Treatment of diseases, even those known to doctors, can be a difficult task. To adopt the best treatment, sometimes you must dive deep into the genomic sequence of patients to understand exactly where the problem is. This is not an easy task, considering that there are 3 billion different arrangements of nucleic acids in every one of us. An Israeli startup, however, has developed a system that expands on this information and analyzes it, to understand exactly the source of the problem - and thereby treat it.
Narrowing down the sea of possibilities
The Israeli startup Geneyx developed a system that operates in the cloud and provides medical teams with the link between disease symptoms and genetic variants. Geneyx’s system goes through the results of genetic sequencing performed on patients and identifies anomalies. The initial genetic sequencing is performed in three stages. First, an initial analysis is done on a machine that reads the DNA sample chemically optically and produces files describing the genomic sequence according to the four nucleic acids (CTAG) – which appear in the genome about 3 billion times in different arrangements. After arranging the information into a readable file, the secondary analysis compares the sequenced genome to a reference genome – a genome that is supposed to be normal and disease-free– and then the analysis flags any discrepancies between the two samples.
"Such a discrepancy is one variant, and at the end of this process, the file produced a list of variants," says David Yizhar, CEO and one of the company's founders, in a conversation with Geektime. After getting to the list of variants, Geneyx performs an analysis to sort out tens of thousands of variants observed and pinpoint those caused by the disease described by the doctor. Geneyx’s algorithms know how to filter the suspicious variants within minutes and give them a 'score' that reflects the degree of certainty that these are variants that are usually identified after a person suffers from a certain disease.
"In certain diseases, we are talking about the relationship of one gene - versus one disease. That is, in all the examined cases, a full correlation was found between the presence of the variant in the particular gene and the disease. These are the relatively 'easy' cases to decipher, and they give the doctor and the researchers an 'address' responsible for the symptoms described," Yizhar added. He further explains that there are cases in which the disease or syndrome results from a structural change of longer segments in the genome: duplications, inversions, and deletions of segments in sequence.
And this is where the technology they developed comes into the picture, which can go through the entire genomic sequence of a person and sort the variants and analyze them – partly by analyzing databases of scientific articles in search of mentions of the connections between symptoms and genes. In the last step, a report is produced for the attending physician and according to the company, this is a tool that supports the decision doctors can then make – but they are the ones who make the final diagnosis for them.
Yizhar says that at Ichilov Hospital in Tel Aviv they treated patients who suffered from intestinal polyps that caused severe pain and internal bleeding. In the case of one patient, it was discovered that his brother and mother suffered from a similar problem, but to a lesser extent. However, even though several partial genome sequences were performed and tested in several different laboratories – they were unable to pinpoint the reason for this. After performing full genome sequencing, and using the Geneyx system, the mutation responsible for the disease was found. "The finding is validated by testing the sick and healthy relatives, and a complete match was found: the healthy relatives did not have a mutation and the sick one did. Locating the mutation allowed the doctors treating the patient to adjust the medicine to be more precise which greatly improved the patient’s situation," explained Yizhar. He then mentioned that another advantage of the system is the ability to help people select embryos – to make sure that an unpleasant genetic disease like this is not passed on to the next generation.
The Israeli company was founded in 2018 by David Yizhar, Raviv Itzhaky, Dvir Dahary and Ofer Barnea. To date, the startup has raised $10 million, partly from Accenture's investment arm. Geneyx employs 25 people in the development center in Herzliya and its offices in the U.S., England, and Italy. To date, approximately 150,000 analyzes have been performed. Geneyx is a graduate of the Microsoft for Startups program in Israel.