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- Razzaghian, Hamid Reza, et al.
(författare)
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Post-Zygotic and Inter-Individual Structural Genetic Variation in a Presumptive Enhancer Element of the Locus between the IL10Rβ and IFNAR1 Genes
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:9, s. e67752-
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Tidskriftsartikel (refereegranskat)abstract
- Although historically considered as junk-DNA, tandemly repeated sequence motifs can affect human phenotype. For example, variable number tandem repeats (VNTR) with embedded enhancers have been shown to regulate gene transcription. The post-zygotic variation is the presence of genetically distinct populations of cells in an individual derived from a single zygote, and this is an understudied aspect of genome biology. We report somatically variable VNTR with sequence properties of an enhancer, located upstream of IFNAR1. Initially, SNP genotyping of 63 monozygotic twin pairs and multiple tissues from 21 breast cancer patients suggested a frequent post-zygotic mosaicism. The VNTR displayed a repeated 32 bp core motif in the center of the repeat, which was flanked by similar variable motifs. A total of 14 alleles were characterized based on combinations of segments, which showed post-zygotic and inter-individual variation, with up to 6 alleles in a single subject. Somatic variation occurred in similar to 24% of cases. In this hypervariable region, we found a clustering of transcription factor binding sites with strongest sequence similarity to mouse Foxg1 transcription factor binding motif. This study describes a VNTR with sequence properties of an enhancer that displays post-zygotic and inter-individual genetic variation. This element is within a locus containing four related cytokine receptors: IFNAR2, IL10R beta, IFNAR1 and IFNGR2, and we hypothesize that it might function in transcriptional regulation of several genes in this cluster. Our findings add another level of complexity to the variation among VNTR-based enhancers. Further work may unveil the normal function of this VNTR in transcriptional control and its possible involvement in diseases connected with these receptors, such as autoimmune conditions and cancer.
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- Forsberg, Anders, et al.
(författare)
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Landmark-Based Software for Anatomical Measurements : A Precision Study
- 2009
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Ingår i: Clinical anatomy (New York, N.Y. Print). - : Wiley. - 0897-3806 .- 1098-2353. ; 22:4, s. 456-462
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to develop a software program, called Landmarker, which would aid studies of complex anatomical morphometry by simplifying the manual identification of landmarks in 3D images. We also tested its precision on routine magnetic resonance imaging (MRI) scans. To understand human biological variation, there is a need to identify morphological characteristics from the exterior and the interior of human anatomy. MRI, as opposed to other radiographic methods (mainly based on X-ray techniques), supplies good soft tissue contrast, which allows for more complex assessments than what bony landmarks can provide. Because automation of this assessment is highly demanding, one of the primary goals for the new software was to enable more rapid identification of landmark sets in 3D image data. Repeat acquisition of head MRIs having a resolution of 0.94 x 0.94 x 1.20 mm3 were performed on 10 volunteers. Intra- and interoperator, as well as interacquisition variations of manual identification of exterior, craniofacial interior, and brain landmarks were studied. The average distances between landmarks were <1.8 mm, <2.3 mm, and <2.0 mm in the intra- and interoperator, and interacquisition evaluations, respectively. This study presents new software for time efficient identification of complex craniofacial landmarks in 3D MRI. To the best of our knowledge, no evaluation of software for rapid landmark-based analysis of complex anatomies from 3D MR data has yet been presented. This software may also be useful for studies in other anatomical regions and for other types of image data.
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- Johansson, Anders, et al.
(författare)
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[11C]-PIB imaging in patients with Parkinson's disease : preliminary results
- 2008
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Ingår i: Parkinsonism & Related Disorders. - : Elsevier BV. - 1353-8020 .- 1873-5126. ; 14:4, s. 345-347
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Tidskriftsartikel (refereegranskat)abstract
- [11C]-PIB positron emission tomography ([11C]-PIB PET) is a sensitive marker of amyloid in Alzheimer's disease (AD), but its specificity has not been fully evaluated. Vascular amyloid-β deposition is common in Parkinson's disease (PD) and α-synuclein, the major component of the Lewy bodies in PD, forms amyloid fibrils. We investigated five apparently cognitively normal PD patients with [11C]-PIB PET. The results were compared to 16 patients with AD and six healthy controls from a previous study. [11C]-PIB retention was not significantly increased in our patients who all had early stage PD. Further studies of more advanced PD patients are warranted.
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- Forsberg, Anders
(författare)
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Kvalitetsbedömning vid adressmatchning
- 1999
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- En metod för att bedöma kvalitet vid adressmatchning har genom att upprätta ett testdataset tagits fram. Testdatat, som finns tillgängligt via Internet, kan nyttjas för att bedöma olika adressmatchningsmetoder, programvaror och databaser. Testdatat består av 374 belägenhets-adresser från Kiruna kommun och finns i en korrekt och i en delvis felaktig version. I den felaktiga versionen har ca 20% av adresserna inplanterade fel. I projektet har några olika adressmatchningsförsök gjorts där testdatat har nyttjats. Försöken visar några sätt att bedöma kvalitet. Kvalitetsaspekter som bedömts är matchningsgrad, läges-noggrannhet och feltolerans. Med feltolerans avses en metods möjlighet att klara en matchning vid olika typer av fel i en adress. Tre olika försök har utförts med det korrekta testdatat. I det två första försöken har program-varorna ArcView och MapInfo testats med vägdatabasen Tätort 2000. I det tredje försöket har matchning skett mot fastighetsdatasystemets adressregister, FDS/AR. FDS/AR gav de bästa resultatet av de undersökta metoderna. Matchningsgraden var 90%. Medelfelet var 24 m och 85% av alla matchade adresser avvek mindre än 30 m från det korrekta läget. ArcView och MapInfo hade ungefär samma medelfel (68 respektive 70 m). Däremot gav ArcView ett bättre matchningsresultat än MapInfo (72% jämfört med 60%). Detta beror på att den testade versionen av ArcView är bättre anpassad till svenska adressnamn än motsvarande version av MapInfo. Ungefär 12% av adresserna i testdatat var landsbygdsadresser. Som väntat var matchnings-graden för dessa låg. Om landsbygdsadresser utesluts ur testdatat stiger matchningsgraden till 95% för FDS/AR, 81% för ArcView och 68% för MapInfo.
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