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Brunner Syndrome via MAOA Gene Sequencing with CNV Detection

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

Sequencing with CNV

Test Code Test Copy GenesPriceCPT Code Copy CPT Codes
10697 MAOA$890 81479,81479 Add to Order
Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

For Sanger Sequencing click here.
Targeted Testing

For ordering sequencing of targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 26 days.

Clinical Sensitivity

Only a handful of individuals have been identified with Brunner syndrome despite widespread screening of X-linked intellectual disability cohorts, suggesting it is a rare X-linked disorder (Bortolato et al. 2018. PubMed ID: 29748850; Brunner et al. 1993. PubMed ID: 8211186; Palmer et al. 2016. PubMed ID: 25807999). Since this test covers all protein coding exons of MAOA, its analytical sensitivity to detect protein truncating or missense variants is presumed to be nearly 100%.

With respect to autism spectrum disorder (ASD) phenotypes, genetic evaluation of ASD patients is estimated to identify a cause in up to 40% of cases. The combined diagnostic yield of chromosomal microarray testing and FMR1 CGG-repeat expansion testing is approximately 11%-15% (Schaefer and Mendelsohn. 2013. PubMed ID: 23519317). The role of nucleotide substitutions and small insertions/deletions in autism-related genes is less clear, but may be as high at 15%, depending on the penetrance of the candidates (Schaefer and Mendelsohn. 2013. PubMed ID: 23519317; Casanova et al. 2016. PubMed ID: 26985359). To date, almost 1,000 genes have documented associations with ASD. It has been reported that nearly 60% of the total variation occurs in approximately 200 genes each of which have several ASD-associated variants (Stenson et al. 2014. PubMed ID: 24077912).

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Clinical Features

Brunner syndrome is a rare neurodevelopmental disorder characterized by intellectual disability, autism spectrum disorder (ASD), and impulsive, aggressive behavioral outbursts trigged by a reaction to stress. Individuals also present with reduced 5-hydroxyindolacetic acid (5-HIAA, a metabolite of serotonin), homovanillic acid (HVA), and vanillylmandelic acid (VMA), and increased serotonin levels in urine (Brunner et al. 1993. PubMed ID: 8211186; Palmer et al. 2016. PubMed ID: 25807999; Bortolato et al. 2018. PubMed ID: 29748850). In at least one family, aggressive outbursts have been associated with the consumption of foods and drinks high in tyramine (beer, cheese, foods with yeast extract). Symptoms were ameliorated by treatment with a selective serotonin reuptake inhibitor (SSRI) and dietary restriction of tyramine. As such, SSRIs have been suggested as a treatment option for some individuals with Brunner syndrome (Palmer et al. 2016. PubMed ID: 25807999).

Features of Brunner syndrome have also been reported with other neurodevelopmental disorders having additional clinical features. These include MAO deletion syndrome (sudden loss of muscle tone) and atypical Norrie disease (congenital blindness) (Saito et al. 2014. PubMed ID: 23414621; Bortolato et al. 2018. PubMed ID: 29748850).

ASD encompasses several neurodevelopmental disorders characterized by varying degrees of social impairment, communication ability, and propensity for restricted interests and repetitive behavior(s) (Levy et al. 2009. PubMed ID: 19819542). ASD usually presents by age 3. Diagnosis is based on the degree and severity of symptoms and behaviors (Diagnostic and Statistical Manual of Mental Disorders (DSM-5); McPartland et al. 2016). Comorbidities occur in more than 70% of cases and include intellectual disability (ID), epilepsy, language deficits, and gastrointestinal problems (Sztainberg and Zoghbi. 2016. PubMed ID: 27786181). Recent studies using whole exome trios have identified novel gene candidates, with familial and de novo variants from several hundred genes now implicated in the development of ASD (Bourgeron. 2016. PubMed ID: 27289453).

Genetics

Pathogenic variants in the X-linked MAOA gene cause Brunner syndrome. Missense, nonsense, and frameshift variants inherited by affected males from their carrier mothers have been exclusively reported (no de novo cases have been reported). Females heterozygous for MAOA pathogenic variants do not present with the hallmark behavioral features of Brunner syndrome (Bortolato et al. 2018. PubMed ID: 29748850). Multi-gene deletions including MAOA have been reported in individuals presenting with MAO deletion syndrome (deletion of both monoamine oxidases, MAOA and MAOB) and atypical Norrie disease (deletion of MAOA, MAOB, and NDP) (Saito et al. 2014. PubMed ID: 23414621; Suárez-Merino et al. 2001. PubMed ID: 11385715; Bortolato et al. 2018. PubMed ID: 29748850).

MAOA (monoamine oxidase A) encodes one of two monoamine oxidases that catalyze the metabolism of neurotransmitters including dopamine, norepinephrine, serotonin, and minor amines such as tyramine (Palmer et al. 2016. PubMed ID: 25807999; Bortolato et al. 2018. PubMed ID: 29748850; Saito et al. 2014. PubMed ID: 23414621). Buildup of these compounds can be neurotoxic, and defects in their metabolism have been suggested to impact behavior (Bortolato et al. 2018. PubMed ID: 29748850; Brunner et al. 1993. PubMed ID: 8211186). Mutant forms of MAOA may selectively metabolize certain neurotransmitters more effectively than others. For example, build-up of serotonin (resulting in serotonin syndrome features) has been reported in some, but not all individuals with Brunner syndrome (Palmer et al. 2016. PubMed ID: 25807999; Nandigama et al. 2001. PubMed ID: 11732903).

Testing Strategy

For this Next Generation Sequencing (NGS) test, 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 regions not captured or with insufficient number of sequence reads.

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.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This test provides full coverage of all coding exons of the MAOA gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

Individuals diagnosed with Brunner syndrome or those presenting with behavioral anomalies and an abnormal urine profile are good candidates for this test. A panel (or exome/genome) sequencing test would nearly always be more appropriate for patients with ASD, behavioral, or neurodevelopmental disorder features, unless previous clinical knowledge of features implicates the MAOA gene. For example, a symptomatic male with affected male siblings or maternal uncles having a known MAOA pathogenic variant and/or clinical features may consider MAOA testing (targeted Sanger sequencing for the known variant may be most appropriate).

Gene

Official Gene Symbol OMIM ID
MAOA 309850
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Monoamine Oxidase A Deficiency XLR 300615

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Autism Spectrum Disorders Sequencing Panel with CNV Detection
X-Linked Intellectual Disability Sequencing Panel with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Bortolato et al. 2018. PubMed ID: 29748850
  • Bourgeron. 2016. PubMed ID: 27289453
  • Brunner et al. 1993. PubMed ID: 8211186
  • Casanova et al. 2016. PubMed ID: 26985359
  • Levy et al. 2009. PubMed ID: 19819542
  • McPartland et al. 2016.
  • Nandigama et al. 2001. PubMed ID: 11732903
  • Palmer et al. 2016. PubMed ID: 25807999
  • Saito et al. 2014. PubMed ID: 23414621
  • Schaefer and Mendelsohn. 2013. PubMed ID: 23519317
  • Stenson et al. 2014. PubMed ID: 24077912
  • Suárez-Merino et al. 2001. PubMed ID: 11385715
  • Sztainberg and Zoghbi. 2016. PubMed ID: 27786181
Order Kits
TEST METHODS

Exome Sequencing with CNV Detection

Test Procedure

For the PGxome we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus ~10 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from patient specimens. Patient DNA corresponding to these regions is captured using Agilent Clinical Research Exome hybridization probes. Captured DNA is sequenced on the NovaSeq 6000 using 2x150 bp paired-end reads (Illumina, San Diego, CA, USA). The following quality control metrics are generally achieved: >97% of target bases are covered at >20x, and mean coverage of target bases >120x. Data analysis and interpretation is performed by the internally developed software Titanium-Exome. In brief, the output data from the NovaSeq 6000 is converted to fastqs by Illumina Bcl2Fastq, and mapped by BWA. Variant calls are made by the GATK Haplotype caller and annotated using in house software and SnpEff. Variants are filtered and annotated using VarSeq (www.goldenhelix.com).

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.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

Analytical Validity

NextGen Sequencing: 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.

Copy Number Variant Analysis: The PGxome test detects most larger deletions and duplications including intragenic CNVs and large cytogenetic events; however aberrations in a small percentage of regions may not be accurately detected due to sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size (e.g., 1-3 exons vs. 4 or more exons), and inadequate coverage. In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of four exon size or larger is >95%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region.

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 sequencing does not reveal any heterozygous differences from the reference sequence, we cannot be certain that we were able to detect both patient alleles.

For technical reasons, the PGxome test is not 100% sensitive. Some exons cannot be efficiently captured, and some genes cannot be accurately sequenced because of the presence of multiple copies in the genome. Therefore, a small fraction of sequence variants will not be detected.

We sequence coding exons for most given transcripts, plus ~10 bp of flanking non-coding DNA for each exon. Unless specifically indicated, test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions, uncharacterized alternative exons, chromosomal rearrangements, repeat expansions, epigenetic effects, and mitochondrial genome variants.

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 amplification.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes if taken 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.

Balanced translocations or inversions are only rarely detected.

Certain types of sex chromosome aneuploidy may not be detected.  

Our ability to detect CNVs due to somatic mosaicism is limited.

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.

A negative finding does not rule out a genetic diagnosis.

Genetic counseling to help to explain test results to the patients and to discuss reproductive options is recommended.

Order Kits

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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