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Aicardi-Goutières Syndrome 7 and Singleton-Merton Syndrome 1 via the IFIH1 Gene

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

NGS Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
3819 IFIH1$690.00 81479 Add to Order
Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information.

For Sanger Sequencing click here.
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 28 days.

Clinical Sensitivity

Approximately 3% of Aicardi-Goutières Syndrome is due to heterozygous missense variants in the IFIH1 gene (Crow et al. 2015). It is difficult to estimate the clinical sensitivity of sequencing for Singleton-Merton Syndrome 1. It is a rare disorder with only three index cases reported in the literature. For these cases, the causative variants were all detectable by sequencing. Due to the heterogeneity of clinical features, the prevalence of IFIH1 pathogenic variants in the population is currently unknown.

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Clinical Features

Aicardi-Goutières Syndrome 7 is a phenotypically heterogeneous inflammatory disorder linked to inappropriate upregulation of Type I interferon. The symptoms can appear similar to those of neonatal Aicardi-Goutières Syndrome 1, which include irritability, hepatomegaly with elevated liver enzymes, and thrombocytopenia. In one alternate form of the disease, developmental progress is normal until 13-15 months of age, at which point rapid neurological regression occurs. A third type of the condition involves only spastic paraparesis, with adult patients displaying normal neuroimaging (Rice et al. 2014). A heightened state of inflammation affecting blood vessels, teeth and bones is present in Singleton-Merton syndrome 1 (SMS1). This rare autosomal dominant disorder can cause severe childhood aortic and valvular calcification, dental anomalies and skeletal abnormalities such as osteoporosis and osteolysis. Less commonly, affected individuals may have generalized muscle weakness, psoriasis, early onset glaucoma, and particular facial features. (Feigenbaum et al. 2013).

Genetics

An atypical form of Aicardi-Goutieres Syndrome (Aicardi-Goutieres 7) and SMS1 are both caused by autosomal dominant pathogenic variants in IFIH1. This gene encodes a cytoplasmic protein that senses double-stranded viral RNAs and mediates an immune activation. Heterozygous IFIH1 missense variants have been detected in 15 individuals from 13 families with atypical Aicardi-Goutieres syndrome (Crow et al. 2015; Rice at al. 2009; Oda et al. 2014). Most IFIH1 variants are located within the Hel1 and Hel2 helicase domains of the IFIH1 protein. Functional studies indicate that the variants are gain of function variants because they confer an induction of interferon activity that is consistently higher than in mutation-negative family members. Testing of parental samples demonstrated that the pathogenic variants arose de novo in the majority of patients. In one family, a mutation positive father with an affected son was not clinically affected, a finding that indicates that IFIH1 pathogenic variants may not be fully penetrant.

Whole exome sequencing identified a unique IFIH1 missense variant in a patient with SMS1. This variant was also located in the Hel2 helicase domain, displayed an autosomal dominant mode of transmission, and was linked to upregulation of interferon. Sanger sequencing identified the presence of this variant in additional family members of the proband and in two other SMS1 families. In one family, the IFIH1 pathogenic variant appeared to have arisen de novo. In two other SMS1 families, no unaffected member was found to possess the pathogenic variant, and the pathogenic variant segregated with the disorder, though disease symptoms and severity differed among affected family members. (Rutch et al 2015). The clinical variability in Aicardi-Goutières Syndrome 7 and SMS1 families suggests that external factors such as differential pathogen exposure or other genetic or epigenetic influences may modify the penetrance of IFIH1 pathogenic variants. A separate clinical disorder, Singleton-Merton syndrome 2, shares many clinical features with SMS1 but is linked to pathogenic variants in DDX58. The protein product of DDX58 also functions as an double-stranded RNA sensor that up regulates type 1 interferon through the same pathway as IFIH1 (Jang et al. 2015).

The observation of the inflammatory nature of IFIH1 gain of function pathogenic variants suggests that the pathology of the associated disorders is progressive. Early treatment may therefore result in disease attenuation. Antibodies targeted against interferon alpha subtypes and the type I interferon receptor are in clinical trials for a related immune disorder (Crow et al. 2013).

Testing Strategy

For this NextGen test, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for the gene listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Indications for Test

Patients with clinical features consistent with AGS, chronic leukocytosis, and increased interferon-alpha (INF-a) and neopterin in Cerebrospinal fluid.

Gene

Official Gene Symbol OMIM ID
IFIH1 606951
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
Aicardi-Goutieres Syndrome 7 AD 615846
Singleton-Merten Syndrome 1 AD 182250

Related Tests

Name
Aicardi-Goutières Syndrome Sequencing Panel
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Crow Y.J. et al. 2014. Clinical and Experimental Immunology. 175: 1-8. PubMed ID: 23607857
  • Crow Y.J. et al. 2015. American Journal of Medical Genetics. Part A. 167A: 296-312. PubMed ID: 25604658
  • Feigenbaum A. et al. 2013. . American Journal of Medical Genetics. Part A. 161A: 360–70. PubMed ID: 23322711
  • Jang M.A. et al. 2015. American Journal of Human Genetics. 96: 266-74. PubMed ID: 25620203
  • Oda H. et al. 2014. American Journal of Human Genetics. 95: 121-5. PubMed ID: 24995871
  • Rice G.I. et al. 2014. Nature Genetics. 46: 503-9. PubMed ID: 24686847
  • Rutsch F. et al. 2015. American Journal of Human Genetics. 96: 275-82. PubMed ID: 25620204
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TEST METHODS

NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most 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 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.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

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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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