| 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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| 3. |
- Ali, M, et al.
(författare)
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Protocol for the development of the international population registry for aphasia after stroke (I-PRAISE)
- 2022
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Ingår i: Aphasiology. - : Informa UK Limited. - 0268-7038 .- 1464-5041. ; 36:4, s. 534-554
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Tidskriftsartikel (refereegranskat)abstract
- Background: We require high-quality information on the current burden, the types of therapy and resources available, methods of delivery, care pathways and long-term outcomes for people with aphasia.Aim: To document and inform international delivery of post-stroke aphasia treatment, to optimise recovery and reintegration of people with aphasia.Methods & Procedures: Multi-centre, prospective, non-randomised, open study, employing blinded outcome assessment, where appropriate, including people with post-stroke aphasia, able to attend for 30 minutes during the initial language assessment, at first contact with a speech and language therapist for assessment of aphasia at participating sites. There is no study-mandated intervention. Assessments will occur at baseline (first contact with a speech and language therapist for aphasia assessment), discharge from Speech and Language Therapy (SLT), 6 and 12-months post-stroke. Our primary outcome is changed from baseline in the Amsterdam Nijmegen Everyday Language Test (ANELT/Scenario Test for participants with severe verbal impairments) at 12-months post-stroke. Secondary outcomes at 6 and 12 months include the Therapy Outcome Measure (TOMS), Subjective Index of Physical and Social Outcome (SIPSO), Aphasia Severity Rating Scale (ASRS), Western Aphasia Battery Aphasia Quotient (WAB-AQ), stroke and aphasia quality of life scale (SAQoL-39), European Quality of Life Scale (EQ-5D), lesion description, General Health Questionnaire (GHQ-12), resource use, and satisfaction with therapy provision and success. We will collect demography, clinical data, and therapy content. Routine neuroimaging and medication administration records will be accessed where possible; imaging will be pseudonymised and transferred to a central reading centre. Data will be collected in a central registry. We will describe demography, stroke and aphasia profiles and therapies available. International individual participant data (IPD) meta-analyses will examine treatment responder rates based on minimal detectable change & clinically important changes from baseline for primary and secondary outcomes at 6 and 12 months. Multivariable meta-analyses will examine associations between demography, therapy, medication use and outcomes, considering service characteristics. Where feasible, costs associated with treatment will be reported. Where available, we will detail brain lesion size and site, and examine correlations with SLT and language outcome at 12 months.Conclusion: International differences in care, resource utilisation and outcomes will highlight avenues for further aphasia research, promote knowledge sharing and optimise aphasia rehabilitation delivery. IPD meta-analyses will enhance and expand understanding, identifying cost-effective and promising approaches to optimise rehabilitation to benefit people with aphasia.
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| 5. |
- Bellenguez, C, et al.
(författare)
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New insights into the genetic etiology of Alzheimer's disease and related dementias
- 2022
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 54:4, s. 412-436
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Tidskriftsartikel (refereegranskat)abstract
- Characterization of the genetic landscape of Alzheimer’s disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/‘proxy’ AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele.
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| 7. |
- De Souza, S, et al.
(författare)
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PATIENT AND PUBLIC INVOLVEMENT IN CLINICAL TRIAL DESIGN
- 2020
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Ingår i: ANNALS OF THE RHEUMATIC DISEASES. - : BMJ. - 0003-4967 .- 1468-2060. ; 79, s. 1285-1286
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Patient and public involvement (PPI) is gaining increasing recognition as important in ensuring research is relevant and acceptable to participants. Rheuma Tolerance for Cure (RTCure) is a 5 year international collaboration between academia and industry; focusing on earlier detection and prevention of rheumatoid arthritis (RA) through the use of immune-tolerising treatments.Objectives:To bring lived experience and insight into scientific discussions; and to evolve collaboration between lay representatives and academia/industry.Methods:9 Patient Research Partners (PRPs) from 5 European countries were recruited via the EULAR PARE Network and institutions within the RTCure Consortium (8 PRPs with RA and 1 ‘at risk’). They were asked to enter into a legal agreement with the Consortium. PRPs participated in teleconferences (TCs) and were invited to attend face-to-face (F2F) meetings at least annually. Requests for input/feedback were sent from researchers to PRPs via the project’s Patient Engagement Expert [SK].Results:PRP involvement has given researchers and industry partners a new perspective on patient priorities, and focused thought on the ethics of recruitment for and participation in clinical trials of people ‘at risk’ of developing RA. PRPs have helped define the target populations, given their thoughts on what types of treatments are acceptable to people ‘at risk’ and have aided the development of a survey (sent to EULAR PARE members) regarding the use of animal models in biomedical research. Positive informal feedback has been received from researchers and industry regarding the contribution of PRPs to the ongoing project (formal evaluation of PPI in RTCure will be carried out in 2020 and at the project end in 2022).Challenges:Legal agreements- Many PRPs refused to sign the Consortium’s complex PRP Agreement; feeling it unnecessary, incomprehensible and inequitable. After extensive consultation with various parties (including EULAR and the Innovative Medicines Initiative) no similar contract was found. Views for its requirement even varied between legal experts. After 2 years of intense discussion, a simple non-disclosure agreement was agreed upon. Ideally any contract, if required, should be approved prior to project onset.Meeting logistics- Other improvements identified were to locate the meeting venue and accommodation on the same site to minimise travel, and to make it easier for PRPs to take breaks when required. This also facilitates informal discussions and patient inclusivity. We now have agreed a policy to fund PRPs extra nights before and after meetings, and to bring a carer if needed.Enabling understanding– Future annual meetings will start with a F2F meeting between PRPs and Work Package Leads. Researchers will be encouraged to start presentations with a summary slide in lay language. Additionally, an RTCure Glossary is in development.Enabling participation– SK will provide monthly project updates and PRP TCs will be held in the evening (as some PRPs remain employed). PRPs will be invited to all project TCs and F2F meetings. Recruitment is underway to increase the number of ‘at risk’ PRPs as their viewpoint is vital to this study.Conclusion:Currently PPI in RTCure is an ongoing mutual learning process. Universal guidance regarding what types of contracts are needed for PPI would be useful. Communication, trust and fruitful discussions have evolved through F2F meetings (both formal and informal) between PRPs, academia and industry. It is important that all parties can be open with each other in order to make PPI more meaningful.Acknowledgments:This work has received support from the EU/EFPIA Innovative Medicines Initiative 2 Joint Undertaking RTCure grant number 777357.Disclosure of Interests:Savia de Souza: None declared, Ruth Williams: None declared, Eva Johansson: None declared, Codruta Zabalan: None declared, Tom Esterine: None declared, Margôt Bakkers: None declared, Wolfgang Roth: None declared, Neil Mc Carthy: None declared, Meryll Blake: None declared, Susanne Karlfeldt: None declared, Martina Johannesson: None declared, Karim Raza Grant/research support from: KR has received research funding from AbbVie and Pfizer, Consultant of: KR has received honoraria and/or consultancy fees from AbbVie, Sanofi, Lilly, Bristol-Myers Squibb, UCB, Pfizer, Janssen and Roche Chugai, Speakers bureau: KR has received honoraria and/or consultancy fees from AbbVie, Sanofi, Lilly, Bristol-Myers Squibb, UCB, Pfizer, Janssen and Roche Chugai
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| 8. |
- Khashayar, P., et al.
(författare)
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Designing an Iran FRAX model and defining intervention and assessment thresholds for osteoporosis
- 2021
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Ingår i: Iranian Journal of Epidemiology. - 1735-7489. ; 16:4, s. 296-304
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Tidskriftsartikel (refereegranskat)abstract
- Background and Objectives: The purpose of this study was to adopt and calibrate the fracture risk assessment algorithm FRAX® for the Iranian population and to provide the required guidance on how to apply it in clinical practice. Methods: The age-specific ten-year probability of major osteoporotic fractures was calculated in women with an average BMI to determine the fracture probability at two potential intervention thresholds. The first threshold was the age-specific fracture probability associated with a femoral neck T-score of -2.5 SD and the other was age-specific fracture probability in women with a history of fracture without BMD. Current Iranian guidelines were used to define these thresholds. The effect of adding BMD values to the assessment of these thresholds was also evaluated separately. Results: Similar to women with a previous fracture, the 10-year probability of a major osteoporotic fracture increased from 4.9% at the age of 50 years to 17% at the age of 80 years. When using a BMD T-score of ≤−2.5 SD as the intervention threshold, the FRAX probability was twice as high in women aged 50 years as in women of the same age with an average BMD and no risk factor. The FRAX probability increased with age but a T-score of -2.5 SD was actually protective after 80 years or age. Conclusion: Intervention thresholds based on BMD alone cannot effectively identify high-risk women for fracture, particularly in advanced ages. Using fracture probability based on ‘fracture threshold’ can help to improve the identification of these women. © 2021, Iranian Epidemiological Association. All rights reserved.
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