Usporedba programa u molekularnoj analizi sindroma fragilnog X kromosoma

master's thesis

• Title (english): Software comparison in the molecular analysis of Fragile X Syndrome
• Author: Valeria Fabijanić
• Mentor: Marija Grdić Rajković (mentor)
• Mentor: Ivana Rako (mentor)
• Committee member: Marija Grdić Rajković (predsjednik povjerenstva)
• Committee member: Sandra Šupraha-Goreta (član povjerenstva)
• Committee member: Ivana Rako (član povjerenstva)
• Granter: University of Zagreb; Faculty of Pharmacy and Biochemistry; (Department of medical biochemistry and haematology); Zagreb
• Defense date and country: 2024-09-20, Croatia
• Scientific / art field, discipline and subdiscipline: BIOMEDICINE AND HEALTHCARE; Pharmacy; Medical Biochemistry

Abstract

Sindrom fragilnog X kromosoma najčešći je nasljedni oblik mentalne retardacije i poteškoća u razvoju.
Posljedica je dinamičke mutacije u FMR1 genu X kromosoma koja se očituje ekspanzijom CGG
ponavljajućeg slijeda u 5'-nekodirajućoj regiji gena. S obzirom na broj CGG ponavljanja, razlikuju se četiri
klase alela: normalni (5-44 CGG), intermedijarni (45-54 CGG), premutacijski (55-200 CGG) te aleli s punom
mutacijom (>200 CGG). U sindromu fragilnog X karakterističan je i mozaicizam, prisutnost različitih alela u
različitim subpopulacijama stanica. Cilj ovog rada bio je usporediti rezultate dobivene pomoću GeneMapper
i AmplideX Reporter softwarea te utvrditi može li automatizirani AmplideX Reporter zamijeniti GeneMapper
software u rutinskoj dijagnostici. Analizirano je ukupno 130 uzoraka, uključujući 129 uzoraka pacijenata i 1
negativan kontrolni uzorak. Analizirani uzorci obuhvaćali su sve četiri kategorije alela, dok je u 3 uzoraka
utvrđen mozaicizam. U 41 uzorku pronađene su razlike u broju ponavljanja za 1 ili 2 CGG tripleta između
dva programa što, međutim, ne predstavlja klinički značajnu razliku. U AmplideX Reporter softwareu uočen
je rascjep alela u 19 uzoraka te su detektirani dodatni pikovi u 11 uzoraka. Usporedbom je utvrđena veća
osjetljivost i specifičnost AmplideX Reporter softwarea u otkrivanju mozaicizama zbog automatskog izračuna
broja CGG ponavljanja s obzirom na CGG profil i ROX ljestvicu veličine te razmatranja kontrole kvalitete
prilikom analize. Potrebna je optimizacija sustava kako bi u potpunosti bila zadovoljena kontrola kvalitete
svakog analiziranog uzorka te se osigurala točnost dobivenih rezultata.

Abstract (english)

Fragile X syndrome is the most common inherited form of mental retardation and developmental disorders.
It results from a dynamic mutation in the FMR1 gene on the X chromosome, characterized by the expansion
of a CGG repeat sequence in the 5'-untranslated region of the gene. Based on the number of CGG repeats,
four allele classes are distinguished: normal (5-44 CGG), intermediate (45-54 CGG), premutation (55-200
CGG), and full mutation (>200 CGG). The syndrome is also characterized by mosaicism, the presence of
different alleles in different subpopulations of cells. The aim of this study was to compare the results obtained
using GeneMapper and AmplideX Reporter software and to determine whether the automated AmplideX
Reporter can replace GeneMapper software in routine diagnostics. A total of 130 samples were analysed,
including 129 patient samples and 1 negative control sample. The analysed samples covered all four
categories of alleles, and mosaicism was detected in 3 samples. Differences in the number of repeats by 1 or
2 CGG triplets between the two programs were found in 41 samples but with no significance in clinical
interpretation. In the AmplideX Reporter software, allele splitting was observed in 19 samples, and additional
peaks were detected in 11 samples. The comparison showed greater sensitivity and specificity of the
AmplideX Reporter software in mosaicism detection due to its automatic calculation of the number of CGG
repeats based on the CGG profile and ROX size ladder, as well as its consideration of quality control during
the analysis. System optimization is needed to fully satisfy the quality control requirements for each analysed
sample and to ensure the accuracy of the obtained results.

• Keywords: sindrom fragilnog X kromosoma; FMR1; dinamična mutacija
• Keywords (english): fragile X syndrome; FMR1; dynamic mutation
• Language: croatian
• URN:NBN: urn:nbn:hr:163:449745
• Study programme: Title: Medical biochemistry - integrated undergraduate and graduate - university study; Study programme type: university; Study level: integrated undergraduate and graduate; Academic / professional title: sveučilišni magistar medicinske biokemije i laboratorijske medicine (sveučilišni magistar medicinske biokemije i laboratorijske medicine)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-10-10 12:13:01