Exome Sequencing Identifies Susceptibility Loci for Sarcoidosis Prognosis

Many sarcoidosis-associating immunological genes have been shown to be shared between other immune-mediated diseases. In Finnish sarcoidosis patients, good prognosis subjects more commonly have HLA-DRB1*03:01 and/or HLA-DRB1*04:01-DPB1*04:01 haplotype, but no marker for persistent disease have been found. The objective was to further pinpoint genetic differences between prognosis subgroups in relation to the HLA markers. Whole-exome sequencing was conducted for 72 patients selected based on disease activity (resolved disease, n = 36; persistent disease, n = 36). Both groups were further divided by the HLA markers (one/both markers, n = 18; neither of the markers, n = 18). The Finnish exome data from the Genome Aggregation Database was used as a control population in the WES sample. Statistical analyses included single-variant analysis for common variants and gene level analysis for rare variants. We attempted to replicate associated variants in 181 Finnish sarcoidosis patients and 150 controls. An association was found in chromosome 1p36.21 (AADACL3 and C1orf158), which has recently been associated with sarcoidosis in another WES study. In our study, variations in these genes were associated with resolved disease (AADACL3, p = 0.0001 and p = 0.0003; C1orf158, p = 7.03E-05). Another interesting chromosomal region also peaked, Leucocyte Receptor Complex in 19q13.42, but the association diminished in the replication sample. In conclusion, this WES study supports the previously found association in the region 1p36.21. Furthermore, a novel to sarcoidosis region was found, but additional studies are warranted to verify this association.Peer reviewe

Screening of variants for lactase persistence/non-persistence in populations from South Africa and Ghana

<p>Abstract</p> <p>Background</p> <p>Lactase non-persistence is a condition where lactase activity is decreased in the intestinal wall after weaning. In European derived populations a single nucleotide polymorphism (SNP) C/T_-13910residing 13.9 kb upstream from the lactase gene has been shown to define lactase activity, and several other single nucleotide polymorphisms (G/C_-14010T/G_-13915, C/G_-13907and T/C_-13913) in the same region have been identified in African and Middle East populations.</p> <p>Results</p> <p>The T_-13910allele most common in European populations was present in 21.8% mixed ancestry (N = 62) individuals and it was absent in the Xhosa (N = 109) and Ghana (N = 196) subjects. Five other substitutions were also found in the region covering the previously reported variants in African and Middle East populations. These included the G/C_-14010variant common in Kenyan and Tanzanian populations, which was present in 12.8% of Xhosa population and in 8.1% of mixed ancestry subjects. Two novel substitutions (C/T_-14091and A/C_-14176) and one previously reported substitution G/A_-13937(rs4988234) were less common and present only in the Xhosa population. One novel substitution G/A_-14107was present in the Xhosa and Ghanaian populations. None of the other previously reported variants were identified.</p> <p>Conclusion</p> <p>Identification of the G/C_-14010variant in the Xhosa population, further confirms their genetic relatedness to other nomadic populations members that belong to the Bantu linguistic group in Tanzania and Kenya. Further studies are needed to confirm the possible relationship of the novel substitutions to the lactase persistence trait.</p

Diversity of Extended HLA-DRB1 Haplotypes in the Finnish Population

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SNP Variants in Major Histocompatibility Complex Are Associate with Sarcoidosis Susceptibility - A Joint Analysis in Four European Populations

Sarcoidosis is a multiorgan inflammatory disorder with heritability estimates up to 66%. Previous studies have shown the major histocompatibility complex (MHC) region to be associated with sarcoidosis, suggesting a functional role for antigen-presenting molecules and immune mediators in the disease pathogenesis. To detect variants predisposing to sarcoidosis and to identify genetic differences between patient subgroups, we studied four genes in the MHC Class III region (LTA, TNF, AGER, BTNL2) and HLA-DRA with tag-SNPs and their relation to HLA-DRB1 alleles. We present results from a joint analysis of four study populations (Finnish, Swedish, Dutch, and Czech). Patients with sarcoidosis (n = 805) were further subdivided based on the disease activity and the presence of Lofgren's syndrome. In a joint analysis, seven SNPs were associated with non-Lofgren sarcoidosis (NL; the strongest association with rs3177928, P = 1.79E-07, OR = 1.9) and eight with Lofgren's syndrome [ Lofgren syndrome (LS); the strongest association with rs3129843, P = 3.44E-12, OR = 3.4] when compared with healthy controls (n = 870). Five SNPs were associated with sarcoidosis disease course (the strongest association with rs3177928, P = 0.003, OR = 1.9). The high linkage disequilibrium (LD) between SNPs and an HLA-DRB1 challenged the result interpretation. When the SNPs and HLA-DRB1 alleles were analyzed together, independent association was observed for four SNPs in the HLA-DRA/BTNL2 region: rs3135365 (NL; P = 0.015), rs3177928 (NL; P <0.001), rs6937545 (LS; P = 0.012), and rs5007259 (disease activity; P = 0.002). These SNPs act as expression quantitative trait loci (eQTL) for HLA-DRB1 and/or HLA-DRB5. In conclusion, we found novel SNPs in BTNL2 and HLA-DRA regions associating with sarcoidosis. Our finding further establishes that polymorphisms in the HLA-DRA and BTNL2 have a role in sarcoidosis susceptibility. This multi-population study demonstrates that at least a part of these associations are HLA-DRB1 independent (e.g., not due to LD) and shared across ancestral origins. The variants that were independent of HLA-DRB1 associations acted as eQTL for HLA-DRB1 and/or -DRB5, suggesting a role in regulating gene expression.Peer reviewe

Mutations of complement lectin pathway genes MBL2 and MASP2 associated with placental malaria

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FinnGen provides genetic insights from a well-phenotyped isolated population

Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10–11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.publishedVersionPeer reviewe

GENETIC VARIANTS PREDISPOSING TO PROGNOSIS IN PULMONARY SARCOIDOSIS

Sarcoidosis is a systemic, granulomatous disease of unknown etiology. Clinical phenotypes range from resolved to persistent disease, leading to the hypothesis that sarcoidosis might not be one disease, but consists of several disease entities each with distinct genetic associations. Many immunological genes have been found to associate with sarcoidosis and many of these loci have been shown to be shared among other immune-mediated diseases. The strongest association is found for the Major Histocompatibility Complex (MHC) genes. In Finnish patients, subjects with good prognosis sarcoidosis are more likely to have the MHC markers HLA-DRB1*03:01 and/or HLA-DRB1*04:01-DPB1*04:01 haplotype, but no diagnostically applicable markers have been found. The overall aim of this thesis was to find genetic variants predisposing to different phenotypes of sarcoidosis, to help distinguish the disease phenotype at the early stages of the disease. This aim was assessed by candidate-gene analysis in the angiotensin converting enzyme (ACE) gene in chromosome 17 (I) and in the MHC II and III regions (II). Marker combination of the MHC and ACE was analyzed to evaluate more powerful prognostic markers (III) and finally, the study was extended throughout the genome by utilizing whole-exome sequencing (IV). In study I, the single nucleotide polymorphisms (SNPs) were genotyped from the ACE gene region. These SNPs included the tag SNP for insertion/deletion (I/D) polymorphism, previously known to associate with the prognosis of sarcoidosis. No association was detected with I/D genotypes, but a novel SNP (rs9905945) was found to be moderately associated with favorable disease. In study II, SNPS from the MHC II and III regions (AGER, LTA, TNF, BTNL2 and HLA-DRA) were genotyped and the study was conducted as a joint analysis in four study populations (Finnish, Swedish, Dutch and Czech). Due to high linkage disequilibrium (LD) in the MHC, the independent association from HLA-DRB1 alleles was evaluated and the functionality of these SNPs was assessed by expression quantitative trait loci (eQTL). Three SNPs in the HLA-DRA/BTNL2 region were found to associate with persistent disease and one SNP in the same region with resolved disease when compared to controls. In study III, the combination of previously found good prognosis HLA markers was assessed with the ACE SNP (I). The strongest association for good disease prognosis was found for a combination of either/or both HLA markers and ACE SNP. In study IV, whole-exome sequencing was conducted. A genetic region was found in chromosome 1p36.21 (AADACL3 and C1orf158), in which an association has recently been found in another WES study. In our study, these genes were found to associate with resolved disease. In conclusion, a novel SNP in the ACE gene was discovered with prospective, although moderate and population-specific association with favorable disease prognosis. Our findings further establish that polymorphisms in the HLA-DRA and BTNL2 in the MHC region have a role in sarcoidosis susceptibility. However, this study did not bring prognostic information to be used in clinical practice. Interestingly, the combination of the ACE SNP and the previously found HLA-DRB1 markers enhanced the accuracy for predicting disease course. The whole-exome analysis revealed genetic regions which associated with disease prognosis in Finnish sarcoidosis. Together all these studies further characterize genetic differences among Finnish sarcoidosis patients with different prognosis.Sarkoidoosi on etiologialtaan tuntematon systeeminen granulomatoottinen sairaus. Kliinisesti tauti vaihtelee itsellään paranevasta hyvän ennusteen taudista aina krooniseen huonon ennusteen tautiin. Näiden vuoksi on esitetty hypoteesi, että sarkoidoosi ei ehkä ole yksittäinen tauti, vaan koostuu useista alamuodoista, joilla on erilainen geneettinen alttius. Useiden immunologisten geenien on todettu liittyvän sarkoidoosiin ja monien näistä geenialueista on löydetty altistavan myös muille immuunivälitteisille sairauksille. Vahvin assosiaatio on löydetty Major Histocompatibility Complex (MHC)-geeneistä. Suomalaisilla hyvän ennusteen potilailla on todennäköisimmin MHC-merkkiaineet HLA-DRB1*03:01 ja/tai HLA-DRB1*04: 01-DPB1*04:01 haplotyyppi verrattuna huonon ennusteen potilaisiin. Diagnostisena apuna käytettäviä geenimarkkeereja ei ole vielä suomalaisesti populaatiosta löytynyt. Tämän väitöskirjan yleisenä tavoitteena oli löytää sarkoidoosin eri alamuotoihin altistavia geneettisiä muunnoksia, joiden avulla taudin eri fenotyypit voitaisiin erottaa jo taudin alkuvaiheissa. Tämä tavoite toteutettiin kandidaatti-geeni-analyysillä angiotensiinikonvertaasientsyymi-geenistä (ACE) (I) sekä MHC II- ja III-alueiden geeneistä (II). MHC:n ja ACE:n markkeeriyhdistelmää analysoitiin tehokkaampien prognostisten markkereiden (III) löytämiseksi ja lopuksi tutkimusta laajennettiin koko genomiin hyödyntämällä eksomisekvensointimenetelmää (IV). Tutkimuksessa I yksittäiset nukleotidipolymorfismit (SNP) genotyypitettiin ACE-geenialueelta. Nämä SNP:t sisälsivät insertio/deletio (I/D) polymorfismiin liittyvän SNP:n, jonka on aikaisemmin havaittu liittyvän sarkoidoosin ennusteeseen. I/D-genotyypeillä ei havaittu yhteyttä sarkoidoosiin, mutta tutkimuksessa löytyi uusi SNP (rs9905945), jonka havaittiin liittyvän hyvän ennusteen tautiin. Tutkimuksessa II MHC II- ja III-alueet (AGER, LTA, TNF, BTNL2 ja HLA-DRA) genotyypitettiin ja tutkimusmateriaalina oli neljä eri populaatiota (Suomi, Ruotsi, Hollanti ja Tšekki). Kolme SNP:iä HLA-DRA / BTNL2-alueella todettiin liittyvän huonon ennusteen tautiin ja yhden SNP:n samalta alueelta todettiin liittyvän hyvän ennusteen tautiin verrattuna verrokkiryhmään. Tutkimuksessa III arvioitiin aiemmin löydettyjen hyvän ennusteen HLA-markkeereiden yhdistelmää ACE SNP:n kanssa (I). Vahvin yhdistelmä hyvän taudin ennusteeksi havaittiin joko/tai molempien HLA-markkeereiden ja ACE SNP:n yhdistelmästä. Tutkimuksessa IV hyödynnettiin eksomisekvensointimenetelmää. Hyvän ennusteen tautiin liittyvä geneettinen alue löytyi kromosomista 1p36.21 (AADACL3 ja C1orf158), joka on äskettäin yhdistetty lapsuuden sarkoidoosiin toisessa eksomisekvensointitukimuksessa. Yhteenvetona, hyvän ennusteen potilailta löytyi ACE-geenistä uusi SNP, mutta assosiaatio oli lievä. Tuloksemme osoittavat lisäksi, että polymorfismeilla MHC-alueen geeneissä HLA-DRA ja BTNL2 on rooli sarkoidoosin alttiudessa. Mielenkiintoista on, että ACE SNP:n ja aiemmin löydettyjen HLA-DRB1-markkeerien yhdistelmä tehosti taudin fenotyyppien erottelua. Eksomisekvensointianalyysi paljasti uusia geneettisiä alueita, jotka liittyivät sairauden ennusteeseen. Yhdessä nämä tutkimukset edelleen lisäävät tietämystä suomalaisten sarkoidoosipotilaiden geneettisistä eroista taudin eri ennusteissa