1. NGS panel - Genetic testing for Aicardi-Goutieres syndrome

Aicardi-Goutieres syndrome

May 30, 2017

Clinical features

Aicardi-Goutieres syndrome is a rare inherited disorder that mainly affects the brain, immune system, and skin. Most characteristically, Aicardi-Goutières syndrome (AGS) manifests as an early-onset encephalopathy which results in severe intellectual and physical disabilities. Many affected infants present at birth with abnormal neurologic findings, hepatosplenomegaly, thrombocytopenia (clinical findings frequently suggestive of congenital infection). Otherwise, newborns have a short phase of normal development, after which they start to show subacute onset of a severe encephalopathy characterized by slowing of head growth, extreme irritability, and loss of previously learned skills. Soon thereafter, many affected infants (~40% 1) develop chilblain skin lesions on their fingers, toes, and ears. It is becoming apparent that atypical, sometimes milder, cases of AGS also exist.

Aicardi-Goutières syndrome can be considered an early-onset encephalopathy accompanied by intellectual and physical disabilities, and it should be suspected in individuals with the following clinical and other findings:

  • Encephalopathy and/or significant intellectual disability
  • Acquired microcephaly during the first year of life
  • Dystonia and spasticity
  • Sterile pyrexias (increased body temperature without infective agents)
  • Hepatosplenomegaly (enlarged liver and spleen)
  • Chilblain lesions on the skin of the feet, hands, ears, and/or more generalized
  • Neuroimaging shows calcification of the basal ganglia, cerebral atrophy, which may be progressive, cerebellar atrophy and brain stem atrophy, bilateral striatal necrosis and intracerebral vasculopathy
  • Peripheral blood findings include positive interferon (IFN) signature, elevated liver enzymes, and thrombocytopenia
  • Cerebrospinal fluid (CSF) shows the presence of chronic CSF leukocytosis, elevated concentrations of IFN-α, increased concentration of neopterin (purine nucleotide, indicator of pro-inflammatory immune status).

Aside from characteristic clinical features, AGS cannot be diagnosed purely based on clinical and laboratory/imaging findings. Many forms of AGS have a genetic background and thus analysis of AGS-associated genes has become a routine part of the diagnostic procedure. Genes closely associated with AGS include the following: ADAR, IFIH1, TREX1, RNASEH2A, RNASEH2B, RNASEH2C, and SAMHD1 (Table 1).


Overview of the genes in CENTOGENE´s Aicardi-Goutieres syndrome panel

Gene
Protein
OMIM
chr. locus
% of mutations Allelic and associated disorders
(OMIM)
ADAR
Adenosine deaminase RNA-specific
146920
1q21.3
7%2 Aicardi-Goutieres syndrome 6 (615010)
Dyschromatosis symmetrica hereditaria (127400)
IFIH1
Interferone-induced helicase
60695
2q24.2
3% Aicardi-Goutieres syndrome 7 (615846)
Singleton-Merten syndrome 1 (182250)
TREX1
DNASe III
606609
3p21.31
23% Aicardi-Goutieres syndrome 1 (225750)
Chilblain lupus (610448)
Vasculopathy, retinal, with cerebral leukodystrophy (192315)
RNASEH2A
Ribonuclease H2 subunit A
606034
19p13.13
5% Aicardi-Goutieres syndrome 4 (610333)
RNASEH2B
Ribonuclease H2 subunit B
620326
13q14.3
36% Aicardi-Goutieres syndrome 2 (610181)
RNASEH2C
Ribonuclease H2 subunit C
610330
11q13.1
12% Aicardi-Goutieres syndrome 3 (610329)
SAMHD1
Ribonuclease H2 subunit A
606754
20q11.23
13% Aicardi-Goutieres syndrome 5 (612952)
Chilblain lupus 2 (614415)

The majority of pathogenic variants in the ADAR gene result in autosomal recessive disease. Missense, nonsense, frameshift, and splice site pathogenic variants have been reported. One missense variant, p.Pro193Ala, is common in individuals of European origin 1, 3. One dominant variant, p.Gly1007Arg, has been reported 3, 4.

All IFIH1 pathogenic variants associated with AGS to date have been missense variants that cause dominant disease. IFIH1 encodes the interferon-induced helicase C domain-containing protein 1, a cytosolic double-stranded RNA receptor 1, 2.

The majority of pathogenic variants in RNASEH2A are missense; but splicing and frameshift pathogenic variants have also been reported 2, 3.

The frequency of some RNASEH2B alleles identified in affected individuals is determined 3:

  • p.Ala177Thr (62%)3
  • p.Thr163Ile (7%)3
  • p.Val185Gly (7%)3
  • c.136+1delG (4%)3.

All pathogenic variants identified in RNASEH2C so far are missense 5 and one of the RNASEH2C alleles has the highest frequency: ~72% for p.Arg69Trp 2, 3.

The majority of pathogenic variants in the SAMHD1 gene are missense, splice site, nonsense, or frameshift variants 6. A recurrent deletion including exon 1 has been observed in several affected individuals of Ashkenazi Jewish ancestry and it is considered a founder variant 7. Furthermore, a recurrent splice acceptor site pathogenic variant (c.1411-2A>G) in intron 12 is seen in persons of Amish ancestry and represents an ancient founder variant 8.

All pathogenic variants associated with TREX1-related AGS were detectable by sequence analysis. A recurrent p.Arg164Ter founder variant in TREX1 is seen in individuals of Cree ancestry 9. The most prevalent TREX1 variant in AGS is a missense change (p.Arg114His) that is particularly common in people from northern Europe 1, 2, 5.

Treatment of manifestations for AGS mainly includes treatment of respiratory complications as well as chest physiotherapy. Special diet and feeding methods are used to assure adequate caloric intake and avoid aspiration; management of seizures is performed using standard protocols. Clinical trials are in progress with new possible drugs being tested for AGS treatment (for example: Reverse transcriptase inhibitors: Zidovudine, Lamivudine, Abacavir).

CENTOGENE offers the Aicardi-Goutieres syndrome panel, including full gene sequencing (genes: ADAR, IFIH1, TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1) and deletion/duplication analysis of selected genes (RNASEH2B, RNASEH2A, TREX1, RNASEH2C, and SAMHD1). In addition, any of the genes in the Aicardi-Goutieres syndrome panel can also be ordered individually, for full gene sequencing and deletion/duplication analysis.


Differential diagnosis

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

  • TORCH congenital infections
  • Band-like calcification polymicrogyria (BLC-PMG; pseudo-TORCH syndrome)
  • The microcephaly-intracranial calcification syndrome (MICS)
  • Mitochondrial cytopathies, including Leigh syndrome
  • Leukoencephalopathy, brain calcifications, and cysts (Labrune syndrome)
  • Alexander disease, megalencephalic leukoencephalopathy with subcortical cysts, and childhood ataxia with central nervous system hypomyelination/vanishing white matter disease
  • Neonatal lupus erythematosus
  • Classic Cockayne syndrome (CS type 1)
  • Cerebroretinal microangiopathy with calcifications and cysts (CRMCC; Coats plus).

Testing strategy

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

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for Aicardi-Goutieres syndrome 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 Aicardi-Goutieres syndrome panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the Aicardi-Goutieres syndrome panel, based on the approval and consent, we further recommend to continue the bioinformatics analysis of the data obtained by whole genome sequencing to cover genes that are either implicated in an overlapping phenotype or could be involved in a similar pathway but not strongly clinically implicated based on the current information in literature.


Referral reasons

The following individuals are candidates for Aicardi-Goutieres syndrome panel gene testing:

  • Individuals with a family history of Aicardi-Goutieres syndrome and presentation of the most common symptoms such as: early onset encephalopathy, hepatosplenomegaly, thrombocytopenia and others
  • Individuals without a positive family history of Aicardi-Goutieres syndrome, but with symptoms resembling this disease
  • Individuals with a negative but suspected family history for Aicardi-Goutieres syndrome, in order to perform proper genetic counseling (prenatal analyses are recommended in families with affected individuals).

Test utility

Sequencing, deletion/duplication of Aicardi-Goutieres syndrome -related genes (ADAR, IFIH1, TREX1, RNASEH2A, RNASEH2B, RNASEH2C, and SAMHD1) should be performed in all individuals suspected for Aicardi-Goutieres syndrome. 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 Aicardi-Goutieres syndrome-associated genes.

Confirmation of a clinical diagnosis of Aicardi-Goutieres syndrome 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 Aicardi-Goutieres syndrome, to identify at-risk family members, provide reproductive risks as well as possible preventive therapy or preconception/prenatal options, and allow for appropriate referral for patient support and/or resources.


More information on CENTOGENE´s Aicardi-Goutieres syndrome panel can be found in our genetic test catalogue.