Browsing by Subject "genetiikka"

Suomalainen perinnöllinen amyloidoosi on kromosomissa 9 vallitsevasti periytyvä systeeminen amyloidoosi, joka tunnetaan myös nimillä Meretojan ja Kymenlaakson tauti. Taudin kuvasi vuonna 1969 Jouko Meretoja, joka arveli potilaiden yhteisen esi-isän olevan lähtöisin 1300- luvulta Kymenlaaksosta. Taudin aiheuttaa pistemutaatio c.640G > A p.D187N gelsoliini-geenissä. Hiljattain osoitettiin SNP-siru genotyypitykseen perustuen, että suomalaisilla potilailla on todennäköisesti yhteinen esi-isä. Tutkimuksen tavoitteena on arvioida, kuinka monen sukupolven päässä sijaitsee suomalaisten gelsoliiniamyloidoosipotilaiden viimeisin yhteinen esi-isä. Toisena tavoitteena on arvioida uuden perustajahaplotyypin säilymiseen perustuvan iänmääritysmenetelmän toimivuutta. Verifioiduksi kontrollimenetelmäksi tämän rinnalle valittiin laajasti iänmääritykseen käytetty alleeliassosiaation hajoamiseen perustuva menetelmä geenin ympärillä sijaitsevia polymorfisia toistojaksoja hyödyntäen. Polymorfisiin toistojaksoihin perustuva menetelmä arvioi etäisyyden yhteiseen esi-isään olevan noin 31 sukupolvea eli noin 775 vuotta. Tämä ei ollut linjassa perustajahaplotyypin säilymiseen nojaavan menetelmän kanssa, joka arvioi etäisyyden yhteiseen esi-isään olevan noin 79 sukupolven päässä.

Triglycerides are a type of lipid that enters our body with fatty food. High triglyceride levels are often caused by an unhealthy diet, poor lifestyle, poorly treated diseases such as diabetes and too little exercise. Other risk factors found in various studies are HIV, menopause, inherited lipid metabolism disorder and South Asian ancestry. Complications of high triglycerides include pancreatitis, carotid artery disease, coronary artery disease, metabolic syndrome, peripheral artery disease, and strokes. Migration has made Singapore diverse, and it contains several subpopulations. One third of the population has genetic ancestry in China. The second largest group has genetic ancestry in Malaysia, and the third largest has genetic ancestry in India. Even though Singapore has one of the highest life expectancies in the world, unhealthy lifestyles such as poor diet, lack of exercise and smoking are still visible in everyday life. The purpose of this thesis was to introduce GWAS-analysis for quantitative traits and apply it to real data, and also to see if there are associations between some variants and triglycerides in three main subpopulations in Singapore and compare the results to previous studies. The research questions that this thesis answered are: what is GWAS analysis and what is it used for, how can GWAS be applied to data containing quantitative traits, and is there associations between some SNPs and triglycerides in three main populations in Singapore. GWAS stands for genome-wide association studies designed to identify statistical association between genetic variants and phenotypes or traits. One reason for developing GWAS was to learn to identify different genetic factors which have an impact on significant phenotypes, for instance susceptibility to certain diseases Such information can eventually be used to predict the phenotypes of individuals. GWAS have been globally used in, for example, anthropology, biomedicine, biotechnology, and forensics. The studies enhance the understanding of human evolution and natural selection and helps forward many areas of biology. The study used several quality control methods, linear models, and Bayesian inference to study associations. The research results were examined, among other things, with the help of various visual methods. The dataset used in this thesis was an open data used by Saw, W., Tantoso, E., Begum, H. et al. in their previous study. This study showed that there are associations between 6 different variants and triglycerides in the three main subpopulations in Singapore. The study results were compared with the results of two previous studies, which differed from the results of this study, suggesting that the results are significant. In addition, the thesis reviewed the ethics of GWAS and the limitations and benefits of GWAS. Most of the studies like this have been done in Europe, so more research is needed in different parts of the world. This research can also be continued with different methods and variables.

Hammaspuutokset ovat yleisin kraniofakiaalinen anomalia. Ne voivat esiintyä sekä erillisinä anomalioina että oireyhtymien yhteydessä. Niiden vaikutus elämänlaatuun on negatiivinen muun muassa heikentyneen suunterveyden ja sosiaalisten suhteiden vaikeutumisen kautta. Pekka Niemisen tutkimusryhmä Helsingin yliopistosta löysi hammaspuutospotilaiden perimätutkimuksissa kaksi uutta mahdollisesti hammaspuutoksia aiheuttavaa geenimutaatiota geenissä RNF43. RNF43-proteiini on normaalisti toimiessaan osa hampaiden kehitykseen ja kasvuun vaikuttavan WNT-viestinnän negatiivista takaisinkytkentää. Mutaatioiden arvellaan häiritsevän hampaiden kehitystä WNT-viestinnän aktiivisuuden muuntelemisen kautta. Tutkimuksessamme tutkimme mutaatioiden vaikutusta RNF43-proteiinin määrään ja sijoittumiseen solussa ja pyrimme näin todistamaan mutaatioiden patogeenisyyden. Käytimme tutkimuksessa HEK293-soluja. Transfektoimme niitä villityypin ja kahden eri mutaation plasmideilla, jotka sisälsivät myös GFP-proteiinin. Värjäsimme niitä membraani- ja tumaväriaineilla, jotta pystyimme hahmottamaan GFP:n ja siten proteiinin sijaintia solussa fluoresenssi- ja konfokaalimikroskooppien avustuksella. Mutaatioilla ei havaittu olevan vaikutusta RNF43:n tuotannon määrään tai sijoittumiseen soluissa, emmekä näin ollen voineet tässä tutkimuksessa todentaa niiden patogeenisyyttä. Veimme tutkimuksellamme kuitenkin kyseisten mutaatioiden ja hammaspuutosten genetiikan tutkintaa eteenpäin. Tästä tutkimuksesta saatujen havaintojen pohjalta voidaan RNF43-geenin mutaatioiden tutkimusta jatkaa muilla menetelmillä.

Familial combined hyperlipidemia (FCH) is a complex and common familial dyslipidemia characterized by elevated total cholesterol and/or triglyceride levels with over five-fold risk of coronary heart disease. The genetic architecture and contribution of rare Mendelian and common variants to FCH susceptibility is unknown. In 53 Finnish FCH families, we genotyped and imputed nine million variants in 715 family members with DNA available. We studied the enrichment of variants previously implicated with monogenic dyslipidemias and/or lipid levels in the general population by comparing allele frequencies between the FCH families and population samples. We also constructed weighted polygenic scores using 212 lipid-associated SNPs and estimated the relative contributions of Mendelian variants and polygenic scores to the risk of FCH in the families. We identified, across the whole allele frequency spectrum, an enrichment of variants known to elevate, and a deficiency of variants known to lower LDL-C and/or TG levels among both probands and affected FCH individuals. The score based on TG associated SNPs was particularly high among affected individuals compared to non-affected family members. Out of 234 affected FCH individuals across the families, seven (3%) carried Mendelian variants and 83 (35%) showed high accumulation of either known LDL-C or TG elevating variants by having either polygenic score over the 90th percentile in the population. The positive predictive value of high score was much higher for affected FCH individuals than for similar sporadic cases in the population. FCH is highly polygenic, supporting the hypothesis that variants across the whole allele frequency spectrum contribute to this complex familial trait. Polygenic SNP panels improve identification of individuals affected with FCH, but their clinical utility remains to be defined.

Canine uveal melanoma (UM) usually manifests as a slowly developing, darker pigmented and well distinguishable mass in the iris. Less than a third of them are considered malignant, which is much less than with other melanocytic cancers. In contrast, in humans, 90% of UM occurs in the choroid and half of the patients eventually develop aggressive and often lethal metastases. Understanding the disease process and genetic background in dogs might also help us further the knowledge and improve the treatment options of humans. There is a hereditary component to the oncogenesis of the UM: the disease is more common in a Caucasian race and is also found in certain families. It is also more prevalent in certain dog breeds; Labrador Retrievers seem to be overrepresented. Several susceptibility genes have been identified in humans. One with the strongest association with UM is a tumor suppressor gene BAP1, which is dysfunctional or missing in nearly half of the human uveal melanomas. This gene is a so-called secondary driver of the UM and mutations in it spark the metastasizing process. There is a germline mutation of BAP1 in fourth of Finnish UM families and these mutations are also connected to various other cancers. Moreover, BAP1 shows over 98% protein product homology and almost 80% mRNA homology between dogs and humans, making it an appealing study target also for canines. Should a single variant account for high UM risk, a DNA test could be developed to be used in breeding and veterinary diagnostics. In this work, I mapped the BAP1 germline mutations of seven Labrador Retrievers with diagnosed uveal melanomas or melanocytomas. It was found that four dogs shared the same set of five heterozygous single nucleotide variants (SNV). One of the SNVs within exon 17 was synonymous, g.37,363,076G>A, p.(Ser721Ser), while the other four SNVs were intronic, residing close to exons 4, 10, 11 and 14. In the future, variant comparisons with healthy Labradors are needed to study the role of the identified variants for the development of UM, as the SNVs now found could also just be a part of a common variation in the Labrador Retriever gene pool. To grasp a bigger picture of the UM tumor development, the tumors themselves should also be analyzed for somatic mutations. Moreover, when we know that the disease is likely affected by over a hundred genes, studying just one gene is unnecessarily self-restricting. Modern full genome sequencing techniques should be used for catching all the predisposing genes simultaneously.