Analysis of fragmentation patterns of cell-free dna

A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to perform a method for analyzing a biological sample, including a mixture of cell-free DNA molecules from a plurality of tissues types that includes a first tissue type, the method comprising:

• analyzing a plurality of cell-free DNA molecules from the biological sample of a subject, each of the plurality of cell-free DNA molecules having a left end and a right end, wherein analyzing a cell-free DNA molecule includes:
• determining a left ending position in a reference genome corresponding to the left end of the cell-free DNA molecule;
• determining a right ending position in the reference genome corresponding to the right end of the cell-free DNA molecule;
• identifying a left set of left genomic positions, each having a local maximum of left ends of the plurality of cell-free DNA molecules corresponding to one of the left set of left genomic positions;
• identifying a right set of right genomic positions, each having a local maximum of right ends of the plurality of cell-free DNA molecules corresponding to one of the right set of right genomic positions;
• and
• identifying a first set of genomic positions as being specific to the first tissue type by:
• comparing left genomic positions of the left set to right genomic positions of the right set to identify the first set of genomic positions where a distance from a left genomic position to a nearest right genomic position is greater than a first threshold distance, the first threshold distance being at least 5 genomic positions in the reference genome.