Molecular Genetics Comprehensive Brain Malformations Panel

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Test Code:

1095
Department:

Molecular Genetics
Test Synonyms:

ACTB • ACTG1 • AHI1 • ARFGEF2 • ARL13B • ARX • ASPM • ATR • ATRX • C5ORF42 • CASK • CC2D2A • CDK5RAP2 • CDKL5 • CDON • CENPJ • CEP152 • CEP290 • CEP41 • COL4A1 • CUL4B • DCX • DHCR7 • DISP1 • DLL1 • EMX2 • EOMES • EXOSC3 • EZH2 • FGF8 • FKRP • FKTN • FLNA • FOXG1 • FOXH1 • GAS1 • GLI2 • GLI3 • GPR56 • HESX1 • IER3IP1 • KIAA1279 • KIF7 • L1CAM • LAMC3 • LARGE • MCPH1 • MECP2 • MED12 • MKS1 • MRPS16 • MYCN • NFIX • NIPBL • NODAL • NPHP1 • NSD1 • OFD1 • OPHN1 • OTX2 • PAFAH1B1 • PCNT • PHF6 • PIK3CA • POMGNT1 • POMT1 • POMT2 • PQBP1 • PTCH1 • PTEN • RAB18 • RAB3GAP1 • RAB3GAP2 • RARS2 • RBBP8 • RELN • RPGRIP1L • SHH • SIX3 • SLC25A19 • SLC9A6 • SOX2 • SRPX2 • STIL • TCF4 • TCTN1 • TCTN2 • TGIF1 • TMEM138 • TMEM216 • TMEM237 • TMEM67 • TSEN2 • TSEN34 • TSEN54 • TTC21B • TUBA1A • TUBA8 • TUBB2B • TUBB3 • UBE3A • UPF3B • VLDLR • VRK1 • WDR62 • ZEB2 • ZIC2
CPT Code(s):

81408

Background:

Disorders causing brain malformations are phenotypically heterogeneous; mutations in certain genes have been associated inherited conditions causing brain developmental issues. These conditions could present with dysmorphologic features including holoprosencephaly, microcephaly and macrocephaly. Other clinical phenotypes include dysmorphologies observed in MRIs, seizures, developmental delays and intellectual disability. These conditions could include lissencephalies, cerebellar hypoplasia, Joubert syndrome and Joubert-like disorders. Conditions causing brain malformations can be inherited in an autosomal dominant, recessive and X-linked pattern.

Reasons for Referral:

Suspected genetic etiology of a brain malformation
Carrier testing
Positive family history

Methodology:

Next generation sequencing will analyze the exons or coding regions of 107 Comprehensive Brain Malformation-associated genes using Illumina NextSeq 500 technology. Samples are prepared using hybridization probes to enrich exonic regions. Promoter, intronic, etc. regions are not assessed on our assay, but may contain variants that impact gene function. Additionally, the assay does not assess coding regions with incompletely coverage including regions of high homology (pseudogenes), regions of high GC content and polynucleotide repeats, etc.

Coding region coverage for the Comprehensive Brain Malformations panel genes

Gene Name	Coverage
ACTB, ACTG1, AHI1, ARFGEF2, ARL13B, ASPM, ATR, ATRX, CASK, CC2D2A, CDK5RAP2, CDKL5, CDON, CENPJ, CEP152, CEP290, CEP41, COL4A1, CUL4B, DCX, DHCR7, DISP1, DLL1, EMX2, EXOSC3, EZH2, FGF8, FKTN, FLNA, GLI3, GPR56, HESX1, IER3IP1, L1CAM, LAMC3, LARGE, MCPH1, MECP2, MED12, MKS1, MRPS16, NFIX, NIPBL, NODAL, NPHP1, NSD1, OFD1, OPHN1, OTX2, PAFAH1B1, PCNT, PHF6, PIK3CA, POMGNT1, POMT1, POMT2, PQBP1, PTCH1, PTEN, RAB18, RAB3GAP1, RAB3GAP2, RARS2, RBBP8, RELN, RPGRIP1L, SLC25A19, SLC9A6, SOX2, SRPX2, STIL, TCF4, TCTN1, TCTN2, TGIF1, TMEM138, TMEM216, TMEM237, TMEM67, TSEN2, TTC21B, TUBA1A, TUBA8, TUBB3, UBE3A, UPF3B, VLDLR, VRK1, WDR62, ZEB2	95%-100%
C5orf42, EOMES, KIAA1279, KIF7,TSEN34, TSEN54	90%-95%
FKRP, FOXG1, FOXH1, GLI2, MYCN, SHH, SIX3, TUBB2B	75%-90%
ARX, GAS1, ZIC2*	50%-75%

Coding regions below 95% may be covered upon request if further assessment of a gene is necessary (some exceptions may apply). Please contact Knight Diagnostic Laboratories for more information.
*ARX gene complete coverage and expansions in the polyalanine tract not available.

Related Tests: Knight Diagnostic Laboratories offers smaller, focused panels:

Specimen Requirements:

Blood: EDTA or ACD (Solution A or B):

Adult: 5 mL
Child: 5 mL
Infant: 2-3 mL

Saliva: 1 ORAgene Saliva Kit (OGR-500)
Skin Fibroblast: Punch Biopsy, or 2 T-25 confluent flasks
DNA: 1-2µg at a minimum of 50-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS)

For routine testing of blood, saliva and buccal swabs, KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed outside of the above windows, please contact our lab.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information, including ethnicity, clinical history, and family history.

Test Performed (Days):

Weekly

Turn Around Time:

8 weeks

Shipment Sensitivity Requirements: