Quantitative analysis of short double-stranded cell free dna in liquid biopsy

The present invention relates to a method for identifying a cfDNA derived biomarker for a physiological condition, disease or disorder of interest, comprising: a) isolating cfDNA from a sample containing cfDNA of a subject known to be in the physiological condition of interest or suffer from the disease or disorder of interest; b) selecting short double-stranded cfDNA fragments; c) determining the nucleic acid sequences of said short double-stranded cfDNA fragments; d) comparing the nucleic acid sequences of said short double-stranded cfDNA fragments to a reference; and; e) based on said comparison in step d) identifying at least one cfDNA derived biomarker associated with the physiological condition, disease or disorder of interest. Moreover, the present invention relates to a method for assessing a physiological condition, disease or disorder of interest in a sample of a subject suspected to suffer therefrom, comprising a) isolating cfDNA from a sample containing cfDNA of said subject; b) selecting short double-stranded cfDNA fragments; c) determining the nucleic acid sequences of said short double-stranded cfDNA fragments; and d) determining the presence, absence or abundance of at least one disease or disorder associated cfDNA derived biomarker associated with the physiological condition, disease or disorder of interest within the determined of the nucleic acid sequences of said short double-stranded cfDNA fragments. Further, the present invention contemplates a method for determining efficacy of treating a physiological condition, disease or disorder of interest in a sample of a subject known to be in said condition or suffer from said disease or disorder comprising: a) isolating cfDNA from a sample containing cfDNA of said subject; b) selecting short double-stranded cfDNA fragments; c) determining the nucleic acid sequences of said short double-stranded cfDNA fragments; d) determining the presence, absence or abundance of at least one cfDNA derived biomarker associated with the physiological condition disease, or disorder of interest within the determined nucleic acid sequences of said short double-stranded cfDNA fragments; e) repeating steps a) to d); and f) determining efficacy of therapy based on the determination over time. Also, the present invention relates to the use of a cfDNA derived biomarker in a sample for assessing a disease or disorder in a subject suspected to suffer therefrom as well as a device for detecting at least one cfDNA derived biomarker in a liquid biopsy sample.