Matches in SemOpenAlex for { <https://semopenalex.org/work/W2025323279> ?p ?o ?g. }
- W2025323279 endingPage "163" @default.
- W2025323279 startingPage "163" @default.
- W2025323279 abstract "The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing number of unconventional transcripts, such as novel isoforms, non-coding RNAs, somatic gene fusions and deletions have been associated with the tumoral state. Massively parallel sequencing techniques provide a framework for exploring the transcriptional complexity inherent to cancer with a limited laboratory and financial effort. We developed a deep sequencing and bioinformatics analysis protocol to investigate the molecular composition of a breast cancer poly(A)+ transcriptome. This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts.We analyzed over 132,000 Roche 454 high-confidence deep sequencing reads from a primary human lobular breast cancer tissue specimen, and detected a range of unusual transcriptional events that were subsequently validated by RT-PCR in additional eight primary human breast cancer samples. We identified and validated one deletion, two novel ncRNAs (one intergenic and one intragenic), ten previously unknown or rare transcript isoforms and a novel gene fusion specific to a single primary tissue sample. We also explored the non-protein-coding portion of the breast cancer transcriptome, identifying thousands of novel non-coding transcripts and more than three hundred reads corresponding to the non-coding RNA MALAT1, which is highly expressed in many human carcinomas.Our results demonstrate that combining 454 deep sequencing with a normalization step and careful bioinformatic analysis facilitates the discovery and quantification of rare transcripts or ncRNAs, and can be used as a qualitative tool to characterize transcriptome complexity, revealing many hitherto unknown transcripts, splice isoforms, gene fusion events and ncRNAs, even at a relatively low sequence sampling." @default.
- W2025323279 created "2016-06-24" @default.
- W2025323279 creator A5002559498 @default.
- W2025323279 creator A5005312066 @default.
- W2025323279 creator A5006505062 @default.
- W2025323279 creator A5007173998 @default.
- W2025323279 creator A5009341406 @default.
- W2025323279 creator A5016274127 @default.
- W2025323279 creator A5018950136 @default.
- W2025323279 creator A5021012929 @default.
- W2025323279 creator A5023805612 @default.
- W2025323279 creator A5023828670 @default.
- W2025323279 creator A5030417567 @default.
- W2025323279 creator A5034654303 @default.
- W2025323279 creator A5040640445 @default.
- W2025323279 creator A5048693547 @default.
- W2025323279 creator A5051867363 @default.
- W2025323279 creator A5061239406 @default.
- W2025323279 creator A5066133225 @default.
- W2025323279 creator A5079506878 @default.
- W2025323279 creator A5084518228 @default.
- W2025323279 creator A5090644269 @default.
- W2025323279 date "2009-01-01" @default.
- W2025323279 modified "2023-10-16" @default.
- W2025323279 title "A transcriptional sketch of a primary human breast cancer by 454 deep sequencing" @default.
- W2025323279 cites W1923010649 @default.
- W2025323279 cites W1969182616 @default.
- W2025323279 cites W1970086542 @default.
- W2025323279 cites W1976884224 @default.
- W2025323279 cites W1977678165 @default.
- W2025323279 cites W1994658343 @default.
- W2025323279 cites W2002354671 @default.
- W2025323279 cites W2005636452 @default.
- W2025323279 cites W2007006753 @default.
- W2025323279 cites W2007015770 @default.
- W2025323279 cites W2015858554 @default.
- W2025323279 cites W2016066165 @default.
- W2025323279 cites W2031820172 @default.
- W2025323279 cites W2034023446 @default.
- W2025323279 cites W2038617558 @default.
- W2025323279 cites W2045160632 @default.
- W2025323279 cites W2053150867 @default.
- W2025323279 cites W2064469303 @default.
- W2025323279 cites W2067410483 @default.
- W2025323279 cites W2073551150 @default.
- W2025323279 cites W2079265437 @default.
- W2025323279 cites W2082534286 @default.
- W2025323279 cites W2092454702 @default.
- W2025323279 cites W2102304447 @default.
- W2025323279 cites W2105714972 @default.
- W2025323279 cites W2108698786 @default.
- W2025323279 cites W2109968848 @default.
- W2025323279 cites W2110185499 @default.
- W2025323279 cites W2111823617 @default.
- W2025323279 cites W2112012175 @default.
- W2025323279 cites W2113597140 @default.
- W2025323279 cites W2119389886 @default.
- W2025323279 cites W2119526776 @default.
- W2025323279 cites W2120158278 @default.
- W2025323279 cites W2121828161 @default.
- W2025323279 cites W2122000580 @default.
- W2025323279 cites W2124050695 @default.
- W2025323279 cites W2127640118 @default.
- W2025323279 cites W2128114769 @default.
- W2025323279 cites W2130022567 @default.
- W2025323279 cites W2130077037 @default.
- W2025323279 cites W2133086081 @default.
- W2025323279 cites W2134652985 @default.
- W2025323279 cites W2136145671 @default.
- W2025323279 cites W2139522545 @default.
- W2025323279 cites W2144040380 @default.
- W2025323279 cites W2144603545 @default.
- W2025323279 cites W2146516445 @default.
- W2025323279 cites W2150533948 @default.
- W2025323279 cites W2151804955 @default.
- W2025323279 cites W2153525556 @default.
- W2025323279 cites W2154431984 @default.
- W2025323279 cites W2156392314 @default.
- W2025323279 cites W2157221164 @default.
- W2025323279 cites W2159006685 @default.
- W2025323279 cites W2159895250 @default.
- W2025323279 cites W2160073543 @default.
- W2025323279 cites W2161271012 @default.
- W2025323279 cites W2166265186 @default.
- W2025323279 cites W2166564409 @default.
- W2025323279 cites W2169907253 @default.
- W2025323279 cites W2916427899 @default.
- W2025323279 doi "https://doi.org/10.1186/1471-2164-10-163" @default.
- W2025323279 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2678161" @default.
- W2025323279 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19379481" @default.
- W2025323279 hasPublicationYear "2009" @default.
- W2025323279 type Work @default.
- W2025323279 sameAs 2025323279 @default.
- W2025323279 citedByCount "208" @default.
- W2025323279 countsByYear W20253232792012 @default.
- W2025323279 countsByYear W20253232792013 @default.
- W2025323279 countsByYear W20253232792014 @default.
- W2025323279 countsByYear W20253232792015 @default.