A new method for targeted sequencing using ultra-long oligonucleotides is described. The method involves synthesizing biotinylated RNA "baits" on a microarray, which are then used to capture genomic DNA fragments of interest. These baits are designed to target specific regions of the genome, such as exons and genomic regions associated with diseases. The RNA baits are synthesized from PCR-amplified oligonucleotides, allowing for high concentrations of bait to drive hybridization. The captured DNA fragments are then PCR-amplified and sequenced using next-generation sequencing technology. The method was tested with 170-mer baits targeting over 15,000 coding exons and four genomic regions. Sequencing of the captured DNA fragments revealed that about 90% of uniquely aligning bases fell on or near the bait sequence, with up to 50% lying on exons. The uniformity of coverage allowed for high-confidence genotype calling for 89% of the targeted exon space. The method was also tested on four genomic regions, where 94% of the sequence fell within the targeted regions. The method demonstrated high specificity, with 82% of the uniquely aligning human sequence falling on or near the bait sequence. The coverage was uniform, with over 60% of the bases within baits achieving at least half the mean coverage. The method was also shown to be reproducible, with high consistency between technical replicates and between different sources of DNA. The method was also tested for its ability to detect SNPs, with high accuracy and sensitivity. The method was able to detect SNPs with high confidence, with a low discordance rate. The method was also shown to be effective in capturing short and dispersed targets such as exons, with high coverage and uniformity. The method was found to be efficient and scalable, with the ability to target a wide range of genomic regions. The method was also shown to be flexible, with the ability to target any arbitrary sequence. The method was also shown to be compatible with a variety of sequencing platforms, including Illumina and 454. The method was found to be effective in reducing the cost of sequencing, with the ability to target specific regions of the genome with high efficiency. The method was also shown to be effective in capturing repetitive sequences, with the ability to target regions that are difficult to sequence with traditional methods. The method was also shown to be effective in capturing ancient DNA that is heavily contaminated with unwanted DNA. The method was also shown to be effective in deep sequencing of viral populations in patient material and metagenomic analyses of environmental or medical specimens.A new method for targeted sequencing using ultra-long oligonucleotides is described. The method involves synthesizing biotinylated RNA "baits" on a microarray, which are then used to capture genomic DNA fragments of interest. These baits are designed to target specific regions of the genome, such as exons and genomic regions associated with diseases. The RNA baits are synthesized from PCR-amplified oligonucleotides, allowing for high concentrations of bait to drive hybridization. The captured DNA fragments are then PCR-amplified and sequenced using next-generation sequencing technology. The method was tested with 170-mer baits targeting over 15,000 coding exons and four genomic regions. Sequencing of the captured DNA fragments revealed that about 90% of uniquely aligning bases fell on or near the bait sequence, with up to 50% lying on exons. The uniformity of coverage allowed for high-confidence genotype calling for 89% of the targeted exon space. The method was also tested on four genomic regions, where 94% of the sequence fell within the targeted regions. The method demonstrated high specificity, with 82% of the uniquely aligning human sequence falling on or near the bait sequence. The coverage was uniform, with over 60% of the bases within baits achieving at least half the mean coverage. The method was also shown to be reproducible, with high consistency between technical replicates and between different sources of DNA. The method was also tested for its ability to detect SNPs, with high accuracy and sensitivity. The method was able to detect SNPs with high confidence, with a low discordance rate. The method was also shown to be effective in capturing short and dispersed targets such as exons, with high coverage and uniformity. The method was found to be efficient and scalable, with the ability to target a wide range of genomic regions. The method was also shown to be flexible, with the ability to target any arbitrary sequence. The method was also shown to be compatible with a variety of sequencing platforms, including Illumina and 454. The method was found to be effective in reducing the cost of sequencing, with the ability to target specific regions of the genome with high efficiency. The method was also shown to be effective in capturing repetitive sequences, with the ability to target regions that are difficult to sequence with traditional methods. The method was also shown to be effective in capturing ancient DNA that is heavily contaminated with unwanted DNA. The method was also shown to be effective in deep sequencing of viral populations in patient material and metagenomic analyses of environmental or medical specimens.