Long read sequencing highlights dark matters associated with human diseases

 

Department of Human Genetics, Yokohama City University

Naomichi Matsumoto, M.D., Ph.D.

 

We have been involved in isolation of novel genes causative for rare diseases as one of comprehensive gene/genome analysis centers with the support of AMED grants. Using short-read-based whole exome sequencing, a total of 70 human diseases have been genetically solved in our center ahead of any other groups and the genetic solution rate of patients with various rare diseases is approximately 35% (2696/7534 independent patients) as of March 2021. In other words, two thirds of patients remain unsolved. Therefore, it is indeed important for us to provide genetic solutions to them. Long read sequencing technologies recently acquired high throughputs of sequencing capacity such as >50 Gb in PromethION (ONT) and 150 Gb in Sequel II (PacBio) which are equivalent to >18x or 50x coverage of human genome (3 Gb). Therefore, it is indeed reasonable to apply the long read technology to disease genome analysis in humans. One of advantages of long read technologies is the >10-kb read length which surpasses less than a few hundred bases of short reads in Illumina technology and easily accesses to the dark matters in human genome such as simple repeat regions and complex structured regions. We have developed the algorithm, tandem-genotypes (Genome Biol 2019), for the abnormally expanded simple repeats among a million of simple repeat regions, which was indeed useful in detecting NOTCH2NLC repeat expansions in neuronal intranuclear inclusion disease (Nat Genet 2019). Although the long read technologies are useful to capture such repeat expansions, their technological weak point is inaccuracy (approximately only 85% accuracy in one read) which hampers the identification of disease-causative defects in human diseases. To overcome the inaccuracy, Cas9-based enrichment technology is useful to collect many reads for making their consensus sequence. I will show you how to apply such a new technology using BAFME patients to obtain scientifically and clinically useful genomic information (Brain 2021).

 

Publications

Genome Biol. 2019 Mar 19;20(1):58.

Nat Genet. 2019 Aug;51(8):1215-12212.

Brain. 2021 Apr 1:awab021. doi: 10.1093/brain/awab021