Long-read sequencing 'illuminates' inaccessible parts of the genome

Since the Human Genome Project concluded in 2003, genome sequencing has become cheaper and more accessible. But current technology has its limitations. Now, for the first time, Stanford University researchers have used long-read whole-genome sequencing to diagnose a patient.

Sequencing a genome involves determining the order of nucleotide base pairs, or “letters,” in that individual’s DNA. This is done by snipping DNA into pieces that a sequencer can read, and then using a computer to put these fragments in order.

Current short-read technology chops DNA up into “words” that are about 100 letters long. Long-read sequencing makes words that can be thousands of letters long, said Euan Ashley, the study’s senior author and a professor of cardiovascular medicine, genetics and biomedical data science at Stanford, in a statement.

“This allows us to illuminate dark corners of the genome like never before,” Ashley said. Cutting up DNA into smaller pieces means there are more breaks between individual segments. Some parts of the genome can be missed—about 5% of it, the researchers wrote. Any mutations—deletions or insertions—that exceed a certain length are undetectable with short-read sequencing.

The Stanford team used long-read sequencing to make a diagnosis for Ricky Ramon, a patient whose symptoms pointed to Carney complex, a rare genetic condition caused by mutations in the PRKAR1A gene. But short-read sequencing found no disease-causing gene variants in Ramon’s genome.

Carney complex is characterized by an increased risk for several types of tumors, including benign tumors in the heart. Ramon has undergone multiple surgeries to remove these tumors, called myxomas, from his heart. He is being considered for a heart transplant, but the transplant team needed a solid diagnosis to move forward.

Using long-read technology from Menlo Park, CA-based Pacific Biosciences, the Stanford team discovered a deletion of more than 2,000 base pairs in Ramon’s genome, confirming a diagnosis of Carney complex.

While short-read sequencing now costs less than $1,000 per genome, Ashley estimates the cost of the long-read sequencing used in this study to be between $5,000 to $6,000.

“If we can get the cost of long-read sequencing down to where it’s accessible for everyone, I think it will be very useful,” he said.