Univariate and multivariate statistical tests in genetic association studies

Genome-wide association studies have identified hundreds of genomic loci associated with a wide range of human conditions and quantitative traits, such as cholesterol level and diabetes. However, most of these studies have focused on analysing single traits, even the studies involving multiple related traits. Growing evidence for pleiotropy, where the same genetic locus is associated with multiple traits, supports the idea that multivariate methods could provide a remarkable boost in statistical power compared to univariate methods. In this thesis the main research question is to compare the multivariate Wald test to the corresponding univariate test, and to see when multivariate testing is more useful. My second research question is to compare the multivariate Wald test and another multivariate method called Canonical Correlation Analysis (CCA), and to see if they yield the same result. To examine these topics I performed a simulation study in which I simulated data set with 1,000 genotypes and 1,000 individuals. In addition I simulated bivariate phenotypes that were differently correlated with each other, and the genotypes. I performed the univariate Wald test for each trait against each genotype, and the multivariate Wald test for each trait pair against each genotype. I also performed the corresponding CCA to compare those results with the Wald test. In addition to the simulation study I performed the similar analyses for real data from The National FINRISK Study. I used three different blood lipid measurements, HDL-cholesterol, LDL-cholesterol and triglycerides as example traits, and 157 genomic loci previously known to associate with blood lipid levels. These blood lipid levels were appropriate example traits for this study because they are correlated differently with each other, and they are differently associated with the 157 genomic loci used here. Therefore I found many different combinations of correlation between traits, and directions of genetic effects for different traits. Based on my simulation studies I can say that the multivariate testing is never much worse in terms of power to detect associations than the corresponding univariate tests, and in some cases it is much more powerful. Thus there is no reason not to do the multivariate analysis first in case of studying multiple related traits. Multivariate testing is more powerful in cases where the correlation between the traits is large and the genetic effects for the traits show opposite directions compared to the trait correlation. The least effective multivariate testing is compared to univariate testing when the correlation between the traits is small, and the directions of genetic effects is consistent with the trait correlation. Based on my results multivariate Wald test and CCA yield the same results, with some minor approximation differencies in small sample sizes.Perimänlaajuisten assosiaatioanalyysien avulla on löydetty satoja perimän kohtia, jotka ovat yhteydessä useisiin sairauksiin tai ominaisuuksiin kuten kolesterolitasoihin ja diabetekseen. Useimmat näistä tutkimuksista ovat kuitenkin tutkineet ainoastaan yhtä ominaisuutta kerrallaan, vaikka tutkimus käsittelisikin useita toisiinsa liittyviä muuttujia. Kasvava näyttö siitä, että yksi perimän kohta on yhteydessä useisiin ominaisuuksiin (pleiotropia) tukee ajatusta, että monimuuttujamenetelmät voisivat olla tehokkaampia kuin yhden muuttujan menetelmät. Tutkielmani päätutkimuskysymys on vertailla moniulotteista Waldin testiä vastaavaan yhden muuttujan testiin, ja katsoa millaisissa tilanteissa on tehokkaampaa käyttää monimuuttujatestausta. Toinen tutkimuskysymykseni on vertailla moniulotteista Waldin testiä toiseen monimuuttujamenetelmään, kanoniseen korrelaatioanalysiin (CCA) ja katsoa tuottavatko nämä menetelmät saman tuloksen. Tutkiakseni näitä asioita tein simulaatiotutkimuksen, jossa simuloin aineiston, jossa on 1,000 genotyyppiä 1,000 henkilölle. Tämän lisäksi simuloin muuttujapareja, jotka ovat eri tavoin yhteydessä toisiinsa, sekä simuloituihin genotyyppeihin. Tein jokaiselle muuttujalle yhden muuttujan Waldin testin jokaista genotyyppiä vastaan, sekä jokaiselle muuttujaparille moniulotteisen Waldin testin jokaista genotyyppiä vastaan. Tein myös vastaavat kanoniset korrelaatioanalyysit jotta voin vertailla näitä tuloksia moniulotteisen Waldin testin tuloksiin. Simulaatiotutkimuksen lisäksi tein vastaavat analyysit myös aineistolle FINRISKI-tutkimuksesta. Esimerkkimuuttujinani käytin kolmea veren lipidiarvoa, HDL-kolesterolia, LDL-kolesterolia ja triglyserideja, sekä 157 perimän kohtaa, joiden tiedetään olevan yhteydessä veren lipiditasoihin. Lipiditasot olivat hyvä esimerkki tähän tutkimukseen, koska ne ovat erilailla yhteydessä keskenään, sekä näiden 157 perimän kohtien kanssa. Näin ollen löysin useita erilaisia yhdistelmiä lipidien välisistä yhteyksistä sekä perimän vaikutuksista eri lipideille. Simulaatiotutkimusteni perusteella voimme sanoa, että monimuuttujatestaus on lähes aina vähintään yhtä voimakas havaitsemaan yhteyksiä kuin vastaavat yhden muuttujan testit, ja joissain tapauksissa se on paljon voimakkaampi. Näin ollen ei ole mitään syytä olla suorittamatta monimuuttujatestausta ensin, kun on kyse useista toisiinsa liittyvistä muuttujista. Monimuuttujatestaus on selkeästi voimakkaampi tilanteissa, joissa muuttujien välinen korrelaatio on suurta ja perimän vaikutus näihin muuttujiin on erisuuntaista. Vähiten monimuuttujatestaamisesta on hyötyä yhden muuttujan testiin verrattuna silloin, kun muuttujien välinen korrelaatio on pientä, ja perimän vaikutus muuttujiin on samansuuntaista. Tutkimusteni perusteella voimme myös sanoa, että moniulotteinen Waldin testi ja CCA tuottavat saman tuloksen, joskin pienillä otoskoilla huomataan pieniä approksimaatioeroja

Moyamoya angiopathy: long-term follow-up study in a Finnish population

Moyamoya angiopathy (MMA) is a chronic cerebrovascular disorder predominantly starting in childhood or early adulthood and thus affects the whole lifetime. Little is known on MMAs long-term outcomes in European patients. We report long-term follow-up data on Finnish MMA patients.Peer reviewe

Lipidome- and Genome-Wide Study to Understand Sex Differences in Circulatory Lipids

Background Despite well-recognized differences in the atherosclerotic cardiovascular disease risk between men and women, sex differences in risk factors and sex-specific mechanisms in the pathophysiology of atherosclerotic cardiovascular disease remain poorly understood. Lipid metabolism plays a central role in the development of atherosclerotic cardiovascular disease. Understanding sex differences in lipids and their genetic determinants could provide mechanistic insights into sex differences in atherosclerotic cardiovascular disease and aid in precise risk assessment. Herein, we examined sex differences in plasma lipidome and heterogeneity in genetic influences on lipidome in men and women through sex-stratified genome-wide association analyses. Methods and Results We used data consisting of 179 lipid species measured by shotgun lipidomics in 7266 individuals from the Finnish GeneRISK cohort and sought for replication using independent data from 2045 participants. Significant sex differences in the levels of 141 lipid species were observed (PPeer reviewe

Sleep apnoea is a risk factor for severe COVID-19

Background Obstructive sleep apnoea (OSA) is associated with higher body mass index (BMI), diabetes, older age and male gender, which are all risk factors for severe COVID-19. We aimed to study if OSA is an independent risk factor for COVID-19 infection or for severe COVID-19. Methods OSA diagnosis and COVID-19 infection were extracted from the hospital discharge, causes of death and infectious diseases registries in individuals who participated in the FinnGen study (n=260 405). Severe COVID-19 was defined as COVID-19 requiring hospitalisation. Multivariate logistic regression model was used to examine association. Comorbidities for either COVID-19 or OSA were selected as covariates. We performed a meta-analysis with previous studies. Results We identified 445 individuals with COVID-19, and 38 (8.5%) of them with OSA of whom 19 out of 91 (20.9%) were hospitalised. OSA associated with COVID-19 hospitalisation independent from age, sex, BMI and comorbidities (p-unadjusted=5.13x10(-5), OR-adjusted=2.93 (95% CI 1.02 to 8.39), p-adjusted=0.045). OSA was not associated with the risk of contracting COVID-19 (p=0.25). A meta-analysis of OSA and severe COVID-19 showed association across 15 835 COVID-19 positive controls, and n=1294 patients with OSA with severe COVID-19 (OR=2.37 (95% 1.14 to 4.95), p=0.021). Conclusion Risk for contracting COVID-19 was the same for patients with OSA and those without OSA. In contrast, among COVID-19 positive patients, OSA was associated with higher risk for hospitalisation. Our findings are in line with earlier works and suggest OSA as an independent risk factor for severe COVID-19.Peer reviewe

Human essential hypertension : no significant association of polygenic risk scores with antihypertensive drug responses

Polygenic risk scores (PRSs) for essential hypertension, calculated from>900 genomic loci, were recently found to explain a significant fraction of hypertension heritability and complications. To investigate whether variation of hypertension PRS also captures variation of antihypertensive drug responsiveness, we calculated two different PRSs for both systolic and diastolic blood pressure: one based on the top 793 independent hypertension-associated single nucleotide polymorphisms and another based on over 1 million genome-wide variants. Using our pharmacogenomic GENRES study comprising four different antihypertensive monotherapies (n similar to 200 for all drugs), we identified a weak, but (after Bonferroni correction) statistically nonsignificant association of higher genome-wide PRSs with weaker response to a diuretic. In addition, we noticed a correlation between high genome-wide PRS and electrocardiographic left ventricular hypertrophy. Finally, using data of the Finnish arm of the LIFE study (n=346), we found that PRSs for systolic blood pressure were slightly higher in patients with drug-resistant hypertension than in those with drug-controlled hypertension (p=0.03, not significant after Bonferroni correction). In conclusion, our results indicate that patients with elevated hypertension PRSs may be predisposed to difficult-to-control hypertension and complications thereof. No general association between a high PRS and less efficient drug responsiveness was noticed.Peer reviewe

Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

Autosomal genetic analyses of blood lipids have yielded key insights for coronary heart disease (CHD). However, X chromosome genetic variation is understudied for blood lipids in large sample sizes. We now analyze genetic and blood lipid data in a high-coverage whole X chromosome sequencing study of 65,322 multi-ancestry participants and perform replication among 456,893 European participants. Common alleles on chromosome Xq23 are strongly associated with reduced total cholesterol, LDL cholesterol, and triglycerides (min P = 8.5 × 10-72), with similar effects for males and females. Chromosome Xq23 lipid-lowering alleles are associated with reduced odds for CHD among 42,545 cases and 591,247 controls (P = 1.7 × 10-4), and reduced odds for diabetes mellitus type 2 among 54,095 cases and 573,885 controls (P = 1.4 × 10-5). Although we observe an association with increased BMI, waist-to-hip ratio adjusted for BMI is reduced, bioimpedance analyses indicate increased gluteofemoral fat, and abdominal MRI analyses indicate reduced visceral adiposity. Co-localization analyses strongly correlate increased CHRDL1 gene expression, particularly in adipose tissue, with reduced concentrations of blood lipids

Geographic Variation and Bias in the Polygenic Scores of Complex Diseases and Traits in Finland

Polygenic scores (PSs) are becoming a useful tool to identify individuals with high genetic risk for complex diseases, and several projects are currently testing their utility for translational applications. It is also tempting to use PSs to assess whether genetic variation can explain a part of the geographic distribution of a phenotype. However, it is not well known how the population genetic properties of the training and target samples affect the geographic distribution of PSs. Here, we evaluate geographic differences, and related biases, of PSs in Finland in a geographically well-defined sample of 2,376 individuals from the National FINRISK study. First, we detect geographic differences in PSs for coronary artery disease (CAD), rheumatoid arthritis, schizophrenia, waist-hip ratio (WHR), body-mass index (BMI), and height, but not for Crohn disease or ulcerative colitis. Second, we use height as a model trait to thoroughly assess the possible population genetic biases in PSs and apply similar approaches to the other phenotypes. Most importantly, we detect suspiciously large accumulations of geographic differences for CAD, WHR, BMI, and height, suggesting bias arising from the population's genetic structure rather than from a direct genotype-phenotype association. This work demonstrates how sensitive the geographic patterns of current PSs are for small biases even within relatively homogeneous populations and provides simple tools to identify such biases. A thorough understanding of the effects of population genetic structure on PSs is essential for translational applications of PSs.Peer reviewe

Increased Risk of Preeclampsia in Women With a Genetic Predisposition to Elevated Blood Pressure

Background: Preeclampsia causes significant maternal and perinatal morbidity. Genetic factors seem to affect the onset of the disease. We aimed to investigate whether the polygenic risk score for blood pressure (BP; BP-PRS) is associated with preeclampsia, its subtypes, and BP values during pregnancy. Methods: The analyses were performed in the FINNPEC study (Finnish Genetics of Pre-Eclampsia Consortium) cohort of 1514 preeclamptic and 983 control women. In a case-control setting, the data were divided into percentiles to compare women with high BP-PRS (HBP-PRS; >95th percentile) or low BP-PRS (Peer reviewe