LongTREC presents:
The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance
Nadja Nolte, Marko Petek, Pablo Angulo Lara, Logan Mulroney, Francesco Nicassio, Fabio Marroni, Lauren McIntyre
We inherit two copies of most genes, one from each parent, and these copies (alleles) are not always equally active. Measuring this “allelic imbalance” helps reveal how genetic differences shape traits and disease. However, current methods often produce wrong counts: reads can be assigned to the wrong copy or gene because of biases when matching them to the reference genome, leading to many false results.
The authors show that long-read RNA sequencing, which reads whole RNA molecules, together with simple quality control steps, can reduce these biases. They tested this in four very different species: the fruit fly, the potato (which carries multiple copies of each chromosome), the Sumatran orangutan and humans. They recommend matching reads to a personalized genome of the individual studied, tracking reads that match several places and tuning the matching settings, and checking extreme imbalances, which can reveal errors in the genome assembly or annotation.
These steps are straightforward, and the authors recommend tools for each one. The study offers practical guidelines that make allele-specific expression analyses more reliable across a wide range of organisms, from crops to humans.
Read the full text here: https://doi.org/10.1093/nargab/lqag071
