The device is intended for rapid and accurate analysis of PCR products in real-time (RT PCR). It enables to analyze up to 32 samples in one run of the device. We investigate thrombophilic mutations, the response to hormonal stimulation in women and screening of fragile X syndrome with RT PCR in our laboratory. The listed genetic examinations are most frequently carried out in women with recurrent miscarriages or primary sterility before the treatment with procedures of assisted reproduction.
Roche Diagnostics MagNA Pure Compact System
The device enables rapid isolation of nucleic acids (DNA, RNA) from samples of patients. We mainly isolate DNA from peripheral blood or buccal swab. We isolate fetal DNA for further genetic examinations from the amniotic fluid or placental tissue in pregnant women. This automatized isolation method enables us to obtain very clean DNA. MagNA Pure Compact can isolate up to 8 samples at a time and therefore significantly accelerates work in comparison with manual isolation of DNA by a laboratory assistant.
Qiagen QIA Symphony SP DNA
The device QIA Symphony is a fully automatic system that fulfills the demanding requirements for isolation of nucleic acids of up to 96 samples at a time. This leads to a significant acceleration and higher quality of the performed genetic examinations. The device is mainly used in our laboratory for DNA isolation from peripheral blood and isolation of cfDNA (cell-free DNA) from blood plasma of pregnant women in non-invasive prenatal examination of the most frequent cases of fetal chromosomal aneuploidy, especially Down syndrome (cfDNA test of GENNET).
Ion Torrent Proton (ThermoFisher)
This device for sequencing of the next generation (NGS - Next Generation Sequencing) can be used in multiple applications for targeted exome sequencing of DNA, RNA sequencing and sequencing of genomes of viruses and bacteria. It is a part of algorithm of cfDNA test in our facility - non-invasive prenatal examination of most frequent cases of fetal chromosomal aneuploidy, in particular Down syndrome, from the blood of pregnant women. CfDNA (cell-free DNA) is formed by a mixture of DNA segments from placental cells (therefore both maternal and fetal DNA) and by its further processing with NGS on Iontorrent we obtain sequences which can be assigned to corresponding locations in human chromosomes. Then we evaluate statistically significant differences in the number of DNA segments of individual chromosomes in comparison with the expected number according to default values (reference values). CfDNA test is a part of prenatal screening program of GENNET. In addition to the risk of Down syndrome it also assesses the risk of other frequent cases of fetal aneuploidy - trisomy 18 (Edwards syndrome) and trisomy 13 (Patau syndrome) and enables to determine the sex of the fetus as well.
ABI Prism 3130 a 3130xl Genetic Analyzers (Applied Biosystems)
ABI Prism 3130 enables the genetic analysis of fluorescence on the basis of capillary electrophoresis and is mainly intended for direct sequencing of DNA segments, i.e. determination of the exact sequence of individual DNA nucleotides of the patient in the tested probe and for additional procedures - fragmentation analysis and MLPA analysis (Multiplex ligation-dependent probe amplification). As to the fact that we carry out a large number of investigations (see below), we have in total two devices in our laboratory - one with four capillaries and a high-capacity device with sixteen capillaries. Direct sequencing of PCR products enables us to verify the findings of pathogenic mutations from NGS examinations (oncopanel CZECANCA), since each mutation must always be confirmed from the patient´s second sample before the result is transmitted to the patient. Direct DNA sequencing of deaf patients helps us find changes (mutations) in genes that are responsible for the emergence of deafness. Fragmentation analysis enables us to investigate mutations of the gene for cystic fibrosis and Y chromosome microdeletion, most commonly in cases of male infertility (in the event of bad results of semen analysis). With the very rapid method QF-PCR we discover the most frequent cases of fetal chromosomal aneuploidy (21,18, 13 and sex chromosomes) from invasive examination of the pregnant woman (amniocentesis, placental tissue or umbilical cord blood) and that is why we can inform the patients about the outcome as soon as the second day after the procedure. Paternity tests and DNA kinship testing are also based on this principle of examination. With fragmentation analysis in the tumor tissue of colon and rectum carcinoma we determine the so-called microsatellite instability. High instability in the tumor indicates possible congenital hereditary predisposition for CRC and it is a reason for another genetic testing of the patient (oncopanel CZECANCA). MLPA method determines differences in the number of gene copies for serious hereditary muscular diseases (spinal muscular atrophy) and we detect large deletions or duplications in genes which are responsible for oncological diseases (such as BRCA genes for hereditary breast and ovarian cancer).
Sciclone NGS Workstation (PerkinElmer)
The purpose of this automatic workstation is preparation of DNA samples for sequencing of the next generation (NGS - Next Generation Sequencing). The system can be used for multiple NGS applications including whole genome sequencing, RNA sequencing, targeted and amplicon sequencing. It is currently used for preparation of NGS libraries for non-invasive prenatal cfDNA testing for detection of the most frequent cases of fetal aneuploidy and for oncopanel CZECANCA, which tests congenital genetic predisposition for cancer. Automatization shortens the preparation time of the required library, eliminates contaminations and mistakes and has a high capacity at the same time - up to 96 samples in one run of the device. This allows us to investigate more patients in a shorter time and we are therefore able to perform urgent genetic examinations in oncological patients, where we need to find out the result of the genetic examination before the actual operation. The extent of the surgical procedure is determined according to the result of genetic examination (such as in patients with mutation of BRCA gene it is appropriate to remove the entire breast or even both breasts due to high risk of a secondary tumor).
In addition we also take part in international quality controls and we support international research projects.
The cytogenetic and molecular genetic laboratories participate in the annual interlaboratory quality controls, both on the national and international level.