Copy-number changes and cancer

25. CNVs and cancer predisposition:
first hits to the tumor genome
• The goal of cancer genetics is to discover all
that predispose to neoplasms.
• To this end, have been the most widely studied form
of genetic variation and, by using massive GWA studies,
many common SNPs have been shown to be associated
with cancer and other complex traits.
• However, the results of these efforts have not explained
much of the .
• This is perhaps because GWA studies have mostly ignored
the inter-individual genetic variation provided by CNVs,
which affect more than 10% of the human genome.

26. • CNVs, especially smaller variants, have been essentially
hidden from view until recently; thus, only a handful of
studies have found an association of CNVs with cancer.
• Once these CNVs have been identified, one can only
assume that CNVs will explain a larger portion of the
genetic basis of cancer.
• Once identified, common and rare CNVs should be
considered separately, as they may have very different roles
in cancer.
CNVs and cancer predisposition:
first hits to the tumor genome

27. Common cancer CNVs :Distribution of common
cancer CNVs in the human genome
As with SNPs, CNVs that are found frequently in the healthy population (common
CNVs) are very likely to have a role in cancer etiology.

28. Common cancer CNVs
:this is essential for DNA repair by homologous
recombination and has been shown by a GWA study to
contain a SNP that is strongly associated with
.
that seems to be associated with
a small deletion in Mtus1 is associated with a
decreased risk of familial and high-risk

29. Rare cancer CNVs
• There are over 200 cancer syndromes and although most
arise infrequently, they account for 5-10% of all cancer
cases.
• These are caused by base-pair-sized germline mutations
in many central
- such as: TP53, APC, BRCA1,
BRCA2, PTEN, and RB1
• and (fewer) , including HRAS and RET.

31. Proposed model for CNVs in tumorigenesis.

32. CNVs and tumor genomes: Copy
number alterations(CNA)
• Genome-scale analyses have found many formerly invisible
CNAs.
• In an analysis of 371 lung adenocarcinoma samples, Weir et al.
identified and
.
• The most significant amplification, at and containing
the novel oncogene .
• Mullighan et al found copy number changes in PAX5, a gene
within the B-cell development pathway, in 57 of 192 cases.

33. • In glioblastoma, CNA information, mRNA expression
levels and methylation changes have been measured and
nucleotide mutational analyses have been carried out.
• Integrative analysis has shown that over 70% of tumors
carry alterations in the retinoblastoma, p53 and receptor
tyrosine kinase pathways.
• Although cancer is driven primarily by alterations of the
genome, CNA profiles can be combined with other high-
throughput data to create insights that are 'greater than
the sum of their parts'.
CNVs and tumor genomes: Using
CNAs to define the key pathways of a
tumor

34. • CGH analysis has also shown that CNVs are associated
with , breast cancer, and
.
• Tse et al identified eight regions with CNVs including six
(on chromosomes 3, 6, 7, 8 and 19), and two
(on chromosomes 7 and 12) that were
significantly overrepresented in
patients compared with healthy
controls.
Examples of cancer associated
with CNVs

35. • Among these CNVs and gene deletions
on chromosome 6p21.3 showed the highest
association signal.
• Examining 51 BRCA1-associated ovarian cancer
patients, and 47 healthy women via Affymetrix
Genome-Wide Human SNP Array 6.0, Yoshihara et al
identified in BRCA1 associated ovarian
cancer patients.
Examples of cancer associated
with CNVs

36. Potential mechanism of the UGT2B17
CNV in prostate cancer pathogenesis.

39. Single-nucleotide
polymorphisms(SNPs) effect on
Pharmacogenomics
 Single Nucleotide Polymorphism (SNP):
GAATTTAAG
GAATTCAAG
 SNPs are defined as Single base-pair positions
in genomic DNA that vary among individuals
in one or several populations.
 SNPs are believed to underlie susceptibility
to such common diseases as cancer, diabetes,
and heart disease and to contribute to the
traits that make individuals unique.
 SNPs are used as genomic biomarkers.
 Hence SNP analysis can be used to enhance
drug discovery and development.
DNA molecule 1 differs from DNA
molecule 2 at a single base-pair
location (a C/T polymorphism)

40. Examples of drugs where pharmacogenomics
testing is useful are listed in this Table

41. CVN and Pharmacogenetics in oncology
Pharmacogenetics focused on the effects of genetics in cancer
treatment.
 Pharmacogenetics And selection of anticancer drugs:
• Thiopurine
• Irinotecan،
• Tamoxifen

42.  Thiopurine such as :
 6-mercaptopurine (6-MP)
 thioguanine
 and azathioprine (TPMT)
 Metabolized by: thiopurine-S-methyl transferase (TPMT)
CVN and Pharmacogenetics in oncology

43. Metabolism of 6-mercaptopurin to
6-methylmercaptopurin by the methylator
TPMT.

44. Various alleles of the gene
TPMT and their SNPs

46. Irinotecan
 Irinotecan
7-ethyl-10- hydroxycamptothecin (SN-38)
(UGT1A1) UDP- glucuronosyl transferase
Active
metab
olite
Deto
xifica
tion

47. Irinotecan

48.  Tamoxifen (estrogen receptor-positive breast
cancer)
 Tamoxifen is a prodrug
 endoxifen (4-hydroxy-N-desmethyl-tomoxifer)
Tamoxifen
By CYP2D6

49. Conclusions
• The study of cancer and CNVs is in its infancy but is
maturing quickly.
• In considering the effect of this form of genetic variation
on cancer predisposition, cancer gene expression and
tumor genome profiling, there is much to learn from past
studies on genomic disorders.
• Denser micro-arrays, next-generation sequencing and
integrative informatics analyses are around the corner and
promise to uncover new CNVs and CNAs.

50. Conclusions
• There are, therefore, many exciting questions to be addressed:
• what role do CNVs have in cancer predisposition and how can we
use this newly discovered form of genetic variation to identify
those most at risk?
• Which cancer-related genes are affected by CNVs and, of these
changes, which are both necessary and sufficient to cause
neoplastic growth?
• Can incipient cancer cells use these constitutional deletions and
duplications to induce or accelerate tumorigenesis and tumor
proliferation?

51. • As these questions are resolved, the potential value of
cancer CNVs as novel biomarkers of cancer
susceptibility and initiation, and of cancer progression
and metastases, will become apparent. Whether
cancer CNVs offer insight into genes that might be
targets for novel drug development remains to be
determined.
Conclusions

53. References
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55. • Tie-Lin Yang, Yan Guo,Christopher J. Papasian and
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56. “Human beings are ultimately
nothing but carriers-passageways-
for genes.
They ride us into the ground like
racehorses from generation to
generation. Genes don't think about
what constitutes good or evil.
They don't care whether we are happy or
unhappy. We're just means to an end for them.
The only thing they think about is what is
most efficient for them.”
Haruki Murakami, 1Q84