| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)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. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Carlevaro-Fita, J, et al.
(författare)
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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
- 2020
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1, s. 56-
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Tidskriftsartikel (refereegranskat)abstract
- Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
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| 4. |
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| 5. |
- Gu, Yi, et al.
(författare)
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Optical properties of InGaAsBi/GaAs strained quantum wells studied by temperature-dependent photoluminescence
- 2013
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Ingår i: Chinese Physics B. - : IOP Publishing. - 1674-1056. ; 22:3, s. 037802-
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Tidskriftsartikel (refereegranskat)abstract
- The effect of bismuth on the optical properties of InGaAsBi/GaAs quantum well structures is investigated using the temperature-dependent photoluminescence from 12 K to 450 K. The incorporation of bismuth in the InGaAsBi quantum well is confirmed and found to result in a red shift of photoluminescence wavelength of 27.3 meV at 300 K. The photoluminescence intensity is significantly enhanced by about 50 times at 12 K with respect to that of the InGaAs quantum well due to the surfactant effect of bismuth. The temperature-dependent integrated photoluminescence intensities of the two samples reveal different behaviors related to various non-radiative recombination processes. The incorporation of bismuth also induces alloy non-uniformity in the quantum well, leading to an increased photoluminescence linewidth.
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| 6. |
- Rheinbay, E, et al.
(författare)
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 102-
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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| 7. |
- Song, Yuxin, 1981, et al.
(författare)
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Dilute bismides for near and mid-infrared applications
- 2013
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Ingår i: 2013 15th International Conference on Transparent Optical Networks (ICTON). - 2162-7339. - 9781479906826 ; , s. 6602735-
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Konferensbidrag (refereegranskat)abstract
- Dilute bismides are a group of emerging materials with unique properties. Incorporation of a small amount of Bi in common III-V host materials results in large band-gap reduction and strong spin-orbit splitting, leading to potential applications in near-infrared (NIR) and mid-infrared (MIR) optoelectronics. Recent progresses on molecular beam epitaxy (MBE) of novel III-Sb-Bi, i.e. GaSbBi and InSbBi thin films from our group are summarised in this paper. Quantum well structures based on GaSbBi and InGaAsBi aiming for the optical communication window were grown and characterized.
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| 8. |
- Wang, Shu Min, 1963, et al.
(författare)
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Novel Dilute Bismides for IR Optoelectronics Applications
- 2013
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Ingår i: Asia Communications and Photonics Conference, ACP. - Washington, D.C. : OSA. - 2162-108X.
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Konferensbidrag (refereegranskat)abstract
- III-V-Bi compounds reveal a number of attractive physical properties promising for novel IR optoelectronic applications [1,2] and have received considerable attention as witnessed by the dedicated international workshops on this topic in the consecutive past four years. The isoelectronic nature of Bi atoms in III-Vs induces strong interactions with the energy bands of host materials leading to large band-gap reduction, less temperature sensitive band-gap and large spin-orbit split band. So far the most studied material is Ga(N)AsBi, while other dilute bismides have also been reported recently. In this paper, we shall briefly review several novel bismides: GaSbBi, InSbiBi, InAsBi, InPBi and InGaAsBi, and the Bi surfactant effect from our group, all grown by molecular beam epitaxy (MBE).
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| 9. |
- Ye, Hong, 1987, et al.
(författare)
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High quality strain-compensated multiple InAs/AlGaNAs quantum dot layers grown by MBE
- 2013
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Ingår i: Physica Status Solidi (C) Current Topics in Solid State Physics. - : Wiley. - 1610-1642 .- 1862-6351. ; 10:5, s. 765-768
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Tidskriftsartikel (refereegranskat)abstract
- Intermediate band solar cells have attracted significant interest as a possible means of achieving high conversion efficiency. Under optimized growth parameters, we successfully achieve a high density of uniform InAs QDs grown on various matrixes by molecular beam epitaxy. Incorporating N atoms into GaAs and AlGaAs barriers effectively compensates the internal compressive strain and avoids formation of dislocations and defects. The 50 stacking of high density and uniform InAs QDs was demonstrated without detectable dislocations using 26 nm GaNAs as a barrier.
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| 10. |
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