Variants of nine breast cancer genes associated with severe disease

Breast cancer risk genes are generally associated with triple-negative and high-grade disease, but differ substantially in their associated pathology, a large case-control analysis shows.

The findings have potential implications for genetic testing, risk prediction, variant classification, and screening, the authors noted.

To assess links between pathogenic germline variants in nine major breast cancer (BC) susceptibility genes and pathological features of nonmetastasized breast tumors, investigators from the Breast Cancer Association Consortium compared 42,680 women with breast cancer and 42,387 population-matched controls from the BRIDGES large-scale sequencing study.

They looked specifically at features relevant to prognosis and distinct therapeutic options, including tumor subtype, morphology, size, stage, and lymph node involvement, and found substantial differences in tumor subtype distribution by gene.

“Pathogenic [protein-truncating variants and pathogenic missense variants] in these ... susceptibility genes were disproportionately associated with more aggressive breast caner, particularly among younger women,” they wrote, noting that carriers of rare genetic variants in the nine genes comprised more than 27% of women diagnosed at age 40 or younger with triple-negative disease (driven mainly by BRCA1) and about 16% of those diagnosed with hormone receptor (HR)–positive, HER2-negative high-grade disease.

All together, the nine genes were associated with 14.4% of tumors in women aged 40 years and younger, but less than 4% in women over age 60 years, and among younger women, the prevalence of variants combined was higher in those with triple-negative and HR-positive, HER2-negative disease versus other subtypes, they said.

The findings were published online on Jan. 27, 2022, in JAMA Oncology.

Study subjects were women aged 18-79 years who were sampled, independently of family history, from 38 international population- or hospital-based studies conducted between 1991 and 2016.

The genes assessed included ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53.

Substantial heterogeneity was observed in the distribution of intrinsic subtypes by gene. For example, RAD51C, RAD51D, and BARD1 variants were associated mainly with triple-negative disease (odds ratios, 6.19, 6.19, and 10.05 respectively), and CHEK2 variants were associated with all subtypes (with ORs ranging from 2.21-3.17) except for triple-negative disease, the authors found.

“For ATM variants, the association was strongest for [HR-positive, HER2-negative]high-grade subtype (OR, 4.99). BRCA1 was associated with increased risk of all subtypes, but the ORs varied widely, being highest for triple-negative disease (OR, 55.32),” they wrote.

BRCA2 and PALB2 variants were also associated with triple-negative disease, TP53 variants were most strongly associated with HR-positive, HER2-negative and HR-negative, HER2-positive subtypes, and tumors occurring in pathogenic variant carriers were of higher grade, they added, noting that for most genes and subtypes, a decline in ORs was observed with increasing age.

All genes except CHEK2 were more strongly associated with high-grade disease.

These and other findings from the study can “inform guidelines for eligibility for gene panel sequencing and breast cancer surveillance in the general population,” the authors explained, adding that tumor characteristics can also be used to determine whether variants of uncertain significance are likely to be pathogenic.

The data should therefore “improve the precision of variant classification algorithms and extend them to a larger set of genes,” they noted.

“This case-control study suggests that rare variants in BC susceptibility genes display marked heterogeneity with respect to tumor phenotype, but also similarities between genes that are consistent with known biological functions. This present study provides detailed quantification of subtype-specific breast cancer risks; these can potentially improve risk prediction models and breast cancer prevention strategies,” they concluded.

More specifically, women found to be carrying variants in these genes may be offered enhanced screening, including by MRI, risk-reducing surgery, chemoprevention, and genetic counseling, corresponding author Nasim Mavaddat, MBBS, PhD, explained in an interview.

“Understanding tumor pathology associated with the genes can inform breast cancer risk prediction models, and management and treatment of women harboring pathogenic variants,” she noted.

The findings “enhance our understanding of breast cancer biology and aid efforts to classify whether genetic variants of uncertain significance are also likely to be pathogenic,” added Dr. Mavaddat, a senior research associate at the University of Cambridge (England).

She also said the investigators are taking steps to include the results in “CanRisk,” a cancer risk prediction model used by genetic counselors and other clinicians, and are “exploring whether variants in these genes are associated with contralateral breast cancer risk and survival after a breast cancer.”

As most participants were European, analyses should be extended to women of other racial and ethnic groups, she added.

The BRIDGES panel sequencing was supported by the European Union Horizon 2020 research and innovation program BRIDGES and the Wellcome Trust. The Breast Cancer Association Consortium is also funded by the European Union Horizon 2020 research and innovation program, the PERSPECTIVE I&I project, which is funded by the Government of Canada, and the Confluence project, which is funded with intramural funds from the National Cancer Institute. Dr. Mavaddat reported grants from the University of Cambridge, European Union Horizon 2020, Wellcome Trust, Genome Canada, Canadian Institutes of Health Research, and National Cancer Institute during the conduct of the study.

Breast cancer risk genes are generally associated with triple-negative and high-grade disease, but differ substantially in their associated pathology, a large case-control analysis shows.

The findings have potential implications for genetic testing, risk prediction, variant classification, and screening, the authors noted.

To assess links between pathogenic germline variants in nine major breast cancer (BC) susceptibility genes and pathological features of nonmetastasized breast tumors, investigators from the Breast Cancer Association Consortium compared 42,680 women with breast cancer and 42,387 population-matched controls from the BRIDGES large-scale sequencing study.

They looked specifically at features relevant to prognosis and distinct therapeutic options, including tumor subtype, morphology, size, stage, and lymph node involvement, and found substantial differences in tumor subtype distribution by gene.

“Pathogenic [protein-truncating variants and pathogenic missense variants] in these ... susceptibility genes were disproportionately associated with more aggressive breast caner, particularly among younger women,” they wrote, noting that carriers of rare genetic variants in the nine genes comprised more than 27% of women diagnosed at age 40 or younger with triple-negative disease (driven mainly by BRCA1) and about 16% of those diagnosed with hormone receptor (HR)–positive, HER2-negative high-grade disease.

All together, the nine genes were associated with 14.4% of tumors in women aged 40 years and younger, but less than 4% in women over age 60 years, and among younger women, the prevalence of variants combined was higher in those with triple-negative and HR-positive, HER2-negative disease versus other subtypes, they said.

The findings were published online on Jan. 27, 2022, in JAMA Oncology.

Study subjects were women aged 18-79 years who were sampled, independently of family history, from 38 international population- or hospital-based studies conducted between 1991 and 2016.

The genes assessed included ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53.

Substantial heterogeneity was observed in the distribution of intrinsic subtypes by gene. For example, RAD51C, RAD51D, and BARD1 variants were associated mainly with triple-negative disease (odds ratios, 6.19, 6.19, and 10.05 respectively), and CHEK2 variants were associated with all subtypes (with ORs ranging from 2.21-3.17) except for triple-negative disease, the authors found.

“For ATM variants, the association was strongest for [HR-positive, HER2-negative]high-grade subtype (OR, 4.99). BRCA1 was associated with increased risk of all subtypes, but the ORs varied widely, being highest for triple-negative disease (OR, 55.32),” they wrote.

BRCA2 and PALB2 variants were also associated with triple-negative disease, TP53 variants were most strongly associated with HR-positive, HER2-negative and HR-negative, HER2-positive subtypes, and tumors occurring in pathogenic variant carriers were of higher grade, they added, noting that for most genes and subtypes, a decline in ORs was observed with increasing age.

All genes except CHEK2 were more strongly associated with high-grade disease.

These and other findings from the study can “inform guidelines for eligibility for gene panel sequencing and breast cancer surveillance in the general population,” the authors explained, adding that tumor characteristics can also be used to determine whether variants of uncertain significance are likely to be pathogenic.

The data should therefore “improve the precision of variant classification algorithms and extend them to a larger set of genes,” they noted.

“This case-control study suggests that rare variants in BC susceptibility genes display marked heterogeneity with respect to tumor phenotype, but also similarities between genes that are consistent with known biological functions. This present study provides detailed quantification of subtype-specific breast cancer risks; these can potentially improve risk prediction models and breast cancer prevention strategies,” they concluded.

More specifically, women found to be carrying variants in these genes may be offered enhanced screening, including by MRI, risk-reducing surgery, chemoprevention, and genetic counseling, corresponding author Nasim Mavaddat, MBBS, PhD, explained in an interview.

“Understanding tumor pathology associated with the genes can inform breast cancer risk prediction models, and management and treatment of women harboring pathogenic variants,” she noted.

The findings “enhance our understanding of breast cancer biology and aid efforts to classify whether genetic variants of uncertain significance are also likely to be pathogenic,” added Dr. Mavaddat, a senior research associate at the University of Cambridge (England).

She also said the investigators are taking steps to include the results in “CanRisk,” a cancer risk prediction model used by genetic counselors and other clinicians, and are “exploring whether variants in these genes are associated with contralateral breast cancer risk and survival after a breast cancer.”

As most participants were European, analyses should be extended to women of other racial and ethnic groups, she added.

The BRIDGES panel sequencing was supported by the European Union Horizon 2020 research and innovation program BRIDGES and the Wellcome Trust. The Breast Cancer Association Consortium is also funded by the European Union Horizon 2020 research and innovation program, the PERSPECTIVE I&I project, which is funded by the Government of Canada, and the Confluence project, which is funded with intramural funds from the National Cancer Institute. Dr. Mavaddat reported grants from the University of Cambridge, European Union Horizon 2020, Wellcome Trust, Genome Canada, Canadian Institutes of Health Research, and National Cancer Institute during the conduct of the study.

Breast cancer risk genes are generally associated with triple-negative and high-grade disease, but differ substantially in their associated pathology, a large case-control analysis shows.

The findings have potential implications for genetic testing, risk prediction, variant classification, and screening, the authors noted.

To assess links between pathogenic germline variants in nine major breast cancer (BC) susceptibility genes and pathological features of nonmetastasized breast tumors, investigators from the Breast Cancer Association Consortium compared 42,680 women with breast cancer and 42,387 population-matched controls from the BRIDGES large-scale sequencing study.

They looked specifically at features relevant to prognosis and distinct therapeutic options, including tumor subtype, morphology, size, stage, and lymph node involvement, and found substantial differences in tumor subtype distribution by gene.

“Pathogenic [protein-truncating variants and pathogenic missense variants] in these ... susceptibility genes were disproportionately associated with more aggressive breast caner, particularly among younger women,” they wrote, noting that carriers of rare genetic variants in the nine genes comprised more than 27% of women diagnosed at age 40 or younger with triple-negative disease (driven mainly by BRCA1) and about 16% of those diagnosed with hormone receptor (HR)–positive, HER2-negative high-grade disease.

All together, the nine genes were associated with 14.4% of tumors in women aged 40 years and younger, but less than 4% in women over age 60 years, and among younger women, the prevalence of variants combined was higher in those with triple-negative and HR-positive, HER2-negative disease versus other subtypes, they said.

The findings were published online on Jan. 27, 2022, in JAMA Oncology.

Study subjects were women aged 18-79 years who were sampled, independently of family history, from 38 international population- or hospital-based studies conducted between 1991 and 2016.

The genes assessed included ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53.

Substantial heterogeneity was observed in the distribution of intrinsic subtypes by gene. For example, RAD51C, RAD51D, and BARD1 variants were associated mainly with triple-negative disease (odds ratios, 6.19, 6.19, and 10.05 respectively), and CHEK2 variants were associated with all subtypes (with ORs ranging from 2.21-3.17) except for triple-negative disease, the authors found.

“For ATM variants, the association was strongest for [HR-positive, HER2-negative]high-grade subtype (OR, 4.99). BRCA1 was associated with increased risk of all subtypes, but the ORs varied widely, being highest for triple-negative disease (OR, 55.32),” they wrote.

BRCA2 and PALB2 variants were also associated with triple-negative disease, TP53 variants were most strongly associated with HR-positive, HER2-negative and HR-negative, HER2-positive subtypes, and tumors occurring in pathogenic variant carriers were of higher grade, they added, noting that for most genes and subtypes, a decline in ORs was observed with increasing age.

All genes except CHEK2 were more strongly associated with high-grade disease.

These and other findings from the study can “inform guidelines for eligibility for gene panel sequencing and breast cancer surveillance in the general population,” the authors explained, adding that tumor characteristics can also be used to determine whether variants of uncertain significance are likely to be pathogenic.

The data should therefore “improve the precision of variant classification algorithms and extend them to a larger set of genes,” they noted.

“This case-control study suggests that rare variants in BC susceptibility genes display marked heterogeneity with respect to tumor phenotype, but also similarities between genes that are consistent with known biological functions. This present study provides detailed quantification of subtype-specific breast cancer risks; these can potentially improve risk prediction models and breast cancer prevention strategies,” they concluded.

More specifically, women found to be carrying variants in these genes may be offered enhanced screening, including by MRI, risk-reducing surgery, chemoprevention, and genetic counseling, corresponding author Nasim Mavaddat, MBBS, PhD, explained in an interview.

“Understanding tumor pathology associated with the genes can inform breast cancer risk prediction models, and management and treatment of women harboring pathogenic variants,” she noted.

The findings “enhance our understanding of breast cancer biology and aid efforts to classify whether genetic variants of uncertain significance are also likely to be pathogenic,” added Dr. Mavaddat, a senior research associate at the University of Cambridge (England).

She also said the investigators are taking steps to include the results in “CanRisk,” a cancer risk prediction model used by genetic counselors and other clinicians, and are “exploring whether variants in these genes are associated with contralateral breast cancer risk and survival after a breast cancer.”

As most participants were European, analyses should be extended to women of other racial and ethnic groups, she added.

The BRIDGES panel sequencing was supported by the European Union Horizon 2020 research and innovation program BRIDGES and the Wellcome Trust. The Breast Cancer Association Consortium is also funded by the European Union Horizon 2020 research and innovation program, the PERSPECTIVE I&I project, which is funded by the Government of Canada, and the Confluence project, which is funded with intramural funds from the National Cancer Institute. Dr. Mavaddat reported grants from the University of Cambridge, European Union Horizon 2020, Wellcome Trust, Genome Canada, Canadian Institutes of Health Research, and National Cancer Institute during the conduct of the study.