TY - JOUR

T1 - Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

AU - Nygaard, Sanne

AU - Jacobsen, Anders

AU - Lindow, Morten

AU - Eriksen, Jens

AU - Balslev, Eva

AU - Flyger, Henrik

AU - Tolstrup, Niels

AU - Moller, Soren

AU - Krogh, Anders

AU - Litman, Thomas

PY - 2009

Y1 - 2009

N2 - ABSTRACT: 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. CONCLUSIONS: 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.

AB - ABSTRACT: 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. CONCLUSIONS: 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.

U2 - 10.1186/1755-8794-2-35

DO - 10.1186/1755-8794-2-35

M3 - Journal article

C2 - 19508715

VL - 2

SP - 35

JO - BMC Medical Genomics

JF - BMC Medical Genomics

SN - 1755-8794

IS - 1

ER -