New study IDs better method to detect gene defects in sporadic ALS
Long-read DNA sequencing found more accurate than short-read method
Long-read DNA sequencing is a more accurate method than short-read sequencing for detecting certain defects in genes associated with an increased risk of sporadic amyotrophic lateral sclerosis (ALS), a new study suggests.
A relatively new technique, long-read sequencing can capture data on thousands to hundreds of thousands of nucleotides, the building blocks of DNA. In comparison, the standard short-read sequencing — while highly accurate up to 300 nucleotides — can miss certain genetic defects that occur over longer stretches of DNA, the researchers found.
“We believe that our findings … will help [elucidate] … ALS molecular mechanisms and consequently identify potential therapeutic targets,” the researchers wrote. This ultimately may help in treating people with sporadic ALS — patients who have no known family history of the progressive neurological disease.
Titled “Comprehensive identification of pathogenic tandem repeat expansions in sporadic amyotrophic lateral sclerosis: advantages of long-read vs. short-read sequencing,” the study was published in the journal Experimental Biology and Medicine.
ALS is marked by the gradual death of motor neurons, the nerve cells that control movement. Although more than 30 genes have been linked to the disease, in sporadic cases, about 10% of people — and not the other 90% or so — are shown to have mutations in known ALS genes.
Some genetic variations may increase risk of sporadic ALS
Still, there are some genetic variations that may increase susceptibility to sporadic ALS, and knowing which ones may be potentially useful for earlier diagnoses and more effective treatments for these patients.
For example, many genes contain short tandem repeats, or STRs, which are segments of DNA that are repeated multiple times and are essential for regulating gene activity. But sometimes STRs can duplicate or expand and become longer than usual — a so-called STR expansion — and disrupt gene function, causing disease.
An STR expansion in the C9ORF72 gene is the most common ALS-causing mutation, and a sizable number of sporadic ALS patients carry STR expansions.
The standard approach for detecting STRs is known as short-read sequencing; this method can read up to 300 nucleotides. While the strategy boasts high accuracy and cost-effectiveness, it’s unable to read long sequences.
Long-read sequencing, conversely, is a relatively new technique that excels in capturing lengthier DNA fragments, often spanning thousands to hundreds of thousands of nucleotides. Initially, high error rates and costs limited its use, but recent technological advances have made it more accurate and accessible.
Still, only a few studies have applied long-read sequencing to characterize disease-associated STR expansions. Most studies on ALS-linked STRs were performed using short-read sequencing.
“STR expansions could represent a valuable starting point to further investigate and clarify the genetic predisposition of sporadic cases,” the researchers wrote.
Researchers conclude long-read sequencing ‘should be preferred’
Here, the team compared short-read versus long-read sequencing to detect STR expansions in a group of sporadic ALS (sALS) patients.
First, the scientists collected blood samples from 47 adults with sporadic ALS, more than two-thirds of whom (68%) were women. Short-read sequencing was used to detect STR expansions in 12 genes, including C9ORF72, associated with various neurodegenerative disorders.
Among the 47 patients, 46 showed STR lengths within the normal range. In the remaining patient, short-read sequencing detected disease-causing STR expansions in the HTT, ATXN2, and CACNA1A genes. Intermediate-length STRs were identified in the ATXN3 and DM1-AS genes of this patient.
When researchers applied long-read sequencing to this patient’s blood sample, however, none of the STR expansions in these genes found by short-read sequencing were detected.
[Short-read sequencing] might fail in identifying pathological [disease-causing] repeats as well as misidentify existing pathological repeats.
Focusing solely on the C9ORF72 gene, short-read sequencing failed to find any STR expansions among the patient samples. In comparison, long-read sequencing detected two STR expansions in the C9ORF72 gene of an ALS patient with motor neuron disease symptoms and dementia.
“In this paper, we compared [short-read sequencing] and [long-read sequencing] on a cohort of sALS patients and showed that [short-read sequencing] might fail in identifying pathological [disease-causing] repeats as well as misidentify existing pathological repeats,” the researchers wrote. “Our findings suggest that [long-read sequencing] should be preferred to [short-read sequencing] for accurate identification of pathological … repeat expansions.
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