FMR1 linked haplotype analysis in a mentally retarded male population

Funding Information: The study was supported by Riga Stradins University ESF projects No. 2004/0005/VPD1/ ESF/PIAA/04/NP/3.2.3.1./0001/0004/0066 and No. 2009/0147/1DP/1.1.2.1.2/09/IPIA/VIAA/009. We are grateful to Dr. K. Eiklid, Ulleval University Hospital, Oslo, Norway, and Prof. R. A. Wevers and Dr. H. Yntema, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands for technical help and inspiration for this project.Fragile X syndrome is caused by dynamic mutation of FMR1 gene CpG island CGG repeats. The underlying mutational mechanism is not fully understood. Different microsatellite markers and SNP have previously been reported as markers associated with FMR1 CGG repeat instability. The aim of the present study was to identify specific haplotypes among Latvian FXS patients and the control group with respect to allelic stability. Eleven male FXS patients and 122 control male patients participated in the study. In total, 27 different DXS548-FRAXAC1-ATL1-FRAXAC2 haplotypes were found. The prevalent haplotype in the control group was 7-4-A-5+ (rel. frequency 0.327). The prevalent haplotype associated with the FXS group was 2-2-G-4 (rel. frequency 0.818; p < 0.0001). Grey zone alleles with a long uninterrupted CGG tract at the 3' end were significantly associated with the 2-2-G-4 haplotype (p = 0.0022). Our findings suggest that, for the Latvian population, the haplotype 2-2-G-4 is a marker of CGG tract instability. We conclude that a founder effect could not be an explanation for our findings on the basis of heterogeneity exhibited by the Latvian population and lack of studies throughout this geographical region. This data may provide evidence of different mutational pathways of expansion in the Baltic States region.publishersversionPeer reviewe

Analysis of possible genetic risk factors contributing to development of childhood acute lymphoblastic leukaemia in the Latvian population

Publisher Copyright: Copyright © 2016 Termedia & Banach.Introduction: Childhood acute lymphoblastic leukaemia (ALL) is a complex disease caused by a combination of genetic susceptibility and environmental exposure. Previous genome-wide association studies have reported several single nucleotide polymorphisms (SNPs) associated with the incidence of ALL. Several variations in genes encoding enzymes involved in carcinogenesis are suggested as being associated with an increased risk of ALL development. Material and methods: We enrolled 77 paediatric ALL patients and 122 healthy controls, and in addition parental DNA was also available for 45 probands. SNPs rs10821936 (ARID5B), rs4132601(IKZF1), rs2239633 (CEBPE), rs3731217 (CDKN2A) and rs1800566 (NQO1) and the presence of GSTT1 and GSTM1 null variants were detected. For statistical analysis the hybrid method of two designs 'Haplin' was used as well as linkage disequilibrium for family-based association studies. Results: We identified the SNP rs10821936 in the ARID5B gene as being statistically significantly associated with childhood ALL, especially if the C allele is in a homozygous state, relative risk (RR) 4.65, 95% CI: 2.03-10.6, p = 0.0006. Statistically significant differences were not found in other SNPs. We found risk combinations including all five variations, the strongest association being found in a combination where all five genetic variants are in a homozygous state, CCTTTTTTCC, p = 0.032. Conclusions: The identified SNP rs10821936 could serve as a potential risk marker for childhood ALL development. Further studies in an independent population are needed for verification.publishersversionPeer reviewe

The fragile X syndrome13 years of experience

Funding Information: The study was approved by the Latvian Central Medical Ethics Committee and the Rîga Stradiòð University Medical Ethics Committee, and supported by ESF project No. 2009/ 0147/1DP/1.1.2.1.2/09/IPIA/VIAA/009.Fragile X syndrome (FXS; MIM #300624; FRAXA, Xq27.3) is well known and a common cause of X-linked mental retardation. The syndrome is caused by dynamic mutation of FMR1 gene CpG island CGG repeats. Clinically FXS patients demonstrate delayed developmental milestones, particularly speech, attention-deficit/hyperactivity disorder, autistic features, and psychomotor development delay. Dysmorphic face and macroorchidism are important features in the postpubertal age. We present our 13-year experience with FXS patients who were confirmed by molecular diagnostic. Phenotype-genotype evaluation was made for 12 male FXS patients. Genotype-phenotype analysis did not reveal significant correlation between clinical symptoms observed in FXS patients and genotypes obtained from leucocytes DNA analysis. The prevalence of the fragile X syndrome in the Latvian male population was estimated to be 1/6428 (95% CI 5538-7552) or 15.55/100 000 males (95% CI 13.24 - 18.05). The prevalence of the fragile X syndrome among mentally retarded male patients was estimated to be 2.67%. The low number of diagnosed patients with fragile X syndrome demonstrated in our study led to the conclusion that fragile X syndrome is generally clinically unrecognised.publishersversionPeer reviewe

Association between inherited monogenic liver disorders and chronic hepatitis C

Aim: To determine the frequencies of mutations that cause inherited monogenic liver disorders in patients with chronic hepatitis C. Methods: This study included 86 patients with chronic hepatitis C (55 men, 31 women; mean age at diagnosis, 38.36 ± 14.52 years) who had undergone antiviral therapy comprising pegylated interferon and ribavirin. Viral load, biochemical parameter changes, and liver biopsy morphological data were evaluated in all patients. The control group comprised 271 unrelated individuals representing the general population of Latvia for mutation frequency calculations. The most frequent mutations that cause inherited liver disorders [gene (mutation): ATP7B (H1069Q), HFE (C282Y, H63D), UGT1A1 (TA)7, and SERPINA1 (PiZ)] were detected by polymerase chain reaction (PCR), bidirectional PCR allele-specific amplification, restriction fragment length polymorphism analysis, and sequencing. Results: The viral genotype was detected in 80 of the 86 patients. Viral genotypes 1, 2, and 3 were present in 61 (76%), 7 (9%), and 12 (15%) patients, respectively. Among all 86 patients, 50 (58%) reached an early viral response and 70 (81%) reached a sustained viral response. All 16 patients who did not reach a sustained viral response had viral genotype 1. Case-control analysis revealed a statistically significant difference in only the H1069Q mutation between patients and controls (patients, 0.057; controls, 0.012; odds ratio, 5.514; 95%CI: 1.119-29.827, P = 0.022). However, the H1069Q mutation was not associated with antiviral treatment outcomes or biochemical indices. The (TA) 7 mutation of the UGT1A1 gene was associated with decreased ferritin levels (beta regression coefficient = -295.7, P = 0.0087). Conclusion: Genetic mutations that cause inherited liver diseases in patients with hepatitis C should be studied in detail.publishersversionPeer reviewe

Monogenic Versus Multifactorial Inheritance in the Development of Isolated Cleft Palate : A Whole Genome Sequencing Study

Funding Information: This project was funded by the Latvian Research Council, Grant no: lzp-2020/2-0374 “Deciphering the genetic mechanisms of the individuals with isolated cleft palate by whole genome sequencing”. SP was supported by an Estonian Research Council grant (MOBTP175). Publisher Copyright: Copyright © 2022 Lace, Pajusalu, Livcane, Grinfelde, Akota, Mauliņa, Barkāne, Stavusis and Inashkina.Craniofacial morphogenesis is highly complex, as is the anatomical region involved. Errors during this process, resulting in orofacial clefts, occur in more than 400 genetic syndromes. Some cases of cleft lip and/or palate (CLP) are caused by mutations in single genes; however, complex interactions between genetic and environmental factors are considered to be responsible for the majority of non-syndromic CLP development. The aim of the current study was to identify genetic risk factors in patients with isolated cleft palate (CP) by whole genome sequencing. Patients with isolated CP (n = 30) recruited from the Riga Cleft Lip and Palate Centre, Institute of Stomatology, Riga, were analyzed by whole genome sequencing. Pathogenic or likely pathogenic variants were discovered in genes associated with CP (TBX22, COL2A1, FBN1, PCGF2, and KMT2D) in five patients; hence, rare disease variants were identified in 17% of patients with non-syndromic isolated CP. Our results were relevant to routine genetic counselling practice and genetic testing recommendations. Based on our data, we propose that all newborns with orofacial clefts should be offered genetic testing, at least for a panel of known CLP genes. Only if the results are negative and there is no suggestive family history or additional clinical symptoms (which would support additional exome or genome-wide investigation), should multifactorial empiric recurrence risk prediction tools be applied for families.publishersversionPeer reviewe

Association of BMP4 polymorphisms with non-syndromic cleft lip with or without cleft palate and isolated cleft palate in Latvian and Lithuanian populations

Cleft 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.publishersversionPeer reviewe

The most common European HINT1 neuropathy variant phenotype and its case studies

Funding Information: The study was funded by Latvian Science Council Project No. FLPP lzp-2021/1-0327. Publisher Copyright: Copyright © 2023 Rozevska, Rots, Gailite, Linde, Mironovs, Timcenko, Linovs, Locmele, Micule, Lace and Kenina.HINT1 is an ubiquitous homodimeric purine phosphoramidase belonging to the histidine-triad superfamily. In neurons, HINT1 stabilizes the interaction of different receptors and regulates the effects of their signaling disturbances. Changes in HINT1 gene are associated with autosomal recessive axonal neuropathy with neuromyotonia. Aim of the study was detailed description of patients' phenotype with HINT1 homozygous NM_005340.7: c.110G>C (p.Arg37Pro) variant. Seven homozygous and three compound heterozygous patients were recruited and evaluated using standardized tests for CMT patients, in four patients' nerve ultrasonography was performed. The median age of symptom onset was 10 years (range 1–20), with initial complaints being distal lower limb weakness with gait impairment, combined with muscle stiffness, more pronounced in the hands than in the legs and worsened by cold. Arm muscles became involved later, presenting with distal weakness and hypotrophy. Neuromyotonia was present in all reported patients and is thus a diagnostic hallmark. Electrophysiological studies demonstrated axonal polyneuropathy. Impaired mental performance was observed in six out of ten cases. In all patients with HINT1 neuropathy, ultrasound examination showed significantly reduced muscle volume as well as spontaneous fasciculations and fibrillations. The nerve cross-sectional areas of the median and ulnar nerves were closer to the lower limits of the normal values. None of the investigated nerves had structural changes. Our findings broaden the phenotype of HINT1-neuropathy and have implications for diagnostics and ultrasonographic evaluation of HINT1-neuropathy patients.publishersversionPeer reviewe

Initial experience with Edwards SAPIEN valve transcatheter implantation in native RVOT in Latvia

© Lietuvos mokslų akademija, 2020.Transcatheter pulmonary valve implantation has been a well-known method for more than a decade, but there are still many challenging cases when a personalized solution is needed. We report a case of a 15-year-old female patient with tetralogy of Fallot, who underwent a surgical correction during infancy. Because of progressive pulmonary regurgitation, stenosis, and right ventricle dilatation, transcatheter pulmonary valve implantation in the native right ventricle outflow tract (RVOT) using Edwards SAPIEN valve was performed. A "landing zone" was created prior to the intervention of stenting the RVOT and the right pulmonary artery. The transcatheter approach for pulmonary valve replacement in a native RVOT is a reasonable alternative to the surgical approach.publishersversionPeer reviewe

Population Genetics of Latvians in the Context of Admixture between North-Eastern European Ethnic Groups

Publisher Copyright: © 2018 Astrida Krumiņa et al., published by Sciendo.This article presents a review on population genetics of Latvians, which alongside Lithuanians are the two extant Baltic speaking populations. The article provides a description of genome-wide single nucleotide polymorphism (SNP) data and contains a comparative analysis of the results of studies performed on classical autosomal genetic markers, mitochondrial DNA (mtDNA) and the non-recombining part of the Y chromosome (NRY), with data on neighbouring populations. The study also covers data of recently performed ancient DNA (aDNA) studies carried out on samples from the territory of today's Latvia. The results of population genetic studies have shown a mixture of eastern and western genetic traits in present-day Latvians with only small differences between Latvian subpopulations. Studies of the Baltic "tribal gene" LWb, as well as the gene's SERPINA1 allele PIZ have indicated the presence of a considerable Baltic admixture in the neighbouring Finno-Ugric and Slavic populations. Although mtDNA analyses have shown that Latvians genetically in general belong to the same common gene pool as most of the Europeans, the Y-chromosomal lineage composition suggests that they are most similar to Northern and Eastern European populations of Lithuanians, Estonians, and Eastern-Slavic populations, which are ethnogenetically closest to them. The analysis of aDNA from the Early and Middle Neolithic did not present any genomic evidence of gene-flow from Central European farmers or any mitochondrial or Y-chromosomal haplogroups that are typical for them in the hunter-gatherers from the territory of today's Latvia and Lithuania.publishersversionPeer reviewe

Human Mitochondrial HMG-CoA Synthase Deficiency: Role of Enzyme Dimerization Surface and Characterization of Three New Patients.

Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency (mitochondrial HMG-CoA synthase deficiency or mHS deficiency, OMIM #605911) is an inborn error of metabolism that affects ketone body synthesis. Acute episodes include vomiting, lethargy, hepatomegaly, hypoglycemia and dicarboxylic aciduria. The diagnosis is difficult due to the relatively unspecific clinical and biochemical presentation, and fewer than 30 patients have been described. This work describes three new patients with mHS deficiency and two missense mutations c.334C>T (p.R112W) and c.430G>T (p.V144L) previously not reported. We developed a new method to express and measure the activity of the enzyme and in this work the study is extended to ten new missense variants including those of our patients. Enzymatic assays showed that three of the mutant proteins retained some but seven completely lacked activity. The identification of a patient homozygous for a mutation that retains 70% of enzyme activity opens the door to a new interpretation of the disease by demonstrating that a modest impairment of enzyme function can actually produce symptoms. This is also the first study employing molecular dynamics modelling of the enzyme mutations. We show that the correct maintenance of the dimerization surface is crucial for retaining the structure of the active center and therefore the activity of the enzyme.post-print1746 K