Analysis options for high-throughput sequencing in miRNA expression profiling

BMC Research Notes

Knut Krohn²  Ralf Paschke¹  Barbara Jarząb⁵  Krzysztof Fujarewicz⁴  Michał Świerniak³  Markus Eszlinger¹  Tomasz Stokowy⁵ 

[1] Division of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany;Interdisciplinary Center for Clinical Research (IZKF), University of Leipzig, Liebigstr. 21, 04103 Leipzig, Germany;Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, Warsaw, Poland;Systems Engineering Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland;Nuclear Medicine and Endocrine Oncology Department, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland

关键词: Microarrays;    miRNA expression;    Follicular thyroid cancer;    High-throughput sequencing;   

Others  :  1134282
DOI  :  10.1186/1756-0500-7-144

 received in 2013-09-02, accepted in 2014-02-28,  发布年份 2014

【 摘 要 】

Background

Recently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling.

Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression.

Methods

We compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors.

Results

High correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers.

Conclusions

Compared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail.

【 授权许可】

   
2014 Stokowy et al.; licensee BioMed Central Ltd.

【 图 表 】

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