A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients

被引：54

作者：

Chatterjee, Aniruddha ^{[1
,2
]}

Leichter, Anna L. ^{[1
]}

Fan, Vicky ^{[3
]}

Tsai, Peter ^{[3
]}

Purcell, Rachel V. ^{[4
]}

Sullivan, Michael J. ^{[5
]}

Eccles, Michael R. ^{[1
,2
]}

机构：

[1] Univ Otago, Dunedin Sch Med, Dept Pathol, 270 Great King St, Dunedin 9054, New Zealand

[2] Maurice Wilkins Ctr Mol Biodiscovery, Auckland, New Zealand

[3] Univ Auckland, Bioinformat Inst, Auckland 1, New Zealand

[4] Univ Otago, Childrens Canc Res Grp, Christchurch, New Zealand

[5] Royal Childrens Hosp, Melbourne, Vic, Australia

来源：

SCIENTIFIC REPORTS | 2015年 / 5卷

关键词：

DIFFERENTIAL EXPRESSION; GENE-EXPRESSION; TISSUE; SEQUENCES; SUMMARIES; ALIGNMENT; PATTERNS; FROZEN;

D O I：

10.1038/srep10438

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Although formalin fixed paraffin embedded (FFPE) tissue is a major biological source in cancer research, it is challenging to work with due to macromolecular fragmentation and nucleic acid crosslinking. Therefore, it is important to characterise the quality of data that can be obtained from FFPE samples. We have compared three independent platforms (next generation sequencing, microarray and NanoString) for profiling microRNAs (miRNAs) using clinical FFPE samples from hepatoblastoma (HB) patients. The number of detected miRNAs ranged from 228 to 345 (median=294) using the next generation sequencing platform, whereas 79 to 125 (median=112) miRNAs were identified using microarrays in three HB samples, including technical replicates. NanoString identified 299 to 372 miRNAs in two samples. Between the platforms, we observed high reproducibility and significant levels of shared detection. However, for commonly detected miRNAs, a strong correlation between platforms was not observed. Analysis of 10 additional HB samples with NanoString identified significantly overlapping miRNA expression profiles, and an alternative pattern was identified in a poorly differentiated HB with an aggressive phenotype. This investigation serves as a roadmap for future studies investigating miRNA expression in clinical FFPE samples, and as a guideline for the selection of an appropriate platform.

引用

页数：13

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