Nucleic acids and methods for detecting chromosomal abnormalities

A method of characterizing fetal DNA in a maternal blood sample, comprising:

• a) obtaining a DNA sample isolated from a maternal blood sample;
• b) capturing a plurality of target sequences from target sites in the DNA sample using a population of molecular inversion probes (MIPs), wherein each MIP in the population of MIPs comprises:
• i) a pair of targeting polynucleotide arms comprising a first targeting polynucleotide arm and a second targeting polynucleotide arm, wherein the first targeting polynucleotide arm has a different nucleotide sequence than the second targeting polynucleotide arm;
• ii) a unique molecular tag;
• and
• iii) a polynucleotide linker
• in a sequence:
• the first targeting polynucleotide arm-the unique molecular tag-the polynucleotide linker-the second targeting polynucleotide arm;
• wherein the pairs of targeting polynucleotide arms in the population of MIPs are identical, and wherein the first targeting polynucleotide arm and the second targeting polynucleotide arm are substantially complementary to pairs of first and second regions that flank each target sequence in the plurality of target sequences in the DNA sample, and wherein the capturing comprises hybridizing the population of MIPs to the DNA sample to produce hybridized MIPs comprising MIPs, from the population of MIPs, hybridized at first target sites and MIPs, from the population of MIPs, hybridized at second target sites, wherein the first target sites comprise target sequences found on a single chromosome and wherein the second target sites comprise target sequences found on multiple chromosomes;
• c) circularizing hybridized MIPs to produce MIP replicons;
• d) amplifying MIP replicons obtained in step c) to form MIP amplicons;
• e) sequencing MIP amplicons obtained in step d) to produce sequence reads;
• f) using the sequence reads to determine a number of first capture events based on the unique molecular tags from the MIPs hybridized at first target sites in step b);
• g) using the sequence reads to determine a number of second capture events based on the unique molecular tags from the MIPs hybridized at second target sites in step b);
• h) providing first site capture metrics by determining, for each target site of the first target sites, a first site capture metric based at least in part on the number of first capture events determined in step f);
• i) identifying a first subset of the first site capture metrics determined in step h) that satisfy at least one criterion;
• j) providing second site capture metrics by determining, for each target site of the second target sites, a second site capture metric based at least in part on the number of second capture events determined in step g);
• k) identifying a second subset of the second site capture metrics determined in step j) that satisfy the at least one criterion;
• l) normalizing a first measure determined from the first subset of first site capture metrics identified in step i) by a second measure determined from the second subset of second site capture metrics identified in step k) to obtain a test ratio;
• and
• m) detecting a difference between the test ratio and a plurality of reference ratios that are computed based on reference DNA samples isolated from reference subjects known to exhibit euploidy or aneuploidy, to characterize the fetal DNA in the maternal blood sample.