Whole genome resequencing
The reference genomes of a large number of organisms are now available and the major challenge at present is to maintain and catalogue the nucleotide and structural variations and to understand their biological effects. The sequences obtained from resequencing are aligned to the reference genome to identify genomic variants such as SNPs, CNVs, indels and chromosomal rearrangements.
Figure : Identification of SNPs, CNVs, indels and chromosomal rearrangements
The genomic DNA is fragmented and used to construct libraries for sequencing.
This step involves repairing the ends of the fragments and adding a specific adapter to both ends. If the initial quantities of DNA are small (< 1µg), a PCR amplification step is performed. Next, the libraries are quality controlled on a Bioanalyser (Agilent) and quantified by qPCR, then sequenced. The sequences obtained are aligned to the reference genome to identify the nucleotide and structural variations. To detect the CNVs and large chromosomal rearrangements with accuracy, a mate-pair protocol can be used (see description sheet for de novo sequencing).
The platforms of the France Génomique network are able to satisfy requests for whole genome resequencing.
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