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- Dadaev, T, et al.
(author)
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Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants
- 2018
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1, s. 2256-
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Journal article (peer-reviewed)abstract
- Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling.
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- Chen, C., et al.
(author)
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A gigabit transceiver for the ATLAS inner tracker pixel detector readout upgrade
- 2019
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In: Journal of Instrumentation. - 1748-0221. ; 14
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Journal article (peer-reviewed)abstract
- This paper presents the design and simulation results of a gigabit transceiver Application Specific Integrated Circuit (ASIC) called GBCR for the ATLAS Inner Tracker (ITk) Pixel detector readout upgrade. GBCR has four upstream receiver channels and a downstream transmitter channel. Each upstream channel operates at 5.12 Gbps, while the downstream channel operates at 2.56 Gbps. In each upstream channel, GBCR equalizes a signal received through a 5-meter 34-American Wire Gauge (AWG) twin-axial cable, retimes the data with a recovered clock, and drives an optical transmitter. In the downstream channel, GBCR receives the data from an optical receiver and drives the same type of cable as the upstream channels. The output jitter of an upstream channel is 26.5 ps and the jitter of the downstream channel after the cable is 33.5 ps. Each upstream channel consumes 78 mW and each downstream channel consumes 27 mW. Simulation results of the upstream test channel suggest that a significant jitter reduction could be achieved with minimally increased power consumption by using a Feed Forward Equalizer (FFE) + Decision Feedback Equalization (DFE) in addition to the linear equalization of the baseline channel. GBCR is designed in a 65-nm CMOS technology.
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- Fröjdh, Erik, et al.
(author)
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Timepix3 : first measurements and characterization of a hybrid-pixel detector working in event driven mode
- 2015
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In: Journal of Instrumentation. - 1748-0221. ; 10
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Journal article (peer-reviewed)abstract
- Timepix3 is a hybrid pixel detector readout chip. It features a data driven readout mode where the chip sends out a data packet containing pixel coordinate, time over threshold and time of arrival immediately after the hit is processed by the pixel. The maximum hit rate is 40 Mhits/cm(2)/s with a minimum time step in the arrival time measurement of 1.56 ns. The pixel matrix consist of 256 x 256 square pixels at a 55 m m pitch and the pixel front end noise is 61 e(-) RMS. In this paper we present the first radiation measurements with Timepix3 bump bonded to a 300 m m thick silicon sensor. The chip is calibrated per pixel, using internal test pulses and the calibration is verified using X-ray fluorescence. The energy resolution, threshold dispersion and gain dispersion is measured. The energy resolution in time over threshold mode under normal operation conditions is 4.07 keV FWHM at 59.5 keV. At 10.5 keV an energy resolution of 0.72 keV FWHM was achieved in photon counting mode and in time over threshold mode, by optimizing the energy response, we achieved a 1.38 keV FWHM. We also investigate the time walk and present first results on using the time information for track reconstruction.
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