Biotinylated probes of 120 bases are used to capture regions of interest. When added to the DNA library in solution, the probes hybridise with their targets. The targeted DNA fragments bound to the probes are captured using magnetic beads coupled with streptavidin, which has a high affinity for the biotin present on the probes. Non-targeted DNA is removed through successive washes, whilst the probe-target sequence complex is retained by magnetisation. A short PCR amplification step increases the quantity of sequences and degrades the probes. Sequencing can be performed independently on an Illumina MiSeq i100 or NextSeq 2000 (depending on the number of targets and/or samples).
Benefits
- Capture of panels of varying sizes (up to 24 MB)
- Tolerance to polymorphisms: a probe panel can be used on closely related species
- Advanced technology for the extraction of ancient or degraded DNA
- It is possible to focus on specific areas of interest by increasing the density of the sensors (tilling)
Disadvantages
- Requires high-quality DNA
- Probe non-specificity can lead to hybridisation at other regions of the genome (off-target)
Services
SureSelect capture of DNA and methylated DNA, on panels ranging from 0.5 Mb to 24 Mb, for a few samples up to several hundred. Sequencing is carried out on Illumina sequencer
Requirements
Depending on the protocol used, 1 to 3 µg of DNA, quantified by fluorescence (e.g. Qubit).
The probes are designed by Agilent Technologies. The PGTB can assist the user with this step (preparation of the reference genome and the BED file containing the target regions).
Results
Sent by email or uploaded to a server
- Demultiplexed FASTQ files
- Sequencing run report (MultiQC)
Associated publications
Lesur I, Rogier O, Sow MD, Boury C, Duplan A, Garnier A, Senhaji-Rachik A, Civan P, Daron J, Delaunay A, Duvaux L, Benoit V, Guichoux E, Le Provost G, Sanou E, Ambroise C, Plomion C, Salse J, Segura V, Tost J, Maury S., 2024. A strategy for studying epigenetic diversity in natural populations: proof of concept in poplar and oak. J Exp Bot. DOI: 10.1093/jxb/erae266
Lesur, I., Alexandre, H., Boury, C., Chancerel, E., Plomion, C., Kremer, A., 2018. Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand. Frontiers in Plant Sciences 9, 996. https://doi.org/10.3389/fpls.2018.00996