| 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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| 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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