The impact of genetics on breast cancer William D. Foulkes MBBS PhD FRCPC Department of Human...

The impact of genetics on breast cancer

William D. Foulkes MBBS PhD FRCPCDepartment of Human Genetics

McGill University2015 Joint Congress on Medical Imaging and Radiation Sciences

May 28, 2015Montreal, 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 approaches3. 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?

1. PRACTICAL BREAST CANCER GENETICSWho to refer to genetics …why…and who test….

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….

CA Ovary 42

?CA Breast 32

CA Ovary 55 Road Traffic Accident 28

CA Breast 72

CA Breast 49 CA breast 55

1

2 3 5

6

4

Prophylactic mastectomy

CA Ovary 42

?CA Breast 32


CA Breast 72


1

2 3 5

6

4


Inability to confirm diagnosis

CA Ovary 42

?CA Breast 32


CA Breast 72


1

2 3 5

6

4


Premature death in a gene carrier

CA Ovary 42

?CA Breast 32


CA Breast 72


1

2 3 5

6

4


Non-penetrance

CA Ovary 42

?CA Breast 32


CA Breast 72


1

2 3 5

6

4


Male transmission of a condition affecting mainly women

CA Ovary 42

?CA Breast 32


CA Breast 72


1

2 3 5

6

4


Prophylactic surgery in gene carriers

CA Ovary 42

?CA Breast 32


CA Breast 72


1

2 3 5

6

4


Founder effects in ethnic groupsAdoption

Non-paternity Family conflicts/estrangement

Small families

• Male transmission• Cancers on both sides of family• Ethnic origin• Small families/preponderance of males• No living affected relatives

Be aware of:

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 cancer-

related 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: Number of affected vs non affected females

Br 40

Br

3

Br

Asking the right types of questions: Age considerations

58

Br 40

80 3

75 70

Br 53

65 60

Br 56

73

Asking the right types of questions: Age considerations

40

Br 40

59 56 50

Br 56

47

Br 53

61 5560 46

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

Br 28

75 8284

2

Asking the right types of questions: Male:male transmission

Br 28

75 8284

Br 37 Ov 37

Br 452

• Expand family history to a minimum of 3 generations• Ask about :

both maternal and paternal sides of familytotal number of cases of breast/ovarian cancerage-at-onset of diagnosesnumber and ages of unaffected femalesfamily structure (size, male/female ratios)

• Confirm all reported diagnoses where possible

Summary

Br 52

Br 42

Br 40

Br 60 Br 38

Br 48

70y

82y

55y 62y

40y

58y 42y

80y

MI 79

MI 75

78y80s

70s

•Multiple generations affected•Autosomal dominant•Early age of diagnosed (under 50y)

2. GENETIC EVALUATION – WHAT DOES IT INVOLVE?

Standard model vs newer approaches

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….

3. CAN GENETICS BE USED TO PREVENT BREAST CANCER?

If so, how?

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

BRCA1

BRCA2

breast

breast

ovary

ovary

Antoniou et al 2003

Risks to age 70

BRCA1 and BRCA2 – we know a lot….

The FAMOUS FIVE

BARD1/BRCA1/PALB2/BRCA2/RAD51

Livingston, Science, 2009

4. CAN GENETICS BE USED TO HELP DIAGNOSE BREAST CANCERS EARLY?

MRI, mammography, ultrasound?

We know it works…

Mammography and MRI

5. CAN GENETICS ASSIST IN TREATMENT DECISIONS?

Chemotherapy and beyond….

BRCA1/2 mutations result in specific vulnerabilities

Hoeijmakers, J.H. Nature, 411;366-373, 2001

Sensitivity of Brca1 or Brca2 null cells toplatinum agents

Tutt Cold Spring Harbour Symposia Quant Biol 2005Bhattacharyya, A. et al. J. Biol. Chem. 2000;275:23899-23903

Carboplatin Sensitivity ofBRCA2 deficient V-C8 cells

0 50 100 150 200 250 30010 -5

10 -4

10 -3

10 -2

10 -1

10 0

VC8

VC8 BAC

Carboplatin Conc M.

BRCA2 null

BRCA2 Wt

Carboplatin (M)

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

DNA DAMAGE DNA DAMAGE

normal tumour

A B C A B CxREPAIR MECHANISMS

Exploitation of tumour specific DNA repair defects by targeting “back up” DNA repair

x XLethal

Slide courtesy Andrew Tutt, MD PhD

Hypothesis

DNA DAMAGE DNA DAMAGE

normal BRCA1 or BRCA2 deficient

HR NHEJ SSA BER NER etc HR NHEJ SSA BER NER etc

Tumour Selective Killing

x xx


So how does PARP inhibition work?

Mechanism of LOH and inactivation of WT copy of a tumor suppressor gene

Foulkes, NEJM, 2008

Parp Inhibitor

BRCA1 functional

BRCA1 defective

Farmer et al Nature 2005

Kudos/AZ PARP inhibitor

KU-0058684PARP-1 IC50 =

3.2nM

KU-0058948PARP-1 IC50 = 3.4nM

450 fold difference SF50BRCA1 deficient vs functional

1000 fold difference SF50BRCA2 deficient vs functional

Farmer et al Nature 2005 434:917-21. Slide courtesy Andrew Tutt, MD PhD

Farmer, H et al. Nature, 434;917-920, 2005

Response to drugs that force cells to repair by HR


Farmer, H et al. Nature, 434;917-920, 2005Slide courtesy Andrew Tutt, MD PhD

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

6. WHAT NEW GENETIC TESTS ARE ON OFFER AND HOW SHOULD THEY BE EVALUATED?

Beyond BRCA1 and BRCA2?

0.000001 0.00001 0.0001 0.001 0.01 0.1 11

10

Allele frequency

Rela

tive

Risk

BRCA1

BRCA2TP53

PALB2

CHEK2 ATM

CDH1

STK1

PTEN NBBC Genes

Risk SNPs

Gene variants and breast cancer risk

Outliers?

Adapted from a slide created by Peter Devilee and Doug Easton

F J Couch et al. Science 2014;343:1466-1470

Fraction of familial risk explained-high, medium and low risk alleles….

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……

WHAT PANELS ARE AVAILABLE NOW?A Rough Guide to Panels

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 testedAKT1, 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 riskGene Risk associated

truncating variantsRisk associated

missense variants

Estimated relative risks

(90% CI)

P-value Absolute risk by age 80

Comments Other associated cancers

>2 fold risk

>4 fold risk

BRCA1 Yes Yes Yes 11.4 75% Estimates based on the BOADICEA model for woman born in 1960.

Ovary

BRCA2 Yes Yes Yes 11.7 76% Estimates based on the BOADICEA model for woman born in 1960.

Ovary, prostate, pancreas

TP53 Yes Yes Yes 105 (62-165)

Most published risk estimates subject to ascertainment bias

Childhood sarcoma, adrenocortical carcinoma, brain tumours

PTEN Unknown Unknown Yes - Published risk estimates subject to ascertainment bias

Thyroid, endometrial

CDH1 Likely Unknown Unknown 6.6 (2.2-19.6)

.004 47% Lobular breast cancer specific

Diffuse gastric

Genes with an established association between protein-truncating variants and breast cancer risk part 2

Gene Risk associated truncating variants

Risk associated

missense variants

Estimated relative risks

(90% CI)

P-value Absolute risk by age 80

Comments

>2 fold risk

>4 fold risk

STK11 Unknown Unknown Unknown - Published risk estimates subject to ascertainment bias

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% c.7272G>T is associated with higher risk

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 25% Most data are limited to c.1100delC

p.I157T associated with ~1.3-fold 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

Gene Comments Estimated RR (90%CI)

P-value Other associated cancers

AKT1 Germline AKT1 mutations predispose to rare form of Cowden like syndrome. Breast cancer risk unknown

-

APC No published evaluation of risk - Colorectal

ATR No published evaluation of risk -

AXIN1 No published evaluation of risk - Colorectal

BAP1 Case reports of breast cancers in families segregating germline BAP1 mutations – no systematic study

- Uveal / cutaneous melanoma

BARD1 Deleterious mutations found ~9/1824 triple negative cases. No published evaluation of risk

-

BLM Evidence relates to p.Q548X in Slavic populations and c.2207_2212delATCTGAinsTAGATTC in Ashkenazim. Evidence of increased breast cancer risk in homozygotes

2.4 (1.6-3.6) 0.0002 Colorectal

BMPR1A Germline mutations predispose to Juvenile Polyposis Syndrome. No published evaluation of breast cancer risk

- Colorectal

BRIP1 Single case-control study of familial cases Most data for R798X 2.0 (1.3-3.0) 0.012 Ovary

CDK4 Case reports in families – no published evaluation of risk - Melanoma

CDKN2A Case reports in families – no published evaluation of risk - Melanoma, pancreas

CTNNB1 No published evidence -

EPCAM No evidence on truncating mutations. Suggestive evidence for association for missense variant p.Thr115Met

- Colorectal

FAM175A No evidence of truncating mutations in high-risk families. No published evaluation of risk

-

FANCC Evidence from one exome sequencing study plus replication (4/1395 cases vs. 0/2210 controls)

- 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


P-value

Other associated cancers

FANCM Evidence from one exome sequencing study plus targeted genotyping of nonsense variant (p.Q1701X)

1.9 (1.3-2.6)

0.002

GEN1 Most data relate to polymorphic truncating mutation c.2515_2519delAAGTT, ~4% frequency

1.1 (0.81-1.5)

0.63

HOXB13 Analyses relate to p.G84E prostate cancer susceptibility variant 1.6 (0.98-2.8)

0.11 Prostate

MEN1 Suggestive evidence from cohort MEN1 carriers

2.0 (1.5-2.6)

2x10-5 Pituitary, parathyroid and pancreatic neuroendocrine tumors

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

- Colorectal, endometrial, ovary

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 (0.86-2.1)

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


P-value Other associated cancers

PALLD No published evaluation of risk -

PIK3CA Germline PIK3CA mutations predispose to rare form of Cowden-like syndrome. Breast cancer risk unknown

-

PMS2 See MLH1 - Colorectal, endometrial, ovary

PPM1D Association in one case-control study. Genotypes mosaic lymphocytes, not inherited

15.3 (3.3-350) 0.0002 Ovary

RAD50 Analyses based on four case-control studies, three of Finnish founder variant c.697delT

2.20 (0.98-4.7) 0.11

RAD51 No evidence of association. No truncating variants found in large case-control study

-

RAD51C Initial evidence for association through breast-ovarian cancer families, but little evidence for breast cancer risk after adjustment for ovarian cancer risk in family-based analysis

0.91 (0.50-1.7) 0.79 Ovary

RAD51D Evidence for association in breast-ovarian families but no evidence of breast cancer association after adjustment for ovarian cancer risk

1.3 (0.68-2.5) 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 No published evaluation of breast cancer risk -

XRCC2 Suggestive evidence exome sequencing followed by replication case-control study (truncating + rare likely deleterious missense)

- 0.02

XRCC3 No published evaluation of breast cancer risk - -

What could possibly go wrong?

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

Published on-line at nejm.org on 27 May, 2015

Further reading on panel testing for breast cancer -

Comments? Questions?

Thank you!

The impact of genetics on breast cancer William D. Foulkes MBBS PhD FRCPC Department of Human...

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