Using large-scale cohorts to identify genetic backgrounds of complex traits

Most cases of diseases with heritable components are not explained by single-gene variants following Mendelian inheritance. The majority of such heritable traits result from the combined contributions of many genes, environmental factors, and chance. These are called complex traits, and include phenotypes such as intelligence, neuropsychiatric disorders, and susceptibility to infection. In this thesis, I investigate how the genetic component of complex traits can be explained using rare and common variation. The first study investigated the genetic etiology of rare idiopathic intellectual disability and syndromic comorbidities in an extreme population isolate in Northern Finland affected by several genetic bottlenecks. Here, I found that there is a significant common variant component in ID, in addition to the rare variant burden expected by nature of the phenotype and study design. I then sought to improve our understanding of general differences in rare variant burden. I analyzed the phenotypes of rare disease-associated copy number variants (CNVs) among patients with epilepsy and comorbid features from several neurology specialist clinics in Europe and the US. Pathogenic CNVs were detected in 10.9% of cases and associated with non-neurological but not neurological phenotypes. The results indicate that in syndromic epilepsy, rare CNV impact associates with other organ systems instead of along neurological disease severity. Next, to investigate the impact rare pathogenic CNVs have on general quality of life in unaffected carriers, I analyzed the impact on general health and socioeconomic factors in two Finnish population cohorts. I found that in the unaffected population, there is an average socioeconomic impact of high-risk CNVs, although one that is less than the impact of polygenic risk scores (PRSs) for educational attainment and intelligence. Finally, to improve understanding of chronic and complicated infections of the upper respiratory tract, I performed a genome-wide association study (GWAS) of these diseases in the biobank-scale FinnGen study. I detected an underlying genetic structure impacting several heritable inflammatory traits of the upper respiratory tract, including their shared and distinct genetic signals. Several important results of the biology of these diseases were recognized, although the majority of the expected high heritability remains unexplained. In conclusion, the studies of this thesis highlight distinct features of both rare and common variation. Rare variant analysis studies the extent of phenotypic variation, with biology inferred from the extreme. For common variation, shared effects observed along the disease spectrum can be leveraged to highlight broad biological impact—as observed here in infectious and inflammatory upper respiratory diseases. These results challenge the single-gene hypothesis for complex traits and highlight a joint contribution of common and rare variation.Vain pieni osa perinnöllisyyteen pohjautuvasta yksilöllisestä vaihtelusta selittyy Mendelin lakeja noudattavien yhden geenin varianttien avulla. Valtaosa perinnöllisten piirteiden vaihtelusta selittyy sen sijaan lukuisten geenien, ympäristötekijöiden ja satunnaisvaihtelun yhdistelmästä. Tällä tavoin ilmentyviä piirteitä ovat esimerkiksi älykkyys, neuropsykiatriset tautitilat sekä infektioalttius, ja tätä periytymistapaa kutsutaan kompleksiseksi periytymiseksi. Tässä väitöskirjassa tarkastelen geneettisen taustan vaikutusta kompleksisesti periytyviin sairauksiin ja piirteisiin. Ensimmäisessä osatyössä etsin harvinaiselle idiopaattiselle älylliselle kehitysvammalle altistavia perintötekijöitä pohjoissuomalaisessa erittäin isoloituneessa väestössä. Havaittiin, että harvinaisten tautivarianttien lisäksi myös tavalliseen älykkyyden vaihteluun liitetyillä geenimuodoilla oli osuutta älyllisen kehitysvammaisuuden synnyssä. Seuraavassa osatyössä tutkin epilepsiaa ja ainakin yhtä muuta neurologista tautia sairastavien potilaiden aineistoa, joka oli kootty ympäri Eurooppaa ja Yhdysvaltoja. Voitiin havaita, että perimän harvinaisten tautiliitännäisten kopiolukuvariaatioiden (CNV:n) löytyminen ei korreloinut epilepsian vaikeusasteen kanssa, vaan liittyi siihen miten runsaasti potilailla esiintyi muita kuin neurologisia löydöksiä. Aiemmista tuloksista poiketen harvinaisten CNV:n vaikutus ei siis liittynyt vakavaan neurologiseen tautiin vaan häiriöihin myös muissa elinjärjestelmissä. Kolmannessa osatyössä tarkastelin kahdessa suomalaisessa väestöaineistossa, miten tiettyihin tauteihin liitetyt CNV:t vaikuttivat terveessä väestössä esiintyessään näiden henkilöiden yleiseen terveyteen ja sosioekonomisiin tekijöihin. Työssä kävi ilmi, että terveissäkin kantajissa tauteihin liitetyillä CNV:lla on keskimäärin vaikutusta sosioekonomisiin tekijöihin, mutta vaikutus on vähäisempi kuin mitä havaitaan koulutukselle ja älykkyydelle lasketuilla polygeenisilla riskipisteillä (PRS:llä). Viimeisessä osatyössä tutkin perinnöllistä alttiutta komplisoituneisiin ylähengitystieinfektioihin genominlaajuisella assosiaatioanalyysillä (GWAS) käyttäen aineistona FinnGen-tutkimuksen biopankkiaineistoa. Havaitsin, että erilaisia ylähengitysteiden sairauksia sairastavilla vaikutti olevan osittain samankaltainen altistava geenitausta, johon sisältyi myös selvästi eriäviä geneettisiä tekijöistä. Useita tärkeitä havaintoja näiden tautien biologian suhteen tehtiin, vaikka suurin osa näissä taudeissa havaitusta perinnöllisestä alttiudesta ei näillä tuloksilla selitykään. Loppupäätelmänä tämän väitöskirjan osatyöt havainnollistavat eroja harvinaisten ja tavallisten perinnöllisten tekijöiden välillä. Harvinaisen geenivaihtelun tutkiminen pyrkii selvittämään ilmentymisvaihtelun laajuutta, etsien biologisia johtolankoja ääri-ilmiöistä. Väestössä tavallisten geenivarianttien tutkimisessa hyödynnetään tavallisten tautitilojen ja ominaisuuksien koko ilmentymiskirjoa laajan biologisen vaikutuksen havaitsemiseksi – kuten tässä vaikutusta tulehduksellisiin ylähengitystietauteihin. Osatöiden tulokset haastavat yhden aiheuttajageenin hypoteesia kompleksisissa piirteissä, ja havainnollistavat tavallisen ja harvinaisen geenivaihtelun yhteisvaikutusta

Polygenic burden has broader impact on health, cognition, and socioeconomic outcomes than most rare and high-risk copy number variants

Copy number variants (CNVs) are associated with syndromic and severe neurological and psychiatric disorders (SNPDs), such as intellectual disability, epilepsy, schizophrenia, and bipolar disorder. Although considered high-impact, CNVs are also observed in the general population. This presents a diagnostic challenge in evaluating their clinical significance. To estimate the phenotypic differences between CNV carriers and non-carriers regarding general health and well-being, we compared the impact of SNPD-associated CNVs on health, cognition, and socioeconomic phenotypes to the impact of three genome-wide polygenic risk score (PRS) in two Finnish cohorts (FINRISK, n = 23,053 and NFBC1966, n = 4895). The focus was on CNV carriers and PRS extremes who do not have an SNPD diagnosis. We identified high-risk CNVs (DECIPHER CNVs, risk gene deletions, or large [\u3e1 Mb] CNVs) in 744 study participants (2.66%), 36 (4.8%) of whom had a diagnosed SNPD. In the remaining 708 unaffected carriers, we observed lower educational attainment (EA; OR = 0.77 [95% CI 0.66-0.89]) and lower household income (OR = 0.77 [0.66-0.89]). Income-associated CNVs also lowered household income (OR = 0.50 [0.38-0.66]), and CNVs with medical consequences lowered subjective health (OR = 0.48 [0.32-0.72]). The impact of PRSs was broader. At the lowest extreme of PRS for EA, we observed lower EA (OR = 0.31 [0.26-0.37]), lower-income (OR = 0.66 [0.57-0.77]), lower subjective health (OR = 0.72 [0.61-0.83]), and increased mortality (Cox\u27s HR = 1.55 [1.21-1.98]). PRS for intelligence had a similar impact, whereas PRS for schizophrenia did not affect these traits. We conclude that the majority of working-age individuals carrying high-risk CNVs without SNPD diagnosis have a modest impact on morbidity and mortality, as well as the limited impact on income and educational attainment, compared to individuals at the extreme end of common genetic variation. Our findings highlight that the contribution of traditional high-risk variants such as CNVs should be analyzed in a broader genetic context, rather than evaluated in isolation

Diagnostic implications of genetic copy number variation in epilepsy plus

Objective Copy number variations (CNVs) represent a significant genetic risk for several neurodevelopmental disorders including epilepsy. As knowledge increases, reanalysis of existing data is essential. Reliable estimates of the contribution of CNVs to epilepsies from sizeable populations are not available. Methods We assembled a cohort of 1255 patients with preexisting array comparative genomic hybridization or single nucleotide polymorphism array based CNV data. All patients had "epilepsy plus," defined as epilepsy with comorbid features, including intellectual disability, psychiatric symptoms, and other neurological and nonneurological features. CNV classification was conducted using a systematic filtering workflow adapted to epilepsy. Results Of 1097 patients remaining after genetic data quality control, 120 individuals (10.9%) carried at least one autosomal CNV classified as pathogenic; 19 individuals (1.7%) carried at least one autosomal CNV classified as possibly pathogenic. Eleven patients (1%) carried more than one (possibly) pathogenic CNV. We identified CNVs covering recently reported (HNRNPU) or emerging (RORB) epilepsy genes, and further delineated the phenotype associated with mutations of these genes. Additional novel epilepsy candidate genes emerge from our study. Comparing phenotypic features of pathogenic CNV carriers to those of noncarriers of pathogenic CNVs, we show that patients with nonneurological comorbidities, especially dysmorphism, were more likely to carry pathogenic CNVs (odds ratio = 4.09, confidence interval = 2.51-6.68; P = 2.34 x 10(-9)). Meta-analysis including data from published control groups showed that the presence or absence of epilepsy did not affect the detected frequency of CNVs. Significance The use of a specifically adapted workflow enabled identification of pathogenic autosomal CNVs in 10.9% of patients with epilepsy plus, which rose to 12.7% when we also considered possibly pathogenic CNVs. Our data indicate that epilepsy with comorbid features should be considered an indication for patients to be selected for a diagnostic algorithm including CNV detection. Collaborative large-scale CNV reanalysis leads to novel declaration of pathogenicity in unexplained cases and can promote discovery of promising candidate epilepsy genes.Peer reviewe

Duplications at 19q13.33 in patients with neurodevelopmental disorders

Objective After the recent publication of the first patients with disease-associated missense variants in the GRIN2D gene, we evaluate the effect of copy number variants (CNVs) overlapping this gene toward the presentation of neurodevelopmental disorders (NDDs). Methods We exploredClinVar (number ofCNVs = 50,794) andDECIPHER (number ofCNVs = 28,085) clinical databases of genomic variations for patients with copy number changes overlapping the GRIN2D gene at the 19q13.33 locus and evaluated their respective phenotype alongside their frequency, gene content, and expression, with publicly available reference databases. Results We identified 11 patients with microduplications at the 19q13.33 locus. The majority of CNVs arose de novo, and comparable CNVs are not present in control databases. All patients were reported to have NDDs and dysmorphic features as the most common clinical phenotype (N = 8/11), followed by seizures (N = 6/11) and intellectual disability (N = 5/11). All duplications shared a consensus region of 405 kb overlapping 13 genes. After screening for duplication tolerance in control populations, positive gene brain expression, and gene dosage sensitivity analysis, we highlight 4 genes for future evaluation: CARD8, C19orf68, KDELR1, and GRIN2D, which are promising candidates for disease causality. Furthermore, investigation of the literature especially supports GRIN2D as the best candidate gene. Conclusions Our study presents dup19q13.33 as a novel duplication syndrome locus associated with NDDs. CARD8, C19orf68, KDELR1, and GRIN2D are promising candidates for functional follow-up.Peer reviewe

The relative proportion of comorbidities among rhinitis and rhinosinusitis patients and their impact on visit burden

Background The aim was to evaluate the relative proportion of Non-steroidal anti-inflammatory drug exacerbated respiratory disease (NERD) and other comorbidities, and their impact on the burden of outpatient visits due to allergic rhinitis (AR), non-allergic rhinitis (NAR), acute rhinosinusitis (ARS), and chronic rhinosinusitis with nasal polyps (CRSwNP) and without (CRSsNP). Methods We used hospital registry data of a random sample of 5080 rhinitis/rhinosinusitis patients diagnosed during 2005-2019. International Statistical Classification of Diseases and Related Health Problems (ICD10) diagnoses, visits, and other factors were collected from electronic health records by using information extraction and data processing methods. Cox's proportional hazards model was used for modeling the time to the next outpatient visit. Results The mean (+/- standard deviation) age of the population was 33.6 (+/- 20.7) years and 56.1% were female. The relative proportion of AR, NAR, ARS, CRSsNP and CRSwNP, were 33.5%, 27.5%, 27.2%, 20.7%, and 10.9%, respectively. The most common other comorbidities were asthma (44.4%), other chronic respiratory diseases (38.5%), musculoskeletal diseases (38.4%), and cardiovascular diseases (35.7%). Non-steroidal anti-inflammatory drug exacerbated respiratory disease existed in 3.9% of all patients, and 17.7% of the CRSwNP group. The relative proportion of subjects having 1, 2, 3 and >= 4 other diseases were 18.0%, 17.6%, 17.0%, 37.0%, respectively. All diseases except AR, ARS, and mouth breathing, were associated with a high frequency of outpatient visits. Conclusions Our results revealed a high relative proportion of NERD and other comorbidities, which affect the burden of outpatient visits and hence confirm the socioeconomic impact of upper airway diseases.Peer reviewe

Heterozygous TYROBP deletion (PLOSLFIN) is not a strong risk factor for cognitive impairment

Biallelic loss-of-function mutations in TYROBP and TREM2 cause a rare disease that resembles early-onset frontotemporal dementia with bone lesions called polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL). Some PLOSL-causing variants in TREM2 have also been associated with Alzheimer's disease when heterozygous. Here, we studied the PLOSLFIN TYROBP deletion that covers 4 of the gene's 5 exons. We genotyped 3220 older Finns (mean age 79, range 58-104) and found 11 deletion carriers (mean age 78, range 60-94). The carrier prevalence was 0.0034 (1 in 293) that matches previous findings in younger cohorts suggesting no significant early mortality. By comparing Mini-Mental State Examination (MMSE) scores and diagnoses of dementia, we did not find any significant differences between TYROBP deletion carriers and noncarriers (all p-values >0.5). Neuropathological analysis of 2 deletion carriers (aged 89 and 94 years) demonstrated only minimal beta amyloid pathology (Consortium to Establish a Registry for Alzheimer's Disease (CERAD) score 0). Collectively these results suggest that heterozygous carriership of the TYROBP deletion is not a major risk factor of cognitive impairment. (C) 2017 Elsevier Inc. All rights reserved.Peer reviewe

Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum

There is a limited understanding about the impact of rare protein-truncating variants across multiple phenotypes. We explore the impact of this class of variants on 13 quantitative traits and 10 diseases using whole-exome sequencing data from 100,296 individuals. Protein-truncating variants in genes intolerant to this class of mutations increased risk of autism, schizophrenia, bipolar disorder, intellectual disability, and ADHD. In individuals without these disorders, there was an association with shorter height, lower education, increased hospitalization, and reduced age at enrollment. Gene sets implicated from GWASs did not show a significant protein-truncating variants burden beyond what was captured by established Mendelian genes. In conclusion, we provide a thorough investigation of the impact of rare deleterious coding variants on complex traits, suggesting widespread pleiotropic risk.Peer reviewe

Polygenic burden has broader impact on health, cognition, and socioeconomic outcomes than most rare and high-risk copy number variants

Copy number variants (CNVs) are associated with syndromic and severe neurological and psychiatric disorders (SNPDs), such as intellectual disability, epilepsy, schizophrenia, and bipolar disorder. Although considered high-impact, CNVs are also observed in the general population. This presents a diagnostic challenge in evaluating their clinical significance. To estimate the phenotypic differences between CNV carriers and non-carriers regarding general health and well-being, we compared the impact of SNPD-associated CNVs on health, cognition, and socioeconomic phenotypes to the impact of three genome-wide polygenic risk score (PRS) in two Finnish cohorts (FINRISK, n = 23,053 and NFBC1966, n = 4895). The focus was on CNV carriers and PRS extremes who do not have an SNPD diagnosis. We identified high-risk CNVs (DECIPHER CNVs, risk gene deletions, or large [>1 Mb] CNVs) in 744 study participants (2.66%), 36 (4.8%) of whom had a diagnosed SNPD. In the remaining 708 unaffected carriers, we observed lower educational attainment (EA; OR = 0.77 [95% CI 0.66-0.89]) and lower household income (OR = 0.77 [0.66-0.89]). Income-associated CNVs also lowered household income (OR = 0.50 [0.38-0.66]), and CNVs with medical consequences lowered subjective health (OR = 0.48 [0.32-0.72]). The impact of PRSs was broader. At the lowest extreme of PRS for EA, we observed lower EA (OR = 0.31 [0.26-0.37]), lower-income (OR = 0.66 [0.57-0.77]), lower subjective health (OR = 0.72 [0.61-0.83]), and increased mortality (Cox's HR = 1.55 [1.21-1.98]). PRS for intelligence had a similar impact, whereas PRS for schizophrenia did not affect these traits. We conclude that the majority of working-age individuals carrying high-risk CNVs without SNPD diagnosis have a modest impact on morbidity and mortality, as well as the limited impact on income and educational attainment, compared to individuals at the extreme end of common genetic variation. Our findings highlight that the contribution of traditional high-risk variants such as CNVs should be analyzed in a broader genetic context, rather than evaluated in isolation.Peer reviewe

Genome-wide association study indicates novel associations of annexin A13 to secretory and GAS2L2 with mucous otitis media

To evaluate the genetics of chronic nonsuppurative otitis media (OM). We performed a genome-wide association study of 429,599 individuals included in the FinnGen study using three different case definitions: combined chronic nonsuppurative OM (7034 cases) (included serous and mucous chronic OM), mucous chronic OM (5953 cases), and secretory chronic OM (1689 cases). Individuals without otitis media were used as controls (417,745 controls). We used immunohistochemistry (IHC) of the murine middle ear to evaluate the expression of annexin A13. Four loci were significantly associated (p < 1.7 × 10−8) with nonsuppurative OM. Three out of the four association signals included missense variants in genes that may play a role in otitis media pathobiology. According to our subtype-specific analyses, one novel locus, located near ANXA13, was associated with secretory OM. Three loci (near TNFRSF13B, GAS2L2, and TBX1) were associated with mucous OM. Immunohistochemistry of murine middle ear samples revealed annexin A13 expression at the apical pole of the Eustachian tube epithelium as well as variable intensity of the secretory cells of the glandular structure in proximity to the Eustachian tube. We demonstrated that secretory and mucous OM have distinct and shared genetic associations. The association of GAS2L2 with ciliary epithelium function and the pathogenesis of dysfunctional mucosa in mucous OM is suggested. The abundant expression of annexin A13 in the Eustachian tube epithelium, along with its role in apical transport for the binding and transfer of phospholipids, indicates the role of annexin A13 and phospholipids in Eustachian tube dysfunction.Peer reviewe

Genetic predictors of lifelong medication-use patterns in cardiometabolic diseases

Peer reviewe