service

Interpretation

This patient has a 28.12% chance of developing breast cancer within her remaining lifetime up to age 85 which is considered a potentially high risk. This does not mean that the patient will develop breast cancer over this time frame.

As this is a potentially high risk (in consultation with the prescribing medical practitioner), genetic counselling is advisable.

The risk scores are patient-specific and cannot be used to estimate risk in relatives. These results should be interpreted by a healthcare provider in the context of the patient’s full clinical history particularly for patients close to a threshold risk value and where any SNPs are undetermined.

Clinical Responses

Does the patient have a medical history of any breast cancer or ductal carcinoma in situ (DCIS) or lobular carcinoma in situ (LCIS)? No
Does the patient have a mutation in either the BRCA1 or BRCA2 gene, or a diagnosis of a genetic syndrome that may be associated with elevated risk of breast cancer? No
What is the patient’s age? 45
What is the patient’s race/ethnicity? Caucasian
How many first-degree relatives have had breast cancer? (mother, sister, daughter) 2 or more
What was the age of the youngest first-degree relative when they were diagnosed with breast cancer? Unknown
How many second-degree relatives have had breast cancer? (aunts, nieces, grandparents, grandchildren, half-siblings, and double cousins 1
What is the patient’s height? 1.77 meters
What is the patient’s weight? 75 kilograms
What is the patient’s menopausal status? Post-Menopausal
Has the patient ever had a breast mammogram? Yes
What was the patient’s reported mammographic breast density? 44

About the Test

GeneType for Breast Cancer combines the major determinants of breast cancer risk into a single risk assessment test.

Polygenic Risk Scores based on single-nucleotide polymorphisms (SNPs), mammographic density, age, family history of breast cancer, body mass index and menopausal status are combined with incidence and mortality data for breast cancer derived from the Australian Institute of Health and Welfare (AIHW), in a proprietary algorithm to provide an absolute estimate of the 5 year and remaining lifetime risk of developing breast cancer

Indication: GeneType for Breast Cancer is a breast cancer risk assessment test for women age 35 or older who lack hereditary status. The test is intended to better inform decision-making for breast cancer screening and preventative care

Validation: GeneType for Breast Cancer is currently validated in women 35 years or older of Caucasian descent and relies on the patient correctly reporting their ethnicity. Other ethnicities are under investigation but not yet available

Limitations: GeneType for Breast Cancer is a breast cancer risk prediction test only. An increased risk score does not mean that a patient will definitely develop breast cancer. A low risk score does not mean that a patient will definitely not develop breast cancer

GeneType for Breast Cancer provides an estimate as to the likelihood that a woman will develop disease at some stage in the future. Cancer is a multifactorial disease and it is not possible to incorporate all potential risk factors into a risk prediction model.

Test results should be interpreted by a healthcare provider in the context of the patient’s full clinical history. Medical management and decision-making for breast cancer screening and prevention practices should not rely solely on a patient’s GeneType for Breast Cancer results.

Measurement of Uncertainty: Estimated potential variation in the polygenic risk score for varying numbers of undetermined SNPs are as follows: 1 = ± 3.92%, 2 = ± 5.77%, 3 = ± 7.16%, 4 = ± 8.33%. For patients that are very close to a clinical risk threshold, such variation may move the patient just above or just below that threshold, however the magnitude of the change is small and their overall risk remains as “close to threshold”. Genotypes which are undetermined are assigned a risk score of 1.00.

Test Methodology: GeneType for Breast Cancer uses PCR arrays to determine the genotype of 77 polymorphic breast cancer susceptibility loci. Genomic DNA is extracted from buccal swab samples using standard DNA extraction methods. SNPs are genotyped using Taqman® chemistry on a customised OpenArray™ system using a QuantStudio™ 12K Flex Real Time PCR platform. The GeneType risk stratifier is calculated using a multiplicative model of breast cancer susceptibility combined with AIHW incidence and mortality data for breast cancer in Australia in a proprietary algorithm to provide an absolute estimate of the lifetime risk of developing breast cancer.

Alternative Testing: This test is not applicable to women who have personal history of breast cancer or who have a mutation in either the BRCA1 or BRCA2 gene, or a diagnosis of a genetic syndrome that may be associated with elevated risk of breast cancer. In this case, the patient should be referred for genetic counselling.

References and Resources

Mavaddat N, Pharoah PD, Michailidou K, et al. Prediction of breast cancer risk based on profiling with common genetic variants. J Natl Cancer Inst 2015;107(5):djv036

NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®); Breast Cancer Screening and Diagnosis. Version 3.2018 – October 2018. NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®); Breast Cancer Risk Reduction. Version 1.2019 – December 2018

For a full list of references supporting the GeneType for Breast Cancer risk assessment test, please visit www.genetype.com

Information for the Patient

Your risk of developing breast cancer is POTENTIALLY HIGH for a woman your age.

Your risk of developing breast cancer over the rest of your life is 28.12%. The risk for an average woman your age is 14%.

Your risk of developing breast cancer over the next 5 years is 12.22%. The risk for an average woman your age is 9.8%.

Understanding Breast Cancer Risk Factors

A risk factor is anything that may increase the chance of developing a disease. Some risk factors are strong and significantly increase your personal risk of the disease while others are weaker and only have a small impact on overall risk. Some risk factors can be modified by making changes to your lifestyle, while others are beyond your control.

Age: Increasing age is one of the strongest risk factors for breast cancer. Most breast cancers occur in women over the age of 50 years. It is important to maintain regular health checks as you get older.

Weight: Being overweight has been shown to increase the risk of breast cancer in post-menopausal women. Speak to your doctor about how to maintain a healthy weight and help to reduce your risk.

Genetics: You are born with a set of genetic markers called Single Nucleotide Polymorphisms (SNPs). This test looks at your SNPs to help determine your risk of developing breast cancer.

Family History: If you have relatives who have been diagnosed with breast cancer, this will impact your risk of developing the disease. The more relatives with breast cancer, the more your risk increases. This test incorporates your extended family history of breast cancer into your final risk score.

Breast Density: Breast density often changes with age, hormonal fluctuation and weight. Women with dense breasts are at increased risk of breast cancer.

Estrogen: Estrogen is a female sex hormone that helps regulate a woman’s reproductive system. Levels of estrogen fluctuate from adolescence through adulthood as a woman goes through changes such as menarche, childbirth and menopause. It is important to understand your medical history as it relates to estrogen. Estrogen is associated with the development of some types of breast cancer.

Hormone Replacement Therapy: Use of hormone replacement therapy, especially for longer periods, has been associated with a modest increase in risk of breast cancer. However, it is important to note that the benefits of these medicines may outweigh the risks for many women. If you are taking combined hormone replacement therapy, review your needs every six to twelve months with your doctor.

Smoking: Smoking increases your risk of developing breast cancer. Talk to your doctor about strategies to help you quit smoking as part of your preventative breast health plan.

Alcohol: Alcohol consumption has been associated with an increased risk of breast cancer in both pre- and post-menopausal women. In order to reduce your risk of breast cancer, it is best not to drink alcohol or, if you drink, limit consumption to 1 standard drink or less per day.

Physical Activity: Moderate physical activity of between 1.5 to 4 hours per week has been shown to reduce risk for breast cancer. The longer the duration of exercise, the greater the reduction in risk.

What You Can Do

A woman can develop breast cancer at any age, regardless of her level of risk. It’s important to know the normal look and feel of your breasts and to perform regular self-examinations. See your doctor if you detect a change in your breasts.

Women at potentially high risk of breast cancer should discuss surveillance options with their doctor. Options may include regular physical breast examinations and breast imaging with mammography, MRI or ultrasound. The type(s) of breast imaging you receive will depend on your age, your mammographic breast density and your level of risk.

For example, mammograms are not as effective in women younger than 40, as the breast tissue in younger women is more dense, making it difficult to accurately detect breast cancers. Your doctor will be able to advise on which types of imaging and the frequency of screening that will be most suitable for you.

Appendix: Detailed SNP Results

SNPNumber NearestGene ChromosomeLocation RiskAllele PatientGenotype Calculated Risk vs Population Mean
rs616488 PEX14 1p36.22 A AA 1.04
rs11552449 SYT6 1p13.2 T CC 0.97
rs11249433 FCGR1B 1p11.2 G AA 0.93
rs6678914 LGR6 1q32.1 G GG 1.01
rs4245739 MDM4 1q32.1 C AA 0.99
rs12710696 OSR1 2p24.1 T CT 1.01
rs4849887 INHBB 2q14.2 C TC 0.93
rs1550623 CDCA7 2q31.1 A AA 1.02
rs1045485 CASP8 2q33.1 G GG 1.01
rs13387042 TNP1 2q35 A AA 1.13
rs16857609 TNS1 2q35 T CC 0.96
rs6762644 ITPR1 3p26.1 G AA 0.95
rs4973768 SLC4A7 3p24.1 T TC 1.00
rs12493607 TGFBR2 3p24.1 C GG 0.96
rs9790517 TET2 4q24 T TC 1.03
rs10069690 TERT 5p15.33 T TC 1.01
rs7726159 TERT 5p15.33 A AC 1.01
rs2736108 TERT 5p15.33 C CC 1.04
rs10941679 MRPS30 5p12 G GA 1.06
rs889312 MAP3K1 5q11.2 C CA 1.05
rs10472076 RAB3C 5q11.2 C CT 1.01
rs1353747 PDE4D 5q11.2 T TT 1.02
rs1432679 EBF1 5q33.3 C CT 1.01
rs11242675 FOXQ1 6p25.3 T TT 1.05
rs204247 RANBP9 6p23 G AA 0.96
rs17529111 FAM46A 6q14 C GA 1.03
rs12662670 ESR1 6q25.1 G TT 0.98
rs2046210 C6orf97 6q25.1 A GG 0.97
rs720475 ARHGEF5 7q35 G AG 0.97
rs9693444 DUSP4 8p12 A AC 1.02
rs6472903 HNF4G 8q21.11 T TT 1.03
rs2943559 HNF4G 8q21.11 G AA 0.98
rs13281615 POU5F1B 8q24.21 G GA 1.01
rs11780156 MYC 8q24.21 T TT 1.12
rs1011970 CDKN2B 9p21.3 T GG 0.98
rs10759243 KLF4 9q31.2 A CC 0.96
rs2380205 ANKRD16 10p15.1 C CC 1.02
rs7072776 MLLT10 10p12.31 A GG 0.97
rs11814448 DNAJC1 10p12.31 C AA 0.99
rs10995190 ZNF365 10q21.2 G GG 1.05
rs704010 ZMIZ1 10q22.3 T TC 1.02
rs2981579 FGFR2 10q26.13 A AG 1.03
rs11199914 FGFR2 10q26.12 C CC 1.04
rs3817198 LSP1 11p15.5 C CT 1.03
rs3903072 SNX32 11q13.1 G TG 1.00
rs554219 CCND1 11q13.3 G CC 0.97
rs78540526 CCND1 11q13.3 T CC 0.99
rs11820646 BARX2 11q24.3 C TC 0.99
rs12422552 ATF7IP 12p13.1 C GG 0.98
rs10771399 PTHLH 12p11.22 A GA 0.89
rs17356907 NTN4 12q22 A AA 1.06
rs2236007 PAX9 14q13.3 G AG 0.95
rs2588809 RAD51B 14q24.1 T CC 0.98
rs941764 CCDC88C 14q32.11 G AA 0.96
rs3803662 TOX3 16q12.1 A GG 0.89
rs17817449 FTO 16q12.2 T GT 0.98
rs11075995 FTO 16q12.2 T UN 1.00
rs13329835 CDYL2 16q23.2 G GA 1.04
rs6504950 STXBP4 17q22 G GG 1.04
rs527616 AQP4 18q11.2 G GG 1.03
rs1436904 CHST9 18q11.2 T UN 1.00
rs2363956 ANKLE1 19P13 T GG 0.98
rs8170 BABAM1 19p13.11 A GG 0.99
rs4808801 ELL 19p13.11 A AA 1.05
rs3760982 KCNN4 19q13.31 A AA 1.06
rs2823093 NRIP1 21q21.1 G GG 1.04
rs132390 EMID1 22q12.2 C TT 0.99
rs999737 RAD51L1 14q23 C CC 1.04
rs11571833 BRCA2 13q13.1 T AA 1.00
rs6001930 SGSM3 22q13.1 C TT 0.97
rs2016394 DLX2 2q31.1 G AG 1.00
rs6828523 ADAM29 4q34.1 C CC 1.03
rs17879961 CHEK2157T 22q12.1 G AA 1.00
rs7904519 TCF7L2 10q25.2 G AA 0.95
rs75915166 FGF3 11q13.3 A CC 1.00
rs865686 KLF4 9q31.2 T GT 0.97
rs1292011 TBX3 12q24.21 A AA 1.07
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