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Barth Syndrome via TAZ 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
8525 TAZ$890 81406,81479 Add to Order

New York State Approved Test

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. If the Sanger option is selected, CNV detection may be ordered through Test #600.

The Sanger Sequencing method for this test is NY State approved.

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

The majority of Barth Syndrome patients have mutations in TAZ (Johnston et al. Am J Hum Genet 61:1053-1058, 1997; Spencer et al. Pediatrics 118:e337-46, 2006).

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Clinical Features

Barth syndrome (BTHS, OMIM 302060) is a rare X-linked disorder of lipid metabolism. Symptoms typically present within the first year of life. Boys with BTHS generally present with skeletal myopathy and abnormal mitochondria along with either dilated cardiomyopathy (DCM, OMIM 115200), left ventricular noncompaction (LVNC, OMIM 300183) or endocardial fibroelastosis (EFE, OMIM 305300) (Barth et al. Neurol Sci 62:327-355, 1983). Additional features include growth delay and elevated urinary 3-methylglutaconic acid and 2-ethylhydracrylic acid. Patients with BTHS are also at risk for bacterial infection due to neutropenia.

Genetics

Barth Syndrome (BTHS) is inherited in an X-linked recessive manner and primarily affects boys with carrier females being asymptomatic. BTHS results from mutations in TAZ, which encodes for the protein tafazzin. Tafazzin is important for the synthesis of cardiolipins and mitochondrial function. Mutations in TAZ can result in a wide-spectrum of cardiomyopathies, including DCM and LVNC without other symptoms associated with Barth Syndrome. (Bione et al. Nat Genet 12:385-389, 1996; D’Adamo et al. J Hum Genet 61:862-867, 1997; Bleyl et al. Am J Med Genet 72:257-265, 1997; Ichida et al. Circulation 103:1256-1263, 2001). Over 100 mutations in TAZ have been identified throughout the entire coding region. The majority of causative variants are missense, nonsense, and splice site mutations. Small insertions and deletions have also been found in patients with BTHS, DCM or LVNC.

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 TAZ gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. 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

Patients with symptoms suggestive of Barth Syndrome. TAZ testing should be considered when males present with cardiomyopathy (DCM or LVNC) along with neutropenia or skeletal muscle weakness.

Gene

Official Gene Symbol OMIM ID
TAZ 300394
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
3-Methylglutaconic Aciduria Type 2 XL 302060

Related Tests

Name
Comprehensive Cardiology Sequencing Panel with CNV Detection
Dilated Cardiomyopathy Sequencing Panel with CNV Detection
Left Ventricular Noncompaction (LVNC) Sequencing Panel with CNV Detection
Pan Cardiomyopathy Sequencing Panel with CNV Detection
Severe Congenital Neutropenia and Neutrophilia via CSF3R Gene Sequencing with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Barth, P. G., et.al. (1983). "An X-linked mitochondrial disease affecting cardiac muscle, skeletal muscle and neutrophil leucocytes." J Neurol Sci 62(1-3): 327-55. PubMed ID: 6142097
  • Bione S, D’Adamo P, Maestrini E, Gedeon AK, Bolhuis PA, Toniolo D. 1996. A novel X-linked gene, G4.5. is responsible for Barth syndrome. Nat. Genet. 12: 385–389. PubMed ID: 8630491
  • Bleyl, S. B., et.al. (1997). "Xq28-linked noncompaction of the left ventricular myocardium: prenatal diagnosis and pathologic analysis of affected individuals." Am J Med Genet 72(3): 257-65. PubMed ID: 9332651
  • D'Adamo, P., et.al. (1997). "The X-linked gene G4.5 is responsible for different infantile dilated cardiomyopathies." Am J Hum Genet 61(4): 862-7. PubMed ID: 9382096
  • Ichida, F., et.al. (2001). "Novel gene mutations in patients with left ventricular noncompaction or Barth syndrome." Circulation 103(9): 1256-63. PubMed ID: 11238270
  • Johnston J, Kelley RI, Feigenbaum A, Cox GF, Iyer GS, Funanage VL, Proujansky R. (1997). Mutation characterization and genotype-phenotype correlation in Barth syndrome. Am J Hum Genet 61(5):1053-8. PubMed ID: 9345098
  • Spencer CT, Bryant RM, Day J, Gonzalez IL, Colan SD, Thompson WR, Berthy J, Redfearn SP, Byrne BJ. (2006). Cardiac and clinical phenotype in Barth syndrome. Pediatrics 118(2):e337-46. PubMed ID: 16847078
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TEST METHODS

Exome Sequencing with CNV Detection

Test Procedure

For PGxome® we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus 10 bases of flanking non-coding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. 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 all available transcripts plus 10 bp of flanking non-coding DNA for each exon. We also sequence other regions within or near genes in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere.  Unless specifically indicated, test reports contain no information about other portions of genes.

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.

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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.

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