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Cancer Genetics:
John A. Martignetti, M.D., Ph.D.Departments of Genetics & Genomic Sciences, Pediatrics, and
O l i l S iOncological Sciences8-6744
What is Cancer?
Hallmarks of cancer
Limitless replicativeLimitless replicativepotential
Evasion ofapoptosis
Cancer is a Genetic Disease
From a genetic point of view, cancer can be divided into two broad categories.
Monogenic diseases - germline mutation within a single gene results in a particular phenotype.
Complex diseases - multiple genes and environmental factors interact to produce the disease phenotype.
Cancer
Sporadic Hereditaryp y
10 109 > 101110 x 109 > 1011
50 x 1012 > 1016
Cell division and replication:
100 x 1015 > 1025
pAn opportunity for genetic
disaster
The Molecular Pathogenesis of Prostate Cancer Development:Cancer is a progression of steps
Normal prostate epithelium
Germline mutations:RNASEL, ELAC2, MSR1
Proliferative inflammatoryatrophy
Normal prostate tissueChromosome 8q gain / 8p loss
TMPRSS2 Fusion
Prostatic intraepithelialneoplasia
L li d t t
Decrease in NKX3.1Loss of sequences:
10q, 13q, 16q
Localized prostatecancer
Metastatic prostate
Gain of sequences:7p, 7q, Xq
Decrease in PTEN
PIN
Androgen-independent
Metastatic prostatecancer
Androgen Receptor:Mutations / Amplifications
Androgen independentcancer
Cancerous tissue
Physical Proof: Tumors arise from previously normal tissues
Removal of a Pedunculated Adenomatous Polyp
2007: 145,500 new cases of colorectal cancer and 55,000 deaths in the U.S.
The adenoma–carcinoma sequence — the progression from normal colonic mucosa to smallcolonic mucosa to small tubular adenomas to larger adenomas and those with more advanced histologic features (villous featuresfeatures (villous features, high-grade dysplasia, or both) to cancer — is a central tenet of our understanding andunderstanding and management of colonic adenomas.
Levine J and Ahnen D. N Engl J Med 2006;355:2551-2557
Epidemiological Proof
TUMORS ARE MONOCLONAL GROWTHSMGIC M
ethylationG
6PD
alleleIg chains (mC
hromosom nes
mm
)m
al abnormmalities
1 cm3
109109
TUMORS ARISE FROM SPECIALIZED CELL TYPES:TYPES:
NOMENCLATUREEPITHELIA - CARCINOMA
- SQUAMOUS CELL CARCINOMAS- ADENOCARCINOMAS
80%
MESENCHYME - SARCOMAS
HEMATOPOIETIC LEUKEMIAS LYMPHOMASHEMATOPOIETIC - LEUKEMIAS, LYMPHOMAS
NEUROECTODERM - GLIOBLASTOMA, NEUROBLASTOMA, RETINOBLASTOMA
OUTLIERS - MELANOMAS, SMALL-CELL LUNG CAOUTLIERS MELANOMAS, SMALL CELL LUNG CA
Human Cancers
Lung Lymphomas:
Leukemias:BloodstreamSome common
carcinomas:Lung
Breast (women)
Lymphomas:Lymph nodes
ColonSome common
BladderProstate (men)
Some common sarcomas:FatBone
Muscle
Cancer Nomenclature
Prefix MeaningCancer Prefixes Identify Origins
adeno- glandchondro- cartilage
th d bl d llerythro- red blood cellhemangio- blood vesselshepato- liverlipo- fatlympho- lymphocyte
l i t llmelano- pigment cellmyelo- bone marrowmyo- muscleosteo- bone
Etiologic Factors In Cancer: Relative ContributionsRelative Contributions
• Genetic susceptibility • ++++• Genetic susceptibility• Alcohol
Diet
• ++++• ++
+++• Diet• Infection
O ti
• +++• ++
• Occupation• Environmental pollution
• ++• +
• Medications• Additional factors
• +• +
• Tobacco • ++++Source: J. Fraumeni, M.D
METASTASIS
Each step is genetically controlled
132 3
4
56
MUTATION
Inheritance
Environment MUTATION
DYSFUNCTION IN GROWTH REGULATING
Environment
Infection
DYSFUNCTION IN GROWTH REGULATINGGENES OR PRODUCTS
GROWTH ADVANTAGEMismatch Repair Genes
IMMORTALIZATIONTelomerase Activation
AUTOSTIMULATION
INVASTION, METASTASIS, ANGIOGENESIS
Oncogenes
Originally identified in RNA tumor viruses as genes thatcould transform cells into an altered state of control of cellproliferation, often resulting in a tumor.
Highly evolutionarily conservedHighly evolutionarily conserved.
Encode proteins that are important in cell cycle progression,ll di i i d diff ti ticell division, and differentiation.
myc myelocytomatosis virusmyc myelocytomatosis virusabl Abelson murine leukemia virussis simian sarcoma virus
t iras rat sarcoma virus
Rous Sarcoma Virus - 1910
Properties / Phenotype of Transformed Cells
Sporadic Cancer
Sporadic tumors: mutations that initiate tumorigenesis occur in somatic cells.p g
Oncogenes : Functions
1. Signal transduction pathways/growth factors - tyrosine kinase receptors, e.g.c-kit, erb-B, RET, ras. Point mutations or deletions of ligand bindingdomain constitutively activate signal transduction and drive cells intoy gthe cell cycle. Cells can become autonomous of growth regulation byendogenous production of polypeptide growth factors which act on theirown external receptors and stimulate their growth.
2. Cell cycle regulatory molecules - i.e. cyclin D1, overexpression expedites theG1 - S phase transition as does loss of inhibitory proteins, ultimatelymaking cells resistant to differentiation factors.
3. Transcription factors - jun, fos, presumably activate a class of genes requiredfor continued proliferation.
4. Regulators of programmed cell death - bcl-2, found at breakpoint of t(14;18)in follicular lymphoma. Overexpression of Bcl-2 protein, present inthe inner mitochondrial membrane, results in prolonged cell survival -escape from apoptotic signals.
O
Mechanisms of Oncogene Activation
Oncogene Cell divisionProliferation
Normal GrowthPoint mutation
Typically, mutations in oncogenesoccur somatically. At the cellular
l
Translocation
ylevel they are dominant. At thegenetic level sporadic.
colon cancer - ras
AmplificationTumorCML - BCR and abl
Amplification
Neuroblastoma - n-myc
Chronic Myelogenous Leukemia (CML):
Chronic Myelogenous Leukemia (CML): the first specific(CML): the first specific
translocation t(9;22)(q34;q11).The Philadelphia chromosome
translocation fuses th b d blthe bcr and abl genes
normal individual Leukemic patient
bcr Bcr-abl
Chr. 22
abl
Chr. 99; 22 Translocationfuses Bcr and Abl
Functional Domains of p160BCR, p145ABL, and p210BCR-ABL
Faderl S et al. N Engl J Med 1999;341:164-172
Tyrosine Kinase
Biochemistry 2nd Ed; 1995:1185
Signaling Pathways of p210BCR-ABL
Faderl S et al. N Engl J Med 1999;341:164-172
O
CH3SO3H
Gleevec®-Tyrosine Kinase Inhibitor:Likely Mode of Action of STI571
ATP in its specific binding site in the kinase domain of the protein is able to phosphorylate tyrosine residues (Y) on selected substrates. The phosphorylated substrate then binds with other molecules and activates downstream
Goldman J and Melo J. N Engl J Med 2001;344:1084-1086
p p ypathways in leukaemogenesis. STI571 occupies the ATP pocket in the BCR-ABL kinase domain and substrates cannot be phosphorylated.
Contribution Of Hereditary Cancer
• Breast Cancer:– 180,000 cases/yr– 10% hereditary = 18,000
• Colon Cancer:– 130,000 cases/yr
5% h dit 7 000– > 5% hereditary = >7,000
• Prostate Cancer:– 180,000 cases/yr– 10% hereditary = 18,000
• Variable Contribution To Other Cancers
Tumor Suppressor Genes
Tumor suppressor genes are normal genes that slow down cell division, repair DNA mistakes, and tell cells when to die (apoptosis or programmed cell death). An important difference between oncogenes and tumor suppressor genes is that oncogenes result from the activation (turning on) of proto-oncogenes, but tumor suppressor genes cause cancer when they are inactivated (turned off). Another major difference is that while the overwhelming majority of oncogenes develop from mutations in normal genes (proto-oncogenes) during the life of the individual (acquired mutations), abnormalities of tumor suppressor genes can be inherited as well as acquired.
Genes that control cell division: RB1 (retinoblastoma)
Genes that repair DNA: HNPCC (hereditary nonpolyposis colon cancer).
Cell "suicide" genes: p53 tumor suppressor gene (Li-Fraumeni syndrome (LFS). People with LFS have a higher risk for developing a number of cancers, including soft-tissue and bone sarcomas, brain tumors, breast cancer, adrenal gland cancer, and leukemia.
-Many sporadic cancers including lung cancers, colon cancers, breast cancers as well as others often have mutated p53 genes within the tumor.
Hereditary Cancers: Recognition
• Early onset, wrong gender• Multiple, bilateral, pleiotropic* (syndromic)• Pedigree shows multiple affected members - Transmitted in
an autosomal dominant pattern
Hereditary cancers: a mutation is present in the germline. This mutation results in an increased predispositionThis mutation results in an increased predisposition
toward developing a specific type(s) of cancer.
Hyperpigmented maculesype p g e ted acu es
Familial breast cancer All breast cancer
Highly penetrant mutationsHighly penetrant mutations
Retinoblastoma: a Paradigm of Hereditary Cancers
Most common intraocular malignancy in childhood:approximately 1:20,000 live births.
Tumor of the retina - nervous tissue lining.P ti i i l d l k i d t biPresenting signs include leukocoria and strabismus.Average age of diagnosis is 12 - 18 months.Association with secondary site tumors:
osteosarcoma Ewing sarcoma leukemiaosteosarcoma, Ewing sarcoma, leukemiaand lymphoma.
Early diagnosis and treatment are critical:90% cure rate by enucleation and radiation.y
First cancer to be directly associated with a geneticabnormality (interstitial deletion 13q14).
Retinoblastoma: a Paradigm of Hereditary Cancers
Sporadic form: always unilateral; approximately 60% of casesSporadic form: always unilateral; approximately 60% of cases.
Familial form: transmitted in an autosomal dominant fashion; approximatelypp y80% are bilateral; 15% are unilateral and 5% are asymptomatic (non-penetrance). 10-15% due to parental transmission, remainder represent de novo mutations - paternal allele (10:1).
The “Two - Hit” HypothesisBased on the epidemiology of retinoblastoma, Alfred Knudson developedp gy , pthe “two-hit” hypothesis. Knudson hypothesized that the responsible gene, RB,was a tumor suppressor gene, or a growth inhibitory gene. Wild type expression of Rb counteracts tumor formation. Because Rb is a growth-inhibitory gene, both copies of this gene need to be inactivated within a single cell to releaseboth copies of this gene need to be inactivated within a single cell to releasethat cell from its growth inhibitory effects. Considering that the rate at whichsomatic mutations occur in a mammalian cell is extremely rare (10-6 to 10-7), the occurrence of two independent somatic mutations at both alleles of the samegene is likely to represent a very rare event (10-12 to 10-14).
In a normal retinal cell, the first somatic mutation (“hit”) at the Rb tumor suppressorgene will not affect the cellular phenotype (because of the recessive nature ofgene will not affect the cellular phenotype (because of the recessive nature ofits growth inhibitory function) and only a second “hit” at the remaining wildtype allele will trigger the tumorigenic process. Hence, the first mutation is recessive at the cellular level, although the clinical condition follows an autosomal dominant mode of inheritance.
In familial retinoblastoma, the first Rb gene mutation is inherited through the germline,and is therefore present in every somatic cell. Only one additional mutation isand is therefore present in every somatic cell. Only one additional mutation isrequired to trigger the tumorigenic process.
The “Two - Hit” HypothesisBased on the epidemiology of retinoblastoma, Alfred Knudson developedp gy , pthe “two-hit” hypothesis. Knudson hypothesized that the responsible gene, RB,was a tumor suppressor gene, or a growth inhibitory gene. Wild type expression of Rb counteracts tumor formation. Because Rb is a grwoth-inhibitory gene, both copies of this gene need to be inactivated within a single cell to releaseboth copies of this gene need to be inactivated within a single cell to releasethat cell from its growth inhibitory effects. Considering that the rate at whichsomatic mutations occur in a mammalian cell is extremely rare (10-6 to 10-7), the occurrence of two independent somatic mutations at both alleles of the samegene is likely to represent a very rare event (10-12 to 10-14).
In a normal retinal cell, the first somatic mutation (“hit”) at the Rb tumor suppressor gene will not affect the cellular phenotype (because of the recessivesuppressor gene will not affect the cellular phenotype (because of the recessive nature of its growth inhibitory function) and only a second “hit” at the remaining Wild type allele will trigger the tumorigenic process. Hence, the first mutation is recessive at the cellular level, although the clinical condition follows an autosomal dominant mode of inheritance.
In familial retinoblastoma, the first Rb gene mutation is inherited through the germline,and is therefore present in every somatic cell. Only one additional mutation isand is therefore present in every somatic cell. Only one additional mutation isrequired to trigger the tumorigenic process.
The “Two - Hit” HypothesisBased on the epidemiology of retinoblastoma, Alfred Knudson developedp gy , pthe “two-hit” hypothesis. Knudson hypothesized that the responsible gene, RB,was a tumor suppressor gene, or a growth inhibitory gene. Wild type expression of Rb counteracts tumor formation. Because Rb is a grwoth-inhibitory gene, both copies of this gene need to be inactivated within a single cell to releaseboth copies of this gene need to be inactivated within a single cell to releasethat cell from its growth inhibitory effects. Considering that the rate at whichsomatic mutations occur in a mammalian cell is extremely rare (10-6 to 10-7), the occurrence of two independent somatic mutations at both alleles of the samegene is likely to represent a very rare event (10-12 to 10-14).
In a normal retinal cell, the first somatic mutation (“hit”) at the Rb tumor suppressorgene will not affect the cellular phenotype (because of the recessive nature ofgene will not affect the cellular phenotype (because of the recessive nature ofits growth inhibitory function) and only a second “hit” at the remaining wildtype allele will trigger the tumorigenic process. Hence, the first mutation is recessive at the cellular level, although the clinical condition follows an autosomal dominant mode of inheritance.
In familial retinoblastoma, the first Rb gene mutation is inherited through the germline, and is therefore present in every somatic cell. Only one additionalgermline, and is therefore present in every somatic cell. Only one additional mutation is required to trigger the tumorigenic process.
Based on the epidemiology of retinoblastoma, Alfred Knudson developed
The “Two - Hit” Hypothesisp gy , p
the “two-hit” hypothesis. Knudson hypothesized that the responsible gene, RB,was a tumor suppressor gene, or a growth inhibitory gene. Wild type expression of Rb counteracts tumor formation. Because Rb is a grwoth-inhibitory gene, both copies of this gene need to be inactivated within a single cell to releaseboth copies of this gene need to be inactivated within a single cell to releasethat cell from its growth inhibitory effects. Considering that the rate at whichsomatic mutations occur in a mammalian cell is extremely rare (10-6 to 10-7), the occurrence of two independent somatic mutations at both alleles of the samegene is likely to represent a very rare event (10-12 to 10-14)gene is likely to represent a very rare event (10 12 to 10 14).
In a normal retinal cell, the first somatic mutation (“hit”) at the Rb tumor suppressorgene will not affect the cellular phenotype (because of the recessive nature ofi h i hibi f i ) d l d “hi ” h i i ildits growth inhibitory function) and only a second “hit” at the remaining wildtype allele will trigger the tumorigenic process. Hence, the first mutation is recessive at the cellular level, although the clinical condition follows an autosomal dominant mode of inheritance.
In familial retinoblastoma, the first Rb gene mutation is inherited through the germline,and is therefore present in every somatic cell. Only one additional mutation isrequired to trigger the tumorigenic process What are some of the epidemiologicrequired to trigger the tumorigenic process. What are some of the epidemiologic and clinical differences between sporadic and inherited retinoblastoma?
Familial Adenomatous Polyposis
Familial Melanoma
Polyposis
Retinoblastoma
Li FraumeniLi Fraumeni Syndrome
Neurofibromatosis
Herditary papillary lrenal cancer
MEN1 Peutz-Jeghers
Cowdens Disease
Chromosomal Abnormalities: Cancer Risk
Numerical abnormalities:Numerical abnormalities:Down syndrome - 20x increased risk for all pediatric leukemias; however, acute megakaryocytic leukemia risk is 400x greater.
Sex chromosome abnormalities:Y chromosome - phenotypic females with Y chromosomal materialhave a greatly increased risk for gonadoblastoma (25% by age 30).
Klinefelter syndrome - associated with mild increased risk of malebreast cancer and leukemia.
Structural abnormalities:WAGR - Wilms tumor, aniridia, genital abnormalities, mental retardation (11p15). Wilms and genital tumors.mental retardation (11p15). Wilms and genital tumors.
Genome instability syndromes: DNA repair genes.HNPCC - mut-L and mut-S genesBloom syndrome - BLM (recQ DNA helicase ). Multiple leukemias,
GI cancersWerner syndrome - WRN. Multiple sarcomas.
Syndrome Genes Associated Predominant Cancer Risk Risk for Cancer, %
(Age Period at Onset)
Hereditary Breast/Ovarian Cancer
BRCA1, BRCA2
Breast, Ovarian, Prostate, Pancreatic cancers
50-80 for breast cancer (a)20 40 for ovarian cancer (a)Breast/Ovarian Cancer BRCA2 cancers 20-40 for ovarian cancer (a)
Familial adenomatous polyposis APC Colon carcinoma, hepatoblastoma
1.6 for hepatoblastoma (c)100 for colon cancer (t -early a)
Gorlin syndrome PTCH Basal cell carcinoma, medulloblastoma90 for basal cell carcinoma (c-a)
5 f d ll bl t (t )y ,
5 for medulloblastoma (t- a)
Hereditary nonpolyposis
colorectal cancer
MLH1, MSH2, MSH6, PMS2
Colon, endometrial, ovarian, renal pelvis, ureter, pancreatic, stomach, small bowel, hepatobilary cancers
70-90 for colon cancer 30-60 for endometrial cancer (teens-adulthood)
Li-Fraumeni syndrome TP53Soft tissue sarcomas, osteosarcomas,
breast cancer, brain tumors, adrenocortical tumors, leukemia
90-100 (c-a)
Multiple endocrine neoplasia type 2A RET Medullary thyroid carcinoma,
pheochromocytoma95-100 for medullary thyroid (c-early a)
50 for pheochromocytomaneoplasia type 2A pheochromocytoma 50 for pheochromocytoma
Neurofibromatosis 1 NF1 Peripheral nerve sheath tumors, optic nerve gliomas, brain tumors, leukemia
10 for peripheral nerve sheath tumors (childhood-adulthood)
Neurofibromatosis 2 NF2/merlinVestibular schwannomas,
menungiomas, spinal tumors, skin 100 for vestibular schwannomas
100 ( d l )g , p ,
tumors 100 (adolescence-a)
Retinoblastoma RB1 Retinoblastoma, pinealoma, osteosarcoma, melanoma
90 for retinoblastoma (inf-c) 50 for osteosarcoma (adolescence-a)
Tuberous sclerosis TSC1 TSC2 Renal cell carcinoma, ependymoma,5-14 for brain tumors (c-early a) 1 f li t i liTuberous sclerosis
complex TSC1, TSC2 Renal cell carcinoma, ependymoma, subependylmal giant cell astrocytoma <1 for malignant angiomyolipoma
<3 for renal cell carcinoma (early a)
Von Hippel-Lindau disease VHL
Clear cell renal cancer, pheochromocytoma, pancreatic islet
cell cancer
40 for renal cell carcinoma, 10-20 for pheochromocytoma,
5-10 for pancreatic islet cell (early a)Offit et al, 2006
Robson M and Offit K. N Engl J Med 2007;357:154-162
MONOGENIC TRAIT: HIGH PENETRANCE
Phenotype
Modifier genesEnvironment
Phenotype
DIAPHYSEAL MEDULLARY STENOSIS - OSTEOSARCOMA (DMS - OS):(DMS OS):
A BONE DYSPLASIA/CANCER SYNDROME
• Autosomal Dominant• 35% Risk of OS• 35% Risk of OS • Phenotype
– Bone Findingsg• Cortical Growth Abnormalities• Bone Infarctions• P th l i F t• Pathologic Fractures• Pain
– Pre-Senile Cataracts• Etiology Unknown
I New York F il
Australian F il
I I
I I I
I
I IC
Family FamilyT
I V
C I I I
I V
C
C
CC
T
T
VV
V IT
T
I
I I
I I I
Vermont Family
I V
V3
C C
C C CC
T
T T T
T T
V I
V I I
T
T
STRs:Simple Tandem Repeatsp p
1. Defined sequences;2. Unique chromosomal
positions;positions;3. Repeat lengths highly
variable between individuals and easily measured;
4. Several hundred well-spacedmarkers can be used
agcttgaa…(GATC)n…..aggcctato examine the entire
genome.
agcttgaa…(GATC) …..aggccta
agcttgaa…(GATCGATC)…..aggcctag g ( ) gg
agcttgaa…(GATCGATCT�GATCGATCGATC)…..aggccta
D9S
934
4
5
D9S
921
D9S
925
D9S
1749
D9S
916
D9S
790
D9S
B3
D9S
932M
D9S
171
D9S
1121
D9S
1118
D9S
304
D9S
301
D9S
1124
D9S
1122
D9S
922
D9S
303
D9S
252
D9S
906
D9S
910
D9S
2026
D9S
930
D9S
302
D9S
907
D9S
918
D9S
915
-6
-5
-4
-3
-2
-1
0
1
2
3
-50
-25 0
5.0
8
11
.4
13
.7
15
.4
16
.5
17
.6
18
.3
18
.5
18
.6
19
.1
19
.7
20
.1
20
.7
21
.2
21
.8
22
.4 23
24
.2
28
.4
31
.7
33
.6
35
.5
38
.5
42
.2
43
.2
43
.8
45
.6
49
.6
52
.2
53
.3
54
.2
55
.5
56
.8 59
61
.7 64
66
.9
69
.9
74
.8 79
85
.4
90
.6
92
.2
93
.9
95
.8
98
.2
98
.9
99
.2
10
0
10
3
10
5
11
0
11
4
11
9
12
4
14
4
16
9
-10
-9
-8
-7
Position in Haldane
D9S925 AL624 AL882 D9S1749 D9S916 D9S976 D9SB3 D9S171186 134 202 135 274 138 142 171186 130 192 135 274 126 144 163
FAMILY 2VI-4
190 134 202 135 274 138 142 171186 130 192 135 274 126 144 163166 132 194 139 272 128 157 162
132 196 149 278 126 157 170166 132 194 127 266 126 157 170190 132 196 149 278 126 155 170166 132 194 139 272 126 142 170182 126 198 139 278 130 142 170186 132 200 144 272 133 142 162
IV-5
IV-6
FAMILY 2
FAMILY 3
IV-7
VI-5
186 132 200 144 272 133 142 162182 128 202 138 266 135 142 160186 132 200 144 275 131 140 162190 134 196 124 266 127 150 160186 132 200 144 275 131 140 162174 130 200 128 269 133 142 172186 132 200 146 275 131 140 162174 130 200 128 272 133 142 162168 149 197 140 274 130 143 164172 149 199 118 280 128 145 162
III-3
V-5
FAMILY 4
IV-4
V-1
V-2
172 149 199 118 280 128 145 162168 149 197 140 274 130 145 164192 149 142 136 145 156
FAMILY 5IV-1
D9S1749 D9S916 D9S976
Chromosome 9
MTAP CDKN2A CDKN2B12kb
1 42 3 4 5 6 7 8 23 2 1 1
Segregation of OS-1 Mutation with Disease Phenotype
Family 5y
COMPLEX TRAIT: LOW PENETRANCE
Phenotypeyp
Single nucleotide polymorphisms (SNPs)
T / TT / T
T / G
G / G
Nature Genetics May, August 2007
Through June 2009, there were 439 published GWA at p < 5 x 10-8
Next-Generation Sequencing
• Genome-wide analysis of sequence and structural variation and mutation
• Digital RNA profiling, including mRNA quantitation, discovery of noveldiscovery of novel transcripts, splicing and allelic variation in expression
• ChIP Seq, small RNA analysis and other applications
Illumina Genome Analyzer
Some Metrics Capillary(E.g. ABI 3730)
Next-Gen Array Based(E.g. Illumina GAIIx, ABI SOLiD 3)
Reads Per Run 96 > 108Reads Per Run 96 > 108
Read Length 500 - 1,000 50 - 200
Sequence Per Run ~ 100 kb ~ 20 Gb
Run time Several hours 7 to 14 days
Data type Analog Digital
A Reinvention of Transcriptomics
Analysis Microarray Sequencing
Novel transcripts No YesNovel transcripts No Yes
Measure abundance < 3 logs > 4 logs
Allelic variation Low Res Yes
Splice variation Low Res Yes
Structural variation Low Res Yes
Analog DigitalData Type Analog hybridization
Digital sequence
Digital, single nucleotide resolution data permits more powerful analysis
Some Challenges
• Data analysisData analysis
• Today’s computational tools are rudimentary relative to the data analysis needs
• Complementing sequence information
•• In the near future, NGS sequencing studies will in general have small sample sizes and may be underpowered
• Therefore complementary computational and experimental strategies• Therefore, complementary computational and experimental strategies are needed
Systems Biology Approach
Make use of pathway, interaction & other associative information
EpigeneticsMethylationMethylation
Alternative SplicingMicroRNA
How is Breast Cancer Treated?
• Treatment depends on stage of cancer• More than one treatment may be usedy• Surgery• Radiation therapyRadiation therapy• Chemotherapy• Hormone therapyHormone therapy• Targeted therapy
Factors Considered in Treatment Decisions
• The stage and grade of the tumor• The stage and grade of the tumor
• The tumor’s hormone receptor status (estrogen receptor [ER] progesterone receptor [PR])receptor [ER], progesterone receptor [PR])
• Factors that may signify an aggressive tumor, such as HER2/neu amplificationsHER2/neu amplifications
• The presence of known mutations to breast cancer genesgenes
• The woman’s menopausal status
• The patient’s age and general health
Of young women diagnosed with breast cancer but whose lymphbreast cancer but whose lymph nodes are unaffected, 80% will be free of disease for five years following surgery and radiotherapy alone. The
i i 20% ill d lremaining 20% will develop metastases, and would benefit from receiving further (adjuvant) therapy. The problem is identifying the patients who fit into y g peach group. b, c, Proportion of patients who, on two types of current predictive criteria (b, NIH Consensus, and c, St Gallen)3, 4, would be advised to receivewould be advised to receive further therapy. The red bars show the proportion of patients who would be cured by surgery and radiotherapy but would then receive unnecessary (and frequently toxic) adjuvant treatment.
Nature 415, 484-485
Nature 415, 530-536: 2002
Of young women diagnosed with breast cancer but whose lymphbreast cancer but whose lymph nodes are unaffected, 80% will be free of disease for five years following surgery and radiotherapy alone. The
i i 20% ill d lremaining 20% will develop metastases, and would benefit from receiving further (adjuvant) therapy. The problem is identifying the patients who fit into y g peach group. b, c, Proportion of patients who, on two types of current predictive criteria (b, NIH Consensus, and c, St Gallen)3, 4, would be advised to receivewould be advised to receive further therapy. d, The situation if the molecular predictor described by Friend and colleagues were validated and used for the basis of advice. The red bars show the proportion of patients who would be cured by surgery and radiotherapy but would then receive unnecessary (andreceive unnecessary (and frequently toxic) adjuvant treatment.
What’s Next?a s e
