Method for determining methylation level of target cpg site of tumor tissue

By combining methylation measurements from mixed tumor tissues and paired adjacent normal tissues, and using the ichorCNA and DSS algorithms to correct the methylation levels of CpG sites in tumor tissues, the bias problem in methylation level measurements in mixed tumor tissues was solved, and more accurate tumor tissue-specific methylation level measurements were achieved.

CN117987556BActive Publication Date: 2026-07-14SHANGHAI WEIHE MEDICAL LAB CO LTD
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Patent Information

Application Number
CN202410205480.9
Authority / Receiving Office
CN · China
Patent Type
Patents(China)
Current Assignee / Owner
Filing Date
2024-02-23
Publication Date
2026-07-14
Estimated Expiration
2044-02-23

AI Technical Summary

Technical Problem

Existing technologies struggle to accurately determine the methylation level of CpG sites in mixed tumor tissues, leading to measurement results that deviate from the true level and affecting the accuracy of downstream analyses.

Method used

By acquiring methylation measurement results of mixed tumor tissue and paired adjacent normal tissue, and combining them with reference adjacent normal tissue samples, the distribution of reads originating from tumor tissue or adjacent normal tissue is determined. The methylation level of tumor tissue is then calculated iteratively using the ichorCNA algorithm and the DSS algorithm for correction.

Benefits of technology

It improves the accuracy of measuring CpG site methylation levels in tumor tissue, reduces the bias in linear model calculations, and avoids the problems of missed screening of early screening markers and false positives of tissue traceability markers.

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Abstract

Embodiments of the present disclosure provide methods, systems, computing devices and media for determining methylation levels of target CpG sites of tumor tissue. The method comprises: obtaining a first methylation measurement of a mixed tumor tissue sample and a second methylation measurement of a paired cancer adjacent tissue sample, the mixed tumor tissue sample comprising tumor tissue and cancer adjacent tissue; determining a distribution of reads comprising target CpG sites in the mixed tumor tissue sample originating from the tumor tissue or the cancer adjacent tissue based on the first methylation measurement and a third methylation measurement of a reference cancer adjacent tissue sample; and determining a methylation level of the target CpG sites of the tumor tissue in the mixed tumor tissue sample based on the determined distribution, the first methylation measurement and the second methylation measurement. In this way, the accuracy of the methylation level measurement can be improved, thereby effectively avoiding the problem of missed screening of early screening markers and false positive of tissue provenance markers.
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