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US 2021/0062264 A1Published application
Use of cfdna fragments as biomarkers in patients after organ transplantation
AssigneeMyway Genetics S.R.L.
InventorValentina FAVALLI
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Abstract
The present invention provides methods for detecting donor cell-free DNA in the circulation of an organ transplant recipient for the early identification of transplant rejection.
Claims15
1-14:
- (canceled)
An in-vitro or ex-vivo method of monitoring the status of a transplanted organ in a subject, comprising:
- a) providing cell-free DNA from a biological sample obtained from a subject who is the recipient of an organ transplant from a donor;
- b) sequencing a panel of 94 single nucleotide polymorphisms (SNPs) from the cell-free DNA, and
- c) calculating the quantity of donor-derived cell-free DNA in the biological sample.
A computer medium comprising instructions which, when executed by a computer, cause the computer to carry the following steps:
- (i) receiving raw data from SNP sequences obtained from the method of claim 1;
- (ii) aligning said sequencing data with the referring genome;
- (iii) pre-processing and preparing raw data for variant calling;
- (iv) identifying SNP variants and calculating the genotype of the recipient for these SNP, identifiable as not mutated (0/0), mutated heterozygous (0/1) or mutated homozygous (1/1), through a germline variant calling process;
- (v) calculating the genotype of the cfDNA mixture and comparing it with the calculated recipient one through a somatic variant calling process;
- (vi) calculating the donor fraction according to the following formula:
- DFi %=(AF(SNPi)−AF(SNPirec))/(AF(SNPidon)−AF(SNPirec))×100, wherein
- DF %=mean DFi %±SD DFi.
5 more elements
Dependencies are inferred from the claim text.