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WuXi NextCode Presents First Results From Healthy Whole-Genome Sequencing Pilot at ACMG


PHOENIX – WuXi NextCode has launched a whole-genome sequencing scan for healthy individuals, called HealthCode, in China and presented first results from a pilot study involving 190 customers at the American College of Medical Genetics and Genomics annual meeting today.

According to Qian Zhao, director of medical genetics at WuXi NextCode in Shanghai, HealthCode was launched last year and is the first whole-genome sequencing-based wellness program in China to date.

For the pilot, WuXi recruited 190 individuals from among its HealthCode customers — 104 men and 86 women, with a mean age of 39 — who signed a consent form and received pre-test counseling from a physician.

The company then collected saliva or blood samples from them and conducted whole-genome sequencing on their DNA in WuXi's CLIA-certified and CAP-accredited Shanghai laboratory using the Illumina HiSeq X system, sequencing to 30x coverage.

WuXi then analyzed 59 genes recommended by the ACMG for secondary findings, determined carrier status for 402 genes associated with recessive diseases, and assessed participants' risks for 28 common polygenic diseases, using an internally developed system called Clinical Sequence Analyzer. Customers received their clinical reports from a doctor and were offered additional post-test counseling with a physician or genetic counselor. All participants also received lifestyle and medical recommendations that were based on their results.

Zhao said the most frequent questions customers had after receiving their results related to diseases featured in their report, whether there are treatments, what their own risk and that of their children is for developing the disease, and what they can do now that they are aware of their risk.

In the ACMG 59 genes, WuXi only reported pathogenic and likely pathogenic variants. Similar to other studies, 1 percent of participants – in this study, two individuals – had a positive finding. One individual had a frameshift mutation in BRCA1, another a frameshift mutation in MSH6. In addition, two people had a pathogenic variant in one copy of the MUTYH gene, but WuXi did not report those because the gene is associated with an autosomal recessive disease.

In one case involving a 40-year-old healthy women, the analysis found a dominant pathogenic variant in the gene MYO7A, which is associated with hearing loss. While the woman was not affected by this at the time, her father had been diagnosed with sensorineural hearing loss but did not have a genetic diagnosis. Based on the result, she was recommended to undergo annual hearing tests.

In terms of carrier status, WuXi reported pathogenic and likely pathogenic variants in 402 recessive disease genes. It also reported heterozygous dominant and homozygous or compound heterozygous pathogenic mutations with special notes, and it reassesses variants of unknown significance every six months against updated reference databases. In all, 37 percent of participants were found to be carriers of at least one disease, the most frequent ones being Usher syndrome, carnitine deficiency, citrin deficiency, and Pendred syndrome.

Among the 28 common diseases analyzed by WuXi were 10 types of cancer, five types of cardiovascular diseases, and type 2 diabetes. The company calculated both the lifetime risk and the relative risk of participants based on a multiplicative genetic model specific for the Chinese population. Results in the report are color coded, with red indicating significantly increased relative risk, yellow slightly increased relative risk, and green below-average relative risk.

Overall, participants had risks elevated more than 1.5 times above average for four out of the 28 diseases. In particular, 18 percent had more than 1.5 times the average risk for type 2 diabetes, which Zhang said is the most prevalent common disease in China with a population incidence of more than 10 percent. According to the World Health Organization, she said, more than 500 million Chinese individuals are prediabetic.

A healthy 39-year-old man, for example, was found to have three times the average genetic risk for type 2 diabetes. He was recommended to receive regular fasting glucose measurements, reduce weight, and exercise, with the goal of detecting any prediabetes early and of preventing him from developing the disease.

Overall, Zhang said, the study showed that the pilot study provided "a wealth of actionable information" that could provide the basis for effective disease prevention strategies. Growing the number of HealthCode customers to tens of thousands, she said, will enable the analysis of common and rare disease risk factors and will complement the disease-based cohorts of China's Precision Medicine Initiative.