Analyses


EXSTAxxx - Standard clinical exome sequencing, with xxx million raw reads

EXSTATRIOxxx - Standard clinical exome sequencing of a trio, with xxx million raw reads per sample

WGACU30 - Acute setting whole-genome sequencing, approximately 30X coverage (2 flow cells yielding approximately 600 M raw reads)

RML250 - Ready made libraries, guaranteed 250M pared reads with accumulated Q30 >80

For exome sequencing, quantity of raw reads can be set between 30 M and 300 M. We will during Q1 2014 provide an estimate of coverage corresponding to various sequencing depths.
The cost of the analyses is provided as part of the master service agreement and updated regularly.

Limitations of the methods


Exome sequencing

The method currently in use utilises enrichment via hybridisation; the inherent nature of this technology does not allow for complete (100%) selection of targeted regions in the exome. Hence it is inevitable that certain regions will not be represented in the final data. Also, the design of the capture kit does not target the entire exome (partly dependent on the definition of the exome). Combining capture efficiency with amplification induced relative differences in copy number of individual molecules causes the representation of the exome to be variable. To assess the completeness of the coverage, we can calculate completeness measures for predefined gene sets. Contact us for further information.

Whole-genome sequencing

The method currently in use for whole-genome sequencing is based on mechanical (random) fragmentation, followed by adapter ligation and purification to remove non-ligated adapters. The protocol contains no amplification steps and is hence significantly more uniform in its representation of the genome than the exome sequencing protocol. Limited by the read lengths, the WGS protocol does not allow mapping of reads to highly repetitive regions. To assess the completeness of the coverage, we can calculate completeness measures for predefined gene sets. Contact us for further information.