Targeted sequencing of crucial cancer causing genes of breast cancer in Saudi patients.
PMID 32994724 | PMCID PMC7499116 | DOI 10.1016/j.sjbs.2020.05.047 · Saudi journal of biological sciences · 2020 · View on PubMed ↗
Breast cancer is the most common cancer among women worldwide, causing 15% of cancer-related deaths among women. Breast cancer incidence rate is increasing in most countries. In Saudi Arabia, breast cancer constitutes nearly 22% of the newly diagnosed cancer cases in women. Breast cancer incidence in the women population of Saudi Arabia is 25.9%, with 18.2% mortality. In this study, targeted sequencing of 164 selected genes was performed on germline and somatic DNA derived from the blood and tissue samples of 50 breast cancer patients using customized panel on Ion torrent platform. This study focused on the identification of genetic variations of different cancer-causing genes, raising the hope for identification of personalized prognosis. After final filtration and validation, we found protein-truncating, non-synonymous missense, and splice site mutations in the known susceptibility genes for breast cancer. We identified a total of 14 point mutations and one deletion in BRCA1, BRCA2, and RAD50 genes from the BRCA panel analysis of breast cancer samples. In the customized panel analysis, we identified 37 potential mutations in 25 breast cancer risk associated genes. Out of these, most mutations were observed in TP53. After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)). Among the mutations detected in our study, TP53 (p.R81X), VHL (p.E52X), and BRCA2 (p.K3326X) mutations, which lead to an aberrant transcript with a premature stop codon, were reported for the first time in breast cancer patients from Saudi Arabia. Our study will help in identifying the damaging mutations and predisposing genes in Saudi breast cancer patients.
Validated evidence
| Type | Entity | Source evidence | Confidence | Extractor |
|---|---|---|---|---|
| gene | BRCA1 | “We identified a total of 14 point mutations and one deletion in BRCA1, BRCA2, and RAD50 genes from the BRCA panel analysis of breast cancer samples.” | 0.98 | hgnc_dict_v1 |
| gene | BRCA2 | “We identified a total of 14 point mutations and one deletion in BRCA1, BRCA2, and RAD50 genes from the BRCA panel analysis of breast cancer samples.” | 0.98 | hgnc_dict_v1 |
| gene | RAD50 | “We identified a total of 14 point mutations and one deletion in BRCA1, BRCA2, and RAD50 genes from the BRCA panel analysis of breast cancer samples.” | 0.98 | hgnc_dict_v1 |
| gene | TP53 | “Out of these, most mutations were observed in TP53.” | 0.98 | hgnc_dict_v1 |
| gene | VHL | “Among the mutations detected in our study, TP53 (p.R81X), VHL (p.E52X), and BRCA2 (p.K3326X) mutations, which lead to an aberrant transcript with a premature stop codon, were reported for the first time in breast cancer patients from Saudi Arabia.” | 0.98 | hgnc_dict_v1 |
| phenotype | breast cancer | “Targeted sequencing of crucial cancer causing genes of breast cancer in Saudi patients.” | 0.98 | phenotype_alias_lexicon_v2 |
| population | Saudi Arabia | “Targeted sequencing of crucial cancer causing genes of breast cancer in Saudi patients. In Saudi Arabia, breast cancer constitutes nearly 22% of the newly diagnosed cancer cases in women. Breast cancer incidence in the women population of Saudi Arabia is 25.9%, with 18.2% mortality. In this study, targeted sequencing of 164 selected genes was performed on germline and somatic DNA derived from the blood and tissue samples of 50 breast cancer patients using customized panel on Ion torrent platform. Among the mutations detected in our study, TP53 (p.R81X), VHL (p.E52X), and BRCA2 (p.K3326X) mutations, which lead to an aberrant transcript with a premature stop codon, were reported for the first time in breast cancer patients from Saudi Arabia. Our study will help in identifying the damaging mutations and predisposing genes in Saudi breast cancer patients.” | 0.95 | saudi_context_rules_v1 |
| variant | p.R81X | “After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)).” | 0.95 | hgvs_regex_v1 |
| variant | p.Y88C | “After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)).” | 0.95 | hgvs_regex_v1 |
| variant | p.R141H | “After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)).” | 0.95 | hgvs_regex_v1 |
| variant | p.V25D | “After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)).” | 0.95 | hgvs_regex_v1 |
| variant | c.59delC | “After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)).” | 0.95 | hgvs_regex_v1 |
| variant | c.327delC | “After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)).” | 0.95 | hgvs_regex_v1 |
| variant | p.E52X | “Among the mutations detected in our study, TP53 (p.R81X), VHL (p.E52X), and BRCA2 (p.K3326X) mutations, which lead to an aberrant transcript with a premature stop codon, were reported for the first time in breast cancer patients from Saudi Arabia.” | 0.95 | hgvs_regex_v1 |
| variant | p.K3326X | “Among the mutations detected in our study, TP53 (p.R81X), VHL (p.E52X), and BRCA2 (p.K3326X) mutations, which lead to an aberrant transcript with a premature stop codon, were reported for the first time in breast cancer patients from Saudi Arabia.” | 0.95 | hgvs_regex_v1 |