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Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis

Rego, Natalia; Bianchi, Sergio; Moreno, Pilar; Persson, Helena LU ; Kvist, Anders LU ; Pena, Alvaro; Oppezzo, Pablo; Naya, Hugo; Rovira, Carlos LU and Dighiero, Guillermo, et al. (2012) In British Journal of Haematology 157(6). p.709-717
Abstract
As an approach to determining the aetiology of chronic lymphocytic leukaemia (CLL), we searched for a virus expressed in human CLL B-cells by combining high-throughput sequencing and digital subtraction. Pooled B-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 (BLAST-like alignment tool) searches. Remaining reads were screened with BLAST against viral databases. Purified B-cells from two CLL patients, with and without stimulation by phorbol-esters, were sequenced using Illumina technology to achieve depth of sequencing. Burrows-Wheeler Aligner mapping and BLAST searches were used for the... (More)
As an approach to determining the aetiology of chronic lymphocytic leukaemia (CLL), we searched for a virus expressed in human CLL B-cells by combining high-throughput sequencing and digital subtraction. Pooled B-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 (BLAST-like alignment tool) searches. Remaining reads were screened with BLAST against viral databases. Purified B-cells from two CLL patients, with and without stimulation by phorbol-esters, were sequenced using Illumina technology to achieve depth of sequencing. Burrows-Wheeler Aligner mapping and BLAST searches were used for the Illumina data. Pyrosequencing resulted in about 400 similar to 000 reads per sample. No viral candidate could be found. Illumina single-end sequencing for 115 cycles yielded an average of 26 +/- 2.5million filtered reads per sample, of which 2.2 +/- 0.6 similar to million remained unmapped to human references. BLAST searches of these reads against viral and human databases assigned nine reads to an Epstein-Barr virus origin, in one sample following phorbol-ester stimulation. Other reads showing a putative viral origin were dismissed after further analysis. Despite an in-depth analysis of the CLL transcriptome reaching more than 100 similar to million sequences, we have not found evidence for a putative viral candidate in CLL. (Less)
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publication status
published
subject
keywords
chronic lymphocytic leukaemia, aetiology, virus, high-throughput, sequencing, digital transcriptome subtraction
in
British Journal of Haematology
volume
157
issue
6
pages
709 - 717
publisher
Federation of European Neuroscience Societies and Blackwell Publishing Ltd
external identifiers
  • wos:000304441600008
  • scopus:84861532176
ISSN
0007-1048
DOI
10.1111/j.1365-2141.2012.09116.x
language
English
LU publication?
yes
id
38c89345-2311-4ff3-9405-16a0e0126df8 (old id 2799648)
date added to LUP
2012-07-03 10:24:54
date last changed
2017-01-15 03:23:47
@article{38c89345-2311-4ff3-9405-16a0e0126df8,
  abstract     = {As an approach to determining the aetiology of chronic lymphocytic leukaemia (CLL), we searched for a virus expressed in human CLL B-cells by combining high-throughput sequencing and digital subtraction. Pooled B-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 (BLAST-like alignment tool) searches. Remaining reads were screened with BLAST against viral databases. Purified B-cells from two CLL patients, with and without stimulation by phorbol-esters, were sequenced using Illumina technology to achieve depth of sequencing. Burrows-Wheeler Aligner mapping and BLAST searches were used for the Illumina data. Pyrosequencing resulted in about 400 similar to 000 reads per sample. No viral candidate could be found. Illumina single-end sequencing for 115 cycles yielded an average of 26 +/- 2.5million filtered reads per sample, of which 2.2 +/- 0.6 similar to million remained unmapped to human references. BLAST searches of these reads against viral and human databases assigned nine reads to an Epstein-Barr virus origin, in one sample following phorbol-ester stimulation. Other reads showing a putative viral origin were dismissed after further analysis. Despite an in-depth analysis of the CLL transcriptome reaching more than 100 similar to million sequences, we have not found evidence for a putative viral candidate in CLL.},
  author       = {Rego, Natalia and Bianchi, Sergio and Moreno, Pilar and Persson, Helena and Kvist, Anders and Pena, Alvaro and Oppezzo, Pablo and Naya, Hugo and Rovira, Carlos and Dighiero, Guillermo and Pritsch, Otto},
  issn         = {0007-1048},
  keyword      = {chronic lymphocytic leukaemia,aetiology,virus,high-throughput,sequencing,digital transcriptome subtraction},
  language     = {eng},
  number       = {6},
  pages        = {709--717},
  publisher    = {Federation of European Neuroscience Societies and Blackwell Publishing Ltd},
  series       = {British Journal of Haematology},
  title        = {Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis},
  url          = {http://dx.doi.org/10.1111/j.1365-2141.2012.09116.x},
  volume       = {157},
  year         = {2012},
}