| 1. |
- amundsen, silja, et al.
(författare)
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A comprehensive screen for SNP associations on chromosome region 5q31-33 in Swedish/Norwegian celiac disease families.
- 2007
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Ingår i: European Journal of Human genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 15:9, s. 980-987
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Tidskriftsartikel (refereegranskat)abstract
- Celiac disease (CD) is a gluten-induced enteropathy, which results from the interplay between environmental and genetic factors. There is a strong human leukocyte antigen (HLA) association with the disease, and HLA-DQ alleles represent a major genetic risk factor. In addition to HLA-DQ, non-HLA genes appear to be crucial for CD development. Chromosomal region 5q31–33 has demonstrated linkage with CD in several genome-wide studies, including in our Swedish/Norwegian cohort. In a European meta-analysis 5q31–33 was the only region that reached a genome-wide level of significance except for the HLA region. To identify the genetic variant(s) responsible for this linkage signal, we performed a comprehensive single nucleotide polymorphism (SNP) association screen in 97 Swedish/Norwegian multiplex families who demonstrate linkage to the region. We selected tag SNPs from a 16 Mb region representing the 95% confidence interval of the linkage peak. A total of 1404 SNPs were used for the association analysis. We identified several regions with SNPs demonstrating moderate single- or multipoint associations. However, the isolated association signals appeared insufficient to account for the linkage signal seen in our cohort. Collective effects of multiple risk genes within the region, incomplete genetic coverage or effects related to copy number variation are possible explanations for our findings.
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| 2. |
- Andrade, Jorge, et al.
(författare)
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The use of grid computing to drive data-intensive genetic research
- 2007
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 15:6, s. 694-702
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Tidskriftsartikel (refereegranskat)abstract
- In genetics, with increasing data sizes and more advanced algorithms for mining complex data, a point is reached where increased computational capacity or alternative solutions becomes unavoidable. Most contemporary methods for linkage analysis are based on the Lander-Green hidden Markov model (HMM), which scales exponentially with the number of pedigree members. In whole genome linkage analysis, genotype simulations become prohibitively time consuming to perform on single computers. We have developed 'Grid-Allegro', a Grid aware implementation of the Allegro software, by which several thousands of genotype simulations can be performed in parallel in short time. With temporary installations of the Allegro executable and datasets on remote nodes at submission, the need of predefined Grid run-time environments is circumvented. We evaluated the performance, efficiency and scalability of this implementation in a genome scan on Swedish multiplex Alzheimer's disease families. We demonstrate that 'Grid-Allegro' allows for the full exploitation of the features available in Allegro for genome-wide linkage. The implementation of existing bioinformatics applications on Grids (Distributed Computing) represent a cost-effective alternative for addressing highly resource-demanding and data-intensive bioinformatics task, compared to acquiring and setting up clusters of computational hardware in house (Parallel Computing), a resource not available to most geneticists today.
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| 3. |
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| 5. |
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| 6. |
- Blom, Elin Susanne, et al.
(författare)
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Low prevalence of APP duplications in Swedish and Finnish patients with early onset Alzheimer's disease
- 2008
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 16:2, s. 171-5
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Tidskriftsartikel (refereegranskat)abstract
- Familial early-onset Alzheimer's disease with cerebral amyloid angiopathy (EOAD/CAA) was recently associated with duplications of the gene for the amyloid-beta precursor protein (APP). In this study, we have screened for duplications of APP in patients with EOAD from Sweden and Finland. Seventy-five individuals from families with EOAD and 66 individuals with EOAD without known familial inheritance were screened by quantitative PCR. On the basis of the initial results, a portion of the samples was also investigated with quantitative multiplex PCR. No duplications of APP were identified, whereby we conclude that this is not a common cause of EOAD in the Swedish and Finnish populations, at least not in our collection of families and cases.
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| 7. |
- Bygren, Lars Olov, 1936-, et al.
(författare)
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Epigenetics or ephemeral genetics? : Reply to Senn
- 2006
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Ingår i: European Journal of Human Genetics. - : Nature publishing group. - 1018-4813 .- 1476-5438.
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Annan publikation (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Devoto, Marcella, et al.
(författare)
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Univariate and bivariate variance component linkage analysis of a whole-genome scan for loci contributing to bone mineral density
- 2005
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 13, s. 781-788
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Tidskriftsartikel (refereegranskat)abstract
- Osteoporosis is a common condition characterized by reduced skeletal strength and increased susceptibility to fracture. The single major risk factor for osteoporosis is low bone mineral density (BMD) and strong evidence exists that genetic factors are in part responsible for an individual's BMD. A cohort of 40 multiplex Caucasian families selected through a proband with osteoporosis was genotyped for microsatellite markers spaced at an average of 10 cM, and linkage to femoral neck (FN), lumbar spine (LS) and trochanter (TR) BMD was analyzed using univariate and bivariate variance component linkage analysis. Maximum univariate multipoint lod-scores were 2.87 on chromosome 1p36 for FN BMD, 1.89 on 6q27 for TR BMD, and 2.15 on 7p15 for LS BMD. Results of bivariate linkage analysis were highly correlated with those of the univariate analysis, although generally less significant, suggesting the possibility that some of these susceptibility loci may exert pleiotropic effects on multiple skeletal sites.
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| 9. |
- Entesarian, Miriam, et al.
(författare)
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FGF10 missense mutations in aplasia of lacrimal and salivary glands (ALSG)
- 2007
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 15:3, s. 379-382
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Tidskriftsartikel (refereegranskat)abstract
- Aplasia of lacrimal and salivary glands (ALSG) is an autosomal dominant congenital anomaly characterized by aplasia, atresia or hypoplasia of the lacrimal and salivary systems. Affected individuals present with irritable eyes and dryness of the mouth with variable expressivity. Mutations in FGF10 were recently described in ALSG and in lacrimo-auriculo-dento-digital (LADD) syndrome which are overlapping clinical entities. We present here two families with ALSG associated with missense mutations (R80S and G138E, respectively) affecting highly conserved residues in FGF10. The clinical features of these patients further broaden the knowledge of FGF10-related phenotypes.
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| 10. |
- Eriksson, Stefan, 1963-, et al.
(författare)
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Potential harms, anonymization, and the right to withdraw consent to biobank research
- 2005
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 13:9, s. 1071-1076
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Tidskriftsartikel (refereegranskat)abstract
- This paper discusses the potential harms involved in biobank research and how ethical review, informed consent, withdrawals, and anonymization of samples should be handled in the light of these harms. There is less risk involved in biobank research than in human subject research; it should therefore be treated differently. In our view, anonymization should not be an automatically permissible response to requests for withdrawal. Nor should a request for withdrawal necessarily stop research on identifiable samples. Apart from not being particularly appropriate for protecting the interests of individuals, anonymization of samples has a negative impact on research. We suggest that the current view on withdrawal from research, supported by the Declaration of Helsinki and subsequent ethical guidelines, be abandoned in the context of biobank research and be replaced by an approach inspired by the Nuremberg Code. This approach requires those wishing to withdraw their samples from research to present sufficient reason for doing so. Our interpretation of 'sufficient reason' includes all those involving genuine, deeply felt concerns that are not based on misconceptions. Still, this underlines the fact that we all share a responsibility for health research and that no one should take withdrawal from biobank research lightly.
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| 11. |
- Everett, K. V., et al.
(författare)
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Linkage and association analysis of CACNG3 in childhood absence epilepsy
- 2007
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Ingår i: Eur J Hum Genet. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 15:4, s. 463-72
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Tidskriftsartikel (refereegranskat)abstract
- Childhood absence epilepsy (CAE) is an idiopathic generalised epilepsy characterised by absence seizures manifested by transitory loss of awareness with 2.5-4 Hz spike-wave complexes on ictal EEG. A genetic component to aetiology is established but the mechanism of inheritance and the genes involved are not fully defined. Available evidence suggests that genes encoding brain expressed voltage-gated calcium channels, including CACNG3 on chromosome 16p12-p13.1, may represent susceptibility loci for CAE. The aim of this work was to further evaluate CACNG3 as a susceptibility locus by linkage and association analysis. Assuming locus heterogeneity, a significant HLOD score (HLOD = 3.54, alpha = 0.62) was obtained for markers encompassing CACNG3 in 65 nuclear families with a proband with CAE. The maximum non-parametric linkage score was 2.87 (P < 0.002). Re-sequencing of the coding exons in 59 patients did not identify any putative causal variants. A linkage disequilibrium (LD) map of CACNG3 was constructed using 23 single nucleotide polymorphisms (SNPs). Transmission disequilibrium was sought using individual SNPs and SNP-based haplotypes with the pedigree disequilibrium test in 217 CAE trios and the 65 nuclear pedigrees. Evidence for transmission disequilibrium (P < or = 0.01) was found for SNPs within a approximately 35 kb region of high LD encompassing the 5'UTR, exon 1 and part of intron 1 of CACNG3. Re-sequencing of this interval was undertaken in 24 affected individuals. Seventy-two variants were identified: 45 upstream; two 5'UTR; and 25 intronic SNPs. No coding sequence variants were identified, although four variants are predicted to affect exonic splicing. This evidence supports CACNG3 as a susceptibility locus in a subset of CAE patients.
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| 12. |
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| 14. |
- Grisoni, Marie-Lise, et al.
(författare)
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Haplotypic analysis of tag SNPs of the interleukin-18 gene in relation to cardiovascular disease events : the MORGAM Project.
- 2008
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 16:12, s. 1512-20
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Tidskriftsartikel (refereegranskat)abstract
- Interleukin-18 (IL-18) is a key inflammatory molecule suspected of being involved in the etiology of cardiovascular diseases (CVD). Five single nucleotide polymorphisms (SNPs) capturing the common genetic variation of the IL-18 gene (tag SNPs) were genotyped in five European prospective CVD cohorts including 1933 cases and 1938 non-cases as part of the MORGAM Project. Not a single SNP was found associated with CVD. However, a significant (P=0.002) gene-smoking interaction was observed. In smokers, the -105T allele was more frequent in cases than in non-cases (0.29 vs 0.25) and associated with an increased risk of disease (odds ratio (OR)=1.25 (1.07-1.45), P=0.005), whereas the inverse relationship tended to be observed in non-smokers (OR=0.90 (0.78-1.02), P=0.131). The gene-smoking interaction was broadly homogenous across the cohorts and was also observed through haplotype analyses. In conclusion, using the concerted effort of several European prospective CVD cohorts, we are able to show that one IL-18 tag SNP interacts with smoking to modulate the risk of developing CVD.
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| 15. |
- Gustafsson Stolt, Ulrica, 1965-, et al.
(författare)
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Information and informed consent in a longitudinal screening involving children : a questionnaire survey
- 2005
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 13, s. 376-383
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Tidskriftsartikel (refereegranskat)abstract
- This empirical study explores participants' perceptions of information and understanding of their children's and their own involvement in a longitudinal screening, the ABIS Study. ABIS (All Babies In Southeast Sweden) is a multicentre, longitudinal research screening for Type 1 diabetes and multifactorial diseases involving 17 005 children and their families. For this study, a random selection of mothers was made, using perinatal questionnaire serial numbers from the ABIS study. In total, 293 of these mothers completed an anonymous questionnaire (response rate 73.3%). Our findings from the questionnaire indicate a marked difference between the reported satisfaction with and understanding of the information provided on the one hand and the significant lack of knowledge of some of the aims and methods of the ABIS screening on the other, namely concerning high-risk identification of involved children, potential prevention and future questionnaires. Two questions evoked by our results are: (1) what information is required for participants in longitudinal studies involving children? and (2) how do we ensure and sustain understanding, and thus in a prolonging, informed consent in these studies? This study underlines the importance of an increased understanding of the ethical issues that longitudinal research on children raise and the need to discuss how information and informed consent strategies should be analysed and designed in longitudinal studies.
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| 16. |
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| 17. |
- Heath, Simon C., et al.
(författare)
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Investigation of the fine structure of European populations with applications to disease association studies
- 2008
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 16:12, s. 1413-1429
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Tidskriftsartikel (refereegranskat)abstract
- An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East-West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North-South gradient from Norway and Sweden to Romania and Spain. Variation of frequencies at markers in three separate genomic regions, surrounding LCT, HLA and HERC2, were strongly associated with this gradient. The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.
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| 18. |
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| 20. |
- Hmani-Aifa, Mounira, et al.
(författare)
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Identification of two new mutations in the GPR98 and the PDE6B genes segregating in a Tunisian family
- 2009
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Ingår i: EUROPEAN JOURNAL OF HUMAN GENETICS. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 17:4, s. 474-482
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Tidskriftsartikel (refereegranskat)abstract
- Autosomal recessive retinitis pigmentosa (ARRP) is a genetically heterogeneous disorder. ARRP could be associated with extraocular manifestations that define specific syndromes such as Usher syndrome (USH) characterized by retinal degeneration and congenital hearing loss (HL). The USH type II (USH2) associates RP and mild-to-moderate HL with preserved vestibular function. At least three genes USH2A, the very large G-protein-coupled receptor, GPR98, and DFNB31 are responsible for USH2 syndrome. Here, we report on the segregation of non-syndromic ARRP and USH2 syndrome in a consanguineous Tunisian family, which was previously used to define USH2B locus. With regard to the co-occurrence of these two different pathologies, clinical and genetic reanalysis of the extended family showed (i) phenotypic heterogeneity within USH2 patients and (ii) excluded linkage to USH2B locus. Indeed, linkage analysis disclosed the cosegregation of the USH2 phenotype with the USH2C locus markers, D5S428 and D5S618, whereas the ARRP perfectly segregates with PDE6B flanking markers D4S3360 and D4S2930. Molecular analysis revealed two new missense mutations, p. Y6044C and p. W807R, occurring in GPR98 and PDE6B genes, respectively. In conclusion, our results show that the USH2B locus at chromosome 3p23-24.2 does not exist, and we therefore withdraw this locus designation. The combination of molecular findings for GPR98 and PDE6B genes enable us to explain the phenotypic heterogeneity and particularly the severe ocular affection first observed in one USH2 patient. This report presents an illustration of how consanguinity could increase familial clustering of multiple hereditary diseases within the same family.
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| 24. |
- Ingman, Max, et al.
(författare)
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A recent genetic link between Sami and the Volga-Ural region of Russia
- 2007
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 15:1, s. 115-120
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Tidskriftsartikel (refereegranskat)abstract
- The genetic origin of the Sami is enigmatic and contributions from Continental Europe, Eastern Europe and Asia have been proposed. To address the evolutionary history of northern and southern Swedish Sami, we have studied their mtDNA haplogroup frequencies and complete mtDNA genome sequences. While the majority of mtDNA diversity in the northern Swedish, Norwegian and Finnish Sami is accounted for by haplogroups V and U5b1b1, the southern Swedish Sami have other haplogroups and a frequency distribution similar to that of the Continental European population. Stratification of the southern Sami on the basis of occupation indicates that this is the result of recent admixture with the Swedish population. The divergence time for the Sami haplogroup V sequences is 7600 YBP (years before present), and for U5b1b1, 5500 YBP amongst Sami and 6600 YBP amongst Sami and Finns. This suggests an arrival in the region soon after the retreat of the glacial ice, either by way of Continental Europe and/or the Volga-Ural region. Haplogroup Z is found at low frequency in the Sami and Northern Asian populations but is virtually absent in Europe. Several conserved substitutions group the Sami Z lineages strongly with those from Finland and the Volga-Ural region of Russia, but distinguish them from Northeast Asian representatives. This suggests that some Sami lineages shared a common ancestor with lineages from the Volga-Ural region as recently as 2700 years ago, indicative of a more recent contribution of people from the Volga-Ural region to the Sami population.
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| 25. |
- Ingman, Max, et al.
(författare)
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SNP frequency estimation using massively parallel sequencing of pooled DNA
- 2008
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 17:3, s. 383-386
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Tidskriftsartikel (refereegranskat)abstract
- Resequencing of genomic regions that have been implicated by linkage and/or association studies to harbor genetic susceptibility loci represents a necessary step to identify causal variants. Massively parallel sequencing (MPS) offers the possibility of SNP discovery and frequency determination among pooled DNA samples. The strategies of pooling DNA samples and pooling PCR amplicons generated from individual DNA samples were evaluated, and both were found to return accurate estimates of SNP frequencies across varying levels of sequence coverage.European Journal of Human Genetics advance online publication, 15 October 2008; doi:10.1038/ejhg.2008.182.
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