1. NGS panel - Genetic testing for Microcephaly

Microcephaly

July 19, 2017

Clinical features

Seckel syndrome is rare autosomal recessive disorder characterized by intrauterine growth retardation, dwarfism, microcephaly with mental retardation, and a characteristic 'bird-headed' facial appearance. The major feature of Seckel syndrome is associated autosomal recessive primary microcephaly (MCPH). Microcephaly is a neurodevelopmental condition characterized by microcephaly present at birth, decreased cerebral cortex size, and non-progressive mental retardation with the absence of visceral abnormalities.

Primary microcephaly has an incidence of less than 1 (0.68) 10,000 in Australia 1, 1:30,000 in Japan 2, 1:250,000 in Netherlands 2 and 1:2,000,000 in Scotland 2, 3.

Microcephaly is divided into primary microcephaly, which is present at birth, and secondary microcephaly, which develops postnatally 4. The crucial difference between these groupings is that primary microcephaly is usually a static developmental anomaly, whereas secondary microcephaly indicates a progressive neurodegenerative condition 5.

The major clinical features of microcephaly include the following:

  • Prenatal onset, during the second trimester of gestation
  • Reduced occipito-frontal circumference (OFC) at birth (<-2 SD) 3. Microcephaly tends to worsen over time and after 6 months of age OFC is at least -3 SD, while it ranges between -4 and -12 SD (mean -8 SD) in older individuals 3.
  • Reduced volume of the cerebral hemispheres, commonly reduced to one third of normal, while the organization and topography of gyri are normal but the pattern may be simplified
  • Reduced size of hindbrain and cerebellum
  • A significant correlation between the severity of microcephaly and both the degree of simplified gyration and the reduction of white matter volume
  • In cases with more severe microcephaly corpus callosum is thinner 6
  • In some affected individuals neuronal migration is abnormal, resulting in heterotopias, or focal pachygyria or polymicrogyria 7.

Cognitive impairment is present in a majority of persons with microcephaly and it ranges from mild to moderate without major motor delay. More severe cognitive impairment has been observed in individuals with Seckel syndrome and in those with isolated microcephaly with brain malformations 3.

A common finding in microcephaly is also short stature, typically between -1 SD and -2 SD and in Seckel syndrome it ranges between -4 and -12 SD 3. Some affected individuals may develop craniosynostosis, secondary to insufficient and slow head growth.

There are many nongenetic and genetic causes of primary microcephaly, such as maternal alcohol overconsumption during pregnancy, congenital infection with toxoplasma, and Rubenstein Taybi syndrome. Microcephaly can be associated with hundreds of syndromal congenital anomalies, including many chromosomal disorders. Microcephaly is also a frequent sign of defects in DNA repair mechanisms and in nucleotide excision repair, in which it often is associated with general growth impairment.

There are a number of genes which have been associated with microcephaly, including the following genes (see Table):

  • Microcephaly phenotype only: MCPH1 (MCPH1), WDR62 (MCPH2), CDK5RAP2 (MCPH3), KNL1 (MCPH4), ASPM (MCPH5), STIL (MCPH7), CEP135 (MCPH8), and CDK6 (MCPH12)
  • Seckel syndrome phenotype only: ATR (SCKL1), NIN (SCKL7), and ATRIP
  • Microcephaly with Seckel syndrome and/or intermediate phenotypes: RBBP8 (SCKL2), CEP152 (MCPH9/SCKL5), CENPJ (MCPH6/SCKL4), CEP63 (SCKL6), and PHC1 (MCPH11).

Overview of microcephaly and Seckel syndrome associated genes

Gene
(OMIM)
chr. locus Mutation frequency Associated/allelic disorders
AKT3
(611223)
1q43-q44 12/41 for MPPH8 MPPH2 (615937)
AP4M1
(602296)
7q22.1 Five families with SPG9 SPG50 (612936)
ARFGEF2
(605371)
20q13.13 Few families with PHM10 ARPHM (608097)
ASPM
(605481)
1q31.3 25%-50%3 MCPH5 (608716)
ASXL3
(615115)
18q12.1 All cases with BRPS11 BRPS (615485)
ATR
(601215)
3q23 4 families3 SCKL1 (210600); FCTCS (614564)
ATRX
(300032)
Xq21.1 95% for ATRX (males)12 MRXHF1 (309580); ATRX (301040); ATMDS (300448)
CASC5
(609173)
15q15.1 Few families3 MCPH4 (604321)
CASK
(300172)
Xp11.4 >95% for MICPCH13 MICPCH (300749); FGS4 (300422)
CDK5RAP2
(608201)
9q33.2 Few families3 MCPH3 (604804)
CDK6
(603368)
7q21.2 1 family14 MCPH12 (616080)
CENPE
(117143)
4q24 Rare MCPH13 (616051)
CENPF
(600236)
1q41 Rare STROMS (243605)
CENPJ
(609279)
13q12.12-q12.13 <5%15 MCPH6 (608393); SCKL4 (613676)
CEP135
(611423)
4q12 <5%3
Majority of SCKS 3
MCPH8 (614673)
CEP152
(613529)
15q21.1 Rare MCPH9 (614852); SCKL5 (613823)
CEP63
(614724)
3q22.2 1 family for SCKS16 SCKL6 (614728)
CHMP1A
(164010)
16q24.3 Rare PCH8 (614961)
CRIPT
(604594)
2p21 Rare Short stature with microcephaly and distinctive facies (615789)
DYRK1A
(600855)
21q22.13 All cases with MRD717 MRD7 (614104)
EFTUD2
(603892)
17q21.31 >95% for MFDGA18 MFDGA (610536)
IER3IP1
(609382)
18q21.1 Rare MEDS (614231)
KATNB1
(602703)
16q21 Rare LIS6 (616212)
KIF11
(148760)
10q23.33 Few families19 MCLMR (152950)
MCPH1
(607117)
8p23.1 <10%3 MCPH1 (251200)
MED17
(603810)
11q21 Rare Microcephaly, postnatal progressive, with seizures and brain atrophy (613668)
MFSD2A
(614397)
1p34.2 Rare MCPH15 (616486)
MSMO1
(607545)
4q32.3 Rare MCCPD (616834)
NDE1
(609449)
16p13.11 Few individuals3 MHAC (605013); LIS4 (614019)
NHEJ1
(611290)
2q35 Few families3 SCID with microcephaly (611291)
NIN
(608684)
14q22.1 2 patients20 SCKL7 (614851)
ORC1
(601902)
1p32.3 Few families21 MGORS1 (224690)
PCNT
(605925)
21q22.3 Few individuals3 MOPD2 (210720)
PHC1
(602978)
12p13.31 Few families3 MCPH11 (615414)
PLK4
(605031)
4q28.1 Few individuals22 MCCRP2 (616171)
PNKP
(605610)
19q13.33 Six unrelated families23 MCSZ (613402); AOA4 (616267)
PYCR2
(616406)
1q42.12 Few individuals24 HLD10 (616420)
QARS
(603727)
3p21.31 Rare MSCCA (615760)
RBBP8
(604124)
18q11.2 2 families with JWDS25 SCKL2 (606744); JWDS (251255)
SASS6
(609321)
1p21.2 Rare MCPH14 (616402)
SLC25A19
(606521)
17q25.1 100% for Amish MCPH26 MCPHA (607196); THMD4 (613710)
STAMBP
(606247)
2p13.1 All MICCAP cases27 MICCAP (614261)
STIL
(181590)
1p33 Common in Indian population 28 MCPH7 (612703)
TRMT10A
(616013)
4q23 Rare MSSGM1 (616033)
TUBB2B
(612850)
6p25.2 Few individuals3 PMGYSA (610031)
TUBGCP4
(609610)
15q15.3 Few families29 MCCRP3 (616335)
TUBGCP6
(610053)
22q13.33 Few families30 MCCRP1 (251270)
WDR62
(613583)
19q13.12 <10%3 MCPH2 (604317)
ZEB2
(605802)
2q22.3 All cases with MOWS31 MOWS (235730)
ZNF335
(610827)
20q13.12 1 large family32 MCPH10 (615095)

Abbreviations: MPPH-Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome; SPG-Spastic paraplegia; ARPHM-Autosomal recessive periventricular heterotopia with microcephaly; BRPS-Bainbridge-Ropers syndrome; SCKL-Seckel syndrome; FCTCS-Familial cutaneous telangiectasia and cancer syndrome; MRXHF-Mental retardation-hypotonic facies syndrome; ATRX-Alpha-thalassemia/mental retardation syndrome ATMDS-Alpha-thalassemia myelodysplasia syndrome, somatic; MICPCH-Mental retardation and microcephaly with pontine and cerebellar hypoplasia; FGS-FG syndrome; PCH-Pontocerebellar hypoplasia; MRD-Mental retardation autosomal dominant; MFDGA-Mandibulofacial dysostosis Guion-Almeida type; MEDS-Microcephaly, epilepsy, and diabetes syndrome; LIS-Lissencephaly; MCCPD-Microcephaly, congenital cataract, and psoriasiform dermatitis; MHAC-Microhydranencephaly; SCID-Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation; MCCRP-Microcephaly and chorioretinopathy; MCSZ-Microcephaly, seizures, and developmental delay; AOA-Ataxia-oculomotor apraxia; HLD-Hypomyelinating leukodystrophy; JWDS-Jawad syndrome; THMD-Thiamine metabolism dysfunction syndrome; MICCAP-Microcephaly-capillary malformation syndrome; MSSGM-Microcephaly, short stature, and impaired glucose metabolism; PMGYSA-Polymicrogyria, symmetric or asymmetric; MOWS-Mowat-Wilson syndrome.

Treatment for patients affected with microcephaly commonly includes supportive therapy, including special education, speech and language therapy, behavioral therapy, occupational therapy, and community services for families. Ritalin® may be helpful in managing hyperkinesia 3. Seizures are usually responsive to monotherapy with standard antiepileptic drugs (AEDs).

CENTOGENE offers full gene sequencing and deletion/duplication analysis for the Microcephaly panel (genes: AKT3, AP4M1, ARFGEF2, ASPM, ASXL3, ATR, ATRX, CASC5, CASK, CDK5RAP2, CDK6, CENPE, CENPF, CENPJ, CEP135, CEP152, CEP63, CHMP1A, CRIPT, DYRK1A, EFTUD2, IER3IP1, KATNB1, KIF11, MCPH1, MED17, MFSD2A, MSMO1, NDE1, NHEJ1, NIN, ORC1, PCNT, PHC1, PLK4, PNKP, PYCR2, QARS, RBBP8, SASS6, SLC25A19, STAMBP, STIL, TRMT10A, TUBB2B, TUBGCP4, TUBGCP6, WDR62, ZEB2, ZNF335).


Differential diagnosis

The differential diagnosis of microcephaly-related disorders – depending on the major symptoms in the initial case – includes the following diseases:

  • Anencephaly
  • Down Syndrome
  • Fetal Alcohol Syndrome
  • Pediatric Craniosynostosis
  • Rett Syndrome
  • Spina Bifida

Testing strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for microcephaly using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the microcephaly panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the microcephaly panel, we recommend continuing the bioinformatics analysis of the data obtained through whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.


Referral reasons

The following individuals are candidates for microcephaly testing:

  • Individuals with a family history of microcephaly and presentation of the most common symptoms
  • Individuals without a positive family history, but with symptoms resembling microcephaly
  • Individuals with a negative but suspected family history of microcephaly, in order to perform proper genetic counseling.

Test utility

Sequencing, deletion/duplication of the panel genes should be performed in all individuals suspected of having microcephaly and suspected phenotypes. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of the microcephaly and related disorders identify at-risk family members, provide disease risks as well as appropriate referral for patient support and/or resources.


More information on CENTOGENE´s Microcephaly panel can be found in our genetic test catalogue.