Release date: 2017-06-26
Euan Ashley and colleagues used long-length long genome sequencing to diagnose a rare disease. This is the first time this technology has been applied to clinical diagnosis.
A few days ago, Stanford University scientists successfully diagnosed a rare genetic disease that had been undiagnosed based on long-term long-sequencing technology (three-generation sequencing). Please follow the small series to find out!
Ricky Ramon found a benign tumor in his left atrium during a routine examination at the age of seven. However, this is only the beginning for Ramon. He did not think of a series of troubles and surgeries that will follow in the next two years.
During this time, benign tumors appeared again in Ramon's heart and other parts of the body, including the pituitary gland, adrenal gland, and thyroid nodules.
But the problem is that doctors can't diagnose what kind of disease he has.
At the age of 18, Ramon believed that his illness might be Carney's syndrome, a genetic disease caused by a mutation in the PRKAR1A gene, but DNA detection did not reveal the causative mutation in the gene.
Today, eight years later, researchers at the Stanford University School of Medicine used Ramet's long-sequencing technology to perform a systematic diagnosis of Ramon, and the condition was finally confirmed. This is also the first time in the clinical use of long-reading whole genome sequencing technology for diagnosis, the research results published in the June 22 issue of the Journal of Genetics in Medicine.
Illuminate the dark corner
The author of the article, Dr. Euan Ashley, a professor of cardiovascular medicine, genetics and biomedical data science, said that the current second-generation sequencing technology breaks DNA into small fragments of hundreds of bases. Long-length long sequencing can break DNA into long fragments of several tens of kb.
“This allows us to illuminate the dark areas of the genome for the first time,†Ashley said. “The development of technology is a powerful force in the medical field. We are able to routinely sequence the patient's genome, which was thought more than a decade ago. I can't think about it."
It is reported that the study was conducted in conjunction with PacBio, which is responsible for the cost of sequencing. The first author of the article is Dr. Jason Merker, Assistant Professor of Pathology, Stanford Clinical Genomics, and Dr. Aaron Wenger of PacBio.
Diagnosis of illness based on long read length sequencing
With the advancement of technology and efficiency, the cost of long-length long sequencing has dropped dramatically. Ashley assessed the cost of sequencing in the study, which is about $5,000 to $6,000 per genome.
Ashley said that although the cost of short-reading long-sequencing (second-generation sequencing) is already less than $1,000, when the DNA is broken into small fragments, some of the genomic sequences cannot be read. A series of repeats, such as GGCGGCGGC, can be repeated to hundreds of base pairs throughout the genome. When the fragment is only 100 bp, we don't know how long these sequences are, and the length of these sequences also determines how susceptible people are to the disease.
In addition, there are some redundant parts in the human genome, that is, most of the 100 bp fragments can be compared to multiple regions, so that we cannot judge how the fragments should be arranged when the genome is assembled. But in the case of long read lengths, the chances of this happening are much smaller.
The researchers pointed out that if this problem is considered, then 5% of the genomes are not uniquely aligned. Any deletion or insertion of more than 50 bp is too long to be detected.
Ashley said that for about one-third of undiagnosed patients, short-length sequencing can help doctors diagnose, but Ramon's case does not.
When the second-generation sequencing technology was originally used to analyze Ramon's genes, it did not identify mutations in genes associated with Carney's syndrome. Therefore, co-author Dr. Tam Sneddon manually scanned Ramon's genome sequencing data, and he noticed some errors. In the end, the researchers used long-length sequencing to sequence the Roman genome and identified a 2.2kb fragment deletion and identified it as Carney syndrome.
This study is a good example of Stanford Medical School's focus on precision medicine, which aims to prevent disease, accurately diagnose and accurately treat diseases in the health field.
About Carney Syndrome
Carney syndrome is derived from mutations in the PRKAR1A gene and is also associated with increased risk in certain types of tumors, especially in the heart and hormone-producing glands such as the ovaries, testes, adrenal glands, pituitary gland and thyroid gland. According to the National Institutes of Health, the number of patients identified as having such diseases is no more than 750.
The most common symptom of the disease is a benign heart tumor or myxoma. In open heart surgery, cardiac myxoma needs to be removed, and when Ramon is 18 years old, he has undergone three such operations. He is considering a heart transplant, so a correct diagnosis of his condition is critical to the transplant. In addition to typical transplants, Ashley said researchers need to confirm that no other health problems are exacerbated by immunosuppressive agents. Immunosuppressive agents are required for heart transplant patients to avoid rejection of donor organs.
Although the research team finally confirmed that Ramon does have Carney syndrome, it means that Ramon can't get rid of his disease. “I am very depressed,†he said. “It took me a long time to accept the fact that this disease will accompany me for a lifetime. Still live in the moment! Bad days are short-lived storms, they will pass.â€
Ramon recently performed his fourth surgery to remove three tumors from the heart. Joseph Woo, president of Cardiothoracic Surgery, completed the operation at Stanford Hospital. Ashley said: “It is very rare to have a tumor in the heart. This is a very brave operation.†Although Ramon is still considering organ transplantation, the demand is no longer there. Urgent.
Long-term long-sequencing technology with great clinical value
Ashley said he and many other doctors believe that long-reading sequencing technology is an important part of future genomics.
"Today we need to think about how to do better." Ashley said, "If we can reduce the cost of long-length sequencing to everyone, then I think this technology will be very useful."
Reference material
[1] Long-read genome sequencing identification causal structural variation in a Mendelian disease
[2] Researchers use long-read genome sequencing for first time in a patient
Source: Sequencing China (micro signal seq114)
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