Long-read sequencing is a newer, more effective way to read DNA, and it can answer questions for people with inherited muscle diseases after years of inconclusive genetic tests. In a new study , a single long-read test found the genetic cause for about 35% of the 31 participants whose previous testing couldn’t explain their symptoms. For those people, it ended a diagnostic odyssey that lasted, on average, 14 years.

This breakthrough not only brings relief to families but also reinforces the case made in Destiny’s Child No Longer: Rewriting Genetic Fate — that reading a person’s DNA fully and early is crucial for uncovering, preventing or managing inherited disease. The new finding goes even further, showing that how we read the genome can matter just as much as whether we read it at all.

Why Standard Tests Miss So Much

Inherited muscle diseases, also called genetic myopathies, slowly weaken and waste the muscles. They can take away the ability to walk, swallow, speak clearly or use the hands. They affect an estimated one in 1,700 to 4,500 people . Over 300 variations are known to cause them.

The genetic changes behind these diseases take many forms. Some are single-letter misspellings in the DNA code. Others are large missing, extra or flipped sections. Some are short stretches of DNA that repeat hundreds or thousands of times, like a stutter. Still others are chemical tags called methyl groups that sit on the DNA and switch genes on or off without changing the letters at all.

Standard sequencing machines can read only several hundred nucleotides at a time. The most widely used platforms produce reads of 50 to 300 letters , so DNA must first be broken into fragments of a few hundred letters . Computers then piece those fragments back together, much like rebuilding a book from torn scraps of paper. The method works well for single-letter misspellings.

Breaking DNA apart and putting it back together is time-consuming, and some changes get lost along the way. Duplications, deletions and inversions are hard to detect because each fragment is too short to show where it belongs. Reads shorter than 300 letters are too short to detect more than 70% of structural variation in the human genome. Long repeats and look-alike stretches of DNA cause similar problems. Chemical tags require a separate test, so a patient may need a different test for each gene and each type of change.

How Long Reads See The Whole Picture

Long-read sequencing reads DNA in continuous stretches of thousands to tens of thousands of letters. The version used here, called nanopore sequencing , threads a single DNA strand through a tiny pore set in a membrane. As each nucleotide passes through, it changes the electrical current across the pore in a unique way, and software converts those changes back into letters. The pores can also accept or reject each DNA strand as it arrives, a method called adaptive sampling , so that only the regions of interest are read. The new test read all 331 regions of the genome tied to muscle disease in one run, mostly in stretches of 16,000 to 48,000 letters or longer.

Those longer reads bring several advantages. First, they span large structural changes from end to end. A review in Frontiers in Genetics notes that long reads can identify more than 68% of structural changes that short reads miss.

Second, long reads pass straight through repeated stretches. In a patient with a genetic disorder that causes progressive muscle weakness and wasting, older tests confirm harmful repeats but can’t measure them. The long-read test can.

Third, long reads show which copy of a gene carries which change. Every person carries two copies of each gene, one from each parent. In recessive diseases, a person becomes sick only when both copies are damaged. Standard tests need parents’ DNA to tell whether two changes sit on the same copy or on different copies. A single long read can cover both changes at once.

Fourth, long reads detect chemical tags directly. Nanopore sequencing reads methyl tags on DNA as it passes through the pore, so it no longer needs a separate chemical test.

Fifth, long reads distinguish look-alike regions. The third most common genetic myopathy, which weakens the face, shoulders and upper arms, arises when a repeated block of DNA shrinks and loses its chemical tags. A nearly identical block on another chromosome does no harm. Diagnosing this myopathy has required up to three separate tests. The new software can tell the two chromosomes apart in a single analysis.

Sixth, long reads are fast. In 2022, a Stanford-led team used nanopore sequencing to read a whole human genome in 5 hours and 2 minutes and reached a genetic diagnosis in 7 hours and 18 minutes . Standard testing usually takes weeks.

Seventh, one long-read test can replace many. A single long-read assay can stand in for the complex combination of genetic tests used today, which saves time and repeat costs. Per test, though, long reads still cost more than short reads. The often-quoted $100 genome refers to short-read sequencing reagents only , not long-read sequencing.

In the study of 53 adults, long-read DNA testing accurately confirmed known genetic diagnoses in nearly all cases. It also corrected a past misdiagnosis and clarified genetic findings between siblings. Among the 31 participants whose muscle disease standard tests couldn’t explain, the new approach identified the cause in 11 people. The test is rapid and flexible, so it can keep pace with newly discovered genes. It helps guide family counseling, clinical monitoring and access to support and to trials that require a genetic diagnosis.

The study also has important limitations. Most critically, it is small and drawn from one country, and its unsolved cases had received different earlier tests. The test reads only its programmed regions, so it cannot discover disease genes outside them. Twenty of the 31 participants remain undiagnosed. Another caveat is that the software was developed partly using data from the same patients it was then tested on. The team plans to validate it independently later.

Reading only the targeted regions costs 2 to 4 times less per person than reading the whole genome with long reads. The study team is working with New South Wales Health Pathology at Concord Hospital in Sydney to bring the test into routine care, and estimates it could be available across Australia in about two years. The approach also reaches beyond muscle.

For families, a diagnosis brings a name, a plan and a path toward treatments in development. For the goal of reading every genome early in life, the lesson is that the reading must be complete. A test that sees single letters but misses repeats, rearrangements and chemical tags leaves families searching. Long-read sequencing shows that one test can see them all, and that years of uncertainty can end with a single sample.