Whole genome sequencing is performed by shotgun sequencing of DNA fragments. While the sample prep and sequencing is routine for whole genome projects, VANTAGE strongly recommends informatics consultation prior to undertaking any whole genome sequencing project.
Standard short-insert Paired-End libraries are generally adequate for whole genome coverage. Mate-pair (or long-insert) 2-5 kb insert libraries can be generated at an added cost and are most effective for use on de novo genome sequencing. The combination of short-insert and long-insert libraries greatly increase the physical coverage and ability to generate long contigs from the short reads.
For review of whole genome sequencing on the Illumina platform:
Bentley et al. "Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry", Nature 456(7218): 53-59 (2008).
Sample submission requirements:
- DNA: 1 to 5 ug genomic DNA, in < 100 ul nuclease-free water or TE. DNA submitted will be assessed for quality, an acceptable sample should have an A260/280 ratio 1.8 - 2.0 and majority of high molecular weight with little migration when run on a 2% agarose gel. FFPE DNA accepted but must be noted on sample submission sheet.