Genome of the Single Human Chromosome 18 as a "Gold Standard" for Its Transcriptome

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Sequencing analysis cutoff levels significantly impact data reliability.
• Choosing appropriate parameters is vital for accurate transcriptome analysis.

Purpose of the Study:

• To determine optimal parameters for reliable RNA transcriptome data analysis.
• To compare different transcriptome analysis platforms for human chromosome 18.

Main Methods:

• Evaluated quantitative polymerase chain reaction, Illumina RNASeq, and Oxford Nanopore Technologies MinION.
• Used HepG2 cells and liver tissue samples for analysis of Chr 18.
• Focused on 275 protein-coding genes encoded by Chr 18.

Main Results:

• The combination of Illumina RNASeq and MinION technologies detected at least one transcript for all 275 protein-coding genes on Chr 18.
• This dual-technology approach achieved complete transcriptome coverage.
• Simultaneous confirmation by short-read (Illumina) and long-read (MinION) sequencing reduced false-positive detection of low-copy transcripts.

Conclusions:

• Combining Illumina RNASeq and MinION nanopore technologies provides comprehensive and reliable RNA transcriptome data.
• This approach enhances the ability to distinguish biological from technical reasons for absent mRNA detection.
• Optimized parameters improve the accuracy of gene expression analysis.