METHOD FOR QUANTITATIVELY DETECTING DNA MODIFICATION FROM NANOPORE SEQUENCING DATA

• Main Author: FENG, Zhixing
• Format: Patent
• Language: Chinese; English; French
• Published: 17.10.2024
• Subjects: CALCULATING; COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS; COMPUTING; COUNTING; INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS; PHYSICS

The invention relates to the technical field of biomedicine, and specifically to a method for quantitatively detecting DNA modification. The method comprises: S01 sequence comparison: using a third-generation-sequencing sequence comparison software such as minimap2 to compare against a reference genome a sequencing read segment contained in a FASTQ file; S02 feature extraction: extracting first to fourth order moments of an obtained sequencing quality score, and the pairwise joint error rates of sites; and S03: constructing and evaluating a machine learning model. The method achieves quantitative detection of DNA modification without the need for a raw signal FAST5 file, but rather merely using a basecalled FASTQ file containing a sequencing DNA sequence and a base sequencing quality; i.e., detecting how many of the sequenced bases of each genome site comprise a modification, so as to provide a technical basis for constructing a large-scale epigenome. L'invention se rapporte au domaine technique de la bioméde