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1.
Identification of spliceogenic variants beyond canonical GT-AG splice sites in hereditary cancer genes
Vita Šetrajčič Dragoš, Ksenija Strojnik, Gašper Klančar, Petra Škerl, Vida Stegel, Ana Blatnik, Marta Banjac, Mateja Krajc, Srdjan Novaković, 2022, original scientific article

Abstract: Pathogenic/likely pathogenic variants in susceptibility genes that interrupt RNA splicing are a well-documented mechanism of hereditary cancer syndromes development. However, if RNA studies are not performed, most of the variants beyond the canonical GT-AG splice site are characterized as variants of uncertain significance (VUS). To decrease the VUS burden, we have bioinformatically evaluated all novel VUS detected in 732 consecutive patients tested in the routine genetic counseling process. Twelve VUS that were predicted to cause splicing defects were selected for mRNA analysis. Here, we report a functional characterization of 12 variants located beyond the first two intronic nucleotides using RNAseq in APC, ATM, FH, LZTR1, MSH6, PALB2, RAD51C, and TP53 genes. Based on the analysis of mRNA, we have successfully reclassified 50% of investigated variants. 25% of variants were downgraded to likely benign, whereas 25% were upgraded to likely pathogenic leading to improved clinical management of the patient and the family members.
Keywords: hereditary cancer, RNA sequencing, spliceogenic
Published in DiRROS: 07.09.2022; Views: 445; Downloads: 231
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2.
Real-world data on detection of germline and somatic pathogenic/likely pathogenic variants in BRCA1/2 and other susceptibility genes in ovarian cancer patients using next generation sequencing
Vida Stegel, Ana Blatnik, Erik Škof, Vita Šetrajčič Dragoš, Mateja Krajc, Brigita Gregorčič, Petra Škerl, Ksenija Strojnik, Gašper Klančar, Marta Banjac, Janez Žgajnar, Maja Ravnik-Oblak, Srdjan Novaković, 2022, original scientific article

Abstract: Detection of germline and somatic pathogenic/likely pathogenic variants (PV/LPV) in BRCA genes is at the moment a prerequisite for use of PARP inhibitors in different treatment settings of different tumors. The aim of our study was to determine the most appropriate testing workflow in epithelial ovarian cancer (EOC) patients using germline and tumor genotyping of BRCA and other hereditary breast and/or ovarian cancer (HBOC) susceptibility genes. Consecutive patients with advanced non-mucinous EOC, who responded to platinum-based chemotherapy, were included in the study. DNA extracted from blood and FFPE tumor tissue were genotyped using NGS panels TruSightCancer/Hereditary and TruSight Tumor 170. Among 170 EOC patients, 21.8% had BRCA germline or somatic PV/LPV, and additionally 6.4% had PV/LPV in other HBOC genes. Sensitivity of tumor genotyping for detection of germline PV/LPV was 96.2% for BRCA genes and 93.3% for HBOC genes. With germline genotyping-only strategy, 58.8% of HBOC PV/LPV and 68.4% of BRCA PV/LPV were detected. By tumor genotyping-only strategy, 96.1% of HBOC PV/LPV and 97.4% of BRCA PV/LPV were detected. Genotyping of tumor first, followed by germline genotyping seems to be a reasonable approach for detection of PV/LPV in breast and/or ovarian cancer susceptibility genes in non-mucinous EOC patients.
Keywords: BRCA, ovarian cancer, tumor genotyping, HBOC
Published in DiRROS: 06.09.2022; Views: 482; Downloads: 265
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Predsimptomatsko genetsko testiranje za dedni sindrom raka dojk in/ali jajčnikov
Barbara Babuder, Simona Hotujec, Ana Blatnik, Ksenija Strojnik, Marta Banjac, Srdjan Novaković, Mateja Krajc, 2021, original scientific article

Abstract: Izhodišče: Kaskadno testiranje je testiranje svojcev prvega dokazanega nosilca patogene različice/verjetno patogene različice (PR/VPR) določenega gena v družini. Uspešnost preventive rakavih bolezni v družini, v kateri je ugotovljena PR/VPR, je odvisna od identifikacije tistih krvnih sorodnikov, ki so prav tako nosilci družinske genetske okvare, pa sami še niso zboleli. Število krvnih sorodnikov iz družin z dednim sindromom za raka dojk in/ali jajčnikov (HBOC), ki se v sklopu obravnave na Onkološkem inštitutu Ljubljana (OIL) odločijo za predsimptomatsko svetovanje in testiranje po novoodkriti PR/VPR v družini, je trenutno neznano. Namen: Namen raziskave je bil ugotoviti število krvnih sorodnikov, ki so se odločili za predsimptomatsko testiranje, ko je bila v družini dokazana PR/VPR v genu BRCA1 in/ali BRCA2, in analizirati njihove značilnosti. Metode: Analizirali smo podatke, ki smo jih pridobili iz podatkovne zbirke Oddelka za onkološko klinično genetiko OIL med letoma 1999 in 2020, o testiranih in njihovih družinskih članih. Uporabili smo deskriptivne statistične metode. Rezultati: Med 5158 napotenimi družinami s sumom na HBOC smo odkrili 785 BRCA1 in BRCA2 pozitivnih, kar pomeni 15,2 %. Od vseh 785 pozitivnih družin se pri 27 % (212/785) družin za genetsko svetovanje še ni odločil nihče od svojcev. V družinah, kjer so se svojci odločili za posvet (573 družin), se jih je 79 % oglasilo v prvih 12 mesecih od razkritja pozitivnega rezultata prvemu testiranemu. V teh 573 družinah se je skupno 1731 oseb odločilo za predsimptomatsko testiranje, od tega je bilo 80,3 % žensk. Povprečno število krvnih sorodnikov, ki so se med letoma 1999 in 2020 odločili za predsimptomatsko svetovanje in testiranje, je dva (2,21) na družino. Če odštejemo družine, v katerih se ni javil nihče od svojcev, pa so se javili povprečno trije (3,02) svojci na družino, torej so poleg nosilca družine na posvet prišli vsaj še trije. Zaključek: Kaskadno testiranje je uspešen način ugotavljanja nosilcev PR/VPR v družini in v populaciji. Trenutno je edini dokazano uspešen način, s katerim lahko zdravim, bolj ogroženim posameznikom omogočimo preventivne ukrepe preprečevanja in zgodnjega odkrivanja raka, s čimer dokazano podaljšujemo življenja. Možnost za odločitev o preventivnih ukrepih bi morali tako imeti vsi krvni sorodniki ob pozitivnem rezultatu prvega testiranega. Treba bo raziskati, zakaj se pri slabi tretjini pozitivnih družin ni javil noben družinski član in kako lahko še izboljšamo klinične poti, da bi povečali odziv svojcev.
Keywords: genetsko testiranje, kaskadno testiranje, dedni sindrom raka dojk in jajčnikov, HBOC, krvni sorodniki, BRCA1/2
Published in DiRROS: 14.12.2021; Views: 735; Downloads: 350
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