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Detection of aneuploidy using multiplex ligation-dependent probe amplification in fetal tissues from aborted pregnancies
Boris Zagradišnik, Špela Stangler Herodež, Alenka Erjavec Škerget, Andreja Zagorac, Nadja Kokalj-Vokač, 2011, izvirni znanstveni članek

Opis: Purpose: About 10-15% of all pregnancies terminate as spontaneous miscarriages. In the first trimester, 50% of spontaneous miscarriages are the result of chromosomal aberrations, mostly chromosomal aneuploidies. Cytogenetic analyses are used to confirm aneuploidy in failed pregnancies. Culture failure or poor quality chromosomes are often problems in those cases. In such situations, methods that are independent of tissue culture areused, and we employed multiplex ligation-dependent probe amplification (MLPA). We determined if MLPA is an appropriate and compatible method compared with classical cytogenetic analyses on fetal tissues. Methods: All fetal samples received from spontaneous abortions were cultured, karyotyped (if possible) and genomic DNA extracted. MLPA analyses were undertaken using subtelomeric probe kits. Additionally, comparative genomic hybridization (CGH) was used to confirm aneuploidy detected by MLPA in cases of failed culture growth. Results: MLPA analyses confirmed an unbalanced chromosome abnormality identified by cytogenetic analyses in all cases in which tissue culture was successful, and provided data in cases of failed culture growth. Several common numeric chromosome aberrations were detected, as well as rare trisomies and other unbalanced chromosome rearrangements. Conclusions: MLPA analyses can provide information about the karyotype of a DNA sample if cytogenetic analyses are not possible because of a lack of viable cells or if only a small amount of genomic DNA is available. These data indicate that MLPA may also be a very useful method for early prenatal aneuploidy screening.
Ključne besede: pomnoževanje od ligacije odvisnih prob, številčne kromosomske preureditve, kariotip
Objavljeno v DKUM: 12.04.2024; Ogledov: 150; Prenosov: 6
.pdf Celotno besedilo (353,36 KB)
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Submicroscopic interstitial deletion of chromosome 11q22.3 in a girl with mild mental retardation and facial dysmorphism: Case report
Danijela Krgović, Nataša Marčun-Varda, Andreja Zagorac, Nadja Kokalj-Vokač, 2011, izvirni znanstveni članek

Opis: Background: Except for terminal deletions that lead to Jacobsen syndrome, interstitial deletions involving the long arm of chromosome 11 are not frequently reported. A clinically distinct phenotype is usually observed in these cases, and no clear genotype-phenotype correlation is proposed. Results: Here we present a case study of a 5-year-old girl with de novo submicroscopic deletion of chromosome 11q22.3 with mild mental retardation and facial dysmorphism. A standard cytogenetic analysis did not reveal any structural aberrations. A contrary array-CGH analysis indicated a small deletion of 11q22.3. Discussion: To our knowledge, this is the smallest 11q22.3 deletion reported in literature, containing nine RefSeq genes. Although none of the deleted genes are obvious candidates for the features observed in our patient, genes CUL5 and SLN could play a key role in the features described.
Ključne besede: 11q22.3 deletion, mild mental retardation, facial dysmorphism
Objavljeno v DKUM: 29.06.2017; Ogledov: 1549; Prenosov: 362
.pdf Celotno besedilo (766,41 KB)
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An evaluation of SOX2 and hTERC gene amplifications as screening markers in oral and oropharyngeal squamous cell carcinomas
Nadja Kokalj-Vokač, Bogdan Čizmarevič, Andreja Zagorac, Boris Zagradišnik, Boštjan Lanišnik, izvirni znanstveni članek

Opis: Background: Oral and oropharyngeal squamous cell carcinomas (OSCC) are among the most common cancers. The poor survival rate among oral cancer patients can be attributed to several factors, one of them being lack of early detection. A key approach to this problem would be to detect potentially malignant lesion at their early stage. Using the FISH technique, oral brush cytology slides can be an easy and rapid screening approach for malignant cell detection. The present study was designed to detect hTERC and SOX2 amplifications in OSSC exfoliative tumor cells and evaluate whether those two gene amplifications might serve as a supportive biomarker in early detection and diagnosis of oral and oropharyngeal SCC. Results: Brush biopsies were collected from exophytic and exulcerated oral and oropharyngeal lesions of the oral cavity of 71 patients and 22 healthy controls. FISH techniques using a TERC-specific DNA probe and a SOX2 DNA specific probe both combined with a centromere 3-specific control probe was performed on the cytology slides. A 100 squamous epithelial cell nuclei of the smears per slide were analysed. As abnormal FISH pattern were considered amplified and polyploid patterns. From 71 brush biopsies of oropharynx and other locations in oral cavity analysed by FISH 49 were considered to be abnormal (69%). The over representation of polyploidy and/or TERC/SOX2 amplification in tumour samples was statistically significant when compared to controls (p = 0.01). Conclusion: SOX2 and TERC gene amplifications are common in all squamous cell carcinomas and their detection in early stages could be crucial for early detection and more accurate prognosis. Our study strongly suggests that early detection by FISH on cytobrushed samples could be a possible non-invasive screening method even before a tissue biopsy is performed.
Ključne besede: SOX and hTERC gene amplifications, brush biopsy, Oral, oropharyngeal squamous cell carcinoma
Objavljeno v DKUM: 29.06.2017; Ogledov: 1328; Prenosov: 386
.pdf Celotno besedilo (1,28 MB)
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TMPRSS2:ERG gene aberrations may provide insight into pT stage in prostate cancer
Zoran Krstanoski, Nadja Kokalj-Vokač, Andreja Zagorac, Boris Pospihalj, Miha Munda, Sašo Džeroski, Rastko Golouh, 2016, izvirni znanstveni članek

Opis: Background: TMPRSS2:ERG gene aberration may be a novel marker that improves risk stratification of prostate cancer before definitive cancer therapy, but studies have been inconclusive. Methods: The study cohort consisted of 202 operable prostate cancer Slovenian patients who underwent laparoscopic radical prostatectomy. We retrospectively constructed tissue microarrays of their prostatic specimens for fluorescence in situ hybridization, with appropriate signals obtained in 148 patients for subsequent statistical analyses. Results: The following genetic aberrations were found: TMPRSS2:ERG fusion, TMPRSS2 split (a non-ERG translocation) and ERG split (an ERG translocation without involvement of TMPRSS2). TMPRSS2:ERG gene fusion happened in 63 patients (42 %), TMPRSS2 split in 12 patients and ERG split in 8 patients. Association was tested between TMPRSS2:ERG gene fusion and several clinicopathological variables, i.e., pT stage, extended lymph node dissection status, and Gleason score, correcting for multiple comparisons. Only the association with pT stage was significant at p = 0.05: Of 62 patients with pT3 stage, 34 (55 %) had TMPRSS2:ERG gene fusion. In pT3 stage patients, stronger (but not significant) association between eLND status and TMPRSS2:ERG gene fusion was detected. We detected TMPRSS2:ERG gene fusion in 64 % of the pT3 stage patients where we did not perform an extended lymph node dissection. Conclusions: Our results indicate that it is possible to predict pT3 stage at final histology from TMPRSS2:ERG gene fusion at initial core needle biopsy. FISH determination of TMPRSS2:ERG gene fusion may be particularly useful for patients scheduled to undergo a radical prostatectomy in order to improve oncological and functional results.
Ključne besede: FISH, predicting pT stage, radical prostatectomy, prostate cancer, TMPRSS2:ERG fusion
Objavljeno v DKUM: 29.06.2017; Ogledov: 1869; Prenosov: 404
.pdf Celotno besedilo (1,06 MB)
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A coalescence of two syndromes in a girl with terminal deletion and inverted duplication of chromosome 5
Danijela Krgović, Ana Blatnik, Ante Burmas, Andreja Zagorac, Nadja Kokalj-Vokač, 2014, izvirni znanstveni članek

Opis: Background: Rearrangements involving chromosome 5p often result in two syndromes, Cri-du-chat (CdC) and Trisomy 5p, caused by a deletion and duplication, respectively. The 5p15.2 has been defined as a critical region for CdC syndrome; however, genotype-phenotype studies allowed isolation of particular characteristics such as speech delay, cat-like cry and mental retardation, caused by distinct deletions of 5p. A varied clinical outcome was also observed in patients with Trisomy 5p. Duplications of 5p10-5p13.1 manifest themselves in a more severe phenotype, while trisomy of regions distal to 5p13 mainly causes mild and indistinct features. Combinations of a terminal deletion and inverted duplication of 5p are infrequent in literature. Consequences of these chromosomal rearrangements differ, depending on size of deletion and duplication in particular cases, although authors mainly describe the deletion as the cause of the observed clinical picture. Case presentation: Here we present a 5-month-old Slovenian girl, with de novo terminal deletion and inverted duplication of chromosome 5p. Our patient presents features of both CdC and Trisomy 5. The most prominent features observed in our patient are a cat-like cry and severe malformations of the right ear. Conclusion: The cat-like cry, characteristic of CdC syndrome, is noted in our patient despite the fact that the deletion is not fully consistent with previously defined cat-like cry critical region in this syndrome. Features like dolichocephaly, macrocephaly and ear malformations, associated with duplication of the critical region of Trisomy 5p, are also present, although this region has not been rearranged in our case. Therefore, the true meaning of the described chromosomal rearrangements is discussed.
Ključne besede: deletion with inverted duplication of 5p, trisomy 5, cri-du-chat syndrome, cat-like cry, ear agenesis
Objavljeno v DKUM: 28.06.2017; Ogledov: 1500; Prenosov: 392
.pdf Celotno besedilo (1,07 MB)
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MTHFR C677T and A1298C genotypes and haplotypes in Slovenian couples with unexplained infertility problems and in embryonic tissues from spontaneous abortions
Špela Stangler Herodež, Boris Zagradišnik, Alenka Erjavec Škerget, Andreja Zagorac, Iztok Takač, Veljko Vlaisavljević, Lidija Lokar, Nadja Kokalj-Vokač, 2013, izvirni znanstveni članek

Opis: The objective of this study was to analyze the methylenetetrahydrofolate reductases (MTHFRs) C677T and A1298C genotype distributions in couples with unexplained fertility problems (UFP) and healthy controls, and to analyze the genotype and haplotype distribution in spontaneously aborted embryonic tissues (SAET) using allele specific polymerase chain reaction (PCR) in 200 probands with UFP, 353 samples of SAET and 222 healthy controls. The analysis revealed a significant overall representation of the 677T allele in male probands from couples with UFP (p = 0.036). The combined genotype distribution for both MTHFR polymorphisms was also significantly altered (χ2 21.73, p <0.001) although female probands made no contribution (c2 1.33, p = 0.72). The overall representation of the 677T allele was more pronounced in SAET (0.5 vs. 0.351 in controls, p <0.001) regardless of the karyotype status (aneuploidy vs. normal karyotype). In addition, the frequencies of the CA and CC haplotypes were significantly lower than in the control group (p = 0.021 and p = 0.001, respectively), whereas the frequency of the TC haplotype was significantly higher than in controls (p <0.0001). The presented findings indicate that only male probands contribute to the association of MTHFR mutations with fertility problems in grown adults and demonstrate a high prevalence of mutated MTHFR genotypes in SAET.
Ključne besede: methylenetetrahydrofolate reductase (MTHFR), genotype, haplotype, infertility, miscarriage
Objavljeno v DKUM: 30.03.2017; Ogledov: 1405; Prenosov: 301
.pdf Celotno besedilo (266,46 KB)
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Kromosomske nepravilnosti pri neplodnosti
Mateja Smogavec, Andreja Zagorac, Nadja Kokalj-Vokač, 2009, izvirni znanstveni članek

Opis: Izhodišča: Analiza podatkov o citogenetskih nepravilnostih, ki so se v Laboratoriju za medicinsko genetiko Univerzitetnega kliničnega centra Maribor izkazale kot vzrok neplodnosti pri parih, ženskah in moških posameznikih ter primerjava dobljenih rezultatov s podatki iz literature, služi za nadaljnje razumevanje in ustreznost napotitve neplodnih oseb na citogenetske analize. Metode: Analizirani so bili podatki kariotipov oseb, ki so bile zaradi neplodnosti obravnavane od januarja 2000 do septembra 2008 v Laboratoriju za medicinsko genetiko Univerzitetnega kliničnega centra Maribor. Proučevana populacija 750 oseb je bila razdeljena na pare (290 parov), na posameznice ženskega (20) in moškega (150) spola. Pri vseh je bila narejena rutinska kromosomska analiza 30 metafaznih celic iz celične kulture periferne krvi s tehnikami proganja GTG, RGH in/ali RBG. Rezultati: V proučevani skupini 750 preiskovancev je imelo 87 (11,6 %) oseb kromosomske nepravilnosti. Od teh je bilo ugotovljenih pri moških 6,8 % kromosomskih nepravilnosti in 4,8 % pri ženskah. Odstotek kromosomskih nepravilnosti proučevanih parov, 8,8 %, je primerljiv s podatki iz literature. Zaključki: Kromosomska analiza je pomemben del preiskav neplodnosti, saj, kot se je izkazalo v naši raziskavi, je pojavnost kromosomskih nepravilnosti v proučevani skupini večja kot v splošni populaciji. Uravnotežene kromosomske preureditve so najpogostejši razlog za spontane splave in prizadetost potomcev pri parih. Anevploidije spolnih kromosomov pa so najpogostejši razlog za neplodnost v ožjem pomenu pri moških in ženskah posameznicah. Pomanjkljivost v citogenetski obravnavi naših preiskovancev na področju neplodnosti je, da se neplodnost mnogokrat ne obravnava celostno - v parih, temveč se na kariotipizacijo napotijo posamezniki z domnevo, da drugi partner ni nosilec kromosomske spremembe.
Ključne besede: kariotipizacija, kromosomske spremembe, azoospermija, spontani splav, amenoreja
Objavljeno v DKUM: 10.07.2015; Ogledov: 2498; Prenosov: 204
.pdf Celotno besedilo (106,88 KB)
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Uporaba primerjalne genomske hibridizacije kot diagnostične metode v medicinskem genetskem laboratoriju : prva uporaba na različnih kliničnih vzorcih
Alenka Erjavec Škerget, Špela Stangler Herodež, Andreja Zagorac, Boris Zagradišnik, Nadja Kokalj-Vokač, 2011, izvirni znanstveni članek

Opis: Purpose: Comparative genomic hybridization (CGH) is a molecular- cytogenetic technique used to identify chromosomal imbalances throughout a genome. Due to its complexity, the use of CGH as a regular diagnostic technique is limited to only a few diagnostic laboratories. In this study, we evaluated the potential applications of CGH as a diagnostic method in different post-natal clinical samples. Methods: Ten patients were recruited with submicroscopic chromosomal abnormalities ranging in size from 3.9 to 37 Mb. For the purpose of confirmation, CGH was applied to five cases where molecular karyotyping with MLPA was previously utilized to detect chromosome aneuploidy. To date, CGH was largely used for the identification of the complex karyotype in haematological malignancies. Results: In eight cases of haematological malignancies, we were able to resolve complex karyotypes with CGH. Utilizing CGH as a diagnostic tool, we detected chromosomal imbalances larger than 8 Mb. In addition, we confirmed all chromosomal aneuploidies that were previously detected with MLPA from embryonic tissues obtained from aborted fetuses. In this tissue, the cells were not mitotically active, and therefore, were inappropriate for the conventional cytogenetics. Conclusion: Because CGH is technically demanding and time consuming, this technique is likely to be inappropriate for screening purposes. However, we found that CGH may be very useful in sporadic cases, where the sample material is not mitotically active or in cases with complex karyotypes. Therefore, our results confirmed that CGH may be useful in laboratories that are unable to use micro-array CGH for economic reasons.
Ključne besede: primerjalna genomska hibridizacija, medicinska genetika, diagnostična metoda
Objavljeno v DKUM: 10.07.2015; Ogledov: 1569; Prenosov: 37
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Kromosomske nepravilnosti pri neplodnosti : raziskovalna naloga
Mateja Smogavec, 2008, raz. nal. na višji ali visoki šoli

Ključne besede: neplodnost, kromosomske nepravilnosti
Objavljeno v DKUM: 07.04.2011; Ogledov: 3964; Prenosov: 427
.pdf Celotno besedilo (636,95 KB)

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