A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines

Author(s):Show less -

Gabriela Pereira Branco ^[1] ; Renan Valieris ^[2] ; Lucas Venezian Povoa ; Luiza Ferreira de Araújo ^[4] ; Gustavo Ribeiro Fernandes ^[5] ; Jorge Estefano Santana de Souza ^[6] ; Maria Galli de Amorim ^[7] ; Elisa Napolitano e Ferreira ; Israel Tojal da Silva ^[9] ; Diana Noronha Nunes ^[10] ; Emmanuel Dias-Neto

Affiliation:Show less -

^[1] A.C.Camargo Cancer Center. Laboratório de Genômica Médica. CIPE - Brasil

^[2] A.C.Camargo Cancer Center. Laboratório de Biologia Computacional - Brasil

^[4] A.C.Camargo Cancer Center. Laboratório de Genômica Médica. CIPE - Brasil

^[5] A.C.Camargo Cancer Center. Laboratório de Genômica Médica. CIPE - Brasil

^[6] Universidade Federal do Rio Grande do Norte. Instituto Metrópole Digital - Brasil

^[7] A.C.Camargo Cancer Center. Laboratório de Genômica Médica. CIPE - Brasil

^[9] A.C.Camargo Cancer Center. Laboratório de Biologia Computacional - Brasil

^[10] A.C.Camargo Cancer Center. Laboratório de Genômica Médica. CIPE - Brasil

• Document type: Journal article
• Source: GENETICS AND MOLECULAR BIOLOGY; v. 43, n. 2 2020-04-27.

Abstract

Abstract Next-generation sequencing (NGS) platforms allow the analysis of hundreds of millions of molecules in a single sequencing run, revolutionizing many research areas. NGS-based microRNA studies enable expression quantification in unprecedented scale without the limitations of closed-platforms. Yet, whereas a massive amount of data produced by these platforms is available, comparisons of quantification/discovery capabilities between platforms are still lacking. Here we compare two NGS-platforms: SOLiD and PGM, by evaluating their microRNA identification/quantification capabilities using two breast-derived cell-lines. A high expression correlation (R2 > 0.9) was achieved, encompassing 97% of the miRNAs, and the few discrepancies in miRNA counts were attributable to molecules that have very low expression. Quantification divergences indicative of artefactual representation were seen for 14 miRNAs (higher in SOLiD-reads) and another 10 miRNAs more abundant in PGM-data. An inspection of these revealed an increased and statistically significant count of uracyls and uracyl-stretches for PGM-enriched miRNAs, compared to SOLiD and to the miRBase. In parallel, adenines and adenine-stretches were enriched for SOLiDderived miRNA reads. We conclude that, whereas both platforms are overall consistent and can be used interchangeably for microRNA expression studies, particular sequence features appear to be indicative of specific platform bias, and their presence in microRNAs should be considered for database-analyses. (AU)

• FAPESP's process: 14/26897-0 - Epidemiology and genomics of gastric adenocarcinomas in Brazil
• Grantee: Emmanuel Dias-Neto
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 11/04399-0 - Discovery and validation of small RNAs predictive of aggressiveness in breast cancer
• Grantee: Gabriela Pereira Branco
• Support Opportunities: Scholarships in Brazil - Master