Guangzhou Kingmed Diagnostics Group has filed a patent for a method of detecting uniparental disomy (UPD) using NGS-trio sequencing data. The method directly deduces the genetic origin of chromosomes for the proband, improving the positive diagnosis rate without increasing costs. It can also assist in the judgment of loss of heterozygosity of large fragments, with a resolution of up to 1 Mbp. The method classifies inheritance patterns, judges genetic relationships, and identifies UPD fragments, including pathogenic ones. GlobalData’s report on Guangzhou Kingmed Diagnostics Group gives a 360-degree view of the company including its patenting strategy. Buy the report here.
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According to GlobalData’s company profile on Guangzhou Kingmed Diagnostics Group, Personalized medicine biomarkers was a key innovation area identified from patents. Guangzhou Kingmed Diagnostics Group's grant share as of September 2023 was 56%. Grant share is based on the ratio of number of grants to total number of patents.
Method for detecting uniparental disomy using ngs-trio sequencing
A recently filed patent (Publication Number: US20230282307A1) describes a method for detecting uniparental disomy (UPD) using next-generation sequencing (NGS) data from a trio of samples. The method involves several steps, including obtaining NGS sequencing data from the trio samples, screening for mutation sites that meet predetermined conditions, merging the mutation site data, and classifying the inheritance patterns at each mutation site. The method also involves judging the genetic relationship, identifying uniparental fragments, analyzing the depth-of-coverage of the fragments, and screening for pathogenic UPD.
In the first step of the method, NGS sequencing data is obtained from a trio of samples, which includes a paternal sample, a maternal sample, and a proband sample. The mutation sites that meet predetermined conditions are then selected, while the remaining mutation sites are classified as unqualified. The unqualified mutation sites are merged, and the mutation sites with identical chromosome coordinates to the unqualified mutation sites are removed from the qualified mutation sites in each trio sample.
Next, the method classifies the inheritance patterns at each mutation site into loci that conform to biparental inheritance, loci that conform to uniparental inheritance only, and loci that are incongruent with heredity laws. The genetic relationship is then judged based on the number of loci incongruent with heredity laws. If the number is smaller than a pre-set value, a follow-up analysis is performed. If the number is larger, the sample is judged to be unqualified.
The method also involves judging uniparental fragments based on the coverage of consecutive loci that conform to either uniparental paternal or maternal inheritance. The fragments are then analyzed for depth-of-coverage, and if a fragment contains a single copy, it is judged to have fragment deletion. Otherwise, the fragment is judged to be a UPD fragment. Pathogenic UPD is determined by screening whether the UPD fragment covers imprinted genes or corresponding bands.
The patent also describes a device for screening UPD based on NGS-trio, which includes modules for obtaining data, analyzing data, and judging UPD. The device follows similar steps as the method described above.
Overall, this patent presents a method and device for detecting UPD using NGS-trio data. The method involves multiple steps, including obtaining data, screening for mutation sites, merging mutation site data, classifying inheritance patterns, judging genetic relationship, judging uniparental fragments, judging UPD, and screening for pathogenic UPD. The device includes modules for each step and can be used for screening UPD.
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