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Query: "author" (Petra Škerl) .

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BAP1-defficient breast cancer in a patient with BAP1 cancer syndrome
Ana Blatnik, Domen Ribnikar, Vita Šetrajčič Dragoš, Srdjan Novaković, Vida Stegel, Biljana Grčar-Kuzmanov, Nina Boc, Barbara Perić, Petra Škerl, Gašper Klančar, Mateja Krajc, 2022, original scientific article

Abstract: BAP1 cancer syndrome is a rare and highly penetrant hereditary cancer predisposition. Uveal melanoma, mesothelioma, renal cell carcinoma (RCC) and cutaneous melanoma are considered BAP1 cancer syndrome core cancers, whereas association with breast cancer has previously been suggested but not confirmed so far. In view of BAP1 immunomodulatory functions, BAP1 alterations could prove useful as possible biomarkers of response to immunotherapy in patients with BAP1-associated cancers. We present a case of a patient with BAP1 cancer syndrome who developed a metastatic breast cancer with loss of BAP1 demonstrated on immunohistochemistry. She carried a germline BAP1 likely pathogenic variant (c.898_899delAG p.(Arg300Glyfs*6)). In addition, tumor tissue sequencing identified a concurrent somatic variant in BAP1 (partial deletion of exon 12) and a low tumor mutational burden. As her triple negative tumor was shown to be PD-L1 positive, the patient was treated with combination of atezolizumab and nab-paclitaxel. She had a complete and sustained response to immunotherapy even after discontinuation of nab-paclitaxel. This case strengthens the evidence for including breast cancer in the BAP1 cancer syndrome tumor spectrum with implications for future cancer prevention programs. It also indicates immune checkpoint inhibitors might prove to be an effective treatment for BAP1-deficient breast cancer.
Keywords: BAP1, breast cancer, hereditary cancer syndromes, immunotherapy
Published in DiRROS: 19.09.2022; Views: 411; Downloads: 168
.pdf Full text (1,12 MB)

4.
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: 439; Downloads: 231
.pdf Full text (778,18 KB)
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5.
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: 466; Downloads: 256
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6.
Določanje mutacije V600E v genu BRAF
Petra Škerl, Alenka Ličar, Srdjan Novaković, 2010, original scientific article

Abstract: Mutacija V600E predstavlja več kot 90 % vseh opisanih mutacij v genu BRAF pri različnih vrstah tumorjev. Protein, ki nastane kot produkt onkogena BRAF z mutacijo V600E (BrafV600E), sproža nenehno signaliziranje prek signalne poti RAS-RAF-MAPK, kar povzroči številnejše delitve celice in njeno maligno transformacijo. Zato ima onkogen BrafV600E pomembno vlogo pri indukciji in napredovanju tumorja ter verjetno predstavlja zgodnji dogodek v procesu maligne transformacije. Po podatkih iz literature je čezmerno izražen v različnih vrstah solidnih tumorjev, kot so melanom, metastatski rak debelega črevesa in danke, papilarni rak ščitnice, rak ledvic (RCC), hepatocelularni karcinom (HCC), velikocelični rak pljuč (NSCLC) in serozni rak jajčnikov. Na Oddelku za molekularno diagnostiko smo uvedli metodo za določanje mutacije V600E v genu BRAF. Metoda temelji na PCR-pomnoževanju in uporabi specifičnih sond. Izkazala se je kot primerna za rutinsko diagnostiko. V primerjavi z neposrednim sekveniranjem, ki velja za zlati standard, sta bili njeni občutljivost in specifičnost 100-odstotni. Zaradi velike specifičnosti je zanesljiva za ločevanje med normalnim in mutiranim genotipom BRAF in je primerna za hitro rutinsko diagnostiko.
Published in DiRROS: 31.08.2018; Views: 2936; Downloads: 652
.pdf Full text (272,73 KB)

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Določanje mutacij pri bolnikih z dedno obliko malignega melanoma kože
Petra Škerl, Barbara Perić, Marko Hočevar, Srdjan Novaković, 2008, original scientific article

Abstract: Gensko testiranje za dedno obliko malignega melanoma kože na OI Ljubljana opravljamo od leta 2005. Izbor bolnikov za testiranje poteka v okviru genetskega svetovanja. Testiramo bolnike in njihove zdrave sorodnike, če sta v družini najmanj dva obolela člana, in bolnike s primarnimi multiplimi melanomi brez obremenjujoče družinske anamneze. Na oddelku za molekularno diagnostiko z metodo sekvenčne analize iščemo in določamo neznane točkovne mutacije ter manjše delecije in insercije v eksonih genov, povezanih z nastankom malignega melanoma kože: CDKN2A, CDK4 in MC1R. Do sedaj smo testirali 70 oseb: 40 bolnikov in njihovih zdravih sorodnikov iz 28 različnih družin, obremenjenih z družinsko anamnezo, ter 30 bolnikov s primarnimi multiplimi melanomi. Sekvenčna analiza genov, povezanih z dedno obliko malignega melanoma kože, je pokazala, da so mutacije CDKN2A p16INK4a pri bolnikih z družinsko anamnezo zelo pogoste (37,5 %). Mutacij CDKN2A p14ARF in CDK4 pri slovenskih bolnikih nismo našli.
Published in DiRROS: 31.08.2018; Views: 3158; Downloads: 714
.pdf Full text (308,29 KB)

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Določanje klonalnosti limfoidnih proliferacij : uvedba nove metode in primerjava z dosedanjo metodo
Petra Škerl, Ira Koković, Veronika Kloboves-Prevodnik, Srdjan Novaković, 2009, professional article

Abstract: Na Oddelku za molekularno diagnostiko smo na področju diagnostike limfomov uvedli dodatno metodo za določanje klonalnosti limfoidnih proliferacij. Tudi nova metoda temelji na verižni reakciji s polimerazo (PCR) in na uporabi različnih konsenzusnih oligonukleotidnih začetnikov. Metoda je validirana in registrirana za diagnostične potrebe (oznaka CE). Z razširjenim naborom oligonukleotidnih začetnikov in uporabo večjega števila začetnikov smo, po naših izračunih, izboljšali občutljivost določanja klonalnosti limfocitov B za 23,1 %, določanje klonalnosti limfocitov T pa za 14,3 %. Teoretično lahko sedaj z obema metodama določimo monoklonalno populacijo limfocitov pri 84,6 % B- in 85,7 % T-limfomov
Published in DiRROS: 31.08.2018; Views: 3285; Downloads: 813
.pdf Full text (1,37 MB)

9.
Dokazovanje mutacij v genu BRCA1 z analizo talitvene krivulje produktov PCR
Srdjan Novaković, Vida Stegel, Petra Škerl, 2006, professional article

Abstract: Rak dojke je z nekaj več kot 1000 novimi bolnicami na leto na prvem mestu po številu obolelih žensk za rakastimi boleznimi v Sloveniji. številka vključuje sporadične in dedne oblike raka na dojki. Dedne oblike raka na dojki so najpogosteje povezane z mutacijami v genih BRCA1 in BRCA2, zato se številni strokovnjaki s tega področja zavzemajo za genetsko testiranje bolnikov, pri katerih obstaja sum na dedno obliko bolezni. Testiranje bolnic/-kov in njihovih sorodnikov je dokaj težavno zaradi zahtevnosti metod genetskega testiranja, stroškov testiranja ter nezadostnega poznavanja in predvidevanja vseh možnih vplivov dokazane mutacije pri nastanku raka na dojki. V tem delu predstavljamo osnovne metodološke podatke za odkrivanje petih različnih mutacij v genu BRCA1 pri bolnicah/-kih s karcinomom dojke in njihovih sorodnikih. Mutacije 1806C>T, 300T>G, 300T>A, 310G>A, 5382insC določamo s polimerazno verižno reakcijo (PCR) v realnem času in analizo talitvene krivulje. Primerjava z neposrednim sekveniranjem je pokazala, da je uporabljena metoda dovolj občutljiva in hitra za dnevno rutinsko določanje mutacij v DNA, izolirani iz periferne krvi.
Published in DiRROS: 31.08.2018; Views: 3029; Downloads: 784
.pdf Full text (711,40 KB)

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