Prevalence of Germline Double Heterozygosity for Pathogenic Variants in Thai Cancer: A Study of 8,068 Patients
Cancer Genetics and Therapeutics
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Primary Categories:
- Cancer
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Secondary Categories:
- Cancer
Introduction:
Germline double heterozygosity for pathogenic variants in hereditary cancer genes was thought to be rare. With the growing use of multi-gene panel testing (MGPT) for cancer-associated genes, there have been increasing reports of double pathogenic variants, though patient characteristics and clinical features remain poorly documented.
In our study, we present cases of hereditary cancer with double heterozygosity for pathogenic variants, suggesting that this phenomenon may be more common than previously thought.
Methods:
In this single-center study at Siriraj Hospital, we analyzed clinical and genomic data from 8,068 Thai patients who underwent MGPT for cancer-associated genes for suspected hereditary cancer syndromes, from January 2016 to October 2024. DNA was extracted from peripheral blood and enriched with a custom library. Next-generation sequencing and Sanger sequencing were used to detect and confirm single nucleotide variants, whereas Multiplex Ligation-dependent Probe Amplification was used to identify copy-number variants. The variants were annotated, classified, and systematically validated according to the 2015 ACMG-AMP standard and guidelines, the 2020 ACMG-ClinGen technical standards for the interpretation and reporting of constitutional copy-number variants, and the ClinGen Expert Panel Specifications for genes with available guidelines.
Results:
A total of 8,068 patients underwent MGPT, revealing pathogenic or likely pathogenic (P/LP) variants in 1,163 individuals. Breast cancer was the most common, affecting 701 patients (60.3%), followed by colorectal cancer (n=243, 20.9%), ovarian cancer (n=97, 8.3%), endometrial cancer (n=51, 4.4%), pancreatic cancer (n=17, 1.5%) and other cancers accounted for the remaining cases (n=54, 4.6%).
Double heterozygosity for pathogenic variants, consisting of 36 single nucleotide variants and 4 copy-number variants, was identified in 20 individuals (1.7%). Of these, 14 cases were diagnosed with breast cancer. Ovarian cancer, colorectal cancer, and pancreatic cancer was found in 2 each.
In breast cancer group, the identified P/LP variants included BRCA2 in 8 cases (57.1%), BRCA1 in 5 cases (35.7%), ATM in 7 cases (50%). Additional variants were RAD50 and PALB2 in 2 individuals each (14.2%), and BARD1, RAD51C, MSH6, and NF1 in 1 individual each (7.1%). The average age at diagnosis for these 14 individuals was 46.7±9 years. Among 14 breast cancer cases, 2 cases were bilateral (85.7%), and 3 cases were triple-negative (21.1%).
Two ovarian cancer patients carried double BRCA1/RAD51D and BRCA1/ERCC2 P/LP variants with age of diagnosis at 49 and 42 years respectively. Two individuals with colon cancer had P/LP variants in MMR genes with other cancer genes—MLH1/POLE and MLH1/BRCA2 with both age of diagnosis at 39 years. For pancreatic cancer patients, one carried pathogenic CDKN2A/RAD51C variants, while the other had BARD1/BRCA2 pathogenic variants, with age of diagnosis at 54 and 65 years respectively.
Conclusion:
Our study identified a substantial number of double heterozygous P/LP variants in Thai hereditary cancer patients. The application of BP5 criteria from the 2015 ACMG-AMP standard and guidelines, when an alternate molecular basis for the disease is found, should be approached with caution in patients with suspected hereditary cancer.
Germline double heterozygosity for pathogenic variants in hereditary cancer genes was thought to be rare. With the growing use of multi-gene panel testing (MGPT) for cancer-associated genes, there have been increasing reports of double pathogenic variants, though patient characteristics and clinical features remain poorly documented.
In our study, we present cases of hereditary cancer with double heterozygosity for pathogenic variants, suggesting that this phenomenon may be more common than previously thought.
Methods:
In this single-center study at Siriraj Hospital, we analyzed clinical and genomic data from 8,068 Thai patients who underwent MGPT for cancer-associated genes for suspected hereditary cancer syndromes, from January 2016 to October 2024. DNA was extracted from peripheral blood and enriched with a custom library. Next-generation sequencing and Sanger sequencing were used to detect and confirm single nucleotide variants, whereas Multiplex Ligation-dependent Probe Amplification was used to identify copy-number variants. The variants were annotated, classified, and systematically validated according to the 2015 ACMG-AMP standard and guidelines, the 2020 ACMG-ClinGen technical standards for the interpretation and reporting of constitutional copy-number variants, and the ClinGen Expert Panel Specifications for genes with available guidelines.
Results:
A total of 8,068 patients underwent MGPT, revealing pathogenic or likely pathogenic (P/LP) variants in 1,163 individuals. Breast cancer was the most common, affecting 701 patients (60.3%), followed by colorectal cancer (n=243, 20.9%), ovarian cancer (n=97, 8.3%), endometrial cancer (n=51, 4.4%), pancreatic cancer (n=17, 1.5%) and other cancers accounted for the remaining cases (n=54, 4.6%).
Double heterozygosity for pathogenic variants, consisting of 36 single nucleotide variants and 4 copy-number variants, was identified in 20 individuals (1.7%). Of these, 14 cases were diagnosed with breast cancer. Ovarian cancer, colorectal cancer, and pancreatic cancer was found in 2 each.
In breast cancer group, the identified P/LP variants included BRCA2 in 8 cases (57.1%), BRCA1 in 5 cases (35.7%), ATM in 7 cases (50%). Additional variants were RAD50 and PALB2 in 2 individuals each (14.2%), and BARD1, RAD51C, MSH6, and NF1 in 1 individual each (7.1%). The average age at diagnosis for these 14 individuals was 46.7±9 years. Among 14 breast cancer cases, 2 cases were bilateral (85.7%), and 3 cases were triple-negative (21.1%).
Two ovarian cancer patients carried double BRCA1/RAD51D and BRCA1/ERCC2 P/LP variants with age of diagnosis at 49 and 42 years respectively. Two individuals with colon cancer had P/LP variants in MMR genes with other cancer genes—MLH1/POLE and MLH1/BRCA2 with both age of diagnosis at 39 years. For pancreatic cancer patients, one carried pathogenic CDKN2A/RAD51C variants, while the other had BARD1/BRCA2 pathogenic variants, with age of diagnosis at 54 and 65 years respectively.
Conclusion:
Our study identified a substantial number of double heterozygous P/LP variants in Thai hereditary cancer patients. The application of BP5 criteria from the 2015 ACMG-AMP standard and guidelines, when an alternate molecular basis for the disease is found, should be approached with caution in patients with suspected hereditary cancer.