Compositions and methods for rapid targeted amplification of genomic regions, sequencing thereof, and analysis

NanoRanger, through reverse PCR and long-read sequencing combined with nanopore sequencing, overcomes the limitations of existing technologies in detecting genomic structural variations, achieving efficient and economical genomic region detection and improving the diagnostic rate of Mendelian diseases and the accuracy of carrier screening.

CN122319249APending Publication Date: 2026-06-30KING ABDULLAH UNIV OF SCI & TECH
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Patent Information

Application Number
CN202480076709.1
Authority / Receiving Office
CN · China
Patent Type
Applications(China)
Current Assignee / Owner
Priority Date
2023-10-05
Filing Date
2024-10-07
Publication Date
2026-06-30

AI Technical Summary

Technical Problem

Existing technologies are insufficient for efficiently and economically detecting genomic structural variations associated with Mendelian diseases. Conventional methods such as chromosome microarrays, whole-genome sequencing, and optical genome mapping have limitations, resulting in low diagnostic rates and high costs, which cannot meet the needs of large-scale Mendelian genomics projects.

Method used

Using the NanoRanger method, reverse PCR and long-read sequencing technologies are employed. Specific primers are used to circularize and amplify genomic DNA, combined with nanopore sequencing, to achieve base-resolution detection of genomic regions. This enables rapid and accurate identification of structural variations and transposable elements.

Benefits of technology

It enables accurate detection of genomic structural variations, reduces the amount of DNA samples required, improves the diagnostic rate, shortens the diagnostic time, and reduces costs, making it suitable for the diagnosis of various genetic diseases and carrier screening.

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Abstract

Compositions and methods for detecting structural variations (SVs) in target genes or for genetic mapping of movable transposable elements are disclosed, the target genes relating to disease pathologies commonly found in large Mendelian genomics projects, and the movable transposable elements relating to genetic diseases, cancer, and aging. The method comprises: (i) contacting a sample containing genomic DNA with a DNA endonuclease for an effective amount of time to cleave the genomic DNA into fragments, the genomic DNA being uncrosslinked; (ii) subjecting the fragments obtained from step (b) to a DNA ligase to obtain circularized DNA; (iii) subjecting the circularized DNA to reverse PCR amplification containing a reverse primer, wherein the reverse primer is designed to match a expected wild-type sequence near a suspected mutant locus in the gene; and (iv) sequencing the amplified products. Exemplary conditions include Bardet-Biedel syndrome; severe upper and lower limb defects; retinitis pigmentosa; syndromic microcephaly; spastic paraplegia; and atypical hemolytic uremic syndrome.
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Citation Information

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