Turnaround times
The quoted turnaround time is from sample receipt in the laboratory, to results authorisation in the Laboratory Information Management system. The times do not include transport of specimen to the laboratory or the administrative process to print and post/email reports. Service users must allow for transport and reporting time when ordering tests.
Clinical background:
Whole genome sequencing (WGS) provides a comprehensive genome-wide view of the known genetic alterations that drive development and progression of tumours.
WGS is now funded by NHS England and available for a subset of eligible patients with haematological malignancies. This includes patients under the age of 25 or any patient where standard genetic testing has been exhausted.
Samples are usually sent from the Newcastle laboratory to the central NEYGLH Leeds laboratory for DNA extraction. Leeds will then coordinate the export of DNA to the Sequencing Centre at the Wellcome Genome Campus in Cambridge for WGS testing.
Post-sequencing data will then be processed by a specific bioinformatic pipeline and uploaded to an interpretation portal. Cancer Clinical Scientists from Newcastle will finally analyse, interpret and report any WGS findings.
Specimen container paediatric:
EDTA
Specimen container adult:
EDTA
Minimum volume paediatric:
5 mL
Minimum volume adult:
5 mL
Special requirements:
Please complete NEHODS request form and also WGS record of discussion form.
Sample Stability:
N/A
Transport requirements:
Samples should be sent to laboratory immediately.
Freq Analysis:
Daily
Add On Test:
Can be added to any genetics sample where enough DNA has been stored. This must be discussed with the NEHODS team and the GTAB meeting.
Quality Assurance:
N/A
Interpretation:
By genetics clinical scientist.
In all cases, WGS results will be discussed at the Genomics Tumour Advisory Board (GTAB) meetings before writing a final report.
Reference Ranges:
N/A
Factors Affecting Result:
Quality and size of sample
Referenced Documents:
N/A
Other Info:
By sequencing the whole genome, WGS can identify nearly all types of mutations, which are small somatic variants (SSV), such as single nucleotide variants (SNVs) and small indels; and copy number and structural variants (CNVs and SVs), such as gains, losses, loss of heterozygosity (LOH), translocations or inversions. Any germline variant that may be present and relevant will also be presented for analysis.