Methylation markers and targeted methylation probe panel

A mixture for processing cell-free DNA fragments, the mixture comprising (a) converted cell-free DNA (cfDNA) molecules or amplification products thereof;

• and (b) a panel of different oligonucleotide probes configured to hybridize to converted cell-free DNA fragments derived from at least 500 target genomic regions;
• wherein the converted cfDNA molecules comprise deaminated nucleotides obtained by treating cfDNA molecules with a deaminating agent;
• wherein each target genomic region of the at least 500 target genomic regions has an anomalous methylation pattern in cancerous samples;
• and
• wherein each of the at least 500 target genomic regions comprises a sequence with complementarity to at least a pair of probes in the panel, wherein each probe of a pair has a first portion and a second portion, wherein the first portions of a probe pair are complementary to the same sequence of at least 25 nucleotides in length, and wherein the second portions of a probe pair are complementary to different sequences at different ends of the sequence complementary to the respective first portions.