With the development and use of high-throughput next-generation sequencing during the last decade, sequencing technology has advanced quickly. Thanks to improvements in bioinformatics analysis, in comparison to traditional germline testing for mutation in a single gene method, the use of targeted NGS-based multigene testing panels to give complete analysis of cancer susceptibility genes has shown to be a feasible option [16–18].
Using Illumina's NGS technology, we designed and validated totally 3 gene panels including Multiplicom BRCA MASTR Plus Dx 2 gen, SOPHİA Hereditary Cancer Solutions 27 genes and SOPHİA Hereditary Cancer Solutions 60 genes. Out of 630 patients, 562 (89.20%) patients were Multiplicom BRCA MASTR Plus Dx, 43 (6.83%, 6.83) patients SOPHİA Hereditary Cancer Solutions 27 genes, and 25 (3.97%) patients were tested with SOPHIA Hereditary Cancer Solutions 60 genes. The Supplementary Material 1 showes Pathogenic germline mutations in Turkis Breast/Ovarian Cancer Families.
Patient demographics: Between 2016 and 2021, 630 ovarian patients applied to Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute labratuary for genetic test. All patients referred for genetic counseling are from all seven region of Turkey. The median age of the patients was 51 (Age range: 25-84 years old.) In this study, we used Next-Generation Sequencing (NGS) to verify three different gene panels for evaluating ovarian cancer mutations in Turkish population. These panels will sequence and analyze the protein-coding areas of the targeted genes to look for cancer-causing mutations in 8 distinct malignancies: breast, ovarian, prostate, uterine, colorectal, pancreatic, stomach cancers, and melanoma. The aim of this research was to evaluate the hereditary cancer panel's analytical and functional capabilities.
The participants in this prospective research were 630 Turkish people, with 546 ( 86.6%) having ovarian cancer, 84 (13.33%) having breast and ovarian cancer together. The total number of patients was 630 (100%). 500 patients out of 630 patients did not carry any mutations in the investigated genes (79.36%), whereas 130 patients (20.64%) carried mutations.
Out of 130 patients with mutation, 81 of them substantially have BRCA1 pathogenic variants, while BRCA2 pathogenic variants were detected 43 in patients. 40 different BRCA1 mutations (52.630%) were detected in patients. In the BRCA1 gene, the three most frequent mutations are as follows: BRCA1 NM_007294.3,EX 19 c.5266dupC p.Gln1756Profs*74 rs431825413 (detected in 13 ovarian patients and 2 breast+ovarian cancer patients), BRCA1 NM_007294.3 EX4 c.181T>G p.Cys61Gly rs28897672( in 5 ovarian+2 breast+ovarian patients), and BRCA1 NM_007294.3 EX 23 c.5444G>A p.Trp1815* rs80356962( in 5 ovarian patients). According to the Breast Cancer Information Core database BRCA1:c.5266dupC is one of the most commonly reported mutations in BRCA1 and in the Ashkenazi Jewesh population, it is recognized founder muatation. c.5266dupC, on the other hand, is less common in the AJ population (0.13 percent) [PubMed] [Google Scholar] and has been found in a variety of other groups, especially in Europe. These mutations in the BRCA1 gene have been identified as the most prevalent alterations in our country's population that cause ovarian cancer. In Turkish ovarian cohort this mutation also can be used as a founder mutation in accordance with the literature.
In 43 of 130 patients, 29 different mutations (38.165%) were found in the BRCA2 gene. The three most common mutations are as follows: BRCA2 NM_000059.3 Ex 25 c.9317G>A p.Trp3106* rs80359205 in 5 patients 4 of whom were diagnosed with ovary and 1 with ovary and breast cancer, BRCA2 NM_000059.3 EX23 c.9097dupA p.Thr3033Asnfs*11 In 3 individuals, 1 of which is over and 2 is over + breast together, BRCA2 NM_000059.3 ex 2 c.67+1G> A rs81002796 was seen in 3 patients with ovarian ca. GeneKor MSA has identified a number of variations in the BRCA2 gene that are pathogenic including BRCA2 NM_000059.3 Ex 25 c.9317G>A p.Trp3106* rs80359205  that we detected in 5 Turkish ovarian patients one with ovarian+breast together. According to literature, the BRCA2 c.9097dupA mutation is the most prevalent in the Turkish population, and it is also highly common in eastern nations  in accordance with our study group. BRCA2 NM_000059.3 ex 2 c.67+1G>A rs81002796 is registered as pathogenic variant in clin var database.
1 patient diagnosed with ovarian ca carries 2 different mutations in BRCA1 and BRCA2. Mutations of this patient; BRCA1 NM_007294.3 Ex1 c.135-2A>G p.? rs80358065 and BRCA2 NM_000059.3 Ex 11 c.6466_6469delTCTC p.Ser2156Asnfs*11 rs879255330,respectively. In the Pakistani community, 539 breast cancer patients who were chosen based on their family history and diagnostic age were invesitgated and BRCA1 NM_007294.3 Ex1 c.135-2A>G p.? rs80358065 was detected as deletirious mutataion .
84 patients diagnosed with both ovarian + breast cancer. A total of 21 different mutations were detected in 27diagnosed both breast+ovarian cancer carrier patients (32.14%). The mutations found in patients diagnosed both breast and ovarian ca are as follows: BRCA1 NM_007294.3 EX 10 c.1151_1154dupAGTG p.Trp385*fs*1 (in 2 patients), BRCA1 NM_007294.3 ex10 c.1016delA p.Lys339Argfs*2 rs80357618 (1 patient), BRCA1 NM_007294.3 ex 10 c.1621C>T p.Gln541* rs80356904( 1 patient), BRCA1 NM_007294.3 ex10 c.3794delA p.Asn1265Ilefs*3 rs80357767 (in 1 patient), BRCA1 NM_007294.3 ex16 c.4717delG p.(Asp1573Metfs*28) (in one patient), BRCA1 NM_007294.3 ex19 c.5209A>T p.Arg1737* rs80357496 ( in one patient), BRCA1 NM_007294.3 ex2 c.66dupA p.(Glu23Argfs*18) rs80357783 (in one patient), BRCA2 NM_000059.3 ex11 c.5576_5579delTTAA p.Ile1859Lysfs*3 rs770318608(in 2 patients), BRCA2 NM_000059.3 ex 11 c.5722_5723delCT p.Leu1908Argfs*2 rs80359530 (in 2 patients), BRCA2 NM_000059.3 ex 9 c.771_775delTCAA p.Asn257Lysfs*17 rs80359675 (in 1 patient), BRCA2 NM_000059.3 ex27 c.9682delA p.Ser3228Valfs*21 rs398122618 ( 1 patient).
A total of 78 individuals were tested using broad panels excpet BRCA1 and BRCA2, and 7 mutations in 6 distinct genes, other than BRCA1 and BRCA2, were discovered in 7 of these patients. ATM NM_000051.3ex53 c.7889T>A p.(Leu2630*) rs1591178998 in one patient with ovarian cancer, CHEK2 NM_001005735.1 ex14 c.1580delC p.(Pro527Argfs*8) rs1555913078 in 1 patient diagnosed with ovarian, CHEK2 NM_001005735.1 ex5 c.609A>G p.(Ile203Met) rs575910805 in a ovarian cancer diagnosed patient, MUTYH NM_001048171.1 ex14 c.1395_1397delGGA p.(Glu466del) rs587778541 was found in one ovarian cancer patient, RAD51C NM_058216.2ex7 c.934C>T p.(Arg312Trp) rs730881932 in 1 patient with ovarian cancer, TP53 NM_000546.5 ex10 c.1024C>Tp.(Arg342*) rs730882029 in 1 patient with ovarian cancer.
The number of total mutations found in 130 patients is 131 (100%).1 patient carries two mutations (0.77%).1 patient carries two mutations (0.77%) and 129 patients are carriers of a single mutation (99.23%). A total of 76 different mutations (100%) including, 1 mutation (1,315%) in ATM, 40 different mutations (52.630%) in BRCA1,29 different mutations in BRCA2 (38.165%), 2 different mutations (2,630) in CHEK2, 1 mutation (1,315%) in ERCC2, 1 mutation (1,315%) in MUTYH, 1 mutation (1,315%) in RAD51C, 1 mutation (1,315%) in TP53 were found.