Urgent TAT for prenatal/neonatal analysis or treatment-focused testing: 4 weeks
TEST METHOD:
Capture-based target enrichment is performed using the Twist Bioscience Enzymatic Fragmentation Library Preparation v1.0 and custom panel. Next-generation sequencing (NGS) is performed on an Illumina MiSeq platform. Variant calls are identified using the Illumina DRAGEN analysis platform v4.0.3. Variant triage and curation is performed using Agilent Alissa Interpret.
For SDHB, SDHC, SDHD, SDHAF1, and SDHAF2 genes, Multiplex Ligation-dependent Probe Amplification (MLPA) kit P226-D1 SDH from MRC-Holland is used to detect copy number variations.
TARGET GENES AND COVERAGE: The coding regions and flanking +/-20bp (encompassing the splice sites) are sequenced in this test. 100% coverage of bases within these regions is achieved by NGS (to a depth of >50x).
LIST OF GENES
ATP7B, CDKL5, CYP24A1, FGFR3, GALT, GLA, GNAS, MECP2, POLG, RET, MAX, SDHAF2*, SDHC*, SDHB*, SDHD*, TMEM127, UBE3A, VHL
*Copy number variations analysis included
Clinically relevant genes associated with rare inherited diseases are analysed.
IMPORTANT NOTES: the speciality of the referring clinician and the clinical presentation should be provided. Failure to provide the information required may delay testing.
Referrals can only come from Genetic Health Service NZ (GHSNZ) or medical specialists group listed in the table below;
List of Genes and disorders:
| Gene name | Disorder | Referral requirements |
| ATP7B | Wilson Disease | Metabolic or Neurology |
| CDKL5 | CKDL Deficiency Disorder/Atypical Rett Syndrome | Paediatric Neurology or Metabolic |
| CYP24A1 | Hypercalcemia | Metabolic or Endocrinology |
| FGFR3 | Achondroplasia | Paediatric Endocrinology or any specialists following input from Genetic Services |
| GALT | Galactosaemia (classic and Duarte variant) | Metabolic or Paediatric Neurology |
| GLA | Fabry Disease | Metabolic or Cardiac Inherited Disease Group |
| GNAS |
McCune-Albright Syndrome
Albright Hereditary Osteodystrophy |
Paediatric Endocrinology |
| MECP2 | Rett Syndrome | Neurology or Metabolic |
| POLG | POLG Related Disorders | Metabolic or Paediatric Neurology |
| RET | Multiple Endocrine Neoplasia type 2 | Endocrinology or Oncology |
| MAX |
Familial Paraganglioma/Phaeochromocytoma Syndrome
-Offered as a single gene test, however if a PHAEO panel is requested this must be sent away |
|
| SDHAF2 | ||
| SDHC | ||
| SDHB | ||
| SDHD | ||
| TMEM127 | ||
| UBE3A | Angelman Syndrome | Paediatrics with Genetic Service involvement, Neurology or Metabolic |
| VHL |
Von Hippel-Lindau Syndrome
-Offered as a single gene test, however if a PHAEO panel is requested this must be sent away |
Endocrinology or Oncology |
To contact the Molecular Genetics team:
Auckland City Hospital
(09) 307 4949
Lablink
ext 22000
Molecular Genetics Office
ext 22014
Transport all bloods between >8 deg C to <25 deg C within 24-48 hours. If necessary specimens can be refrigerated overnight for transport at the temperatures stated above the following day.
For testing of other sample types please contact the laboratory prior to sending.