Single Test for Over 50 Genetic Diseases Cuts Diagnosis from Decades to Days

The diseases covered by the test belong to a class of more than 50 diseases caused by unusually-long repetitive DNA sequences in a person's genes that are known as 'Short Tandem Repeat expansion disorders'. A short tandem repeat (STR) is a short DNA sequence motif, typically 2 to 6 base pairs (bp), repeated consecutively at a given position in the genome.

Clinical Genomic Scientists from the Garvan Institute of Medical Research (Sydney, Australia) and their colleagues extracted high–molecular weight (HMW) genomic DNA from patient blood samples using the Qiagen Gentra PureGene Blood Kit (Qiagen, Hilden, Germany) or the QIAsymphony DSP DNA Midi Kit and suspended in nuclease-free water.

Before Oxford Nanopore Technologies (ONT) library preparations, the DNA was sheared to ~15-kb fragment size using Covaris G-tubes (Woburn, MA, USA) and visualized, after shearing, on an Agilent TapeStation (Santa Clara, CA, USA) and Nanopore sequencing libraries were prepared. Each sample was loaded onto an ONT MinION flow cell (R9.4.1) and sequenced on either an ONT GridION or ONT MinION device (Oxford Nanopore Technologies, Oxford Science Park, UK) with live target selection/rejection executed.

The team reported that their approach enabled accurate, haplotype-resolved assembly and DNA methylation profiling of STR sites, from a list of predetermined candidates. This correctly diagnoses all individuals in a small cohort (n = 37) including patients with various neurogenetic diseases (n = 25). Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing and identifies noncanonical STR motif conformations and internal sequence interruptions. They observed a diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of repeat disorders. They also showed how the inclusion of pharmacogenomic genes as secondary ReadUntil targets can further inform patient care.

Ira W. Deveson, PhD, Head of Genomics Technologies and a senior author of the study, said, “'We correctly diagnosed all patients with conditions that were already known, including Huntington's disease, fragile X syndrome, hereditary cerebellar ataxias, myotonic dystrophies, myoclonic epilepsies, motor neuron disease and more. They are often difficult to diagnose due to the complex symptoms that patients present with, the challenging nature of these repetitive sequences, and limitations of existing genetic testing methods.” The study was published on March 4, 2022 in the journal Science Advances.

Related Links:
Garvan Institute of Medical Research 
Covaris 
Agilent Technologies 
Oxford Nanopore Technologies