GeneDx, Inc.
207 Perry Parkway
Gaithersburg, MD 20877
Phone: 301-519-2100
Fax: 301-519-2892
E-mail: genedx@genedx.com
www.genedx.com
Test Information Sheet
Microcephaly Panel
Sequence Analysis and Exon-Level Deletion/Duplication Testing of 28 Genes
Microcephaly Panel Gene List:
ASPM
ATR
ATRX
CASK
CDK5RAP2
CDKL5
CENPJ
CEP152
DHCR7
FOXG1**
IER3IP1
MCPH1
MECP2
MYCN***
NIPBL
PCNT
RAB18
RAB3GAP1
RAB3GAP2
RBBP8
SLC25A19
SLC9A6
STIL
TCF4
TUBB3
UBE3A
WDR62
ZEB2*
* No sequencing of exon 10 of the ZEB2 gene.
** This panel does not include deletion/duplication testing of FOXG1.
*** Deletion/duplication of the MYCN gene is performed by MS-MLPA.
Clinical Features:
Microcephaly is defined as a small cranium with an occipito-frontal head circumference (OFC) of more than two
1
standard deviations (SD) below the mean for age, sex, and ethnicity. Microcephaly can be congenital (primary
microcephaly) or develop postnatally (secondary microcephaly). Either type can be caused by environmental or
2
genetic factors. Approximately 15-50% of individuals with microcephaly have been reported to have an underlying
1
genetic etiology. Individuals with primary microcephaly have inadequate brain growth during pregnancy, and are
born with a significantly small head size (OFC of < 3 SDs). They may also develop mild to severe intellectual
3
disabilities, seizures, mild short stature, and a narrow sloping forehead due to the reduced cranial size. Imaging
typically reveals a normal brain structure with reduction in size, particularly of the cerebral cortex. The brain size in
4
cases of secondary microcephaly has the expected size at birth but subsequently fails to grow normally. Common
causes of secondary microcephaly include environmental insults, such as infections or a brain injury. In addition,
secondary microcephaly is observed in some metabolic disorders or genetic syndromes, such as Rett syndrome
and Angelman syndrome, in which a progressive reduction in head circumference is seen in infancy or early
5
childhood. Congenital and postnatal microcephaly could present as an isolated finding in an individual, be
associated with other brain malformations such as cerebellar hypoplasia, or as part of an underlying syndrome.
Genetics:
The general incidence of microcephaly at birth varies from 1.3 to 150 per 100,000 live births, depending on the
2
population and the applied SD threshold to define microcephaly. Microcephaly can be caused by chromosomal
abnormalities, inborn errors of metabolism, single gene disorders, trauma and infection. The inheritance patterns
can be autosomal dominant, recessive or x-linked. One type of isolated congenital microcephaly that has a genetic
etiology is primary autosomal recessive microcephaly (MCPH), which is a rare and heterogeneous disorder reported
2
in about 100 families worldwide. The incidence of MCPH in consanguineous populations is approximately one in
2
10,000 and less in non-consanguineous populations. Currently there are seven subtypes of MCPH and between
37-54% of patients with a strictly characterized MCPH diagnosis have a pathogenic variant in the ASPM gene,
3
associated with MCPH5. However, about 20-30% of families with MCPH do not have an identifiable variant in one
2
of the seven loci, indicating further genetic heterogeneity. Syndromic forms of microcephaly are associated with
underlying chromosomal aberrations, contiguous gene deletions, and single gene disorders that are inherited in an
5
autosomal dominant, recessive, or X-linked manner. Several of these syndromes have postnatal onset of
microcephaly, including Rett syndrome and Ataxia-telangectasia with intellectual disability, whereas other
syndromes, such as Cornelia de Lange, Smith-Lemli Opitz, and Seckel, present with congenital microcephaly.
Information Sheet on Microcephaly Panel
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© GeneDx Revision Date: 12/2015
Reason for Referral:
1. Molecular confirmation of a clinical diagnosis.
2. Establish the type of microcephaly and cause in order to provide information regarding prognosis, management
and recurrence risk.
3. Testing of at-risk relatives for specific known variant(s) previously identified in an affected family member.
4. Prenatal diagnosis for known familial pathogenic variant(s) in at-risk pregnancies.
Methods:
Using genomic DNA, coding exons and flanking splice junctions of the genes on this panel are enriched using a
proprietary targeted capture method developed by GeneDx. The products are sequenced on an Illumina instrument
using paired end reads. The sequence data is aligned to reference sequences based on human genome build
GRCh37/UCSC hg19. Sanger sequencing is used to compensate for low coverage and refractory amplifications.
Concurrently, multiplex ligation-dependent probe amplification (MLPA) of the MYCN gene and targeted array CGH
analysis with exon-level resolution is performed to evaluate for a deletion or duplication of one or more exons for
most of the genes included on the panel. If indicated, MLPA of the FOXG1 gene is available as a separate test (test
code 904). The presence of any potentially disease-associated sequence variant(s) or copy number alteration(s) is
confirmed by dideoxy DNA sequence analysis or quantitative PCR, respectively, or by other appropriate methods.
Test Sensitivity:
The clinical sensitivity of sequencing and deletion/duplication analysis of the genes included in this panel depends
on the patient’s clinical phenotype. Specific information about the diagnostic yield for each gene in selected
populations is summarized in the following table. The technical sensitivity of the sequencing test is estimated to be
98%. Deletions involving more than 20 bp and insertions involving more than 10 bp are not reliably detected by the
sequencing methodology, and deletions or duplications of less than 500 bp are not reliably detected by array CGH.
Note that small sections of a few genes have inherent sequence properties that result in suboptimal data and
variants in those regions may not be reliably identified.
Specimen Requirements and Shipping/Handling:
• Blood: Whole blood in EDTA. Adults: 8-10 ml; Children: 4 ml; Infants: 2 ml. Ship blood overnight at
ambient temperature, using a cool pack in hot weather. Blood specimens may be refrigerated for up to 7
days prior to shipping.
• Oral Rinse: Use GeneDx kit only; follow instructions at http://www.genedx.com/order-a-test/specimenrequirements/.
• Extracted DNA: Outside DNA is discouraged; however, high quality extracted DNA can be accepted. This
test requires a minimum of 20 ug of DNA at a concentration of 50 ng/ul of DNA with a minimum volume of
400 ul.
• Other specimens: Buccal brushes and paraffin embedded tissue CANNOT be used for this testing.
• Prenatal Diagnosis (for specific known mutation(s) or deletion(s) only): For prenatal testing for a
known pathogenic variant in a gene on this panel, please refer to the specimen requirements table on our
website at: http://ww.genedx.com/test-catalog/prenatal/. Ship specimen overnight at ambient temperature,
using a cool pack in hot weather.
Test
689
9011/9012/9013
441
902
Description
Microcephaly Panel
DNA sequencing of a relative for one/two/three specific
known variant(s)
Deletion/duplication testing of a relative for specific known deletion or
duplication
Prenatal diagnosis for specific known pathogenic variant(s)
References: 1. Ashwal et al., (2009) Neurology 73: 887-897. 2. Kaindl et al., (2010) Progress in Neurobiology 90:363-383. 3. Passemard et al.,
(2009) Primary Autosomal Recessive Microcephaly. In : GeneReviews at GeneTests: Medical Genetics Information Resource (database online).
Copyright, University of Washington, Seattle. 1997-2010. Available at http://www.genetests.org. 4. Woods CG (2004) Current Opinion in
Neurobiology 14:112-117. 5. Abuelo, D (2007) Semin Pediatr Neurol 14:118-127. 6. Thornton GK and Woods CG (2009) Trends in Genetics
25(11):501-510.
Information Sheet on Microcephaly Panel
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© GeneDx Revision Date: 12/2015
Genes Associated with Non-syndromic Microcephaly
Disorder
Gene
MCPH1
WDR62
(MCPH2)
CDK5RAP2
(MCPH3)
Primary Microcephaly
(Types 1-7)
CEP152
(MCPH9 ;
previously
MCPH4)
ASPM
(MCPH5)
CENPJ
(MCPH6)
STIL
(MCPH7)
Protein
Microcephalin
Inh.
AR
Diagnostic Yield in Selected Population(s)
<5% of MCPH1
WD repeat-containing protein 62
AR
Rare2
Cyclin-dependent kinase 5
regulatory subunit associated
protein 2
AR
<5% of MCPH1
Centrosomal protein of 152 kDa
AR
Rare for MCPH3
Rare in Seckel syndrome4
AR
37-54% of MCPH1
AR
<5% of MCPH1
Rare in Seckel syndrome5
AR
<5% of MCPH1
Abnormal spindle-like,
microcephaly-associated protein
Centromeric associated protein
J
SCL/TAL1-interrupting locus
protein
Alpha-Thalassemia
Intellectual Disability
Syndrome
ATRX
Transcriptional regulator ATRX
XL
~25% in ATRX6
Amish Lethal
Microcephaly
SLC25A19
Nuclear mitochondrial
deoxynucleotide carrier
AR
100% in Old Order Amish population7
Otherwise rare
Complex Cortical
Dysplasia, with Other
Brain Malformations
(CDCBM)
TUBB3
Tubulin beta-3
AD
Rare8
Mental Retardation
and Microcephaly with
Pontine and Cerebellar
Hypoplasia
CASK
Calcium/calmodulin-dependent
serine protein kinase
XL
~4% in cerebellar hypoplasia and intellectual
9-11
disability
References: 1. Passemard et al., (2009) Primary Autosomal Recessive Microcephaly. In: GeneReviews at GeneTests: Medical Genetics
Information Resource (database online). Copyright, University of Washington, Seattle. 1997-2010. Available at http://www.genetests.org. 2. Yu
et al., (2010) Nat Genet 42(11):1015-20. 3. Guernsey et al., (2010) Am J Hum Genet 87(1):40-51. 4. Kalay et al., (2011) Nat Genet 43(1):23-26.
5. Al-Dosari et al., (2010) J Med Genet 47:411-414. 6. Badens et al., (2006) Clin Genet 70(1):57-62. 7. Dunckelmann et al., (2000)
Neuropediatrics 31:35-8. 8. Poirier et al., (2010) Hum Mol Genet 19:4462–4473. 9. Najm et al., (2008) Nat Genet Sep;40(9):1065-7. 10.
Hackett et al., (2010) Eur J Hum Genet May;18(5):544-52. 11. Burglen et al., (2012) Orphanet J Rare Dis Mar 27;7:18.
Information Sheet on Microcephaly Panel
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© GeneDx Revision Date: 12/2015
Genes Associated with Syndromic Microcephaly
Syndrome
Gene
Protein
Inh.
Diagnostic Yield in Selected
Populations
88% females with Rett syndrome1
2-8% females with atypical Rett
syndrome2,3
MECP2
Methyl CpG binding protein 2
XL
CDKL5
Cyclin-dependent kinase-like 5
XL
FOXG1**
Forkhead box protein G1
AD
~1% Rett syndrome overall4
25% congenital variant of Rett5
UBE3A
Ubiquitin protein ligase E3A
AD
11% Angelman syndrome6
SLC9A6
Sodium/hydrogen exchanger 6
XL
6% Angelman-like syndrome7
TCF4
Transcription factor 4
AD
36% Pitt-Hopkins syndrome (PHS)8
2% Angelman syndrome8
Cornelia de Lange
syndrome
NIPBL
Delangin
AD
~37-47% Cornelia de lange syndrome
(CdLS)9-11
Feingold syndrome
MYCN***
N-myc proto-oncogene protein
AD
~65-75% Feingold syndrome12-14
Mowat-Wilson syndrome
ZEB2*
Zinc finger E-box-binding
homeobox 2
AD
95% Mowat Wilson syndrome15-16
Microcephaly with
simplified gyral pattern,
epilepsy and permanent
neonatal diabetes
syndrome (MEDS)
IER3IP1
Immediate-early response 3interacting protein 1
AR
Unknown17-18
ATR
Ataxia-telangiectasia and Rad3related protein
AR
Unknown19
PCNT
Pericentrin
AR
~30% in Seckel syndrome20 100% in
Microcephalic Osteodysplastic Primoridal
Dwarfism type II (MOPDII)20,21
RBBP8
CTBP interacting protein
AR
Unknown22,23
Smith-Lemli Opitz
syndrome
DHCR7
7-dehydrocholesterol reductase
AR
~95% Smith Lemli Opitz (one or both
variants)24
Warburg Micro Syndrome
RAB18
RAS-associated protein
AR
Rare25
AR
~67% Warburg micro syndrome26
AR
Unknown in Warburg micro syndrome27
Unknown in Martsolf syndrome28
Typical/Atypical Rett
syndromes
Angelman/
Angelman-like/
Pitt-Hopkins syndromes
Seckel syndrome
RAB3GAP1
RAB3GAP2
Rab3 GTPase-activating protein
(catalytic subunit)
Rab3 GTPase-activating protein
(non-catalytic subunit)
* No sequencing of exon 10 of the ZEB2 gene.
** This panel does not include deletion/duplication testing of FOXG1.
***Deletion/duplication of the MYCN gene is performed by MS-MLPA.
References: 1. Li et al., (2006) J Hum Genet 52:38-47. 2. Tao et al., (2004) Am J Hum Genet 75:1149-1154. 3. Rosas-Vargas et al., (2008) J
Med Genet 45:172-178. 4. Bahi-Buisson et al., (2010) 11:241-249. 5. Mencarelli et al., (2010) J Med Genet 47:49-53. 6. Lossie et al., (2001) J
Med Genet 38(12):834-845. 7. Gillfillan et al., (2008) Am J Hum Genet 82:1003-1010. 8. de Pontual et al., (2009) Hum Mutat 30:669-676.
9. Pie et al., (2010) Am J Med Genet 152A(4):924-929. 10. Selicorni et al., (2007) Clin Genet 72:98-108. 11. Gillis et al. (2004) Am J Hum
Genet 75:610-623. 12. Marcelis et al., (2008) Human Mutation 29(9):1125-1132. 13. Van Bokhoven et al., (2005) Nat Genet 37:465-467. 14.
Teszas et al., (2006) Am J Med Genet 140A:2254-56. 15. Wilson et al., (2003) Am J Med Genet 119A:257-265. 16. Zweier et al., (2005) Eur J
Med Genet 48:97-111. 17. DeWit et al., (2006) Neurogenetics 7:259-263. 18. Poulton et al. (2011) Am J Hum Genet 89: 265-276. 19. O’Driscoll
et al., (2003) Nature Genetics 33: 495-501. 20. Willems et al., (2010) J Med Genet 47: 797-802. 21. Rauch et al., (2008) Science 319:816-819.
22. Borglum et al., (2001) Eur J Hum Genet 9:753-757. 23. Qvist et al., (2011) PLoS Genet 7:e1002310. 24. Witsch-Baumgartner et al. (2000)
Am J Hum Genet 66:402-412. 25. Bern et al., (2011) Am J Hum Genet 129:45-50. 26. Aligianis et al., (2005) Nat Genet 37:211-223. 27. Borck
et al., (2011) Hum Genet 129:45-50. 28. Aligianis et al., (2006) Am J Hum Genet 78:702-7.
Information Sheet on Microcephaly Panel
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© GeneDx Revision Date: 12/2015