| 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. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Tidskriftsartikel (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. |
- Beecham, Ashley H, et al.
(författare)
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Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
- 2013
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:11, s. 1353-60
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Tidskriftsartikel (refereegranskat)abstract
- Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
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| 3. |
- Karami, Nahid, 1959, et al.
(författare)
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Investigation of an outbreak of CTX-M-15-producing Escherichia coli of sequence types 131 and 1441 in a neonatal surgical ward: comparison of typing methods
- 2010
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Ingår i: 20th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, Austria.
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Konferensbidrag (refereegranskat)abstract
- Objectives: In a surgical ward caring mainly for newborns spread of CTX-M-15-producing E.coli had been ongoing at least since September 2008 when we finally recognized the outbreak in late December. We have compared various typing methods with pulsed-field gel electrophoresis (PFGE) to verify the actual outbreak and subsequently to determine number of affected children. Methods: In addition to clinical sampling 125 children hospitalized between Sept-Dec were screened for extended-spectrum beta-lactamase (ESBL)-producing bacteria in stool during Dec-Feb. From Jan-June 2009 newly admitted children were screened at admission and twice weekly. Fifty-one E coli isolates with ESBL from 27 children were found. These isolates have been typed with PFGE, multiple-locus-variable number tandem repeat analysis (MLVA), a mini multiple-locus-sequence typing (MLST) method (dnaJ, purA and fumC genes) as well as with the Phene Plate (PhP) biochemical fingerprinting system. Results: When the outbreak was revealed five children had developed infections with ESBL-producing E. coli that were of two PFGE-types (A and B) later considered to be the outbreak strains. One or both were spread to 21 children. Six children had multiple types. Altogether 38 isolates (20 children) were of type A (ST 131), 7 isolates (5 children) of type B (ST 1441). In addition E coli of six distinct PFGE-types (C-?) were found in one child each. MLVA gave identical discriminatory results as PFGE for all isolates tested. Mini-MLST could not differentiate ST 131 isolates of to distinct PFGE-types (type A and C) but accurately predicted the ST-types of each PFGE-type when confirmed with standard MLST according to http://mlst.ucc.ie/mlst/dbs/Ecoli. By comparing resistance pattern we thus missed the outbreak by a month. PhP indicated that all initial isolates were singletons and there was hardly any correlation with PFGE. Conclusion: If transmission has been ongoing for a long time several types of ESBL-producing bacteria may be found in an outbreak and all isolates including repeat and screening isolates need to be typed to identify affected patients. Only genetic typing, gave satisfactory results in this outbreak. MLVA gave identical results to PFGE and is thus attractive being faster, cheaper and easier to communicate. Our mini-MLST was somewhat less discriminatory but despite using only three house keeping genes accurately predicted the ST-types.
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