Browsing by Subject "Medical Genetics"

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  • Karppanen, Tiina; Kaartokallio, Tea; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli; Staff, Anne Cathrine; Laivuori, Hannele; Klemetti, Miira M. (Helsingfors universitet, 2016)
    Background Preeclampsia is a common and heterogeneous vascular syndrome of pregnancy. Its genetic risk profile is yet unknown and may vary between individuals and populations. The rs4606 3' UTR polymorphism of the Regulator of G-protein signaling 2 gene (RGS2) in the mother has been implicated in preeclampsia as well as in the development of chronic hypertension after preeclampsia. The RGS2 protein acts as an inhibitor of physiological vasoconstrictive pathways, and a low RGS2 level is associated with hypertension and obesity, two conditions that predispose to preeclampsia. We genotyped the rs4606 polymorphism in 1339 preeclamptic patients and in 697 controls from the Finnish Genetics of Preeclampsia Consortium (FINNPEC) cohort to study the association of the variant with preeclampsia. Results No association between rs4606 and preeclampsia was detected in the analysis including all women. However, the polymorphism was associated with preeclampsia in a subgroup of overweight women (body mass index ≥ 25 kg/m2, and < 30 kg/m2) (dominant model; odds ratio, 1.64; 95% confidence interval, 1.10-2.42). Conclusions Our results suggest that RGS2 might be involved in the pathogenesis of preeclampsia particularly in overweight women and contribute to their increased risk for hypertension and other types of cardiovascular disease later in life.
  • Roininen, Nelli Aurora (Helsingfors universitet, 2016)
    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.
  • Tanskanen, Tomas (Helsingfors universitet, 2013)
    Objective. Early-onset colorectal cancer (CRC), defined here as age of onset less than 40 years, develops frequently in genetically predisposed individuals. Next-generation sequencing is an increasingly available option in the diagnostic workup of suspected hereditary susceptibility, but little is known about the practical feasibility and additional diagnostic yield of the technology in this patient group. Materials and methods. We analyzed 38 young CRC patients derived from a set of 1514 CRC cases. All 38 tumors had been tested in our laboratory for microsatellite instability (MSI), and Sanger sequencing had been used to screen for MLH1 and MSH2 mutations in MSI cases. Also, gastrointestinal polyposis had been diagnosed clinically and molecularly. Family histories were acquired from national registries. If inherited syndromes had not been diagnosed in routine diagnostic efforts (n = 23), normal tissue DNA was analyzed for mutations in a comprehensive set of high-penetrance genes (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, SMAD4, BMPR1A, LKB1/STK11, and PTEN) by exome sequencing. Results. CRC predisposition syndromes were confirmed in 42% (16/38) of early-onset CRC patients. Hereditary nonpolyposis colorectal cancer was diagnosed in 12 (32%) patients, familial adenomatous polyposis in three (7.9%), and juvenile polyposis in one (2.6%) patient. Exome sequencing revealed one additional MLH1 mutation. Over half of the patients had advanced cancers (Dukes C or D, 61%, 23/38). The majority of nonsyndromic patients had unaffected first-degree relatives and microsatellite-stable tumors. Conclusions. Microsatellite instability positivity or gastrointestinal polyposis characterized all patients with unambiguous highly penetrant germline mutations. In our series, exome sequencing produced little added value in diagnosing the underlying predisposition conditions.
  • Karhu, Thomas (Helsingfors universitet, 2016)
    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.
  • Rantakokko, Kirsimarja (Helsingin yliopisto, 2018)
    Seksuaalirikosten uhrit kohtaavat seksuaalisen väkivallan lisäksi muutakin fyysistä väkivaltaa. Uhrin tutkimuksen osana tehdään fyysinen tutkimus, minkä tarkoituksena on, paitsi selvittää tarvitseeko uhri hoitoa, kerätä tietoa mahdollisista väkivallan merkeistä tulevaa oikeusprosessia varten. Tässä tutkielmassa käytettiin materiaalina Helsingin yliopiston oikeuslääkäriasemalla tutkittujen seksuaalirikosten uhrien lääkärin lausunnoista kerättyjä tietoja vuosilta 1954, 1964, 1974, 1984, 1994, 2002 ja 2012. Tarkastelimme väkivallan merkkien määrää uhreissa, riskitekijöitä, jotka vaikuttavat siihen saako uhri väkivallan merkkejä tai tuleeko tämä kuristetuksi, ja kuinka raa’alta heihin kohdistunut väkivalta vaikutti. Ulkoisten vamman merkkien perusteella väkivallan raakuuden arviointia varten kehitimme Violence Severity Scoren (VSS), jonka käyttöä pilotoimme tässä tutkielmassa. Yli puolilla uhreista oli todettavissa ei lainkaan tai hyvin vähän väkivallan merkkejä (VSS 0-5). Vakavaa väkivaltaa kohdanneiden osuus uhreista vaihteli vuosittain 1-15% välillä. Vamman merkeistä yleisin vammatyyppi oli mustelma, kaikkein harvinaisimpia olivat vakavammat merkit kuten murtumat. Yhteensä noin puolet vammojen merkeistä sijaitsi raajojen alueella ja neljäsosa taas erityisen vaarallisella alueella: päässä, kaulalla ja suussa. Aikuiset olivat suuremmassa riskissä saada väkivallan merkkejä ja joutua kuristetuksi kuin lapset. Tuntemattomien raiskaamat uhrit olivat suuremmassa riskissä joutua kuristetuksi kuin tuttujen raiskaamat. Osuus uhreista, joilla oli todettavissa fyysisten väkivallan merkkejä, aluksi kasvoi ollen korkeimmillaan 1984 ja 1994. 2000-luvulla väkivallan merkkejä saaneiden osuus jälleen pieneni. VSS:n avulla tarkastellen näimme samanlaisen kehityksen väkivallan raakuudessa. Kun asiaa tarkasteli pelkillä aikuisilla uhreilla, nähtiin, että vuonna 1954 väkivallan raakuus per uhri on ollut korkeimmillaan ja tämän jälkeen laskenut koko ajan kohti nykypäivää, lukuun ottamatta vuotta 1984, joka erottui poikkeuksellisen väkivaltaisena.
  • Saarentaus, Elmo (Helsingin yliopisto, 2017)
    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.
  • Vesanen, Kari (Helsingfors universitet, 2016)
    Studies have shown that there is a familial risk in developing lymphomas. This thesis aimed to find candidate predisposing mutations for inherited non-Hodgkin lymphoma susceptibility in a Finnish pedigree. Exome sequences were available from two individuals in the pedigree, and common mutations were sought from exomes using bioinformatical tools. The validity and uniqueness of these common mutations were verified, and variation segregation was assessed by sequencing variation areas from all lymphoma patients in the pedigree. After filtering, 13 common variations were found, but due to variation's presence also in healthy control samples or the lack of segregation in the kindred, no candidate variation explaining non-Hodgkin lymphoma clustering in the pedigree was found. However, this study proved a group of mutations that probably do not need further studies as candidate variations for inheritable non-Hodgkin lymphoma. This study also provided rough comparison data for two different DNA sequence analysis programs.
  • Pohjolan-Pirhonen, Risto (Helsingin yliopisto, 2018)
    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.
  • Mäkitie, Sara (Helsingfors universitet, 2016)
    Numerous genome-wide association studies (GWAS), GWAS meta-analyses and mouse studies have demonstrated that Wingless-related integration site 16 (WNT16) is associated with BMD, cortical bone thickness and strength as well as fracture risk. Practically no data exists regarding the significance of WNT16 in childhood-onset osteoporosis and fractures. Mutations and genetic variation in WNT16 were hypothesized to explain the clinical characteristics of some of the patients in question. Therefore, in this study the WNT16 gene was screened by Sanger sequencing in 46 pediatric patients with early-onset osteoporosis and in 60 pediatric patients with multiple fractures. We found altogether 12 variants in WNT16, of which one was a novel change. Inspite of the large amount of genetic variation found in WNT16, no actual mutations were found. None of the changes were statistically significant. It is likely that WNT16 mutations do not play an important role in the development of childhood osteoporosis.
  • Vasilescu, Catalina (Helsingin yliopisto, 2020)
    Next-Generation Sequencing (NGS) technologies enabled the characterization of the human genome and its variation in great detail within large cohorts. The current medical research aims towards personalized medicine, whereby identifying the causal disease mechanisms in each individual will promote more tailored forms of treatment. In genetic studies, NGS technologies involve targeted sequencing panels of known disease genes, whole-exome sequencing (WES) covering the genome's protein-coding part, and whole-genome sequencing (WGS). Our study applied targeted panels and WES for the genetic diagnosis of severe childhood disorders, starting with a progressive neurological syndrome and continuing with a cohort of 66 children diagnosed with cardiomyopathy, a leading cause of pediatric heart transplants. We made substantial progress in understanding the molecular basis of the studied disorders. First, we strengthen the evidence that heat shock response is a novel mechanism underlying leukoencephalopathy. Second, we characterized genetically a cohort of early-onset severe cardiomyopathies (KidCMP), representing the whole of Finland for patients evaluated for cardiac transplantation or receiving inotropic support. Third, we characterized a novel disease gene causing childhood cardiomyopathies, an important step in further deciphering the genetic landscape of these severe heart disorders. Altogether, this thesis highlights the power of novel technologies in identifying causal genetic variants and characterizing novel disease genes. Our findings enhance knowledge of the underlying molecular mechanisms and potentially aid in developing new therapeutic interventions. For families, the genetic diagnosis enables a causative recognition of the disease and identifying individuals at risk. Our cardiomyopathy project also contributed to establishing a protocol for systematic genetic testing of patients and families at the Pediatric Cardiology Department of the University of Helsinki Central Hospital.
  • Kanduri, Chakravarthi (Helsingin yliopisto, 2015)
    Music perception and performance form a useful tool for studying the normal functioning of the human brain. The abundance of neuroscientific literature has demonstrated that music perception and performance alter the human brain structure and function and induce physiological changes through neurochemical modulation. Emerging evidence from molecular genetic studies have suggested a substantial genetic component in musical aptitude and related traits like creativity in music. This thesis puts a step forward in understanding the molecular genetic background of music perception and performance, using a combination of genomics and bioinformatics approaches. Specifically, the role of copy number variations (CNVs; a form of genetic variation) in musical aptitude and creativity in music was investigated both in the largest families of the MUSGEN-project and also in sporadic cases. The effects of listening to music and performing music by playing an instrument on human transcriptional responses were also investigated. The genome-wide CNV analysis principally identified genes like GALM, PCDHA1-9 as the possible candidate genes that could affect musical aptitude and creativity in music. PCDHA1-9 and GALM genes are known to regulate the serotonergic system, which is responsible for neurocognitive and motor functions, the essential biological processes of music related traits. Overall, the detected genes affect neurodevelopment, learning, memory and serotonergic functions. The findings also demonstrated that large and rare CNV burden does not affect normal traits like musical aptitude. Both listening to music and performing music enhanced the activity of genes that are known to be involved in dopaminergic neurotransmission, neuroplasticity, learning, and memory. Most importantly, one of the most up-regulated genes in both studies - synuclein alpha (SNCA) and its upstream transcription regulator GATA2, are located on chromosomal regions 4q22.1 and 3q21 respectively linking the strongest linkage and associated regions of musical aptitude together. In addition, several of the up-regulated genes in both the studies (like SNCA, FOS, and DUSP1) have been known to be regulated during song learning and singing in songbirds, suggesting a possible evolutionary conservation of genes related to sound perception and production. These novel findings give preliminary information about the genes associated with musical aptitude and the effect of music on the human body. It is obvious that replication studies are required to confirm the results. These pioneering findings could guide further research on the molecular genetics of music perception and performance in humans. These findings will also enhance our understanding of the genetic bases of cognitive traits, the evolution of music and music therapy.
  • Mäkelä, Aaro (Helsingfors universitet, 2009)
    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.
  • Vlachopoulou, Efthymia (2015)
    The Human Leukocyte Antigen (HLA) region is located on chromosome 6 (6p21.3) and its main function is to regulate the immune system. This region has been associated with several autoimmune and other inflammatory conditions. However, many aspects of these associations remain unknown due to high polymorphism, high linkage disequilibrium (LD) and high gene density of this region that increase the complexity and create computational challenges. In this Thesis, the aim is to investigate the HLA haplotype variation in the Finnish population, to evaluate the HLA imputation using two of the existed softwares and to analyze the HLA association with Acute Coronary Syndrome (ACS). The main question in this study is whether the HLA region varies in the Finnish population compared to other populations and how this variation can influence the results of further analyses. The HLA haplotypes showed great variation in the Finnish population compared to other European populations due to different linkage disequilibrium (LD) structures and this highlights the diversity of the HLA haplotypes among different populations. The most common European haplotype HLA-A*01~HLA-B*08~HLA-DRB1*03 shows a lower frequency in Finland, whereas the enrichment of the haplotype HLA-A*03~HLA-B*35~HLA-DRB1*01 was observed (I). Furthermore, the poor imputation results of the HLA-DRB1 gene enhance the power of the previously mentioned arguments (from I) due to the inaccurate imputation from other European populations. The study emphasizes the need for population-specific reference materials for a successful imputation (II). The diversity of HLA alleles, the variability in the frequencies of Single Nucleotide Polymorphisms (SNP) among populations, the difference of the rare HLA alleles appearing in various populations and the extremely high amount of combinations of HLA alleles (due to high polymorphism) contribute to the low success rates of imputation. The association (OR = 4.43, 95% CI = 3.57-5.50) of a novel BTNL2;HLA-DRA;HLA-DRB1*01-haplotype with the risk of Acute Coronary Syndrome (ACS) was identified (III). The analysis showed the implication of the HLA-DRB1*01 allele and the BTNL2 gene to the inflammation process. These two genes affect the antigen presentation and its immune response. Overall, the associated haplotype appeared approximately in 15% of ACS patients and in 5% of healthy individuals. Furthermore, the survival analysis shows that the HLA-DRB1*01 allele does not affect the survival time after an ACS event. Our results provide more insight into the detailed patterns of the haplotypes in the Finnish population, into the success of the imputation approaches and into the HLA association with ACS. Genetic diversity is depicted on these haplotypes which might lead to different immune responses. These findings help future development of appropriate statistical tools for the HLA region.
  • Ristolainen, Heikki; Kilpivaara, Outi; Kamper, Peter; Taskinen, Minna; Saarinen, Silva; Leppä, Sirpa; d'Amore, Francesco; Aaltonen, Lauri A. (Helsingfors universitet, 2015)
    Tutkimuksessamme tarkastelimme Lähi-idästä lähtöisin olevaa perhettä, jossa kolmella viidestä lapsesta on todettu nuorellä iällä klassinen Hodgkinin lymfooma (cHL). Perinnöllinen alttius cHL:lle tunnetaan huonosti, eikä taudille mahdollisesti altistavia geenimuutoksia ole aiemmin raportoitui kuin yksi kappale. Geenimuutosten selvittämiseksi eksomisekvensoimme kolmen sairastuneen lapsen verinäytteestä eristetyn DNA:n ja poimimme joukosta kaikkien kolmen jakamat muutokset. Suodatimme lasten jakamien DNA-muutosten joukosta pois omissa vertailujoukoissamme ja useissa julkisissa tietokannoissa esiintyvät geneettiset muutokset ja arvioimme jäljellejääneiden muutosten haitallisuutta kahdella laskennallisella priorisaatioalgoritmilla. Näin saimme järjestettyä jäljelle jääneet 35 jaettua muutosta laskennalliseen haitallisuusjärjestykseen. Jaetuista muutoksista merkittävimmäksi nousi ACAN-geenissä oleva homotsygoottinen 57 emäksen pituinen deleetio c.2836_2892del, jota ei ole aiemmin liitytty cHL-fenotyyppiin.
  • Godbole, Nimish (Helsingin yliopisto, 2018)
    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.
  • Lindell, Rony (Helsingfors universitet, 2016)
    Next-generation sequencing has evolved during the past 10 years to become the go-to method for genome-wide analysis projects. Based on parallelizable PCR methods adopted from the traditional Sanger sequencing, NGS platforms can produce massive amounts of genetic information in a single run and read an entire DNA molecule within a day. The immense amount of nucleotide sequence data produced by a single sample has brought us to an era of algorithmic optimization for analysis and guring out parallelization schema. For cohort projects generally cloud based systems are used due to vast computing power requirements. Anduril is an integration and parallelization framework well suited for NGS analysis, as is shown in this study. After a brief review of the golden standard methods of NGS analysis, we describe the incorporation of the main tools into the new sequencing bundle for Anduril. Tools for alignment (BWA, Bowtie), recalibration (GATK, Picard-tools) and variant calling (GATK, Samtools, VarScan) are in main focus. The Best Practice of Broad Institute, creators of The Genome Analysis Toolkit (GATK), has been a big inspiration in the creation of our sequencing pipeline. The evolution of sequencing bundle tools into a pipeline is discussed through three separate project examples. First, a small group of 8 chronic myeloid leukemia patient samples were analysed after implementation of the main tools of the pipeline. The results were consistent with previous results, but no novel relevant mutations were found. Second, exome sequencing data from 180 breast cancers with controls available in TCGA (The Cancer Genome Atlas) were processed for use in various projects in our lab. The example showed the power of Anduril in gross cohort analysis projects, enabling automatic parallelization and intelligent work ow management system. Third, we analysed exome data from 330 TCGA ovarian cancers with controls and created a prototypical set of database components for creation of a database of annotated variants for use in analytical queries. Compared to other integration frameworks (e.g. GATK, Crossbow and Hadoop), Anduril is a robust contender for the programming oriented scientist. As cloud computing is becoming at an increasing rate a requirement in large genome-wide analysis projects, Anduril provides an e ective generalizable framework for adding tools, creating pipelines and executing entire work ows on multi-nodal computing servers. As technology advances and available computational resources grow, fast multi-processor analysis can be incorporated into health care more and more for detection of disease causing genes, medication kinetics altering polymorphisms and cancer driving mutations in an everyday setting.
  • Hinterding, Helena (Helsingin yliopisto, 2018)
    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.
  • Henrichsson-Helin, Jenni (Helsingin yliopisto, 2016)
    Sepelvaltimotaudin yhtenä taustatekijänä on verisuonitulehdus, jonka taustalla on immunologisia ja geneettisiä tekijöitä. MHC (Major Histocompatibility Complex) – geenialueella on haplotyyppejä, jotka liittyvät sepelvaltimotautiin. HLA-I-luokkaan kuuluvan HLA-DRB1-01*-alleelin tiedetään lisäävän sepelvaltimotautiriskiä mahdollisesti geneettisesti lisääntyvän tulehdustaipumuksen kautta. Tämän tutkimuksen tavoitteena oli etsiä myös muita sepelvaltimotaudille altistavia HLA-alleeleja ja haplotyyppejä. Tutkimusotantana oli 104 COROGENE-tutkimuksen tapausnäytettä ja 96 FINRISKI-tutkimuksen verrokkinäytettä. Sekä COROGENE- tapaus että FINRISKI-verrokkinäytteistä oli aikaisemmin tutkittu HLA-DRB1*01-geenilukumäärä ja BTNL2-SNP-haplotyypin kopiolukumäärä. Potilaat ja kontrollit jaoteltiin BTNL2-kopioluvun perusteella kolmeen eri ryhmään (0,1,2). Näistä ryhmistä tutkittiin DRB1*01- sekä DRB1*13-positiivisuutta sekä haplotyyppiryhmien ja DRB1*01-positiivisuuden välistä yhteyttä. Näytteiden analysoinnissa käytettiin CONEXIO Genomicsin SBT Resolver™ DRB1 exon 2 – menetelmää. Tilastollisina menetelminä käytettiin SPSS – ohjelman khiin neliötestiä ja alleelifrekvenssien analysoinnissa SKDM-HLA-työvälinettä. Tulosten perusteella näyttää siltä, että sepelvaltimotautipotilailla esiintyy kontrolleja enemmän HLA-DRB1*01 ja HLA-DRB1*13-alleeleja sisältäviä haplotyyppejä. Tutkimuksen otanta on kuitenkin liian suppea pidemmälle menevien johtopäätösten tekemiseen. Sepelvaltimotaudin perinnöllisen taustan selvittäminen on tärkeätä, jotta taudin puhkeaminen ja komplikaatioiden syntyminen voitaisiin tulevaisuudessa estää.
  • Muurinen, Mari (Helsingin yliopisto, 2018)
    A large part of the genetic and epigenetic changes contributing to human height and growth remain unknown. Silver-Russell syndrome (SRS) is a rare human growth disorder, where maternal uniparental disomy of chromosome 7 [UPD(7)mat] and loss of methylation at 11p15 (11p15 LOM) are the two major findings. However, a substantial proportion of the SRS patients remain without a molecular diagnosis. SRS is caused by a disturbance of imprinted genes that are expressed solely or predominantly from one parent and are important for growth and development. Imprinted genes may also be especially susceptible to environmental factors, which can cause persistent changes in methylation patterns and affect development of adult-onset diseases. This thesis aims to explore new genetic and epigenetic changes in SRS, as well as epigenetic changes of imprinted genes in growth-restricted children, children of normal growth and individuals born pre-term. In Study I, genomic structural variation of 22 SRS patients was studied with the Affymetrix 250K Sty microarray. Several copy number changes were found, including a heterozygous deletion of 15q26.3 including the insulin-like growth factor 1 receptor (IGF1R) gene. In Study II, CpGs in the insulin-like growth factor 2 (IGF2) gene (located in the 11p15 region) were tested in pre-term and very low birth weight born individuals with elevated levels of cardiovascular risk factors. DNA methylation changes were found in one CpG site of the pre-term born individuals compared to controls. In Study III, genome wide comparisons between the DNA methylation levels of SRS patients that have UPD(7)mat, controls, and an individual with paternal uniparental disomy of chromosome 7 [UPD(7)pat] were done. DNA methylation was studied using the Illumina Infinium HumanMethylation450K BeadChip technology, which is capable of measuring methylation level of more than 450 000 CpG sites across the genome. The study provided new information on the DNA methylation landscape of chromosome 7, suggesting new differentially methylated regions (DMRs) and imprinted genes. In Study IV, DNA methylation levels were compared between three different subgroups of SRS: SRS with UPD(7)mat, SRS with 11p15 LOM and clinical SRS without a known molecular etiology. The promoter region of homeobox A4 (HOXA4) gene was found hypomethylated in all of the subgroups of SRS. This region was subsequently tested in other severely growth-restricted patients and was found hypomethylated. Additionally, the methylation level of the HOXA4 promoter region was found to be associated with the height of school-aged children, suggesting that HOXA4 plays a role not only in SRS but also in the regulation of height in general. These studies found molecular changes in SRS, new differentially methylated regions in chromosome 7 and epigenetic findings potentially relevant for regulation of human growth. The findings provide potential targets for further studies in human growth and development.
  • Kleine, Iida-Marja (Helsingin yliopisto, 2018)
    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.