Lissencephaly Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
5047 ACTB 81479,81479 Order Options and Pricing
ACTG1 81479,81479
ADGRG1 81479,81479
APC2 81479,81479
ARX 81404,81403
CDK5 81479,81479
CEP85L 81479,81479
CRADD 81479,81479
DCX 81405,81479
DYNC1H1 81479,81479
KATNB1 81479,81479
KIF2A 81479,81479
KIF5C 81479,81479
LAMB1 81479,81479
MACF1 81479,81479
NDE1 81479,81479
PAFAH1B1 81406,81405
RELN 81479,81479
TMTC3 81479,81479
TMX2 81479,81479
TUBA1A 81479,81479
TUBA8 81479,81479
TUBB 81479,81479
TUBB2B 81479,81479
TUBB3 81479,81479
TUBG1 81479,81479
TUBGCP2 81479,81479
VLDLR 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
5047Genes x (28)81479 81403(x1), 81404(x1), 81405(x2), 81406(x1), 81479(x51) $1070 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Lissencephaly comprises a group of cerebral malformations due to a defect of neuronal migration. Lissencephaly is characterized by absent (agyria) or decreased (pachygyria) convolutions, cortical thickening, and a smooth cerebral surface. The symptoms of lissencephaly vary with different causes. The major features of lissencephaly include early developmental delay, early diffuse hypotonia, spastic quadriplegia, intellectual disability, infantile spasms and seizures. Additional features include microcephaly, subtle dysmorphic features, failure to thrive, difficult feeding and swallowing, muscle spasms, myoclonic jerks, and poor social interactions (Leventer et al. 2001. PubMed ID: 11502906; Wallerstein et al. 2008. PubMed ID: 18462864; Di Donato et al. 2017. PubMed ID: 28440899; Barkovich et al. 2012. PubMed ID: 22427329; Dobyns. 2010. PubMed ID: 20331703). The prevalence of classical lissencephaly is estimated around 12 per million births (Parrini et al. 2016. PubMed ID: 27781032).

Outside of DNA testing, brain imaging techniques such as CT and MRI are the most powerful tools for diagnosis of lissencephaly. For example, in the cases of tubulinopathies, MRI shows pachygyric cortex with posterior to anterior gradient, enlarged lateral ventricles, and variable degrees of reduced white matter volume (Brock et al. 2018. PubMed ID: 29706637; Poirier et al. 2013. PubMed ID: 23603762; Romaniello et al. 2017. PubMed ID: 28677066).

As lissencephaly can be caused by defects in many genes with variable and overlapping presentations, they can be difficult to diagnose by clinical manifestation and image studies only. Therefore, an accurate molecular diagnosis is critical for treatment, prognosis, and reproductive planning.

Genetics

The genetic etiology of the lissencephaly is heterogeneous. Lissencelphay can be inherited in an autosomal dominant, autosomal recessive or X-linked manner.  This panel covers many well documented genes, as well as newly-discovered genes. Genes within the panel include ARX (Aristaless-related homeobox protein), DCX (doublecortin), RELN (reelin signaling), TUBA1A, TUBB2BTUBB3TUBBTUBG1TUBA8 (tubulins), KATNB1 (Katanin), MACF1 (microtubule-actin cross-linking factor), LAMB1 (extracellular matrix laminin), PAFAH1B1 (platelet-activating factor acetylhydrolase), NDE1 (mitosis-related protein), and a number of others (Di Donato et al. 2018. PubMed ID: 29671837; Parrini et al. 2016. PubMed ID: 27781032). 

The type of pathogenic variant varies with different genes. The vast majority of pathogenic variants in genes involving tubulinopathies occur de novo (Bahi-Buisson and Cavallin et al. 2016. PubMed ID: 27010057; Rodan et al. 2017. PubMed ID: 27770045). Germline mosaicism has been reported in a patient with tubulinopathy (Brock et al. 2018. PubMed ID: 29706637).

See individual gene summaries for information about the molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

Lissencephaly is clinically and genetically heterogeneous. The sensitivity is variable depending on different disorders. In one study with analysis of 17 genes (ACTB, ACTG1, ARX, CRADD, DCX, LIS1, TUBA1A, TUBA8, TUBB2B, TUBB, TUBB3, TUBG1, KIF2A, KIF5C, DYNC1H1, RELN, and VLDLR) a detection rate of 81% was achieved (Di Donato et al. 2018. PubMed ID: 29671837).

 

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 98.4% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

This panel is recommended for patients suspected to have lissencephaly.

Diseases

Name Inheritance OMIM ID
Baraitser-Winter Syndrome 1 AD 243310
Baraitser-Winter Syndrome 2 AD 614583
Cortical Dysplasia, Complex, With Other Brain Malformations AD 614039
Cortical dysplasia, complex, with other brain malformations 10 AR 618677
Cortical dysplasia, complex, with other brain malformations 2 AD 615282
Cortical dysplasia, complex, with other brain malformations 3 AD 615411
Cortical Dysplasia, Complex, with other Brain Malformations 4 AD 615412
Cortical dysplasia, complex, with other brain malformations 6 AD 615771
Lissencephaly 1 AD 607432
Lissencephaly 10 AD 618873
Lissencephaly 2 AR 257320
Lissencephaly 3 AD 611603
Lissencephaly 4 AR 614019
Lissencephaly 5 AR 615191
Lissencephaly 6, with microcephaly AR 616212
Lissencephaly 7 with cerebellar hypoplasia AR 616342
Lissencephaly 8 AR 617255
Lissencephaly 9 with complex brainstem malformation AD 618325
Mental Retardation, Autosomal Dominant 13; MRD13 AD 614563
Mental retardation, autosomal recessive 34, with variant lissencephaly AR 614499
Neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity AR 618730
Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures AR 618737
Polymicrogyria With Optic Nerve Hypoplasia AR 613180
Polymicrogyria, Asymmetric AD 610031
Polymicrogyria, Bilateral Frontoparietal AR 606854
Polymicrogyria, bilateral perisylvian AR 615752
VLDLR-Associated Cerebellar Hypoplasia AR 224050
X-Linked Lissencephaly XL 300067
X-Linked Lissencephaly 2 XL 300215

Related Test

Name
PGxome®

Citations

  • Bahi-Buisson and Cavallin et al. 2016. PubMed ID: 27010057
  • Barkovich et al. 2012. PubMed ID: 22427329
  • Brock et al. 2018. PubMed ID: 29706637
  • Di Donato et al. 2017. PubMed ID: 28440899
  • Di Donato et al. 2018. PubMed ID: 29671837
  • Dobyns. 2010. PubMed ID: 20331703
  • Leventer et al. 2001. PubMed ID: 11502906
  • Parrini et al. 2016. PubMed ID: 27781032
  • Poirier et al. 2013. PubMed ID: 23603762
  • Rodan et al. 2017. PubMed ID: 27770045
  • Romaniello et al. 2017. PubMed ID: 28677066
  • Wallerstein et al. 2008. PubMed ID: 18462864

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

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.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

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.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: $
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