cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Clin Epigenetics. 2016 Nov 21;8:123. doi: 10.1186/s13148-016-0287-1. eCollection 2016.

Abstract

Background: We present the first sequencing data using the combinatorial probe-anchor synthesis (cPAS)-based BGISEQ-500 sequencer. Applying cPAS, we investigated the repertoire of human small non-coding RNAs and compared it to other techniques.

Results: Starting with repeated measurements of different specimens including solid tissues (brain and heart) and blood, we generated a median of 30.1 million reads per sample. 24.1 million mapped to the human genome and 23.3 million to the miRBase. Among six technical replicates of brain samples, we observed a median correlation of 0.98. Comparing BGISEQ-500 to HiSeq, we calculated a correlation of 0.75. The comparability to microarrays was similar for both BGISEQ-500 and HiSeq with the first one showing a correlation of 0.58 and the latter one correlation of 0.6. As for a potential bias in the detected expression distribution in blood cells, 98.6% of HiSeq reads versus 93.1% of BGISEQ-500 reads match to the 10 miRNAs with highest read count. After using miRDeep2 and employing stringent selection criteria for predicting new miRNAs, we detected 74 high-likely candidates in the cPAS sequencing reads prevalent in solid tissues and 36 candidates prevalent in blood.

Conclusions: While there is apparently no ideal platform for all challenges of miRNome analyses, cPAS shows high technical reproducibility and supplements the hitherto available platforms.

Keywords: BGISEQ; Biomarker discovery; Next-generation sequencing; miRNA.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blood
  • Brain Chemistry
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing / instrumentation*
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Myocardium / chemistry*
  • Oligonucleotide Array Sequence Analysis
  • RNA, Small Untranslated / blood
  • RNA, Small Untranslated / genetics*
  • Sequence Analysis, RNA / methods*

Substances

  • RNA, Small Untranslated