117,338 research outputs found
SNP detection by RNA-seq
No full textSNP detection by RNA-seq
L. Xumerle 1 , I. Iacobucci 2 , V. Mijatovic 1 , A. Mori 1 , G. Martinelli 2 , P. F. Pignatti 1 , G.
Malerba 1 ;
1 Biology and Genetics, Verona, Italy, 2 Department of Hematology and Oncological Sciences „L. e A. Seràgnoli“, Bologna, Italy.
The massively parallel sequencing of the transcriptome (RNA-seq) produ ces several millions sequences (reads) that are usually used to quantify digiltally the genes expression over the trascriptome. Since RNA-seq is based on sequencing, it‘s possible to identify loci that are likely to be polimorphic using alignment mismatches between the tested sample and the reference genome sequence. The goal of this study is to compare the most common alignment programs (bowtie2, tophat2, bwa, gsnap) to verify the reliability of SNP detection in RNA-seq samples. For the analysis were used data of 5 RNA-seq samples from individuals (2 leukemia and 3 chronic myeloproliferative syndrome) previously genotyped with the Affymetrix Chip GenomeWideSNP 6. After alignment, genotypes of polimorfic loci were detected directly from the pileup computed by the program samtools. More than 10000 polymorphic loci were detected by RNA-seq and were in common with the corresponding loci on the Chip. In the first analysis an allele was considered a true variant if called by at least five reads. Using this threshold the average genotype error rate between RNA-seq and Chip is ~10%. The same computation performed with no threshold value (1 read was enough to call the alternative allele) shows an error rate of ~ 0,03%. The results suggest that SNP detection is possible using RNA-seq and that variants called by few reads have to be interpreted as true variants and not a background noise. A more detailed study of differential allele counts needs to be performed to ascertain possible biases of RNA-seq
Effects of Duplex-specific nuclease on human cells expression profiling using RNA-seq
No full textEffects of Duplex-specific nuclease on human cells expression profiling using RNA-seqV. Mijatovic 1 , G. Buson 2 , M. Valenti 3 , L. Dalle Carbonare 3 , A. Ferrarini 2 , A. Dal Molin 1 , A. Mori 1 , L. Xumerle 1 , E. Caviola 4 , P. Pertile 4 , M. Delledonne 2 , P. F. Pignatti 1 , G. Malerba 1 ;1 Department of Life and Reproductions Sciences, University of Verona, Verona, Italy, 2 Department of Biotechnology, University of Verona, Verona, Italy, 3 Department of Medicine, Clinic of Internal Medicine, Section D, Verona, Italy, 4 Cutech Srl, Padova, Italy.RNA-seq is a next-generation sequencing method able to characterize tho-ence the estimate of relative expression of less expressed genes, as well as reduce the estimate accuracy of gene expression levels of low expressed genes. Therefore, it would be convenient to apply a method able to reduce excessively abundant mRNA transcripts. A cDNA depletion method for the most represented transcripts called duplex-specific nuclease (DSN) has been effectively used in several studies. Three different cell types were studied: blood, monocytes and keratinocytes. From each cell type two RNA-seq libraries were produced (untreated libraries), for a total of 6 libraries. A part of each library was then treated with DSN, producing a total of 6 DSN treated libraries. Overall, 12 RNA-seq libraries (6 untreated and 6 treated) were prepared. In blood tissue the most abundant transcripts in both DSN-treated and DSN-untreated samples corresponded to globins (HBA2, HBA1 and HBB), accounting for ~70% of total transcripts. In this sample maximum effects of DSN treatment was observed. Transcripts found to be the most expressed in monocyte sample were ~10 times smaller than globins expression in blood sample. Gene expression of keratinocyte libraries was not influenced by DSN treatment. DSN treatment has been able to strongly reduce globins expression. DSN treatment also reduced, even if with a smaller effect, the most expressed genes in monocyte sample
Association of the IL33 gene region with childhood allergic asthma
No full textThe study evaluates the association of the IL33 gene region with childhood allergic asthm
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Analisi di associazione del cluster genico degli interferoni nella regione 9p21 in famiglie italiane con asma allergico
No full textStudio di associazione della regione cromosomica 9p22 in famiglie italiane con asma allergico
No full textSquare Dancing with the Stars to Enhance Dynamic Hirschman Linkages?
No full textIn this Presidential Address, the author takes the reader on a reconnaissance of his life and time as a regional scientist. He points out scenery he found scintillating along the way, hoping that some may pick up the banner and chew on a few of the ideas for a while. He suggests a revisit to Albert O. Hirschman’s notion of key sectors and more empirical analysis related to Marcus Berliant’s and Masahisa Fujita’s notion of knowledge creation and transfer.Presidential Address, San Antonio, Texas, March 29, 2014 (53rd Meetings of the Southern Regional Science Association
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Linkage and association study of allergic asthma with a STAT6 gene olymorphism in a sample of the Italian population
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