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- 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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- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 16. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 17. |
- Alt, Helmut, et al.
(författare)
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Scandinavian Thins on Top of Cake : New and Improved Algorithms for Stacking and Packing
- 2014
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Ingår i: Theory of Computing Systems. - : Springer Science and Business Media LLC. - 1432-4350 .- 1433-0490. ; 54:4, s. 689-714
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Tidskriftsartikel (refereegranskat)abstract
- We show how to compute the smallest rectangle that can enclose any polygon, from a given set of polygons, in nearly linear time; we also present a PTAS for the problem, as well as a linear-time algorithm for the case when the polygons are rectangles themselves. We prove that finding a smallest convex polygon that encloses any of the given polygons is NP-hard, and give a PTAS for minimizing the perimeter of the convex enclosure. We also give efficient algorithms to find the smallest rectangle simultaneously enclosing a given pair of convex polygons.
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- Arkin, Esther M, et al.
(författare)
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Convex transversals
- 2014
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Ingår i: Computational Geometry. - : Elsevier BV. - 0925-7721. ; 47:2, s. 224-239
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Tidskriftsartikel (refereegranskat)abstract
- We answer the question initially posed by Arik Tamir at the Fourth NYU Computational Geometry Day (March, 1987): “Given a collection of compact sets, can one decide in polynomial time whether there exists a convex body whose boundary intersects every set in the collection?”We prove that when the sets are segments in the plane, deciding existence of the convex stabber is NP-hard. The problem remains NP-hard if the sets are regular polygons. We also show that in 3D the stabbing problem is hard when the sets are balls. On the positive side, we give a polynomial-time algorithm to find a convex transversal of a maximum number of pairwise-disjoint segments in 2D if the vertices of the transversal are restricted to a given set of points. Our algorithm also finds a convex stabber of the maximum number of a set of convex pseudodisks in the plane.The stabbing problem is related to “convexity” of point sets measured as the minimum distance by which the points must be shifted in order to arrive in convex position; we give a PTAS to find the minimum shift in 2D, and a 2-approximation in any dimension. We also consider stabbing with vertices of a regular polygon – a problem closely related to approximate symmetry detection.
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| 19. |
- Arkin, Esther M, et al.
(författare)
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Shortest path to a segment and quickest visibility queries
- 2016
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Ingår i: LIPIcs-Leibniz International Proceedings in Informatics. ; , s. 77-100
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Konferensbidrag (refereegranskat)abstract
- We show how to preprocess a polygonal domain with a xed starting point s in order to answer eciently the following queries: Given a point q, how should one move from s in order to see q as soon as possible? This query resembles the well-known shortestpath- to-a-point query, except that the latter asks for the fastest way to reach q, instead of seeing it. Our solution methods include a data structure for a di erent generalization of shortest-path-to-a-point queries, which may be of independent interest: to report eciently a shortest path from s to a query segment in the domain.
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- Bae, Sang Won, et al.
(författare)
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Computing the $ L_1 $ Geodesic Diameter and Center of a Polygonal Domain
- 2016
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Ingår i: 33rd Symposium on Theoretical Aspects of Computer Science. - : Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik. - 9783959770019 ; , s. 14:1-14:14
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Konferensbidrag (refereegranskat)abstract
- For a polygonal domain with h holes and a total of n vertices, we present algorithms that compute the L1 geodesic diameter in O(n2+h4) time and the L1 geodesic center in O((n4+n2h4) (n)) time, where (·) denotes the inverse Ackermann function. No algorithms were known for these problems before. For the Euclidean counterpart, the best algorithms compute the geodesic diameter in O(n7.73) or O(n7(h+log n)) time, and compute the geodesic center in O(n12+) time. Therefore, our algorithms are much faster than the algorithms for the Euclidean problems. Our algorithms are based on several interesting observations on L1 shortest paths in polygonal domains.
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- de Jong, S, et al.
(författare)
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Applying polygenic risk scoring for psychiatric disorders to a large family with bipolar disorder and major depressive disorder
- 2018
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 1, s. 163-
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Tidskriftsartikel (refereegranskat)abstract
- Psychiatric disorders are thought to have a complex genetic pathology consisting of interplay of common and rare variation. Traditionally, pedigrees are used to shed light on the latter only, while here we discuss the application of polygenic risk scores to also highlight patterns of common genetic risk. We analyze polygenic risk scores for psychiatric disorders in a large pedigree (n ~ 260) in which 30% of family members suffer from major depressive disorder or bipolar disorder. Studying patterns of assortative mating and anticipation, it appears increased polygenic risk is contributed by affected individuals who married into the family, resulting in an increasing genetic risk over generations. This may explain the observation of anticipation in mood disorders, whereby onset is earlier and the severity increases over the generations of a family. Joint analyses of rare and common variation may be a powerful way to understand the familial genetics of psychiatric disorders.
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- Thombs, BD, et al.
(författare)
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Overestimation of Postpartum Depression Prevalence Based on a 5-item Version of the EPDS: Systematic Review and Individual Participant Data Meta-analysis
- 2020
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Ingår i: Canadian journal of psychiatry. Revue canadienne de psychiatrie. - : SAGE Publications. - 1497-0015. ; 65:12, s. 835-844
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Tidskriftsartikel (refereegranskat)abstract
- The Maternal Mental Health in Canada, 2018/2019, survey reported that 18% of 7,085 mothers who recently gave birth reported “feelings consistent with postpartum depression” based on scores ≥7 on a 5-item version of the Edinburgh Postpartum Depression Scale (EPDS-5). The EPDS-5 was designed as a screening questionnaire, not to classify disorders or estimate prevalence; the extent to which EPDS-5 results reflect depression prevalence is unknown. We investigated EPDS-5 ≥7 performance relative to major depression prevalence based on a validated diagnostic interview, the Structured Clinical Interview for DSM (SCID). Methods: We searched Medline, Medline In-Process & Other Non-Indexed Citations, PsycINFO, and the Web of Science Core Collection through June 2016 for studies with data sets with item response data to calculate EPDS-5 scores and that used the SCID to ascertain depression status. We conducted an individual participant data meta-analysis to estimate pooled percentage of EPDS-5 ≥7, pooled SCID major depression prevalence, and the pooled difference in prevalence. Results: A total of 3,958 participants from 19 primary studies were included. Pooled prevalence of SCID major depression was 9.2% (95% confidence interval [CI] 6.0% to 13.7%), pooled percentage of participants with EPDS-5 ≥7 was 16.2% (95% CI 10.7% to 23.8%), and pooled difference was 8.0% (95% CI 2.9% to 13.2%). In the 19 included studies, mean and median ratios of EPDS-5 to SCID prevalence were 2.1 and 1.4 times. Conclusions: Prevalence estimated based on EPDS-5 ≥7 appears to be substantially higher than the prevalence of major depression. Validated diagnostic interviews should be used to establish prevalence.
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