A method to detect and isolate DNA sequences that are candidate genes for inherited disorders for which the gene product is unknown, based on the absence of mismatches in DNA sequences between an affected individual and a heterozygous or carrier progenitor. Large DNA segments are prepared from the genomic DNA of the two related individuals in such a way (e.g. by leaving 3'-overhangs) that they will not be degraded by subsequent exonuclease digestion, e.g. by ExoIII. The DNA from one individual is enzymically methylated and annealed with the DNA of the second, heterohybrids (two methylated or two unmethylated strands) are cleaved by appropriate endonucleases, e.g. DpnI and MboI, and the uncleaved duplexes are scanned for single-base mismatches by methyl-directed mismatch repair enzymes that leave single-strand nicks that are attacked by ExoIII. The duplexes that survive all these tests are those that are shared by the two related individuals and are therefore candidates for the affected gene.