Browsing by discipline "Medical Genetics"

Externally visual characteristics such as hair, skin and eye pigmentation or clothes have always been used for suspect identification. Also the opposite - to link unknown body parts or only DNA to a person - is recently tried to be introduced into forensics. I am testing the feasibility of one such method, IrisPlex, in Finnish population. The IrisPlex method was first published by Walsh et al. (2011). IrisPlex uses six single nucleotide polymorphisms (SNPs) in different genes found to affect the most in eye color variation. SNPs were detected from DNA sample by single base extension method, SNaPshot. Based on this information from DNA of a participant, the prediction of the most probable eye color was generated with a multinomial regression model. Also the genotypic information in the six loci and differences between Eastern and Western Finns were studied. In addition, this study supplements the knowledge of eye color frequencies across Europe. This study revealed that IrisPlex does work appropriately in Finns when detecting the blue and brown eye colors: 80% of the study participants' eye colors were predicted correctly. The biggest weakness of IrisPlex is its incapability to predict the intermediately colored eyes. Prediction probability differences between genders were not detected. In the study population 60% of the participants had blue eyes (28 individuals), 13% had brown eyes (6 individuals) and 28% (13 individuals) intermediately colored eyes. When the eyes were divided into two categories, the portion of blue-eyed participants was 77% (36 individuals) and brown-eyed participants 23% (11 individuals). These results are consistent with previous studies and update the color frequencies. Genetic segmentation of Finnish people in Eastern and Western Finland has been established in multiple studies. In addition to previous ones, this study is consistent with the genetic segmentation theory between Eastern and Western Finland. Darker eyes were observed slightly more frequently in participants with north-east heritage than in participants with south-west heritage. However, the studied populations were small and the result was insignificant. Additionally, the studied population sample represents the narrow gene pool of the Finns; almost half of the participants, 42%, reported all or 3 of their grandparents to have been born in the same village. The allele and genotype frequencies were also studied and compared to another study, in which these SNPs have been studied in the Finns and the results were consistent. Altogether, this study strengthens the evidence that IrisPlex has potential in forensic, archeological and anthropological applications even in genetically isolated populations as the Finns. This study supports the IrisPlex method to be further developed and especially addresses the need for better sensitivity for intermediate eye color.

The main focus of this study is a Finnish family, in which four out of eight children presented with an unidentified disease causing a grave developmental disorder. A genetic cause for this disorder was sought by utilizing whole exome sequencing. Both parents, two affected siblings and one healthy sibling were sequenced. After variant filtering and analysis, only the candidate gene UBA5 passed the filtering criteria. The results were validated using Sanger sequencing. Both affected individuals were shown to have compound heterozygous variants of this gene, with one of the variants being novel. No cases of disease in humans associated with UBA5 have prior to this study been reported. However, other unrelated patients with a similar phenotype have since been found to possess pathogenic variants in the gene UBA5, which confirms the claim that it's the disease-causing gene. Therefore, this study enhances our knowledge of the gene's physiological significance.

Genetiska varianter har under senaste åren upptäckts påverka en myriad vanliga samt sällsynta sjukdomar. En viktig grupp varianter i neuropsykiatriska sjukdomar är kromosomavvikelser, speciellt förändringar i antalet genkopior (eng. ”copy number variations”, CNVs). CNVs är associerade med ett brett spektrum olika syndrom, som 22q11.2-deletionssyndrom, samt utvecklingsbetingade neuropsykiatriska sjukdomstillstånd och störningar, som intellektuell funktionsnedsättning, autismspektrets störningar, epilepsi, samt skitsofreni och andra psykotiska sjukdomar. För att undersöka CNVs associeration med neurologiska utvecklingssjukdomar analyserade vi CNVs i två olika kohorter: en kohort med utvecklingsstörda patienter som är värvda i Norra Finland (NFID); och FINRISK-populationskohorten. I en assocationsanalys efter att ha tagit kön, härstamning och genetisk varians (PCA) i beaktande, resulterande i 433 patienter och 1100 kontroller. Det upptäcktes CNVs som beaktades som högst sannolikt patogena i ca 5.3 % av patienter Den vanligaste typen av CNV var 22q11.2-deletionssyndrom (8 st); den vanligaste patogena kriterien var storlek (deletion på över 2 Mb). Associationsanalysens resultat visade en hög association med tidigare igenkända regioner och gener, med deletioner av storleken över 1 Mb fortfarande identifierade i populationen.

Introduction: Parkinson’s disease is the second most common neurodegenerative disease in the Western countries with a prevalence of about 0.3% in the population. Approximately 5 to 10% of patients are estimated to have a hereditary form of the disease. In recent years, 23 gene loci have been found, in which mutations cause hereditary Parkinson’s disease. In Finland, however, only a few disease linked gene variants have been found so far. Aims and methods: To find out if there are gene variants previously found in Parkinson’s disease patients in the Finnish population, we searched variants found in literature search in a novel genetic database, SISu, which contains genetic data of over 10 000 Finns. In addition, to confirm population findings and search for new gene variants, we analyzed 47 patient cohort with a designed gene panel and also another cohort, containing 147 patients, by minisequencing one variant found in the population data. Results: We found 16 variants in five different genes in the population data. Three of them were considered pathogenic and four likely benign after our analysis. In addition, we found nine potentially disease linked variants in eight different patients. Four of the variants were novel. Discussion: Finns seem to carry only few previously described gene variants in genes linked to Parkinson’s disease. It is likely that Finns carry their own unique variants, some of which we also found in our study. Our analysis brings valuable information about the still scarce knowledge of the genetics of this disease in the Finnish population. In addition, we were able to evaluate the disease risk of many variants further by studying their occurrence in Finns. The study of novel gene variants may bring valuable new information about the pathogenic processes related to the disease; especially the location of a novel variant in PARK2 gene found in our study turned out to be crucial for one of the previously suggested disease mechanisms.

Teollisuusmaissa - ja siten Suomessakin - tapaturmakuolemat ovat ylivoimaisesti suurin syy lasten ja nuorten kuolemiin. Maailmanlaajuisesti tapaturmakuolleisuus lasten ja nuorten ikäluokissa on vielä suurempi. Tapaturmat muodostavat maailmassa hiukan alle puolet lasten ja nuorten kuolemista ollen toiseksi yleisin kuolinsyy. Tutkielma käsittelee Oikeuslääketieteen laitoksella vuosina 1996-2005 tutkittuja alle kaksikymmentävuotiaita lapsia ja nuoria, joiden kuolemanluokkana on ollut tapaturma. Tapauksia oli 249, joista 192 valittiin tutkimukseen. Kuolemantapaukset eroteltiin pääluokkiin kuolemantyypin ja -paikan suhteen. Korrelaatioita etsittiin ajan, iän ja sukupuolen suhteen. Poikien tapaturmat olivat yleisempiä kaikissa ikäluokissa, tapaturmatyypeissä ja - paikoissa. Tapaturmakuolemat yleistyivät pojilla iän suhteen, mutta tytöillä vastaavaa ilmiötä ei havaittu. Liikenneonnettomuudet muodostivat yli puolet tapaturmista. Tie ja yksityisasunto olivat yleisimmät tapaturmapaikat. Pienen otoksen takia ajan suhteen ei huomattu merkitsevää muutosta.

Background: Malignant mesothelioma is a fatal cancer of the mesothelial cells characterized by previous exposure to asbestos, long latency period and shorter survival time thereafter. Lack of highly sensitive and specific biomarkers and no curative treatment at present has made the continuous study of mesothelioma important. One of the biomarker under study are the microRNAs (miRNAs) which are small non-coding RNAs of about 20-22 nucleotides long which regulate post-translational gene expression. MiRNAs control several essential biological pathways including the epithelial-mesenchymal transition (EMT) pathway. Their dysregulation can lead to disruption of these pathways and also to the development of cancer. Identifying and understanding the role played by these miRNAs in malignant mesothelioma will help in their development as an effective diagnostic, prognostic and therapeutic target for this cancer. Aims: The study aims to first identify miRNAs previously linked with malignant mesothelioma, invasion and the EMT pathway based on review of literature. The study then aims to characterize miRNAs expression in established mesothelial cell lines used widely in mesothelioma research. Material & methods: Literature review is conducted using peer reviewed articles and limiting the articles published within the last 5 years. For characterizing the miRNAs, 6 mesothelial cell lines are used of which one is non-tumorigenic and used to represent a healthy control. Small RNA sequencing is done of all 6 cell lines and results analyzed using the Chipster analysis software. Results: A comprehensive list of 100 miRNAs was created which were linked to malignant mesothelioma, invasion, metastasis and EMT pathway. Small RNA sequencing of the cell lines revealed 134 miRNAs which were expressed in at least one of the cell lines. 34 of these miRNAs had higher counts in the healthy control as compared to all the cancer cell lines. In addition, we found 19 miRNAs having low counts in the control cell line but showed downregulation to zero in all the cancer cell lines. 4 miRNAs, namely miR-10a-5p, miR- 21-5p, miR-23b-3p and miR-183-5p, were also found in this study which were not previously linked with malignant mesothelioma. Conclusion: Characterization of the available mesothelial cell lines is the first step in understanding the role played by miRNAs in the development of this cancer. Further studies are needed to confirm the entire list of mesothelioma associated miRNAs found here, especially the 4 miRNAs which were not previously linked to mesothelioma. Validation of the miRNAs through comparison with patient samples with higher number of biological replicates and greater depth of libraries along with miRNA pathway analysis will help the development of miRNAs as a diagnostic and prognostic marker for this cancer.

Early-onset cardiomyopathies (CMPs) are disorders that bring a heavy burden for families as they often lead to early death among children. CMP may be defined as a disease affecting the myocardium and its ability to pump blood efficiently. While CMPs can be both of acquired and hereditary origin, heterogeneous genetics often explain the early onset of such diseases with varying phenotypes. This study aimed to offer molecular diagnoses to three patients within the ‘KidCMP cohort’ (n=74, University Hospital Helsinki) and characterize their disease-causing genes in early-onset CMPs. Additionally; it aimed to develop patient-specific tools to study disease mechanisms in more detail. While candidate pathogenic variants were identified through whole-exome sequencing, the validation of these variants was approached through experimental work at RNA and protein level as well as molecular modeling. Using whole-exome sequencing data, we identified novel candidate disease genes in three patients from the ‘KidCMP’ cohort: TMOD1, NRAP and PGM5. While NRAP has been previously reported in a family with autosomal dominant transmission of adult dilated CMP and incomplete penetrance, TMOD1 and PGM5 have not been previously associated with disease. TMOD1 (Tropomodulin-1) presented a homozygous missense mutation in our patient, and the conservation in species and molecular modeling of the identified variant further supported its underlying role in teenage-onset dilated CMP. Cytoskeletal stability and sarcomeric force transmission are likely to be disrupted as a result of the mutation in this actin-binding protein. NRAP (Nebulin-related-anchoring protein) presented a homozygous nonsense mutation in the second patient and RNA analysis from cells and heart tissue revealed mRNA to escape nonsense-mediated decay. This gene occupies an important role in myofibril assembly and anchoring actin filaments to the cell membrane. Based on the induced premature stop codon we judged this variant to lead to a loss of function and to underlie severe early-onset dilated CMP in our patient. PGM5 (Phosphoglucomutase-like protein 5) presented a compound heterozygous missense mutation in the third patient and protein analysis revealed the affected protein to be present in reduced form. PGM5 interacts with actin filaments and occupies an important role in myofibril formation as well as cell-cell contact. Homology modeling showed the variants to cluster in the disease-associated region of the homologous PGM1 gene. Based on this, we judge this variant to underlie early-onset dilated CMP in our patient. Overall, these findings suggest a valuable role of whole-exome sequencing in disclosing the heterogeneous genetic background of this field of diseases. By identifying and characterizing novel disease genes as presented here, we offer important knowledge for targeted treatment options and further research.

This study investigates the metabolic consequences of a biomarker for mitochondrial myopathies, using the mouse as a model organism. The studied biomarker is fibroblast growth factor 21 (FGF21), which is secreted in high amounts from the diseased muscle tissue. It is an endocrine hormone that regulates lipid metabolism, and in healthy individuals it is mainly secreted from the liver. I utilized skeletal muscle samples from mice that were either wild type or had a mitochondrial myopathy, both with or without a whole-body knockout of FGF21. I analysed a data set from a targeted metabolomic experiment conducted on the skeletal muscle samples. The experiment was performed by our collaborator Vidya Velagapudi. Additionally I measured protein and mRNA expression of selected enzymes from the muscle samples. This study shows, that the cytokine FGF21 contributes to the disease progression of mitochondrial myopathy. The aspects of pathophysiology it regulates were all found to center on the metabolic pathway of one carbon (1C) metabolism. Serine de novo synthesis shuttles glucose carbons into 1C metabolism. The transsulfuration pathway produces glutathione using carbon units from the 1C pathway. The results of this study show, that FGF21 mediates the upregulation of alternative carbon donors in one carbon metabolism, especially serine biosynthesis, and the elevated utilisation of carbon units in the transsulfuration pathway. Not all of the metabolic changes characteristic of mitochondrial myopathy were affected by FGF21, e.g. the upregulation of acyl carnitines seen in mitochondrial myopathy was not affected by the knock-out of FGF21.