Author: Rego, Natalia; Bianchi, Sergio; Moreno, Pilar; Persson, Helena; Kvist, Anders; Pena, Alvaro; Oppezzo, Pablo; Naya, Hugo; Rovira, Carlos; Dighiero, Guillermo; Pritsch, Otto
Title: Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis Cord-id: 71fp78kx Document date: 2012_4_10
ID: 71fp78kx
Snippet: As an approach to determining the aetiology of chronic lymphocytic leukaemia (CLL), we searched for a virus expressed in human CLL Bâ€cells by combining highâ€throughput sequencing and digital subtraction. Pooled Bâ€cell mRNA transcriptomes from five CLL patients and five healthy donors were sequenced with 454 Life Sciences technology. Human reads were excluded by BLAST (Basic Local Alignment Search Tool) and BLAT (BLASTâ€like alignment tool) searches. Remaining reads were screened with BLAS
Document: As an approach to determining the aetiology of chronic lymphocytic leukaemia (CLL), we searched for a virus expressed in human CLL Bâ€cells by combining highâ€throughput sequencing and digital subtraction. Pooled Bâ€cell mRNA transcriptomes from five CLL patients and five healthy donors were sequenced with 454 Life Sciences technology. Human reads were excluded by BLAST (Basic Local Alignment Search Tool) and BLAT (BLASTâ€like alignment tool) searches. Remaining reads were screened with BLAST against viral databases. Purified Bâ€cells from two CLL patients, with and without stimulation by phorbolâ€esters, were sequenced using Illumina technology to achieve depth of sequencing. Burrowsâ€Wheeler Aligner mapping and BLAST searches were used for the Illumina data. Pyrosequencing resulted in about 400 000 reads per sample. No viral candidate could be found. Illumina singleâ€end sequencing for 115 cycles yielded an average of 26 ± 2·5 million filtered reads per sample, of which 2·2 ± 0·6 million remained unmapped to human references. BLAST searches of these reads against viral and human databases assigned nine reads to an Epsteinâ€Barr virus origin, in one sample following phorbolâ€ester stimulation. Other reads showing a putative viral origin were dismissed after further analysis. Despite an inâ€depth analysis of the CLL transcriptome reaching more than 100 million sequences, we have not found evidence for a putative viral candidate in CLL.
Search related documents:
Co phrase search for related documents- abundant class and acute respiratory syndrome: 1
- accumulate evidence and acute respiratory: 1
- accumulate evidence and acute respiratory syndrome: 1
- acute respiratory and additional patient: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18
- acute respiratory and additional requirement: 1, 2, 3, 4
- acute respiratory and local alignment search tool: 1, 2, 3, 4, 5
- acute respiratory syndrome and additional patient: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17
- acute respiratory syndrome and additional requirement: 1, 2, 3, 4
- acute respiratory syndrome and local alignment search tool: 1, 2, 3, 4, 5
Co phrase search for related documents, hyperlinks ordered by date