High-throughput genotyping by sequencing low amounts of genetic material

A method for analysis of target nucleic acids, the method comprising the following steps:

• i. in a sample that has been provided and wherein target nucleic acids are present in an amount of 100 pg or less, wherein said target nucleic acids originate from an embryo or fetus or from a cancer or tumor cell, wherein said target nucleic acids are DNA,
• ii. generating a reduced representation library of said target nucleic acids by a method comprising
• fragmenting said target nucleic acids using one or more restriction enzymes;
• ligating adaptors to said fragments;
• and
• selecting a subset of said adaptor-ligated fragments based on the size of said fragments,
• wherein generating a reduced representation library comprises amplifying a subset of fragments which, when combined, comprise only a part of the target nucleic acids, and
• wherein said generating a reduced representation library reduces the complexity at least 5 times,
• iii. massively parallel sequencing said reduced representation library, and
• iv. identifying variants in said target nucleic acids by analyzing results obtained by said sequencing.