Capture-Seq is a method of genotyping consisting of capturing and sequencing specific, targeted regions of the genome.  This methodology presents a more efficient alternative to genotyping by sequencing (GBS).  Capture probes are selected and designed to hybridize to unique regions of interest based on existing reference genomes. The probe design process is carried out in collaboration with the client to satisfy the goals of the project and maximize efficiency of each probe. The laboratory component is fully automated to achieve high-throughput, reliable, and consistent results. We fragment the genomic DNA, ligate barcoded Illumina-compatible adapters to the resulting fragments, and enrich via PCR to prepare the DNA for probe capture. We then perform the capture reactions with the custom-designed probes and sequence the libraries.

The Capture-Seq service includes a series of quality control steps performed throughout the procedure to ensure outstanding data quality regardless of the genome complexity and DNA source.

Once the sequencing data is produced, the files are divided by each individual sample, filtered for quality and aligned to the reference genomes used to design the probes. Based on the alignment results, and information about the population, we perform the SNP identification and genotyping as well as a variety of other analyses.

Additional bioinformatics analyses are available as a packaged service.





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     RAPiD-Seq is a genotyping by sequencing method designed to reduce the representation of genomes by PCR amplification. PCR primers are selected to amplify a defined set of regions equally distributed across the genome to obtain maximum coverage and number of targeted loci.

The first PCR (PCR I) is independently performed for every sample to be genotyped. Modified primers used in this reaction contain a specific sequence that determines the number and distribution of annealing sites in the genome. Therefore, the number of loci that are genotyped can be adjusted by selecting different primers, according to the client needs (low, medium or high marker density) and species. The PCR primer has other properties that stabilize annealing to the genome, to differentiate among samples during sequence processing, and to permit sequencing.

The second PCR (PCR II) is performed on pooled samples derived from the PCR I.  By combining individuals during this reaction that will later be sequenced together, sample preparation throughput is increased. After this reaction, the samples are ready for sequencing in a next-generation DNA sequencer. Genotypic information is obtained using custom-developed algorithms for RAPiD-Seq data.

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The Plant Journal (2013)

Whole-exome targeted sequencing of the uncharacterized pine genome

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What a Character

In the world of genomics, survival of the fittest is a reinforced practice. The weak do not advance. Scientists at Gainesville-based RAPiD Genomics have established a valuable business using that very Darwinian theory… (more)

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