Biology subjects

Johansson, A.

Publications and source records attributed to Johansson, A..

22 records · Page 2Linked to original sources

bioRxiv2017

Genome-wide association analysis identifies 26 novel loci for asthma, hay fever and eczema

The disease risk for asthma, hay fever and eczema include both environmental and genetic risk factors and the comorbidity between the diseases are large. Heritability estimates suggest that the risk of asthma, hay fever and eczema is largely due to genetic factors. In this GWAS, we include 346,545 Caucasian participants from the UK Biobank to increase power to identify novel loci for asthma, hay fever and eczema. We also investigate if associated lead SNPs have a significantly larger effect for one disease phenotype compared to the other phenotypes, to highlight possible disease specific effects.\n\nThis study identifies 141 loci, of which 41 are novel to this study, to be associated (P[≤]3x10-8) with asthma, hay fever or eczema, analysed separately or combined as a single phenotype. At four of the novel loci, TNFRSF8, MYRF, TSPAN8, and BHMG1, the lead SNPs were in LD (> 0.8) with potentially casual missense variants. For seven of the novel GWAS loci, the lead SNP was in LD (> 0.8) with genetic variants associated with gene expression (eQTL) where, for example, increased levels of TMEM258 as well as decreased levels of HHEX and ADAM19 was associated with decreased odds for asthma.\n\nOur study shows that a large amount of the genetic contribution to asthma, hay fever and eczema is shared between the diseases. Nonetheless, a number of SNPs have a significantly larger effect on one of the phenotypes suggesting that part of the genetic contribution is more phenotype specific.

genetics↗

bioRxiv2017

Natural variation at FLOWERING LOCUS T2 mediates local adaptation in a key life history trait in European aspen

BackgroundThe initiation of growth cessation and dormancy represent critical life-history tradeoffs between survival and growth, and have important fitness effects in perennial plants. Such adaptive life history traits often show strong local adaptation along environmental gradients but despite their importance, the genetic architecture of these traits remains poorly understood.\n\nResultsWe integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). We discover a single genomic region containing the PtFT2 gene that mediates local adaptation in the timing of bud set and that explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affect the phenotypic variation in bud set that we observe in wild natural populations.\n\nConclusionsOur results reveal a major effect locus that determine the timing of bud set and that have facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life history trait is remarkable given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

evolutionary biology↗

bioRxiv2017

Breastfeeding And Risk Of Asthma, Hay Fever And Eczema

BackgroundBreastfeeding is commonly proposed to protect against atopic diseases. However, studies aiming to quantify these protective effects have shown conflicting results.\n\nMethodsTo entrench the effects of breastfeeding on risk of asthma, hay fever and eczema, our study included a large study cohort, UK Biobank (N=502,682). Information was collected on whether participants had been breastfeed and on the prevalence of disease. Disease was tested for association with breastfeeding, adjusting or matching for influential covariates.\n\nFindingsA total of 443,068 participants were included in our analyses of which 71{middle dot}2% had been breastfed. The prevalence of asthma was 11{middle dot}4 % and 12{middle dot}7% in the breastfed and non-breastfed groups, and hay fever or eczema (23{middle dot}9% and 24{middle dot}8 % in the two groups respectively. When correcting or matching for potential confounders, we could not see any association between being breastfed and asthma. However, there were increased odds of hay fever and eczema among participants that had been breastfed (P=7{middle dot}78x10-6).\n\nInterpretationThis study reports that breastfeeding is associated with increased odds of hay fever and eczema but it show no evidence for breastfeeding being associated with asthma diagnosis.\n\nFundingThe Swedish Society for Medical Research (SSMF), the Kjell and Marta Beijers Foundation, Goran Gustafssons Foundation, the Swedish Medical Research Council (Project Number 2015-03327), the Marcus Borgstrom Foundation, the [A]ke Wiberg Foundation and the Vleugels Foundation.\n\nEvidence before this studyAtopic diseases affect quality of life for a large part of the human population and pose a very high socio-economic burden. Genetic, environmental, and a number of lifestyle factors influence our risk of developing atopic disorders and high familial prevalence is one of the strongest known risk factors for disease. Several environmental and lifestyle risk factors have already been well established in the scientific community, such as smoking on the risk of developing asthma. Breastfeeding is commonly argued to be protective against atopic diseases. However, studies aiming to quantify these protective effects have shown conflicting results.\n\nAdded value of this studyOur study is, to our knowledge, the largest investigation on how breastfeeding is associated with being diagnosed with asthma, hay fever and eczema at adult age. The study found breastfeeding to be associated with increased odds of being diagnosed with hay fever and eczema during life, while we found no association between breastfeeding and asthma. Our results for hay fever and eczema is in line with the western world hygiene hypothesis, but contradict the general picture of breastfeeding being protective.\n\nImplications of all the available evidenceTo be able to give parents correct advice on lifestyles choices that will protect their kids against atopic diseases, we need to clarify the currently conflicting results on the effect of breastfeeding on risk of atopic diseases. However, these results should not be used to recommend breastfeeding or to discourage it since the present study only investigates the association between breastfeeding history and being diagnosed with asthma, hay fever and eczema during lifetime.\n\nAbbreviations

epidemiology↗

bioRxiv2016

SweGen: A whole-genome map of genetic variability in a cross-section of the Swedish population

Here we describe the SweGen dataset, a high-quality map of genetic variation in the Swedish population. This data represents a basic resource for clinical genetics laboratories as well as for sequencing-based association studies, by providing information on the frequencies of genetic variants in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide population based cohort of over 10,000 individuals. From this sample collection, 1,000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole genome sequencing (WGS). Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a whole-genome map of aggregated variant frequencies in the Swedish population that we hereby release to the scientific community.

genetics↗