Enrichment of targeted genomic regions for multiplexed parallel analysis

A method of determining fetal risk of inheriting a genetic condition, the method comprising:

• (a) preparing a sequencing library from a sample comprising maternal and fetal DNA;
• (b) hybridizing the sequencing library to a pool of double-stranded TArget Capture Sequences (TACS), wherein the pool of TACS comprises a plurality of TACS families directed to variant allele loci of interest associated with different genetic conditions, wherein each TACS family comprises a plurality of member sequences, wherein each member sequence binds to the same locus of interest but has different start and/or stop positions with respect to a reference coordinate system for the locus of interest, and further wherein:
• (i) each member sequence within each TACS family is between 100-500 base pairs in length, each member sequence having a 5′ end and a 3′ end;
• (ii) each member sequence binds to the same locus of interest at least 50 base pairs away, on both the 5′ end and the 3′ end, from regions harboring Copy Number Variations (CNVs), Segmental duplications or repetitive DNA elements;
• and
• (iii) the GC content of the pool of TACS is between 19% and 80%, as determined by calculating the GC content of each member within each family of TACS;
• (c) isolating members of the sequencing library that bind to the pool of TACS to obtain an enriched library;
• (d) amplifying and sequencing the enriched library;
• (e) performing statistical analysis on the enriched library sequences to thereby determine maternal carrier status at the loci of interest associated with different genetic conditions, wherein for a sample with a positive maternal carrier status, the method further comprises:
• (f) obtaining a paternal DNA sample and performing steps (a)-(e) on the paternal DNA sample to determine paternal carrier status for those diseases in which there is a positive maternal carrier status;
• and
• (g) determining fetal risk of inheriting a genetic condition based on maternal carrier status and, when (f) is performed, paternal carrier status,
• wherein the sample comprises DNA fragments, and
• wherein the start and/or stop positions for the member sequences within a TACS family, with respect to a reference coordinate system for the genomic sequence of interest, are staggered by 5 to 10 base pairs.

A method of testing for risk of a genetic abnormality in a DNA sample comprising predominantly fetal or embryonic DNA and comprising genomic sequences of interest, the method comprising:

• (a) preparing a sequencing library from the DNA sample comprising predominantly fetal or embryonic DNA;
• (b) hybridizing the sequencing library to a pool of double-stranded TArget Capture Sequences (TACS), wherein the pool of TACS comprises a plurality of TACS families directed to different genomic sequences of interest, wherein each TACS family comprises a plurality of member sequences, wherein each member sequence binds to the same genomic sequence of interest but has different start and/or stop positions with respect to a reference coordinate system for the genomic sequence of interest, and further wherein:
• (i) each member sequence within each TACS family is between 100-500 base pairs in length, each member sequence having a 5′ end and a 3′ end;
• (ii) each member sequence binds to the same genomic sequence of interest at least 50 base pairs away, on both the 5′ end and the 3′ end, from regions harboring Copy Number Variations (CNVs), Segmental duplications or repetitive DNA elements;
• and
• (iii) the GC content of the pool of TACS is between 19% and 80%, as determined by calculating the GC content of each member within each family of TACS;
• (c) isolating members of the sequencing library that bind to the pool of TACS to obtain an enriched library;
• (d) amplifying and sequencing the enriched library;
• and
• (e) performing statistical analysis on the enriched library sequences to thereby determine risk of a genetic abnormality in the DNA sample,
• wherein the start and/or stop positions for the member sequences within a TACS family, with respect to a reference coordinate system for the genomic sequence of interest, are staggered by 5 to 10 base pairs.