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Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

BACKGROUND: MiRNAs play important roles in cellular control and in various disease states such as cancers, where they may serve as markers or possibly even therapeutics. Identifying the whole repertoire of miRNAs and understanding their expression patterns is therefore an important goal. METHODS: He...

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Autores principales: Nygaard, Sanne, Jacobsen, Anders, Lindow, Morten, Eriksen, Jens, Balslev, Eva, Flyger, Henrik, Tolstrup, Niels, Møller, Søren, Krogh, Anders, Litman, Thomas
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702338/
https://www.ncbi.nlm.nih.gov/pubmed/19508715
http://dx.doi.org/10.1186/1755-8794-2-35
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author Nygaard, Sanne
Jacobsen, Anders
Lindow, Morten
Eriksen, Jens
Balslev, Eva
Flyger, Henrik
Tolstrup, Niels
Møller, Søren
Krogh, Anders
Litman, Thomas
author_facet Nygaard, Sanne
Jacobsen, Anders
Lindow, Morten
Eriksen, Jens
Balslev, Eva
Flyger, Henrik
Tolstrup, Niels
Møller, Søren
Krogh, Anders
Litman, Thomas
author_sort Nygaard, Sanne
collection PubMed
description BACKGROUND: MiRNAs play important roles in cellular control and in various disease states such as cancers, where they may serve as markers or possibly even therapeutics. Identifying the whole repertoire of miRNAs and understanding their expression patterns is therefore an important goal. METHODS: Here we describe the analysis of 454 pyrosequencing of small RNA from four different tissues: Breast cancer, normal adjacent breast, and two teratoma cell lines. We developed a pipeline for identifying new miRNAs, emphasizing extracting and retaining as much data as possible from even noisy sequencing data. We investigated differential expression of miRNAs in the breast cancer and normal adjacent breast samples, and systematically examined the mature sequence end variability of miRNA compared to non-miRNA loci. RESULTS: We identified five novel miRNAs, as well as two putative alternative precursors for known miRNAs. Several miRNAs were differentially expressed between the breast cancer and normal breast samples. The end variability was shown to be significantly different between miRNA and non-miRNA loci. CONCLUSION: Pyrosequencing of small RNAs, together with a computational pipeline, can be used to identify miRNAs in tumor and other tissues. Measures of miRNA end variability may in the future be incorporated into the discovery pipeline as a discriminatory feature. Breast cancer samples show a distinct miRNA expression profile compared to normal adjacent breast.
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spelling pubmed-27023382009-06-27 Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing Nygaard, Sanne Jacobsen, Anders Lindow, Morten Eriksen, Jens Balslev, Eva Flyger, Henrik Tolstrup, Niels Møller, Søren Krogh, Anders Litman, Thomas BMC Med Genomics Research Article BACKGROUND: MiRNAs play important roles in cellular control and in various disease states such as cancers, where they may serve as markers or possibly even therapeutics. Identifying the whole repertoire of miRNAs and understanding their expression patterns is therefore an important goal. METHODS: Here we describe the analysis of 454 pyrosequencing of small RNA from four different tissues: Breast cancer, normal adjacent breast, and two teratoma cell lines. We developed a pipeline for identifying new miRNAs, emphasizing extracting and retaining as much data as possible from even noisy sequencing data. We investigated differential expression of miRNAs in the breast cancer and normal adjacent breast samples, and systematically examined the mature sequence end variability of miRNA compared to non-miRNA loci. RESULTS: We identified five novel miRNAs, as well as two putative alternative precursors for known miRNAs. Several miRNAs were differentially expressed between the breast cancer and normal breast samples. The end variability was shown to be significantly different between miRNA and non-miRNA loci. CONCLUSION: Pyrosequencing of small RNAs, together with a computational pipeline, can be used to identify miRNAs in tumor and other tissues. Measures of miRNA end variability may in the future be incorporated into the discovery pipeline as a discriminatory feature. Breast cancer samples show a distinct miRNA expression profile compared to normal adjacent breast. BioMed Central 2009-06-09 /pmc/articles/PMC2702338/ /pubmed/19508715 http://dx.doi.org/10.1186/1755-8794-2-35 Text en Copyright © 2009 Nygaard et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Nygaard, Sanne
Jacobsen, Anders
Lindow, Morten
Eriksen, Jens
Balslev, Eva
Flyger, Henrik
Tolstrup, Niels
Møller, Søren
Krogh, Anders
Litman, Thomas
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing
title Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing
title_full Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing
title_fullStr Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing
title_full_unstemmed Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing
title_short Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing
title_sort identification and analysis of mirnas in human breast cancer and teratoma samples using deep sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702338/
https://www.ncbi.nlm.nih.gov/pubmed/19508715
http://dx.doi.org/10.1186/1755-8794-2-35
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