Browsing by Author "Kempa, Inga"
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Item Association of BMP4 polymorphisms with non-syndromic cleft lip with or without cleft palate and isolated cleft palate in Latvian and Lithuanian populations(2014) Kempa, Inga; Ambrozaitytė, Laima; Stavusis, Janis; Akota, Ilze; Barkane, Biruta; Krumina, Astrida; Matulevičienė, Aušra; Utkus, Algirdas; Kučinskas, Vaidutis; Lace, Baiba; Scientific Laboratory of Molecular Genetics; Rīga Stradiņš UniversityCleft lip with or without cleft palate (CLP and CL, respectively) and isolated cleft palate (CP) represent one of the most common human birth defects, with a prevalence of approximately 1 in 300-2500 depending on the population. Formation of non-syndromic CL/CLP and CP arises from the interaction of environmental and genetic factors. The objective of this study was to investigate the association between the BMP4 gene (encoding bone morphogenetic protein 4) and non-syndromic CL/CLP and CP in order to clarify the role of this gene in the aetiology of the malformation in Latvian and Lithuanian populations. We genotyped three markers of the BMP4 gene (rs17563, rs2071047 and rs1957860) in order to perform single marker and haplotype association analyses for Latvian and Lithuanian non-syndromic CL/CLP and CP patients and controls. Transmission disequilibrium test was also conducted for Latvian and Lithuanian proband-parent trios. The case-control analysis revealed that SNP rs2071047 allele A was associated with a decreased risk of CL/CLP in the Latvian population, which was confirmed by the haplotype analysis. A modest association was detected between SNP rs1957860 and CP in the Lithuanian population, where allele C was associated with a decreased risk of this cleft phenotype, corroborating haplotype analysis data. Our findings support a role of the BMP4 gene in the aetiology of non-syndromic CL/CLP and CP in the studied populations.Item Causes and Genomic Approaches to Female Reproductive Failure. Doctoral Thesis(Rīga Stradiņš University, 2021) Voložonoka, Ludmila; Miskova, Anna; Kempa, IngaClinical recognition of the genetic causes of female reproductive failure using increasingly advancing genetic technologies to preserve patient safety and move towards personalized treatment application is a major challenge of reproductive medicine in the 21st century. The aim of this thesis was to demonstrate a reliable application of advanced genomic techniques in different stages of female reproductive failure in real-life clinical or research scenarios. Several genetic approaches were exploited – starting from the multifactor genetic testing of preimplantation embryos to select the ones free of inherited monogenic conditions and chromosomal aberrations, then following with the analysis of fetal material in case of early pregnancy loss using array comparative genomic hybridization and short tandem repeat analysis to exclude maternal cell contamination, and finally using next generation sequencing technology to analyze genetic landscape leading to preterm delivery in women with cervical insufficiency. The practical work described here was published as three scientific articles now forming three chapters of this thesis. Array comparative genomic hybridization combined with loci-specific genetic testing techniques allowed for a versatile and reliable analysis of preimplantation embryos to select the ones free of genetic conditions analyzed, and in combination with microsatellite analysis it also allowed to access the chromosomal causes of early pregnancy loss while reducing the misdiagnosis caused by maternal cell contamination. Next generation sequencing application allowed to identify the disruptive variants potentially contributive to the development of non-syndromic cervical insufficiency. Pathway enrichment analysis of variant genes from our cohort revealed an increased variation burden in genes playing roles in tissue mechanical and biomechanical properties. Literature analysis allowed to conclude that number of genes can be reliably attributed to female reproductive failure and an increasing number of genes form a pool of good candidates. In order to develop diagnostic gene panels and facilitate genetic advancement inclusion in the clinical practice of female reproduction, a standardized clinical gene-disease validity assessment of the identified genes has to be performed and best practice guidelines have to be composed.Item Causes and Genomic Approaches to Female Reproductive Failure. Summary of the Doctoral Thesis(Rīga Stradiņš University, 2021) Voložonoka, Ludmila; Miskova, Anna; Kempa, IngaClinical recognition of the genetic causes of female reproductive failure using increasingly advancing genetic technologies to preserve patient safety and move towards personalized treatment application is a major challenge of reproductive medicine in the 21st century. The aim of this thesis was to demonstrate a reliable application of advanced genomic techniques in different stages of female reproductive failure in real-life clinical or research scenarios. Several genetic approaches were exploited – starting from the multifactor genetic testing of preimplantation embryos to select the ones free of inherited monogenic conditions and chromosomal aberrations, then following with the analysis of fetal material in case of early pregnancy loss using array comparative genomic hybridization and short tandem repeat analysis to exclude maternal cell contamination, and finally using next generation sequencing technology to analyze genetic landscape leading to preterm delivery in women with cervical insufficiency. The practical work described here was published as three scientific articles now forming three chapters of this thesis. Array comparative genomic hybridization combined with loci-specific genetic testing techniques allowed for a versatile and reliable analysis of preimplantation embryos to select the ones free of genetic conditions analyzed, and in combination with microsatellite analysis it also allowed to access the chromosomal causes of early pregnancy loss while reducing the misdiagnosis caused by maternal cell contamination. Next generation sequencing application allowed to identify the disruptive variants potentially contributive to the development of non-syndromic cervical insufficiency. Pathway enrichment analysis of variant genes from our cohort revealed an increased variation burden in genes playing roles in tissue mechanical and biomechanical properties. Literature analysis allowed to conclude that number of genes can be reliably attributed to female reproductive failure and an increasing number of genes form a pool of good candidates. In order to develop diagnostic gene panels and facilitate genetic advancement inclusion in the clinical practice of female reproduction, a standardized clinical gene-disease validity assessment of the identified genes has to be performed and best practice guidelines have to be composed.Item Higher CTX-M, TEM, and SHV extended-spectrum beta-lactamase plasmid gene combination frequency in ESBL producing Klebsiella pneumoniae compared with ESBL producing Escherichia coli(Central Bohemia University, 2016) Skuja, Vita; Pekarska, Katrina; Derovs, Aleksejs; Viksna, Ludmila; Piekuse, Linda; Kempa, Inga; Caune, Una; Rudzite, Dace; Lejnieks, Aivars; Krumina, Angelika; Department of Internal Diseases; Rīga Stradiņš University; Scientific Laboratory of Molecular GeneticsItem Identification of Candidate Genes Involved in the Etiology of Non-Syndromic Cleft Lip with or without Cleft Palate and Isolated Cleft Palate. Doctoral Thesis(Rīga Stradiņš University, 2013) Kempa, Inga; Lāce, Baiba; Kloviņš, JānisCleft lip with or without cleft palate and isolated cleft palate (CL/CLP/CP) is one of the most common birth defects worldwide with prevalence of approximately 1 in 700 live births in European populations. Individuals with CL/CLP/CP need multidisciplinary care from birth to adulthood even after surgical repair. CL/CLP/CP affects speech, dental development, hearing, appearance and psychology of person. It has been considered that individuals with this malformation have higher morbidity and mortality of cardiovascular diseases and cancers if compared to unaffected individuals. Despite possibility of surgical repair, this defect remains important health and social problem in nowadays. Formation of orofacial clefts is a result between interaction of environmental and genetic factors. Recent estimates suggest that 2-14 genes could be involved in the formation of CL/CLP/CP. In present study we performed case-control analysis and family based association test in CL/CLP and CP patients, their parents and control group. Identification of possible candidate genes involved in the etiology of non-syndromic cleft lip with or without cleft palate and isolated cleft palate in Latvian population was the objective of the present study. Our results showed very strong association between FGFR1, WNT3, SKI, BMP4 and IRF6 genes and non-syndromic CL/CLP and CP and possible interaction between 19q13 locus and non-syndromic CL/CLP, which continue to support the involvement of these genes in the development of non-syndromic clefts in Caucasians. Results of this study is step further of understanding of this complex malformation and estimating the impact of genes involved in the etiology of non-syndromic cleft lip with or without cleft palate and isolated cleft palate.Item Identification of Candidate Genes Involved in the Etiology of Non-Syndromic Cleft Lip with or without Cleft Palate and Isolated Cleft Palate. Summary of the Doctoral Thesis(Rīga Stradiņš University, 2013) Kempa, Inga; Lāce, Baiba; Kloviņš, JānisCleft lip with or without cleft palate and isolated cleft palate (CL/CLP/CP) is one of the most common birth defects worldwide with prevalence of approximately 1 in 700 live births in European populations. Individuals with CL/CLP/CP need multidisciplinary care from birth to adulthood even after surgical repair. CL/CLP/CP affects speech, dental development, hearing, appearance and psychology of person. It has been considered that individuals with this malformation have higher morbidity and mortality of cardiovascular diseases and cancers if compared to unaffected individuals. Despite possibility of surgical repair, this defect remains important health and social problem in nowadays. Formation of orofacial clefts is a result between interaction of environmental and genetic factors. Recent estimates suggest that 2-14 genes could be involved in the formation of CL/CLP/CP. In present study we performed case-control analysis and family based association test in CL/CLP and CP patients, their parents and control group. Identification of possible candidate genes involved in the etiology of non-syndromic cleft lip with or without cleft palate and isolated cleft palate in Latvian population was the objective of the present study. Our results showed very strong association between FGFR1, WNT3, SKI, BMP4 and IRF6 genes and non-syndromic CL/CLP and CP and possible interaction between 19q13 locus and non-syndromic CL/CLP, which continue to support the involvement of these genes in the development of non-syndromic clefts in Caucasians. Results of this study is step further of understanding of this complex malformation and estimating the impact of genes involved in the etiology of non-syndromic cleft lip with or without cleft palate and isolated cleft palate.Item Impact of the genes UGT1A1, GSTT1, GSTM1, GSTA1, GSTP1 and NAT2 on acute alcohol-toxic hepatitis(2014-02) Piekuse, Linda; Lace, Baiba; Kreile, Madara; Sadovska, Lilite; Kempa, Inga; Daneberga, Zanda; Mičule, Ieva; Sondore, Valentina; Keiss, Jazeps; Krumina, Astrida; Scientific Laboratory of Molecular GeneticsAlcohol metabolism causes cellular damage by changing the redox status of cells. In this study, we investigated the relationship between genetic markers in genes coding for enzymes involved in cellular redox stabilization and their potential role in the clinical outcome of acute alcohol-induced hepatitis. Study subjects comprised 60 patients with acute alcohol-induced hepatitis. The control group consisted of 122 healthy non-related individuals. Eight genetic markers of the genes UGT1A1, GSTA1, GSTP1, NAT2, GSTT1 and GSTM1 were genotyped. GSTT1 null genotype was identified as a risk allele for alcohol-toxic hepatitis progression (OR 2.146, P=0.013). It was also found to correlate negatively with the level of prothrombin (β= -11.05, P=0.037) and positively with hyaluronic acid (β=170.4, P=0.014). NAT2 gene alleles rs1799929 and rs1799930 showed opposing associations with the activity of the biochemical markers γ-glutamyltransferase and alkaline phosphatase; rs1799929 was negatively correlated with γ-glutamyltransferase (β=-261.3, P=0.018) and alkaline phosphatase (β= -270.5, P=0.032), whereas rs1799930 was positively correlated with Γ-glutamyltransferase (β=325.8, P=0.011) and alkaline phosphatase (β=374.8, P=0.011). Enzymes of the glutathione S-transferase family and NAT2 enzyme play an important role in the detoxification process in the liver and demonstrate an impact on the clinical outcome of acute alcohol-induced hepatitis.Item Interaction between IRF6 and TGFA Genes Contribute to the Risk of Nonsyndromic Cleft Lip/Palate(2012-09-20) Letra, Ariadne; Fakhouri, Walid; Fonseca, Renata F.; Menezes, Renato; Kempa, Inga; Prasad, Joanne L.; McHenry, Toby G.; Lidral, Andrew C.; Moreno, Lina; Murray, Jeffrey C.; Daack-Hirsch, Sandra; Marazita, Mary L.; Castilla, Eduardo E.; Lace, Baiba; Orioli, Ieda M.; Granjeiro, Jose M.; Schutte, Brian C.; Vieira, Alexandre R.; Department of Biology and MicrobiologyPrevious evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10-6). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10-6). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10-6 for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans.Item Interaction between IRF6 and TGFA Genes Contribute to the Risk of Nonsyndromic Cleft Lip/Palate(2012-09-20) Letra, Ariadne; Fakhouri, Walid; Fonseca, Renata F.; Menezes, Renato; Kempa, Inga; Prasad, Joanne L.; McHenry, Toby G.; Lidral, Andrew C.; Moreno, Lina; Murray, Jeffrey C.; Daack-Hirsch, Sandra; Marazita, Mary L.; Castilla, Eduardo E.; Lace, Baiba; Orioli, Ieda M.; Granjeiro, Jose M.; Schutte, Brian C.; Vieira, Alexandre R.; Department of Biology and MicrobiologyPrevious evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10-6). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10-6). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10-6 for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans.Item Kandidātgēnu identifikācija nesindromālo lūpas ar/bez aukslēju šķeltņu un izolētas aukslēju šķeltnes attīstībā. Promocijas darba kopsavilkums(Rīgas Stradiņa universitāte, 2013) Kempa, Inga; Lāce, Baiba; Kloviņš, JānisLūpas šķeltne ar/bez aukslēju šķeltnes un izolēta aukslēju šķeltne (LŠ/LŠ+AŠ/AŠ) ir viens no visbiežāk sastopamajiem iedzimtajiem defektiem visā pasaulē, ar prevalenci Eiropas populācijā aptuveni 1 no 700 jaundzimušajiem. Indivīdiem ar LŠ/LŠ+AŠ/AŠ nepieciešama multidisciplināra aprūpe visā dzīves laikā, arī pēc ķirurģiskas operācijas. Lūpas šķeltne ar/bez aukslēju šķeltnes un izolēta aukslēju šķeltne ir saistīta ne tikai ar personas runas, dzirdes traucējumiem, zobu attīstības, bet arī ar izskata un psiholoģiskām problēmām. Tiek uzskatīts, ka indivīdiem ar LŠ/LŠ+AŠ/AŠ, ir paaugstināts sirds-asinsvadu slimību un audzēju saslimstības un mirstības risks, salīdzinot ar veseliem indivīdiem. Neskatoties uz iespēju ķirurģiski labot šo defektu, mūsdienās LŠ/LŠ+AŠ/AŠ ir kļuvusi par vienu no svarīgām sabiedrības veselības problēmām visā pasaulē. LŠ/LŠ+AŠ/AŠ veidojas, mijiedarbojoties ārējās vides faktoriem un ģenētiskajiem faktoriem. Pēdējie pētījumi liecina, ka aptuveni 2-14 gēni varētu būt iesaistīti nesindromālo LŠ/LŠ+AŠ/AŠ veidošanā. Šajā pētījumā tika veikta gadījuma-kontroles analīze un ģimenes asociācijas tests, lai identificētu iespējamos kandidātgēnus, kuri varētu būt iesaistīti nesindromālo lūpas šķeltnes ar/bez aukslēju šķeltņu un izolētas aukslēju šķeltnes attīstībā Latvijas populācijā. Mūsu pētījumā iegūtie rezultāti atklāja ļoti augstu saistību starp FGFR1, WNT3, SKI, BMP4 un IRF6 gēniem un nesindromālajām LŠ/LŠ+AŠ un AŠ, kā arī norāda uz iespējamo saistību starp 19q13 lokusu un nesindromālajām LŠ/LŠ+AŠ. Šie rezultāti turpina apstiprināt minēto gēnu nozīmi nesindromālo lūpas ar/bez aukslēju šķeltņu un izolētas aukslēju šķeltnes attīstībā eiropiešiem. Šis ir pirmais tik liela mēroga pētījums, kas ir veltīts nesindromālo LŠ/LŠ+AŠ/AŠ kandidātgēnu analīzei Latvijā. Pētījumā iegūtie rezultāti ir vērā ņemams ieguldījums šīs sarežģītās patoloģijas izpratnē un iespējamo gēnu ietekmes izvērtēšanā slimības izraisīšanā.Item Lack of Association between Rs2067474 Polymorphism in the Histamine Receptor H2 Gene and Gastric Cancer in Latvian Population(2018-12-01) Moisejevs, Georgijs; Gailite, Linda; Isajevs, Sergejs; Nikitina-Zaķe, Liene; Kempa, Inga; Jančiauskas, Dainius; Kikuste, Ilze; Siviņš, Armands; Ancans, Guntis; Leja, Marcis; Scientific Laboratory of Molecular GeneticsHistamine has an important role in the process of the gastric mucosa inflammation acting via histamine receptor H2 (encoded by the gene HRH2). Single nucleotide polymorphism of the enhancer element of HRH2 gene promoter rs2067474 (1018G>A)may be associated with changes of expression of the receptor. We attempted to clarify the association of this polymorphism with gastric cancer and/or atrophic gastritis in the Latvian (Caucasian) population. The study group consisted of 121 gastric cancer patients and 650 patients with no evidence of gastric neoplasia on upper gastrointestinal endoscopy. Genotyping for rs2067474 was performed with the TaqMan probe-based system using a commercially available probe for RT-PCR. The frequency of the A allele in the gastric cancer group was 0.41% and in the control group - 1.54% (p = 0.231). No significant differences were found comparing genotypes between gastric cancer versus control patients (OR = 0.236, CI95% = 0.030-1.896), patients with (n = 165) versus without (n = 485) gastric metaplastic lesions (OR = 0.854, CI95% = 0.288-2.540) and patients with (n = 297) and without (n = 353) gastric atrophic lesions (OR = 1.145, CI95% = 0.451-2.906). Our findings suggest that the HRH2 -1018G>A polymorphism (rs2067474) is neither associated with gastric cancer nor the grade of atrophic gastritis in the Latvian (Caucasian) population.Item Management of Pregnancy with Cervical Shortening: Real-Life Clinical Challenges(2023-03-26) Kornete, Anna; Voložonoka, Ludmila; Zolovs, Maksims; Rota, Adele; Kempa, Inga; Gailīte, Linda; Rezeberga, Dace; Miskova, Anna; Department of Obstetrics and Gynaecology; Scientific Laboratory of Molecular Genetics; Statistics UnitBackground and Objectives: Preterm birth is the leading cause of neonatal mortality worldwide and may be responsible for lifelong morbidities in the survivors. Cervical shortening is one of the common pathways to preterm birth associated with its own diagnostic and management challenges. The preventive modalities that have been tested include progesterone supplementation and cervical cerclage and pessaries. The study aimed to assess the management strategies and outcomes in a group of patients with a short cervix during pregnancy or cervical insufficiency. Materials and Methods: Seventy patients from the Riga Maternity Hospital in Riga, Latvia, were included in the prospective longitudinal cohort study between 2017 and 2021. Patients were treated with progesterone, cerclage, and/or pessaries. The signs of intra-amniotic infection/inflammation were assessed, and antibacterial therapy was given when the signs were positive. Results: The rates of PTB were 43.6% (n = 17), 45.5% (n = 5), 61.1% (n = 11), and 50.0% (n = 1) in progesterone only, cerclage, pessary, and cerclage plus pesssary groups, respectively. The progesterone therapy was associated with a reduced preterm birth risk (x2(1) = 6.937, p = 0.008)), whereas positive signs of intra-amniotic infection/inflammation significantly predicted the risk of preterm birth (p = 0.005, OR = 3.82, 95% [CI 1.31–11.11]). Conclusions: A short cervix and bulging membranes, both indicators of intra-amniotic infection/inflammation, are the key risk factors in preterm birth risk predictions. Progesterone supplementation should remain at the forefront of preterm birth prevention. Among patients with a short cervix and especially complex anamnesis, the preterm rates remain high. The successful management of patients with cervical shortening lies between the consensus-based approach for screening, follow-up, and treatment on the one side and personalising medical therapy on the other.Item Performance comparison of two whole genome amplification techniques in frame of multifactor preimplantation genetic testing(2018-08-01) Volozonoka, Ludmila; Perminov, Dmitry; Korņejeva, Liene; Alkšere, Baiba; Novikova, Natālija; Pīmane, Evija Jokste; Blumberga, Arita; Kempa, Inga; Miskova, Anna; Gailīte, Linda; Fodina, Violeta; Scientific Laboratory of Molecular Genetics; Department of Obstetrics and GynaecologyPurpose: To compare multiple displacement amplification and OmniPlex whole genome amplification technique performance during array comparative genome hybridization (aCGH), Sanger sequencing, SNaPshot and fragment size analysis downstream applications in frame of multifactor embryo preimplantation genetic testing. Methods: Preclinical workup included linked short tandem repeat (STR) marker selection and primer design for loci of interest. It was followed by a family haplotyping, after which an in vitro fertilization preimplantation genetic testing (IVF-PGT) cycle was carried out. A total of 62 embryos were retrieved from nine couples with a confirmed single gene disorder being transmitted in their family with various inheritance traits—autosomal dominant (genes—ACTA2, HTT, KRT14), autosomal recessive (genes—ALOX12B, TPP1, GLB1) and X-linked (genes—MTM1, DMD). Whole genome amplification (WGA) for the day 5 embryo trophectoderm single biopsies was carried out by multiple displacement amplification (MDA) or polymerase chain reaction (PCR)-based technology OmniPlex and was used for direct (Sanger sequencing, fragment size analysis, SNaPshot) and indirect mutation assessment (STR marker haplotyping), and embryo aneuploidy testing by array comparative genome hybridization (aCGH). Results: Family haplotyping revealed informative/semi-informative microsatellite markers for all clinical cases for all types of inheritance. Indirect testing gave a persuasive conclusion for all embryos assessed, which was confirmed through direct testing. The overall allele dropout (ADO) rate was higher for PCR-based WGA, and MDA shows a better genomic recovery scale. Five euploid embryos were subjected to elective single embryo transfer (eSET), which resulted in four clinical pregnancies and birth of two healthy children, which proved free of disease causative variants running in the family postnataly. Conclusions: A developed multifactor PGT protocol can be adapted and applied to virtually any genetic condition and is capable of improving single gene disorder preimplantation genetic testing in a patient-tailored manner thus increasing pregnancy rates, saving costs and increasing patient reliability.Item Risk Factors that Determine Less Favourable Hospitalisation Course and Outcome in Patients with ESBL Producing Enterobacteriaceae Infection : Preliminary Results(2016-08-01) Skuja, Vita; Pekarska, Katrīna; Caune, Una; Piekuse, Linda; Kempa, Inga; Rudzīte, Dace; Kigitoviča, Dana; Derovs, Aleksejs; Vīksna, Ludmila; Lejnieks, Aivars; Krūmiņa, Angelika; Department of Internal Diseases; Scientific Laboratory of Molecular Genetics; Department of InfectologyHospitalisation course and outcome for patients with extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae infection is less favourable due to extensive antibacterial resistance. This study was conducted to identify possible risk factors that could influence the hospitalisation course and outcome in these patients. The study protocol included demographic, clinical, hospitalisation, bacteriological and plasmid genetic data. The preliminary study results showed that hospitalisation course and outcome was less favourable for internal medicine profile patients with ESBL producing bacteria, TEM gene presence in the bacterial plasmid genome, patient age < 65 years and patients with infectious and musculoskeletal diseases. The study includes preliminary data only and further studies should be carried out to verify the suggested risk factors.Item Role of Single Nucleotide Variants in FSHR, GNRHR, ESR2 and LHCGR Genes in Adolescents with Polycystic Ovary Syndrome(2021-12-11) Lidaka, Lasma; Beķere, Laine; Rota, Adele; Isakova, Jekaterina; Lazdāne, Gunta; Ķīvīte-Urtāne, Anda; Dzīvīte-Krišāne, Iveta; Kempa, Inga; Dobele, Zane; Gailīte, Linda; Department of Obstetrics and Gynaecology; Scientific Laboratory of Molecular Genetics; Institute of Public HealthBackground: Polycystic ovary syndrome (PCOS) is the most common endocrinopathy in women, affecting up to 16.6% of reproductive-age women. PCOS symptoms in adolescents comprise oligomenorrhoea/amenorrhoea and biochemical and/or clinical hyperandrogenism. Long-term health risks of PCOS patients include infertility, metabolic syndrome, type 2 diabetes and cardiovascular disease. Genetic factors have been proven to play a role in development of the syndrome and its symptoms. Objective: To investigate single nucleotide variants (SNVs) in the GNRHR, ESR2, LHCGR and FSHR genes in adolescent patients with PCOS and their association with PCOS symptoms. Methods: We conducted a cross-sectional study comprising of 152 adolescents: 63 patients with PCOS, 22 patients at risk of developing PCOS and 67 healthy controls. Participants were recruited from out-patients attending a gynaecologist at the Children’s Clinical University Hospital, Riga, Latvia, between January 2017 and December 2020. Genomic DNA was extracted from whole blood, and SNVs in the GNRHR, ESR2, LHCGR and FSHR genes were genotyped. The distributions of SNV genotypes were compared among the three groups and genotype-phenotype associations within the PCOS group were evaluated. Results: No statistically significant differences were found in the distributions of genotypes for GNRHR (rs104893837), ESR2 (rs4986938), LHCGR (rs2293275) and FSHR (rs6166, rs6165, rs2349415) among PCOS patients, risk patients and healthy controls. Within the PCOS group, ESR2 rs4986938 minor allele homozygous patients had a significantly higher level of total testosterone than major allele homozygous patients and heterozygous patients. A significantly higher total testosterone level was also observed in PCOS patients carrying the LHCGR rs2293275 minor allele compared with major allele homozygous patients. Conclusions: The SNVs ESR2 rs4986938 and LHCGR rs2293275 play a role in the phenotypic characteristics of PCOS. To fully uncover their influence on the development of PCOS and its symptoms, further studies of larger cohorts and a follow up of this study sample through to adulthood are required. Furthermore, studies of adolescent PCOS patients conducted prior to the latest European Society of Human Reproduction and Embryology (ESHRE) criteria (2018) should be re-evaluated as the study groups might include risk patients according to these updated criteria, thereby potentially significantly impacting the published results.Item Sievietes reproduktīvās mazspējas iemesli un genomiskās pieejas to risināšanai. Promocijas darba kopsavilkums(Rīgas Stradiņa universitāte, 2021) Voložonoka, Ludmila; Miskova, Anna; Kempa, IngaSievietes reproduktīvās mazspējas iemesli un genomiskās pieejas to risināšanai Sievietes reproduktīvās mazspējas ģenētisko cēloņu identificēšana, izmantojot mūsdienīgas ģenētiskās tehnoloģijas, vienlaikus saglabājot pacientu drošību un virzoties uz personalizētas ārstēšanas lietošanu, ir reproduktīvās medicīnas izaicinājums 21. gadsimtā. Darba mērķis bija demonstrēt genomisko tehnoloģiju lietojumu dažādos sievietes reproduktīvās mazspējas etapos reālos klīniskajos vai pētījumu apstākļos. Tika lietotas vairākas genomiskās metodoloģijas – pirmsimplantācijas embriju testēšanai, lai atlasītu embrijus bez iedzimtas monogēnas patoloģijas un hromosomālajām aberācijām, salīdzinošā genoma hibridizācija uz mikročipiem un mikrosatelītu analīze augļa hromosomu analīzei pārtraukušās grūtniecības materiālā, nosakot mātes šūnu kontaminācijas klātbūtni paraugā, un, visbeidzot, nākamās paaudzes sekvencēšana dzemdes kakla nepietiekamības izraisītu priekšlaicīgu dzemdību ģenētiskās etioloģijas raksturošanai. Paveiktais praktiskais darbs tika publicēts trijos zinātniskajos rakstos, kas veido trīs darba sadaļas. Salīdzinošā genoma hibridizācija uz mikročipiem apvienojumā ar lokusa ģenētiskās testēšanas metodēm deva iespēju veikt pirmsimplantācijas analīzi, lai atlasītu embrijus bez testētās patoloģijas, savukārt kombinācijā ar mikrosatelītu analīzi ļāva noteikt hromosomālās patoloģijas izraisošas agrīnas grūtniecības pārtraukšanos, vienlaikus mazinot mātes šūnu kontaminācijas izraisītas kļūdainas diagnozes iespēju. Lietojot nākamās paaudzes sekvencēšanu, tika identificēti gēnu varianti, kas potenciāli veicina nesindromiskas dzemdes kakla nepietiekamības attīstību. Gēnu ceļu bagātināšanas analīze atklāja palielinātu gēnu variācijas slogu gēnos, kas nodrošina audu mehānisko un biomehānisko izturību. Literatūras analīze ļauj secināt, ka gēnu skaits ar zināmu ietekmi uz sievietes reproduktīvās mazspējas attīstību nepārtraukti aug un aizvien lielāks gēnu skaits veido labu kandidātu kopu, kas gaida replikācijas pētījumus. Diagnostisko gēnu paneļu klīniskajai izveidei un lietošanai un ģenētisko sasniegumu iekļaušanai sievietes reprodukcijas klīniskajā praksē nepieciešama standartizēta identificēto gēnu klīniskās validitātes novērtēšana un labās prakses vadlīniju izstrāde.Item A systematic review and standardized clinical validity assessment of genes involved in female reproductive failure(2022-04-22) Volozonoka, Ludmila; Miskova, Anna; Kornejeva, Liene; Kempa, Inga; Bargatina, Veronika; Gailite, Linda; Scientific Laboratory of Molecular Genetics; Department of Obstetrics and GynaecologyGenetic testing is becoming increasingly required at almost every stage of failed female reproduction/infertility. Nonetheless, clinical evidence for the majority of identified gene-disease relationships is ill-defined, thus leading to difficult gene variant interpretation and poor translation of existing knowledge into clinics. We aimed to identify the genes that have ever been implicated in monogenic female reproductive failure in humans and to classify the identified gene-disease relationship pairs using a standardized clinical validity assessment. A PubMed search following PRISMA guidelines was conducted on 20 September 2021 aiming to identify studies pertaining to genetic causes of phenotypes of female reproductive failure. The clinical validity of identified gene-disease pairs was assessed using standardized criteria, counting whether sufficient genetic and experimental evidence has been accumulated to consider a single gene 'characterized' for a single Mendelian disease. In total, 1256 articles were selected for the data extraction; 183 unique gene-disease pairs were classified spanning the following phenotypes: hypogonadotropic hypogonadism, ovarian dysgenesis, premature ovarian failure/insufficiency, ovarian hyperstimulation syndrome, empty follicle syndrome, oocyte maturation defect, fertilization failure, early embryonic arrest, recurrent hydatidiform mole, adrenal disfunction and Mullerian aplasia. Twenty-four gene-disease pairs showed definitive evidence, 36 - strong, 19 - moderate, 81 - limited and 23 - showed no evidence. Here, we provide comprehensive, systematic and timely information on the genetic causes of female infertility. Our classification of genetic causes of female reproductive failure will facilitate the composition of up-to-date guidelines on genetic testing in female reproduction, the development of diagnostic gene panels and the advancement of reproductive decision-making.Item Unravelling the genetic landscape of cervical insufficiency : Insights into connective tissue dysfunction and hormonal pathways(2024-09) Voložonoka, Ludmila; Bārdiņa, Līvija; Kornete, Anna; Krūmiņa, Zita; Rots, Dmitrijs; Minkauskienė, Meilė; Rota, Adele; Strelcoviene, Zita; Vilne, Baiba; Kempa, Inga; Miskova, Anna; Gailīte, Linda; Rezeberga, Dace; Rīga Stradiņš UniversityBACKGROUND: The intricate molecular pathways and genetic factors that underlie the pathophysiology of cervical insufficiency (CI) remain largely unknown and understudied. METHODS: We sequenced exomes from 114 patients in Latvia and Lithuania, diagnosed with a short cervix, CI, or a history of CI in previous pregnancies. To probe the well-known link between CI and connective tissue dysfunction, we introduced a connective tissue dysfunction assessment questionnaire, incorporating Beighton and Brighton scores. The phenotypic data obtained from the questionnaire was correlated with the number of rare damaging variants identified in genes associated with connective tissue disorders (in silico NGS panel). SKAT, SKAT-O, and burden tests were performed to identify genes associated with CI without a priori hypotheses. Pathway enrichment analysis was conducted using both targeted and genome-wide approaches. RESULTS: No patient could be assigned monogenic connective tissue disorder neither genetically, neither clinically upon clinical geneticist evaluation. Expanding our exploration to a genome-wide perspective, pathway enrichment analysis replicated the significance of extracellular matrix-related pathways as important contributors to CI's development. A genome-wide burden analysis unveiled a statistically significant prevalence of rare damaging variants in genes and pathways associated with steroids (p-adj = 5.37E-06). Rare damaging variants, absent in controls (internal database, n = 588), in the progesterone receptor (PGR) (six patients) and glucocorticoid receptor (NR3C1) (two patients) genes were identified within key functional domains, potentially disrupting the receptors' affinity for DNA or ligands. CONCLUSION: Cervical insufficiency in non-syndromic patients is not attributed to a single connective tissue gene variant in a Mendelian fashion but rather to the cumulative effect of multiple inherited gene variants highlighting the significance of the connective tissue pathway in the multifactorial nature of CI. PGR or NR3C1 variants may contribute to the pathophysiology of CI and/or preterm birth through the impaired progesterone action pathways, opening new perspectives for targeted interventions and enhanced clinical management strategies of this condition.