New DNA sequencing technology allows us to test for disease-causing variants in all the genes known to cause a range of Endocrine disorders in a single test (targeted next generation sequencing) rather than analysing just one or two genes at a time. This test enables panels of genes to be tested simultaneously in a cost-effective manner. We are using a targeted capture method (Agilent Sure Select) and Illumina HiSeq® technology to achieve high sensitivity (>99%) for detection of variants previously detected by Sanger sequencing and can also identify large deletions and duplications (Ellard et al 2013 Diabetologia 56:1958 http://link.springer.com/article/10.1007%2Fs00125-013-2962-5). De Franco et al. (2015) highlight how early and comprehensive genomic testing improves clinical care for neonatal diabetes patients.
Which genes/genetic subtypes are included in the test?
|Phaeochromocytoma and Paraganglioma||FH, MAX, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, TMEM127, VHL|
|Hypophosphatemic Rickets||CYP27B1, CYP2R1, DMP1, ENNP1, FAM20C, FGF23, PHEX, SLC34A1, SLC34A3, VDR|
|Familial Isolated Hyperparathyroidism||AP2S1, CASR, CDC73, CDKN1B, MEN1, RET|
|Familial Hypocalciuric Hypercalcaemia||CASR, GNA11, AP2S1|
|Endocrine Neoplasia syndromes||AIP, CDC73, CDKN1B, MEN1, RET|
|Chondrodysplasia Punctata||PEX7, GNPAT, AGPS, ARSL (previously ARSE), EBP|
|Familial Isolated Hypoparathyroidism||AIRE, CASR, GATA3, GCM2,GNA11, PTH, TBCE|
|Generalised Arterial Calcification of Infancy||ENPP1, ABCC6, NT5E|
|Tumoral Calcinosis||FGF23, GALNT3|
|Congenital Generalised Lipodystrophy||AGPAT2, BSCL2, CAV1, CAVIN1, LIPE, LMNA, PLIN1, POLD1, PPARG, ZMPSTE24|
|Congenital Hypothyroidism||DUOX2, DUOXA2, FOXE1, GLIS3, GNAS, HESX1, IGSF1, IRS4, IYD, LXH3, LXH4, NKX2-1, OTX2, PAX8, POU1F1, PRKAR1A, PROP1, SECISBP2, SLC16A2, SLC26A4, SLC26A7, SLC5A5, TBL1X, TG, THRA, THRB, TPO, TRHR, TSHB and TSHR|
|Familial Glucocorticoid Deficiency||MC2R, MRAP, STAR, MCM4, NNT|
|Pseudohypoaldosteronism type 2||WNK1, WNK4, CUL3, KLHL3|
|Primary Pigmented Nodular Adrenocortical Disease||ARMC5, PDE8B, PDE11A, PRKAR1A,|
|Combined Pituitary Hormone Deficiency||BTK, CHD7, FGF8, FGFR1, FOXA2, GH1, GHR, GHRHR, GHSR, GLI2, GLI3, GNRHR, HESX1, IGSF1, LHX3, LHX4, OTX2, PITX2, PNPLA6, POU1F1, PROKR2, PROP1, SOX2, SOX3, TBX19|
When should I request this test and how much does it cost?
Testing for each of the panels can be requested either as the first test (NHS price £650-£750/non-NHS £813-£938) or as a follow-on test if one or more of the genes have already been tested using Sanger sequencing (up to 50% discount applied). Click on the panel name for a copy of our request form. We require 5-10ml venous blood in plastic EDTA bottles or >5µg DNA.
What is the reporting time for this test?
The national target for Next Generation Sequencing tests is 8 weeks. Future technological developments are expected to make testing faster and cheaper.
Can the test identify a variant that is known to cause a disease other than the disorder under investigation?
Potentially, yes. However we will only report findings relevant to the patient’s presentation.
What are the test limitations?
This test will identify the same types of variants detected by Sanger sequencing as well as large deletions or duplications previously identified by a separate dosage assay. The test sensitivity is estimated at >99% (95% CI) for base substitutions and small insertions/deletions and >95% (95% CI) for copy number changes. Balanced translocations, inversions and intronic variants located outside splice site will not be detected. Sequence analysis of the coding regions and intronic regions located within 50 bases upstream and 10 bases downstream of each exon using 100bp paired end reads. There are some parts of the human genome that are not amenable to next generation sequencing. Clinically significant regions with <20X coverage will be analysed using Sanger sequencing. Confirmation of variants identified by targeted NGS is undertaken by Sanger sequencing, MLPA or droplet digital PCR.
Sequencing a greater number of genes will identify more novel/rare variants whose clinical significance is uncertain. These include variants not seen before or identified in a small number of patients where the causal link to the disease is unproven. The clinical report will only include likely disease-causing variants or variants where further investigation is recommended (for example by testing affected relatives to see if they have the same possible variant). New clinical or genetic information may change the interpretation of pathogenicity. In accordance with best practice guidelines, known polymorphisms are not reported.
Where can I find more information?
Click on the panel name in the table above or contact Martina Owens (Martina.Owens@nhs.net or 01392 408249).