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- Clark, M. S., et al.
(författare)
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Multi-omics for studying and understanding polar life
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss ‘omics’ approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
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- Pilheden, M., et al.
(författare)
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Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia
- 2022
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Ingår i: Hemasphere. - : Ovid Technologies (Wolters Kluwer Health). - 2572-9241. ; 6:10
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Tidskriftsartikel (refereegranskat)abstract
- Infant acute lymphoblastic leukemia (ALL) with KMT2A-gene rearrangements (KMT2A-r) have few mutations and a poor prognosis. To uncover mutations that are below the detection of standard next-generation sequencing (NGS), a combination of targeted duplex sequencing and NGS was applied on 20 infants and 7 children with KMT2A-r ALL, 5 longitudinal and 6 paired relapse samples. Of identified nonsynonymous mutations, 87 had been previously implicated in cancer and targeted genes recurrently altered in KMT2A-r leukemia and included mutations in KRAS, NRAS, FLT3, TP53, PIK3CA, PAX5, PIK3R1, and PTPN11, with infants having fewer such mutations. Of identified cancer-associated mutations, 62% were below the resolution of standard NGS. Only 33 of 87 mutations exceeded 2% of cellular prevalence and most-targeted PI3K/RAS genes (31/33) and typically KRAS/NRAS. Five patients only had low-frequency PI3K/RAS mutations without a higher-frequency signaling mutation. Further, drug-resistant clones with FLT3(D835H) or NRAS(G13D/G12S) mutations that comprised only 0.06% to 0.34% of diagnostic cells, expanded at relapse. Finally, in longitudinal samples, the relapse clone persisted as a minor subclone from diagnosis and through treatment before expanding during the last month of disease. Together, we demonstrate that infant and childhood KMT2A-r ALL harbor low-frequency cancer-associated mutations, implying a vast subclonal genetic landscape.
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- Bager, Ninna, et al.
(författare)
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Complex and monosomal karyotype are distinct cytogenetic entities with an adverse prognostic impact in paediatric acute myeloid leukaemia : A NOPHO-DBH-AML study
- 2018
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Ingår i: British Journal of Haematology. - : Wiley. - 0007-1048 .- 1365-2141. ; 183:4, s. 618-628
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Tidskriftsartikel (refereegranskat)abstract
- Data on occurrence, genetic characteristics and prognostic impact of complex and monosomal karyotype (CK/MK) in children with acute myeloid leukaemia (AML) are scarce. We studied CK and MK in a large unselected cohort of childhood AML patients diagnosed and treated according to Nordic Society for Paediatric Haematology and Oncology (NOPHO)-AML protocols 1993-2015. In total, 800 patients with de novo AML were included. CK was found in 122 (15%) and MK in 41 (5%) patients. CK and MK patients were young (median age 2.1 and 3.3 years, respectively) and frequently had FAB M7 morphology (24% and 22%, respectively). Refractory disease was more common in MK patients (15% vs. 4%) and stem cell transplantation in first complete remission was more frequent (32% vs. 19%) compared with non-CK/non-MK patients. CK showed no association with refractory disease but was an independent predictor of an inferior event-free survival (EFS; hazard ratio [HR] 1.43, P = 0.03) and overall survival (OS; HR 1.48, P = 0.01). MK was associated with a poor EFS (HR 1.57, P = 0.03) but did not show an inferior OS compared to non-MK patients (HR 1.14, P = 0.62). In a large paediatric cohort, we characterized AML with non-recurrent abnormal karyotype and unravelled the adverse impact of CK and MK on prognosis.
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- Ekberg, Joakim, 1976-, et al.
(författare)
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Design of an online health-promoting community : Negotiating user community needs with public health goals and service capabilities
- 2013
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Ingår i: BMC Health Services Research. - : BioMed Central. - 1472-6963. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: An online health-promoting community (OHPC) has the potential to promote health and advance new means of dialogue between public health representatives and the general public. The aim of this study was to examine what aspects of an OHPC that are critical for satisfying the needs of the user community and public health goals and service capabilities.Methods: Community-based participatory research methods were used for data collection and analysis, and participatory design principles to develop a case study OHPC for adolescents. Qualitative data from adolescents on health appraisals and perspectives on health information were collected in a Swedish health service region and classified into categories of user health information exchange needs. A composite design rationale for the OHPC was completed by linking the identified user needs, user-derived requirements, and technical and organizational systems solutions. Conflicts between end-user requirements and organizational goals and resources were identified.Results: The most prominent health information needs were associated to food, exercise, and well-being. The assessment of the design rationale document and prototype in light of the regional public health goals and service capabilities showed that compromises were needed to resolve conflicts involving the management of organizational resources and responsibilities. The users wanted to discuss health issues with health experts having little time to set aside to the OHPC and it was unclear who should set the norms for the online discussions.Conclusions: OHPCs can be designed to satisfy both the needs of user communities and public health goals and service capabilities. Compromises are needed to resolve conflicts between users' needs to discuss health issues with domain experts and the management of resources and responsibilities in public health organizations.
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- Hedman, J., et al.
(författare)
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Applying a PCR inhibitor tolerant DNA polymerase blend in forensic DNA profiling
- 2011
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Ingår i: Forensic Science International: Genetics, Supplement Series. - : Elsevier. - 1875-1768. ; 3:1, s. e349-e350
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Tidskriftsartikel (refereegranskat)abstract
- Crime scene samples often contain extraneous compounds that may interfere with PCR-based DNA analysis, resulting in imbalanced, partial or blank/negative DNA profiles. Customising the chemical content of the PCR reaction is a strategy that may increase PCR inhibitor tolerance without manipulating the sample. We have validated a modified version of AmpFlSTR SGM Plus, replacing AmpliTaq Gold DNA polymerase with a customised blend of two alternative polymerases, ExTaq Hot Start and PicoMaxx High Fidelity. Allele calls are identical to standard analysis. Stutter sizes and balance values are indistinguishable. The modified chemistry provides increased resistance to PCR inhibitors, resulting in an elevated number of detected alleles for various problematic crime scene samples.
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