Forms

Classic Lissencephaly via the DCX Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
503 DCX$610.00 81405 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
Mutations in DCX are estimated to cause ~20% of classic lissencephaly cases (Pilz et al. 1998).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 DCX$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote
Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features
Lissencephaly is defined as "smooth brain" with absent gyri (agyria) or abnormally wide gyri (pachygyria) (Barkovich et al. Ann Neurol 1991; 30:139–46). Classic lissencephaly includes the LIS1-associated, DCX-related, and TUBA1A-related forms as well as the rare Baraitser-Winter syndrome (BWS) (Dobyns et al. Neurology 42:1375-88, 1992; Poirier et al. Hum Mutat 28:1055-64, 2007). DCX-related lissencephaly, also known as X-linked Lissencephaly type 1 (LISX1, OMIM# 300076), is a neuronal migration disorder caused by mutations in the DCX gene (des Portes et al. Cell 92: 51-61, 1998). DCX-related lissencephaly includes classic lissencephaly in males and subcortical band heterotopia (SBH)/double cortex syndrome in females (Dobyns et al. Neurology 53: 270-277, 1999; Guerrini et al Am J Med Genet 106:160-173, 2001). Males with classic lissencephaly typically have developmental delay, severe mental retardation and infantile-onset seizures (Dobyns et al. 1999). SBH is a milder form of lissencephaly, in which the severity of symptoms correlates with the degree of the underlying brain malformation. In individuals with SBH, cognitive abilities range from normal to learning disabilities and/or severe mental retardation with or without seizures (Guerrini et al. 2001).
Genetics
DCX-related lissencephaly is inherited in an X-linked manner. Approximately 10% of unaffected mothers of children with a DCX mutation may have somatic mosaicism or germline mosaicism (Mei et al. Neurology 68: 446–450, 2007). DCX gene encodes the DCX protein, which contains two tandem doublecortin domains that bind tubulin (Taylor et al. J Biol Chem 275:34442-34450, 2000). It has also been reported that DCX interacts with LIS1 protein. These proteins have important roles in proper microtubule function in the developing cerebral cortex, which could explain the role of DCX in neuronal migration and early embryonic development (Hirotsune et al. Nat Genet 19: 333-339, 1998; Gleeson et al. Neuron 23:257-271, 1999; Caspi et al. Hum Molec Genet 9:2205-2213, 2000). A mix of missense, nonsense, splice site and small deletion mutations as well as whole and intrageneic deletion and duplication mutations have been reported in the DCX gene (Pilz et al. Hum Mol Genet 7:2029-37; Gleeson et al. Cell 92:63-72, 1998; Gleeson et al. Ann Neurol 45:146-153, 1999; Matsumoto et al. Eur J Hum Genet 9:5-12, 2001; Mei et al. 2007).
Testing Strategy
This test involves bidirectional sequencing using genomic DNA of the 6 coding exon (exons 4-9) of the DCX gene. The full coding region of each exon plus ~10 bp of flanking non-coding DNA on each side are sequenced. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.
Indications for Test
Candidates for this test are patients with symptoms consistent with X-linked lissencephaly 1 and family members of patients who have known DCX mutations.

Gene

Official Gene Symbol OMIM ID
DCX 300121
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
X-Linked Lissencephaly 300067

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Barkovich, A. J., et.al. (1991). "The spectrum of lissencephaly: report of ten patients analyzed by magnetic resonance imaging." Ann Neurol 30(2): 139-46. PubMed ID: 1897907
  • Caspi, M., et.al. (2000). "Interaction between LIS1 and doublecortin, two lissencephaly gene products." Hum Mol Genet 9(15): 2205-13. PubMed ID: 11001923
  • des Portes, V., et.al. (1998). "A novel CNS gene required for neuronal migration and involved in X-linked subcortical laminar heterotopia and lissencephaly syndrome." Cell 92(1): 51-61. PubMed ID: 9489699
  • Dobyns, W. B., et.al. (1992). "Causal heterogeneity in isolated lissencephaly." Neurology 42(7): 1375-88. PubMed ID: 1620349
  • Dobyns, W. B., et.al. (1999). "Differences in the gyral pattern distinguish chromosome 17-linked and X-linked lissencephaly." Neurology 53(2): 270-7. PubMed ID: 10430413
  • Gleeson, J. G., et.al. (1998). "Doublecortin, a brain-specific gene mutated in human X-linked lissencephaly and double cortex syndrome, encodes a putative signaling protein." Cell 92(1): 63-72. PubMed ID: 9489700
  • Gleeson, J. G., et.al. (1999). "Characterization of mutations in the gene doublecortin in patients with double cortex syndrome." Ann Neurol 45(2): 146-53. PubMed ID: 9989615
  • Guerrini, R., Carrozzo, R. (2001). "Epilepsy and genetic malformations of the cerebral cortex." Am J Med Genet 106(2): 160-73. PubMed ID: 11579436
  • Hirotsune, S., et.al. (1998). "Graded reduction of Pafah1b1 (Lis1) activity results in neuronal migration defects and early embryonic lethality." Nat Genet 19(4): 333-9. PubMed ID: 9697693
  • Matsumoto, N., et.al. (2001). "Mutation analysis of the DCX gene and genotype/phenotype correlation in subcortical band heterotopia." Eur J Hum Genet 9(1): 5-12. PubMed ID: 11175293
  • Mei, D., et.al. (2007). "Multiplex ligation-dependent probe amplification detects DCX gene deletions in band heterotopia." Neurology 68(6): 446-50. PubMed ID: 17283321
  • Pilz, D. T., et.al. (1998). "LIS1 and XLIS (DCX) mutations cause most classical lissencephaly, but different patterns of malformation." Hum Mol Genet 7(13): 2029-37. PubMed ID: 9817918
  • Poirier, K., et.al. (2007). "Large spectrum of lissencephaly and pachygyria phenotypes resulting from de novo missense mutations in tubulin alpha 1A (TUBA1A)." Hum Mutat 28(11): 1055-64. PubMed ID: 17584854
  • Taylor, K. R., et.al. (2000). "Patient mutations in doublecortin define a repeated tubulin-binding domain." J Biol Chem 275(44): 34442-50. PubMed ID: 10946000
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TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.
SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.
DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.
CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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