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- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 2. |
- Buchanan, E. M., et al.
(author)
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The Psychological Science Accelerator's COVID-19 rapid-response dataset
- 2023
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In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 10:1
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Journal article (peer-reviewed)abstract
- In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing manipulations on behavioral intentions and affective measures. The data collected (April to October 2020) included specific measures for each experimental study, a general questionnaire examining health prevention behaviors and COVID-19 experience, geographical and cultural context characterization, and demographic information for each participant. Each participant started the study with the same general questions and then was randomized to complete either one longer experiment or two shorter experiments. Data were provided by 73,223 participants with varying completion rates. Participants completed the survey from 111 geopolitical regions in 44 unique languages/dialects. The anonymized dataset described here is provided in both raw and processed formats to facilitate re-use and further analyses. The dataset offers secondary analytic opportunities to explore coping, framing, and self-determination across a diverse, global sample obtained at the onset of the COVID-19 pandemic, which can be merged with other time-sampled or geographic data.
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| 9. |
- Pennings, M., et al.
(author)
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KIF1A variants are a frequent cause of autosomal dominant hereditary spastic paraplegia
- 2020
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In: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 28, s. 40-49
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Journal article (peer-reviewed)abstract
- Variants in the KIF1A gene can cause autosomal recessive spastic paraplegia 30, autosomal recessive hereditary sensory neuropathy, or autosomal (de novo) dominant mental retardation type 9. More recently, variants in KIF1A have also been described in a few cases with autosomal dominant spastic paraplegia. Here, we describe 20 KIF1A variants in 24 patients from a clinical exome sequencing cohort of 347 individuals with a mostly ‘pure’ spastic paraplegia. In these patients, spastic paraplegia was slowly progressive and mostly pure, but with a highly variable disease onset (0–57 years). Segregation analyses showed a de novo occurrence in seven cases, and a dominant inheritance pattern in 11 families. The motor domain of KIF1A is a hotspot for disease causing variants in autosomal dominant spastic paraplegia, similar to mental retardation type 9 and recessive spastic paraplegia type 30. However, unlike these allelic disorders, dominant spastic paraplegia was also caused by loss-of-function variants outside this domain in six families. Finally, three missense variants were outside the motor domain and need further characterization. In conclusion, KIF1A variants are a frequent cause of autosomal dominant spastic paraplegia in our cohort (6–7%). The identification of KIF1A loss-of-function variants suggests haploinsufficiency as a possible mechanism in autosomal dominant spastic paraplegia. © 2019, The Author(s).
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| 10. |
- Galbany, L., et al.
(author)
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An updated measurement of the Hubble constant from near-infrared observations of Type Ia supernovae
- 2023
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In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 679
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Journal article (peer-reviewed)abstract
- We present a measurement of the Hubble constant (H0) using type Ia supernovae (SNe Ia) in the near-infrared (NIR) from the recently updated sample of SNe Ia in nearby galaxies with distances measured via Cepheid period-luminosity relations by the SH0ES project. We collected public near-infrared photometry of up to 19 calibrator SNe Ia and 57 SNe Ia in the Hubble flow (z > 0.01), and directly measured their peak magnitudes in the J- and H-band by Gaussian processes and spline interpolation. Calibrator peak magnitudes together with Cepheid-based distances were used to estimate the average absolute magnitude in each band, while Hubble-flow SNe were used to constrain the zero-point intercept of the magnitude–redshift relation. Our baseline result of H0 is 72.3 ± 1.4 (stat) ±1.4 (syst) km s−1 Mpc−1 in the J-band and 72.3 ± 1.3 (stat) ±1.4 (syst) km s−1 Mpc−1 in the H-band, where the systematic uncertainties include the standard deviation of up to 21 variations of the analysis, the 0.7% distance scale systematic from SH0ES Cepheid anchors, a photometric zero-point systematic, and a cosmic variance systematic. Our final measurement represents a measurement with a precision of 2.8% in both bands. Among all the analysis variants, the largest change in H0 comes from limiting the sample to those SNe from the CSP and CfA programs; they are noteworthy because they are the best calibrated, yielding H0 ∼ 75 km s−1 Mpc−1 in both bands. We explore applying stretch and reddening corrections to standardize SN Ia NIR peak magnitudes, and we demonstrate that they are still useful to reduce the absolute magnitude scatter and, which improves its standardization, at least up to the H-band. Based on our results, in order to improve the precision of the H0 measurement with SNe Ia in the NIR in the future, we would need to increase the number of calibrator SNe Ia, to be able to extend the Hubble–Lemaître diagram to higher redshift, and to include standardization procedures to help reduce the NIR intrinsic scatter.
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