The impact of genetics on breast cancer
William D. Foulkes MBBS PhD FRCPC
Department of Human Genetics
McGill University
2015 Joint Congress on Medical Imaging and Radiation Sciences
May 28, 2015
Montreal, QC, Canada
Preamble
• This presentation will discuss the relevance of
genetic evaluation in the prevention, diagnosis
and treatment of breast cancer
Learning objectives
• Consider the importance of a genetic
evaluation for women with breast cancer
• Identify some of the genetic tests on offer for
breast cancer susceptibility
Outline of this presentation
1. Who gets referred to genetics and why?
2. Genetic evaluation – what does it involve
• - standard model
• - newer approaches
3. Can genetics be used to prevent breast cancer?
4. Can genetics be used to help diagnose breast
cancers early?
5. Can genetics assist in treatment decisions?
6. What new genetic tests are on offer and how
should they be evaluated?
Who to refer to genetics …why…and who test….
1. PRACTICAL BREAST CANCER GENETICS
Familial Breast Cancer
• Women can be classified as
– average (population) risk, (<17%)
– moderate risk (2-3x higher than pop. risk) (17-30%)
– high risk (> 3 times population risk) (>30%)
• family history is an important predisposing
factor for development of breast cancer
• However, for most women, increasing age is
the greatest risk factor
Who to test?
• Risk assessment
– Computer models
– Empiric models
– Clinical judgement
• Provincial standards of practice
• Consensus guidelines
• Commercial testing
• The “10% rule”
How frequent are BRCA1/2 mutations in young
women with breast cancer?
• Depends on how young you are
• Where you live, but more importantly…
• Your ethnicity/population group
membership
Genetic evaluation pitfalls
• Things to look out for…that might obscure a
genetic diagnosis….
1
?CA Breast 32
2
3
Road Traffic
Accident 28
CA Ovary 55
4
CA Breast 72
6
CA Breast 49
Prophylactic
mastectomy
CA breast 55
CA Ovary 42
5
1
Inability to confirm
diagnosis
?CA Breast 32
2
3
Road Traffic
Accident 28
CA Ovary 55
4
CA Breast 72
6
CA Breast 49
Prophylactic
mastectomy
CA breast 55
CA Ovary 42
5
1
?CA Breast 32
2
3
Road Traffic
Accident 28
CA Ovary 55
4
5
CA Breast 72
6
CA Breast 49
Prophylactic
mastectomy
CA breast 55
CA Ovary 42
Premature death in
a gene carrier
1
?CA Breast 32
2
3
Road Traffic
Accident 28
CA Ovary 55
4
5
CA Breast 72
6
CA Breast 49
Prophylactic
mastectomy
CA breast 55
CA Ovary 42
Non-penetrance
1
?CA Breast 32
2
3
Road Traffic
Accident 28
CA Ovary 55
4
5
CA Breast 72
6
CA Breast 49
Prophylactic
mastectomy
CA breast 55
CA Ovary 42
Male transmission of a
condition affecting mainly
women
1
?CA Breast 32
2
3
Road Traffic
Accident 28
CA Ovary 55
4
5
CA Breast 72
6
CA Breast 49
Prophylactic
mastectomy
CA breast 55
CA Ovary 42
Prophylactic surgery in
gene carriers
1
?CA Breast 32
2
3
Road Traffic
Accident 28
CA Ovary 55
4
5
CA Breast 72
6
CA Breast 49
Prophylactic
mastectomy
CA breast 55
CA Ovary 42
Small families
Founder effects in ethnic groups
Adoption
Non-paternity
Family conflicts/estrangement
Be aware of:
• Male transmission
• Cancers on both sides of family
• Ethnic origin
• Small families/preponderance of males
• No living affected relatives
Barriers to eliciting an accurate
family history
• Lack of information
– Geographical proximity to affected relatives
– Deceased relatives
• Lack of communication in family
– Unresolved family tension (can often surround the cancerrelated death of a parent or close relative)
– Estrangement from relatives
– Relatives unwilling to provide consent for ROI
• Issues of confidentiality (e.g. insurability)
• Adoption
– Lack of background information
– Can lead to complicated ethical dilemmas
Summary: why is an accurate family history
important?
• In order to:
– “Correct” inaccurate risk perception
– Provide accurate risk assessment
– Determine eligibility for genetic testing
– Make appropriate recommendations re screening/
cancer risk management
Key information to elicit
• Key screening questions:
– Has anyone on EITHER SIDE of your family had breast
and/or ovarian cancer?
– Has anyone been diagnosed with breast and/or ovarian
cancer at a young age (<50yrs)?
– How big is your family? How many men vs. women in the
family?
– What is your ethnicity?
• Sending pathology with referral can help us a lot!
Asking the right types of questions
‘40 y.o. female with Breast Cancer.
Strong family history: 2 aunts with
breast cancer. ?BRCA testing.
Please assess.’
Asking the right types of questions:
Relatedness
Br 40
Br 40
Asking the right types of questions:
Relatedness
Br 40
Br 40
Asking the right types of questions: Number of
affected vs non affected females
3
Br
Br 40
Br
Asking the right types of questions: Age
considerations
73
80
75
70
65
60
3
Br 53 Br 56
Br 40
58
Asking the right types of questions: Age
considerations
61
60
Br 56
Br 40
59
56
55
Br 53
50
47
46
40
Asking the right types of questions
‘28 y.o. woman with BrCa. No family
history. BRCA testing? Please assess.’
Asking the right types of questions:
Male to Female Ratio
75
84
82
2
Br 28
Asking the right types of questions:
Male:male transmission
75
84
82
2
Br 37
Ov 37
Br 45
Br 28
Summary
• Expand family history to a minimum of 3 generations
• Ask about :
both maternal and paternal sides of family
total number of cases of breast/ovarian cancer
age-at-onset of diagnoses
number and ages of unaffected females
family structure (size, male/female ratios)
• Confirm all reported diagnoses where possible
•Multiple generations affected
•Autosomal dominant
•Early age of diagnosed (under
50y)
78y
80s
70y
Br 48
MI 75
80y
MI 79
Br 52
55y
Br 42
40y
Br 40
70s
82y
58y
62y
Br 60
42y
Br 38
Standard model vs newer approaches
2. GENETIC EVALUATION – WHAT DOES
IT INVOLVE?
Germline breast cancer genetic
testing : the standard model
• Well-established in clinical practice for specific
genes
• Generally applied with reasonably clear clinical
criteria
– Most involve sequencing of BRCA1 and BRCA2 to
identify a putative deleterious variant
• Even with genes such as BRCA1 and BRCA2 that
are well characterised there can be problems
– Pathogenicity of specific variants often cannot be
established
– Assumption of pathogenicity based on class of variant
The process
•
•
•
•
Patient or physician initiate discussion
Physician refers the patient to genetics service
Genetics service perform some kind of triage
Often then request more information to clarify
diagnoses in patient and/or relatives
• Depending on triage, urgent or routine
• Routine appointments might be 12 months or
more later, in the public system
Genetic evaluation
• After gathering relevant information
• Appointment is made
• 45mins -90 mins interview with genetic
counsellor and/or MD
• Decision on genetic testing – or more info.
needed
• Send blood for genetic testing, as appropriate
• Wait for results
• Call patient back in for results
• Follow-up, depending on results….
If so, how?
3. CAN GENETICS BE USED TO PREVENT
BREAST CANCER?
BRCA1/2 – the most important breast
cancer genes
• The basics
The terrain
Foulkes, NEJM, 2008
BRCA1
First identified in 1994
Thousands of different mutations
Numerous founder mutations
High lifetime risk for breast and
ovarian cancer
• Risks at other sites less certain
• Characteristic pathology
• Implicated in key molecular
processes esp. DNA repair
•
•
•
•
BRCA2
• First identified in 1995
• Thousands of different mutations
identified
• Several founder mutations identified
• High lifetime risk for breast and
ovarian cancer
• High risks also for pancreas and
prostate cancer, and possibly CMM and
stomach ca
• Few characteristic pathological findings
• Implicated in DNA repair
BRCA1 and BRCA2
• Approximately 3-5% of breast cancer is due to
highly penetrant autosomal dominant genes
• BRCA1 and BRCA2, together account for around
85% of families with four or more cases of
breast/ovarian cancer
• Mutations in BRCA1 and BRCA2 are spread
throughout the gene
• ~0.11% of women in the general population carry
a mutation in BRCA1
• ~0.12% carry a mutation in BRCA2
• 2.5% of individuals of Ashkenazi Jewish descent
harbour one of three common BRCA1/BRCA2
founder mutations
Risks to age 70
breast
BRCA1
ovary
BRCA2
breast
ovary
Antoniou et al 2003
BRCA1 and BRCA2 – we know a lot….
Livingston, Science, 2009
The FAMOUS FIVE
BARD1/BRCA1/PALB2/BRCA2/RAD51
MRI, mammography, ultrasound?
4. CAN GENETICS BE USED TO HELP
DIAGNOSE BREAST CANCERS EARLY?
Mammography and MRI
We know it works…
Chemotherapy and beyond….
5. CAN GENETICS ASSIST IN TREATMENT
DECISIONS?
BRCA1/2 mutations result in specific
vulnerabilities
Hoeijmakers, J.H. Nature, 411;366-373, 2001
Sensitivity of Brca1 or Brca2 null cells to
platinum agents
Bhattacharyya, A. et al. J. Biol. Chem. 2000;275:23899-23903
Tutt Cold Spring Harbour Symposia Quant Biol 2005
Breast cancer:
metastatic studies using platinum
• In a phase II, open-label study, 20 patients with metastatic
breast cancer who carried a mutation in BRCA1 were treated
with cisplatin 75mg/m2 intravenously every three weeks as part
of a 21-day cycle for six cycles.
• Restaging studies to assess response were performed after
cycles 2 and 6, and every 3 months thereafter.
• Between July 2007 and January 2009, 20 patients were enrolled.
• 65% had prior adjuvant chemotherapy, 55% prior chemotherapy
for metastatic breast cancer; mean age 48 years (ranges 32 70); 30% ER or PR +, 70% ER/PR/HER2 - , and 0% HER2+.
• Overall response rate was 80%; nine patients experienced a
complete clinical response (45%) and seven experienced a
partial response (35%). One-year survival was 93%.
• Cisplatin-related adverse events, including nausea (50%),
anemia (5%) and neutropenia (35%) were mostly mild to
moderate in severity. One patient discontinued therapy due to
grade 4 neutropenia
•
Byrski et al, BRCT
What about newer agents?
• PARP inhibitors…basic principles…
Mechanism of LOH and inactivation of WT copy of a tumor suppressor gene
Foulkes, NEJM, 2008
Turner, N et al. Nature Reviews Cancer, 4;1-6, 2004
Tumour Selective Killing
Exploitation of tumour specific DNA repair defects
by targeting “back up” DNA repair
normal
tumour
DNA DAMAGE
REPAIR MECHANISMS
A
x
B
C
DNA DAMAGE
A
Xx
B
C
Lethal
Slide courtesy Andrew Tutt, MD PhD
Tumour Selective Killing
Hypothesis
normal
DNA DAMAGE
HR NHEJ SSA BER NER etc
x
BRCA1 or BRCA2
deficient
DNA DAMAGE
HR NHEJ SSA BER NER etc
x
x
Slide courtesy Andrew Tutt, MD PhD
So how does PARP inhibition work?
Mechanism of LOH and inactivation of WT copy of a tumor suppressor gene
Foulkes, NEJM, 2008
Kudos/AZ PARP inhibitor
Parp Inhibitor
KU-0058948
PARP-1 IC50 = 3.4nM
BRCA1
functional
KU-0058684
PARP-1 IC50 = 3.2nM
BRCA1
defective
450 fold difference SF50
BRCA1 deficient vs functional
1000 fold difference SF50
BRCA2 deficient vs functional
Farmer et al Nature 2005 434:917-21
.
Farmer et al Nature 2005
Slide courtesy Andrew Tutt, MD PhD
Response to drugs that force cells to repair by HR
Slide courtesy Andrew Tutt, MD PhD
Farmer, H et al. Nature, 434;917-920, 2005
Slide courtesy Andrew Tutt, MD PhD
Farmer, H et al. Nature, 434;917-920, 2005
Parp1 inhibitors in clinical practice…
Waterfall plots…in BRCA carriers
Strikingly
different
results
depending
disease and
on BRCA
status
PARP inhibitors: comparison with other targeted therapies
PI3KCA inhibitors in BRCA1-related
breast cancer
• BKM120 delayed tumor doubling in a mouse
model of BRCA1-related breast cancer
• BKM120 reduced RAD51 foci
• Adding BKM120 to olaparib had a synergistic
effect in mouse model-derived tumors and in
human xenotransplanted BRCA1-deficient tumors
Juvekar et al, Cancer Discovery, 2012
Beyond BRCA1 and BRCA2?
6. WHAT NEW GENETIC TESTS ARE ON OFFER
AND HOW SHOULD THEY BE EVALUATED?
Gene variants and breast cancer risk
CDH1
BRCA1
TP53
10
BRCA2
Relative Risk
STK1
PALB2
PTEN
NBBC Genes
CHEK2
ATM
Risk SNPs
1
0.000001
0.00001
0.0001
0.001
0.01
Allele frequency
Adapted from a slide created by Peter Devilee and Doug Easton
0.1
1
Fraction of familial risk explainedhigh, medium and low risk alleles….
F J Couch et al. Science 2014;343:1466-1470
20 years of decreasing costs: data per $100
That court case
In June 2013, ruling on “Association
for Molecular Pathology v. Myriad
Genetics, Inc.”, the Supreme Court of
the Unites States, unanimously
invalidated specific claims made by
Myriad, with respect to the patenting
of the genomic DNA sequence of
BRCA1 and BRCA2……
A Rough Guide to Panels
WHAT PANELS ARE AVAILABLE NOW?
What is a gene panel test?
• New sequencing technologies reduce costs
substantially
• Sequencing of multiple genes in a single assay
possible to identify disease-associated
variants
• The use of a panel in itself is not a problem
• The specific content of the panel may be a
problem
• Panels vary enormously in their content
Genes tested
AKT1, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2,
EPCAM, FAM175A, GEN1, MRE11A, MUTYH, NBN, PALB2,
PIK3CA, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53, XRCC2
So should we test for more than BRCA1/2??
• Yes
• No
• Maybe So…
Genes with an established association between protein-truncating variants and breast cancer risk
Gene
Risk associated
truncating variants
Risk
Estimated P-value
associated relative
missense risks
variants
(90% CI)
Absolute Comments
risk by
age 80
>2 fold
risk
>4 fold
risk
BRCA1
Yes
Yes
Yes
11.4
75%
BRCA2
Yes
Yes
Yes
11.7
76%
TP53
Yes
Yes
Yes
105
(62-165)
PTEN
Unknown Unknown Yes
CDH1
Likely
-
Unknown Unknown 6.6
(2.2-19.6)
.004
47%
Estimates based
on the BOADICEA
model for woman
born in 1960.
Estimates based
on the BOADICEA
model for woman
born in 1960.
Most published
risk estimates
subject to
ascertainment
bias
Other
associated
cancers
Ovary
Ovary, prostate,
pancreas
Childhood
sarcoma,
adrenocortical
carcinoma, brain
tumours
Published risk
Thyroid,
estimates subject endometrial
to ascertainment
bias
Lobular breast
Diffuse gastric
cancer specific
Genes with an established association between protein-truncating variants and breast cancer risk part 2
Gene
Risk associated truncating Risk
variants
associated
Estimated
P-value
relative risks
missense
variants
(90% CI)
Absolute Comments
risk by age
80
>2 fold
risk
>4 fold
risk
STK11
Unknown
Unknown
Unknown
-
PALB2
Likely
Unknown
Unknown
5.3 (3.0-9.4) 4x10-10
40%
ATM
Likely
Unlikely
Yes
2.8 (2.2-3.7) 5 x 10-11
24%
NF1
Likely
Unlikely
Unknown
2.6 (2.1-3.2) 2.3x10-13 26%
CHEK2
Likely
Unlikely
Yes
3.0 (2.6-3.5) 8x10-37
Published risk estimates
subject to ascertainment
bias
25%
c.7272G>T is associated with
higher risk
Most data are limited to
c.1100delC
p.I157T associated with ~1.3fold risk
NBN
Likely
Unlikely
Unknown
2.7 (1.9-3.7) 5 x 10-7
23%
Almost all data pertain to
c.657del5 in Slavic
populations
Other genes for which protein-truncating variants have been suggested to be associated with breast
cancer, or present on breast cancer testing panels, but where the association has not been established
Estimated RR
P-value Other associated
Gene
Comments
(90%CI)
AKT1
APC
ATR
AXIN1
BAP1
BARD1
BLM
BMPR1A
BRIP1
CDK4
CDKN2A
CTNNB1
EPCAM
FAM175A
FANCC
cancers
Germline AKT1 mutations predispose to rare form of Cowden like syndrome.
Breast cancer risk unknown
No published evaluation of risk
-
No published evaluation of risk
-
No published evaluation of risk
-
Colorectal
Case reports of breast cancers in families segregating germline BAP1 mutations –
no systematic study
-
Uveal / cutaneous
melanoma
Deleterious mutations found ~9/1824 triple negative cases.
-
No published evaluation of risk
Evidence relates to p.Q548X in Slavic populations and
c.2207_2212delATCTGAinsTAGATTC in Ashkenazim. Evidence of increased breast
cancer risk in homozygotes
Germline mutations predispose to Juvenile Polyposis Syndrome. No published
evaluation of breast cancer risk
Single case-control study of familial cases Most data for R798X
Colorectal
-
2.4 (1.6-3.6) 0.0002 Colorectal
-
Colorectal
2.0 (1.3-3.0) 0.012
Ovary
Case reports in families – no published evaluation of risk
-
Melanoma
Case reports in families – no published evaluation of risk
-
Melanoma,
pancreas
No published evidence
-
No evidence on truncating mutations. Suggestive evidence for association for
missense variant p.Thr115Met
No evidence of truncating mutations in high-risk families. No published evaluation of risk
Evidence from one exome sequencing study plus replication (4/1395 cases vs.
0/2210 controls)
Colorectal
0.02
Other genes for which protein-truncating variants have been suggested to be associated with breast cancer,
or present on breast cancer testing panels, but where the association has not been established
part 2
Gene
Comments
Estimated POther associated cancers
RR (90%CI) value
FANCM
Evidence from one exome sequencing study plus targeted
genotyping of nonsense variant (p.Q1701X)
1.9 (1.32.6)
0.002
GEN1
Most data relate to polymorphic truncating mutation
c.2515_2519delAAGTT, ~4% frequency
1.1 (0.811.5)
0.63
HOXB13
Analyses relate to p.G84E prostate cancer susceptibility variant 1.6 (0.98-
0.11
Prostate
2x10-5
Pituitary, parathyroid and pancreatic
neuroendocrine tumors
2.8)
MEN1
Suggestive evidence from cohort MEN1 carriers
2.0 (1.52.6)
MLH1
Evidence from cohort analyses in lynch-syndrome families
inconclusive. 3.95 (1.59- 8.13), P=.001 for mismatch repair
gene mutations combined, in one prospective study
-
MRE11A
Two mutations in 8 multiple case breast cancer families with
tumors that showed loss of all three MRN proteins. Combined
analysis of truncating and rare missense variants affecting key
functional domains in MRE11A, NBN and RAD50: OR 2.88
(1.22-6.78) P=.02
MSH2
see MLH1
-
Colorectal, endometrial, ovary
MSH6
See MLH1
-
Colorectal, endometrial, ovary
MUTYH
Suggestive evidence for increased breast cancer risk in MAP
patients homozygote for MUTYH mutations One case-control
study found no evidence of increased risk
1.3 (0.862.1)
Colorectal, endometrial, ovary
-
0.26
Gastro-intestinal
Other genes for which protein-truncating variants have been suggested to be associated with breast cancer, or present on
breast cancer testing panels, but where the association has not been established part 3
Gene
Comments
Estimated RR
(90%CI)
P-value
Other associated cancers
PALLD
PIK3CA
No published evaluation of risk
Germline PIK3CA mutations predispose to rare form of Cowden-like
syndrome. Breast cancer risk unknown
-
PMS2
See MLH1
-
PPM1D
Association in one case-control study. Genotypes mosaic lymphocytes, not
inherited
15.3 (3.3-350)
RAD50
Analyses based on four case-control studies, three of Finnish founder variant 2.20 (0.98-4.7)
c.697delT
RAD51
No evidence of association. No truncating variants found in large casecontrol study
RAD51C
Initial evidence for association through breast-ovarian cancer families, but 0.91 (0.50-1.7)
little evidence for breast cancer risk after adjustment for ovarian cancer risk
in family-based analysis
0.79
Ovary
RAD51D
Evidence for association in breast-ovarian families but no evidence of breast 1.3 (0.68-2.5)
cancer association after adjustment for ovarian cancer risk
0.49
Ovary
RINT1
Suggestive evidence from exome sequencing and targeted replication
3.2 (1.5-7.0)
0.013
SMAD4
Germline mutations predispose to Juvenile Polyposis Syndrome. No
published evaluation of breast cancer risk
-
VHL
XRCC2
No published evaluation of breast cancer risk
Suggestive evidence exome sequencing followed by replication case-control study (truncating + rare likely deleterious missense)
XRCC3
No published evaluation of breast cancer risk
Colorectal, endometrial, ovary
0.0002
Ovary
0.11
-
-
0.02
-
The results, she said, were “surreal.” She did not have
mutations in the breast cancer genes, but did have one
linked to a high risk of stomach cancer. In people with a
family history of the disease, that mutation is
considered so risky that patients who are not even sick
are often advised to have their stomachs removed. But
no one knows what the finding might mean in
someone like Jennifer, whose family has not had the
disease.
It was a troubling result that her doctors have no idea
how to interpret.
Conclusions on panel testing –
Proceed with Caution
• Multi-gene panels are the inevitable consequence of
falling costs and changing laws
• They are in principle “a good thing”
• But look before you leap
• BRCA1, BRCA2 still the major players
• TP53, PALB2 and possibly ATM and CHEK2 deserve
consideration
• Other genes probably more trouble than they are worth,
at least under the current model of pre-test counselling
• Somatic cancer gene panels will create their own
challenges
• Newer delivery models may change things once again
Further reading on panel testing for
breast cancer -
Published on-line at nejm.org on 27 May, 2015
Comments? Questions?
Thank you!