title: Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.
abstract: BACKGROUND
  High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell.
  
  
  RESULTS
  We present the utility of massively parallel sequencing by synthesis for profiling the transcriptome of a human prostate cancer cell-line, LNCaP, that has been treated with the synthetic androgen, R1881. Through the generation of approximately 20 megabases (MB) of EST data, we detect transcription from over 10,000 gene loci, 25 previously undescribed alternative splicing events involving known exons, and over 1,500 high quality single nucleotide discrepancies with the reference human sequence. Further, we map nearly 10,000 ESTs to positions on the genome where no transcription is currently predicted to occur. We also characterize various obstacles with using sequencing by synthesis for transcriptome analysis and propose solutions to these problems.
  
  
  CONCLUSIONS
  The use of high-throughput sequencing-by-synthesis methods for transcript profiling allows the specific and sensitive detection of many of a cell's transcripts, and also allows the discovery of high quality base discrepancies, and alternative splice variants. Thus, this technology may provide an effective means of understanding various disease states, discovering novel targets for disease treatment, and discovery of novel transcripts.
authors.affiliation: British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada. sjones@bcgsc.ca.
authors.forename: Matthew N
authors.initials: MN
authors.lastname: Bainbridge
authors.forename: René L
authors.initials: RL
authors.lastname: Warren
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
authors.forename: Tammy
authors.initials: T
authors.lastname: Romanuik
authors.forename: Thomas
authors.initials: T
authors.lastname: Zeng
authors.forename: Anne
authors.initials: A
authors.lastname: Go
authors.forename: Allen
authors.initials: A
authors.lastname: Delaney
authors.forename: Malachi
authors.initials: M
authors.lastname: Griffith
authors.forename: Matthew
authors.initials: M
authors.lastname: Hickenbotham
authors.forename: Vincent
authors.initials: V
authors.lastname: Magrini
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Marianne D
authors.initials: MD
authors.lastname: Sadar
authors.forename: Asim S
authors.initials: AS
authors.lastname: Siddiqui
authors.forename: Marco A
authors.initials: MA
authors.lastname: Marra
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology; D017398:Alternative Splicing; D000728:Androgens; D045744:Cell Line, Tumor / Q000737:chemistry / Q000187:drug effects; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics*; D005091:Exons / Q000235:genetics; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D008297:Male; D015741:Metribolone / Q000494:pharmacology; D009376:Neoplasms, Hormone-Dependent / Q000235:genetics* / Q000473:pathology; D020641:Polymorphism, Single Nucleotide; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology; D012333:RNA, Messenger / Q000235:genetics*; D012334:RNA, Neoplasm / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic
chemical_list: D000728:Androgens; D018076:DNA, Complementary; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D015741:Metribolone