| 1. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Alfoeldi, Jessica, et al.
(författare)
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The genome of the green anole lizard and a comparative analysis with birds and mammals
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 477:7366, s. 587-591
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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| 3. |
- Palkopoulou, Eleftheria, et al.
(författare)
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A comprehensive genomic history of extinct and living elephants
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 115:11, s. E2566-E2574
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Tidskriftsartikel (refereegranskat)abstract
- Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an similar to 120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for similar to 500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.
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| 4. |
- Nicolas, Aude, et al.
(författare)
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Genome-wide Analyses Identify KIF5A as a Novel ALS Gene
- 2018
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Ingår i: Neuron. - : Cell Press. - 0896-6273 .- 1097-4199. ; 97:6, s. 1268-1283.e6
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Tidskriftsartikel (refereegranskat)abstract
- To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.
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| 5. |
- Rhind, Nicholas, et al.
(författare)
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Comparative Functional Genomics of the Fission Yeasts
- 2011
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 332:6032, s. 930-936
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Tidskriftsartikel (refereegranskat)abstract
- The fission yeast clade-comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus-occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.
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| 6. |
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| 7. |
- Carneiro, Miguel, et al.
(författare)
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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 345:6200, s. 1074-1079
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Tidskriftsartikel (refereegranskat)abstract
- The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
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| 8. |
- Heiman, Jenny, 1980, et al.
(författare)
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The effect of nonsupervised physical activity before and after breast cancer surgery on quality of life: Results from a randomized controlled trial (PhysSURG-B)
- 2022
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Ingår i: Scandinavian Journal of Surgery. - : SAGE Publications. - 1457-4969 .- 1799-7267. ; 111:4
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Tidskriftsartikel (refereegranskat)abstract
- Background and objective: The PhysSURG-B trial of prehabilitation before breast cancer surgery randomized patients to a nonsupervised physical activity or a control group. The effects of the intervention on short- and long-term quality of life (QoL) were examined, with a subgroup analysis of patients receiving adjuvant chemotherapy. Methods: Female patients planned for surgery were randomly assigned to either an intervention of 30 min of self-administered physical aerobic activity daily 2 weeks before and 4 weeks after surgery or control. QoL was assessed with questionnaires at baseline, 4 weeks and 12 months postoperatively using the instruments FACT-B, RAND-36, and EQ-VAS. Results: Of 354 included participants at 12 months after surgery, 287 were available for analysis. FACT- B scores at 4 weeks and 12 months showed no differences between intervention compared to control, odds ratio (OR) of 0.975 (95% confidence interval (CI) 0.636-1.495) and 0.883 (95% CI 0.581-1.342), respectively. There was no difference in EQ-VAS comparing intervention to control at 4 weeks and 12 months, respectively, OR 1.163 (95% CI 0.760-1.779) and 0.817 (95% CI 0.559-1.300). RAND-36 domains "role limitations due to physical health" and "pain" showed a decrease at 4 weeks in both groups, returning toward baseline at 12 months follow-up. The subgroup who received adjuvant chemotherapy had significantly lower QoL measured using FACT-B at 12 months compared to patients not receiving chemotherapy (OR 0.475; 95% CI 0.300-0.753). Conclusions: An intervention of non-supervised physical activity before and after surgery for breast cancer showed no effect on short or long-term QoL, compared to control.
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| 9. |
- Ullmark, Jenny Heiman, 1980, et al.
(författare)
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Sick leave and predictive factors for sick leave at 12 months after breast cancer surgery in the randomized controlled physical activity trial (PhysSURG-B)
- 2023
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Ingår i: Surgeon-Journal of the Royal Colleges of Surgeons of Edinburgh and Ireland. - : Elsevier BV. - 1479-666X. ; 21:5, s. E229-E237
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To evaluate sick leave 12 months after breast cancer surgery, to analyze the effect of adjuvant chemotherapy and to identify predictive factors for sick leave, based on a randomized controlled trial of a non-supervised physical activity intervention (PhysSURGB).Methods: Sick leave days (for patients age 18-67) were collected from the Swedish Social Insurance Agency, and compared between the intervention and control arm in the trial. A random forest model was used to analyze predictive factors for sick leave, including baseline patient and tumor characteristics as well as patient-reported outcomes measuring quality of life, personality traits, pain, anxiety and depression.Results: A total of 203 patients were analyzed, and when comparing intervention to control, there was no differences in sick leave days (117 vs 55 days, odds ratio 1.21; 95% CI 0.75 -1.96). Adjuvant chemotherapy significantly increased days of sick leave (323 vs 42 days, odds ratio 17.3; 95% CI 9.15-34.2). Factors predicting prolonged sick leave were adjuvant chemotherapy, young age, previous mental health problems and low quality of life (measured as FACT-B score) at baseline.Conclusion: A non-supervised physical activity intervention had no effect on sick leave 12 months after surgery. Significantly longer sick leave was seen in patients treated by adjuvant chemotherapy. Factors predicting prolonged sick leave can be recognized at baseline and utilized when designing future interventions.
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