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- Dahl, F, et al.
(författare)
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Imaging single DNA molecules for high precision NIPT
- 2018
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1, s. 4549-
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Tidskriftsartikel (refereegranskat)abstract
- Cell-free DNA analysis is becoming adopted for first line aneuploidy screening, however for most healthcare programs, cost and workflow complexity is limiting adoption of the test. We report a novel cost effective method, the Vanadis NIPT assay, designed for high precision digitally-enabled measurement of chromosomal aneuploidies in maternal plasma. Reducing NIPT assay complexity is achieved by using novel molecular probe technology that specifically label target chromosomes combined with a new readout format using a nanofilter to enrich single molecules for imaging and counting without DNA amplification, microarrays or sequencing. The primary objective of this study was to assess the Vanadis NIPT assay with respect to analytical precision and clinical feasibility. Analysis of reference DNA samples indicate that samples which are challenging to analyze with low fetal-fraction can be readily detected with a limit of detection determined at <2% fetal-fraction. In total of 286 clinical samples were analysed and 30 out of 30 pregnancies affected by trisomy 21 were classified correctly. This method has the potential to make cost effective NIPT more widely available with more women benefiting from superior detection and false positive rates.
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- Ameur, Adam, et al.
(författare)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Tidskriftsartikel (refereegranskat)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies 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 cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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- Andres, E., et al.
(författare)
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AMANDA : Status, results and future
- 1999
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Ingår i: Proceedings, 8th International Workshop, Venice, Italy, February 23-26, 1999. Vol. 1, 2. ; , s. 63-79
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Konferensbidrag (refereegranskat)abstract
- We review the status of the AMANDA neutrino telescope. We present resultsobtained from the four-string prototype array AMANDA-B4 and describe themethods of track reconstruction and neutrino event separation. We give also firstresults of the analysis of the 10-string detector AMANDA-B10, in particular onatmospheric neutrinos and the search for magnetic monopoles. We sketch thefuture schedule on the way to a cube kilometer telescope at the South Pole,ICECUBE.
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- Bergstrom, L., et al.
(författare)
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The AMANDA experiment : Status and prospects for indirect dark matter detection
- 1996
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Ingår i: The identification of dark matter. Proceedings, 1st International Workshop, Sheffield, UK, September 8-12, 1996. ; , s. 521-528
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Konferensbidrag (refereegranskat)abstract
- At the AMANDA South Pole site, four new holes were drilled to depths 2050m to 2180 m and instrumented with 86 photomultipliers (PMTs) at depths1520-2000 m. Of these PMTs 79 are working, with 4-ns timing resolutionand noise rates 300 to 600 Hz. Various diagnostic devices were deployedand are working. An observed factor 60 increase in scattering length anda sharpening of the distribution of arrival times of laser pulses relative tomeasurements at 800-1000 m showed that bubbles are absent below 1500 m.Absorption lengths are 100 to 150 m at wavelengths in the blue and UV to337 nm. Muon coincidences are seen between the SPASE air shower arrayand the AMANDA PMTs at 800-1000 m and 1500-1900 m. The muon trackrate is 30 Hz for 8-fold triggers and 10 Hz for 10-fold triggers. The presentarray is the nucleus for a future expanded array. The potential of AMANDAfor SUSY dark matter search through the detection of high-energy neutrinosfrom the centre of the Sun or Earth is discussed.
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