| 1. |
- Jiang, X., et al.
(author)
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Shared heritability and functional enrichment across six solid cancers
- 2019
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
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Journal article (peer-reviewed)abstract
- Quantifying the genetic correlation between cancers can provide important insights into the mechanisms driving cancer etiology. Using genome-wide association study summary statistics across six cancer types based on a total of 296,215 cases and 301,319 controls of European ancestry, here we estimate the pair-wise genetic correlations between breast, colorectal, head/neck, lung, ovary and prostate cancer, and between cancers and 38 other diseases. We observed statistically significant genetic correlations between lung and head/neck cancer (r(g) = 0.57, p = 4.6 x 10(-8)), breast and ovarian cancer (r(g) = 0.24, p = 7 x 10(-5)), breast and lung cancer (r(g) = 0.18, p = 1.5 x 10(-6)) and breast and colorectal cancer (r(g) = 0.15, p = 1.1 x 10(-4)). We also found that multiple cancers are genetically correlated with non-cancer traits including smoking, psychiatric diseases and metabolic characteristics. Functional enrichment analysis revealed a significant excess contribution of conserved and regulatory regions to cancer heritability. Our comprehensive analysis of cross-cancer heritability suggests that solid tumors arising across tissues share in part a common germline genetic basis.
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| 2. |
- Ji, Xuemei, et al.
(author)
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Protein-altering germline mutations implicate novel genes related to lung cancer development
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Few germline mutations are known to affect lung cancer risk. We performed analyses of rare variants from 39,146 individuals of European ancestry and investigated gene expression levels in 7,773 samples. We find a large-effect association with an ATM L2307F (rs56009889) mutation in adenocarcinoma for discovery (adjusted Odds Ratio=8.82, P=1.18x10(-15)) and replication (adjusted OR=2.93, P=2.22x10(-3)) that is more pronounced in females (adjusted OR=6.81 and 3.19 and for discovery and replication). We observe an excess loss of heterozygosity in lung tumors among ATM L2307F allele carriers. L2307F is more frequent (4%) among Ashkenazi Jewish populations. We also observe an association in discovery (adjusted OR=2.61, P=7.98x10(-22)) and replication datasets (adjusted OR=1.55, P=0.06) with a loss-of-function mutation, Q4X (rs150665432) of an uncharacterized gene, KIAA0930. Our findings implicate germline genetic variants in ATM with lung cancer susceptibility and suggest KIAA0930 as a novel candidate gene for lung cancer risk. In lung cancer, relatively few germline mutations are known to impact risk. Here the authors looked at rare variants in 39,146 individuals and find novel germline mutations associated with risk, as well as implicating ATM and a new candidate gene for lung cancer risk.
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| 5. |
- Biswas, Dhruva, et al.
(author)
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A clonal expression biomarker associates with lung cancer mortality
- 2019
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In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 25:10, s. 1540-1548
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Journal article (peer-reviewed)abstract
- An aim of molecular biomarkers is to stratify patients with cancer into disease subtypes predictive of outcome, improving diagnostic precision beyond clinical descriptors such as tumor stage(1). Transcriptomic intratumor heterogeneity (RNA-ITH) has been shown to confound existing expression-based biomarkers across multiple cancer types(2-6). Here, we analyze multi-region whole-exome and RNA sequencing data for 156 tumor regions from 48 patients enrolled in the TRACERx study to explore and control for RNA-ITH in non-small cell lung cancer. We find that chromosomal instability is a major driver of RNA-ITH, and existing prognostic gene expression signatures are vulnerable to tumor sampling bias. To address this, we identify genes expressed homogeneously within individual tumors that encode expression modules of cancer cell proliferation and are often driven by DNA copy-number gains selected early in tumor evolution. Clonal transcriptomic biomarkers overcome tumor sampling bias, associate with survival independent of clinicopathological risk factors, and may provide a general strategy to refine biomarker design across cancer types.
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| 8. |
- Brunnström, K, et al.
(author)
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Object Detection in Cluttered Infrared Images.
- 2003
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In: Optical Engineering. - : SPIE-Intl Soc Optical Eng. - 0091-3286 .- 1560-2303. ; 42:2, s. 388-399
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Journal article (peer-reviewed)abstract
- Implementation of the Johnson criteria for infrared images is the probabilities of a discrimination technique. The inputs to the model are the size of the target, the range to it, and the temperature difference against the background. The temperature difference is calculated without taking the background structure into consideration, but it may have a strong influence on the visibility of the target. We investigated whether a perceptually based temperature difference should be used as input. Four different models are discussed: 1. a probability of discrimination model largely based on the Johnson criteria for infrared images, 2. a peak signal-to-noise ratio model, 3. a signal-to-clutter ratio model, and 4. two versions of an image discrimination model based on how human vision analyzes spatial information. The models differ as to how much they try to simulate human perception. To test the models, a psychophysical experiment was carried out with ten test persons, measuring contrast threshold detection in five different infrared backgrounds using a method based on a two-alternative forced-choice methodology. Predictions of thresholds in contrast energy were calculated for the different models and compared to the empirical values. Thresholds depend on the background, and these can be predicted well by the image discrimination models, and better than the other models. Future extensions are discussed.
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| 10. |
- Brunnström, Kjell, 1960-, et al.
(author)
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Video expert assessment of high quality video for Video Assistant Referee (VAR) : A comparative study
- 2024
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In: Multimedia tools and applications. - : Springer Nature. - 1380-7501 .- 1573-7721. ; 83:20, s. 58783-58825
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Journal article (peer-reviewed)abstract
- The International Football Association Board decided to introduce Video Assistant Referee (VAR) in 2018. This led to the need to develop methods for quality control of the VAR-systems. This article focuses on the important aspect to evaluate the video quality. Video Quality assessment has matured in the sense that there are standardized, commercial products and established open-source solutions to measure it with objective methods. Previous research has primarily focused on the end-user quality assessment. How to assess the video in the contribution phase of the chain is less studied. The novelties of this study are two-fold: 1) The user study is specifically targeting video experts i.e., to assess the perceived quality of video professionals working with video production. 2) Six video quality models have been independently benchmarked against the user data and evaluated to show which of the models could provide the best predictions of perceived quality. The independent evaluation is important to get unbiased results as shown by the Video Quality Experts Group. An experiment was performed involving 25 video experts in which they rated the perceived quality. The video formats tested were High-Definition TV both progressive and interlaced as well as a quarters size format that was scaled down half the size in both width and height. The videos were encoded with both H.264 and Motion JPEG for the full size but only H.264 for the quarter size. Bitrates ranged from 80 Mbit/s down to 10 Mbit/s. We could see that for H.264 that the quality was overall very good but dropped somewhat for 10 Mbit/s. For Motion JPEG the quality dropped over the whole range. For the interlaced format the degradation that was based on a simple deinterlacing method did receive overall low ratings. For the quarter size three different scaling algorithms were evaluated. Lanczos performed the best and Bilinear the worst. The performance of six different video quality models were evaluated for 1080p and 1080i. The Video Quality Metric for Variable Frame Delay had the best performance for both formats, followed by Video Multimethod Assessment Fusion method and the Video Quality Metric General model.
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