| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 3. |
- Jimenez, Camilo, et al.
(författare)
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Follow-up of pituitary tumor volume in patients with acromegaly treated with pegvisomant in clinical trials
- 2008
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Ingår i: European Journal of Endocrinology. - 1479-683X. ; 159:5, s. 517-523
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Tidskriftsartikel (refereegranskat)abstract
- Objective: We examined pituitary tumor volumes in patients treated with pegvisomant for 18 months or longer and in whom the tumors were monitored for at least 3 years. We present details on 9 of 304 patients in clinical trials with pegvisomant who experienced tumor growth within the first year of treatment. Method: Magnetic reonance images prior to start of pegvisomant and at last follow-up were examined in 43 patients (14% of participating patients). Twenty-nine had received prior radiation therapy (18% of irradiated patients and all but live received somatostatin analogs between periods of pegvisomant treatment. Results: At follow-up, the received tumor volume was 0.6 cc (range 0.0-19.7 ccl. in comparison with 1.6 cc (0.0-19.7 cc) at baseline (P<0.001). Twenty-five patients, of which 23 received radiation therapy, had tumor volume reduction therapy, had an increase in tumor volume from 1.61 to 1.93 cc. Of the nine patients with tumor growth, six had progressive growth before initiating pegvisomant. Two patients with stable tumors while on octreotide experienced enlargement after octreotide discontinuation but remained stable on long-term pegvisomant therapy. Conclusion: The present data indicate that pegvisomant does not promote tumor growth and suggest that the nine observed cases of tumor progression. which occured within 8 months after commencing pegvisomant, are likely rebound expansions after discontinuation of somatostatin analogs and/or the natural history of aggressively growing pituitary tumors. Continued long-term surveillance of tumor volume, particularly in non-irradiated patients is recommended.
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| 4. |
- Mikkelsen, Tarjei, et al.
(författare)
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Initial sequence of the chimpanzee genome and comparison with the human genome
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 437:7055, s. 69-87
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Tidskriftsartikel (refereegranskat)abstract
- Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
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| 5. |
- Bergström, Anders, et al.
(författare)
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Daily costs of prostaglandin analogues as monotherapy or in fixed combinations with timolol, in Denmark, Finland, Germany and Sweden.
- 2009
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Ingår i: Clinical Ophthalmology. - 1177-5467. ; 3, s. 471-481
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: To compare the daily costs of 3 prostaglandin analogues (bimatoprost, latanoprost, travoprost), alone, and associated with timolol in 4 European countries (Denmark, Finland, Germany, and Sweden). METHODS: Six glaucoma products were sampled by buying 5 bottles from 1 suburban pharmacy in each of the 4 countries. Drops were weighed by a single operator at 1 site according to standardized procedures. Residual drops were then counted. Unit bottle costs were estimated from tariff lists. Eye-drop weights were entered into a nested analysis of variance comprising drug, instillation day, country, the interaction, and a sample factor nested within the country factor. Effectiveness was represented by treatment failure rates estimated from a meta-analysis and a general practitioner survey. RESULTS: Every drug bottle contained sufficient drops to treat 1 patient for 28/31 days. Drop-size heterogeneity between countries was observed for bimatoprost and bimatoprost/timolol. Mean travoprost and travoprost/timolol drop-sizes were the smallest, and drop-counts per bottle were the lowest for latanoprost, or latanoprost/timolol. In all 4 countries annual costs were least for travoprost and travoprost/timolol. CONCLUSIONS: On taking into account drug costs and effectiveness, travoprost and travoprost/timolol were cheaper and more effective than latanoprost and latanoprost/timolol and were cheaper than bimatoprost and bimatoprost/timolol.
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| 6. |
- McCarroll, Steven A, et al.
(författare)
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Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease
- 2008
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 40:9, s. 1107-1112
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Tidskriftsartikel (refereegranskat)abstract
- Following recent success in genome-wide association studies, a critical focus of human genetics is to understand how genetic variation at implicated loci influences cellular and disease processes. Crohn's disease (CD) is associated with SNPs around IRGM, but coding-sequence variation has been excluded as a source of this association. We identified a common, 20-kb deletion polymorphism, immediately upstream of IRGM and in perfect linkage disequilibrium (r2 = 1.0) with the most strongly CD-associated SNP, that causes IRGM to segregate in the population with two distinct upstream sequences. The deletion (CD risk) and reference (CD protective) haplotypes of IRGM showed distinct expression patterns. Manipulation of IRGM expression levels modulated cellular autophagy of internalized bacteria, a process implicated in CD. These results suggest that the CD association at IRGM arises from an alteration in IRGM regulation that affects the efficacy of autophagy and identify a common deletion polymorphism as a likely causal variant.
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