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Marfan Syndrome and Related Aortopathies Sequencing Panel with CNV Detection

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

Sequencing and CNV

Test Code Test Copy GenesCPT Code Copy CPT Codes
1212 ACTA2 81405,81479 Add to Order
CBS 81406,81479
COL3A1 81479,81479
COL5A1 81479,81479
COL5A2 81479,81479
EFEMP2 81479,81479
ELN 81479,81479
FBLN5 81479,81479
FBN1 81408,81479
FBN2 81479,81479
FLNA 81479,81479
FOXE3 81479,81479
LOX 81479,81479
MAT2A 81479,81479
MED12 81479,81479
MFAP5 81479,81479
MYH11 81408,81479
MYLK 81479,81479
NOTCH1 81407,81479
PLOD1 81479,81479
PRKG1 81479,81479
SKI 81479,81479
SLC2A10 81479,81479
SMAD3 81479,81479
SMAD4 81406,81405
SMS 81479,81479
TGFB2 81479,81479
TGFB3 81479,81479
TGFBR1 81405,81479
TGFBR2 81405,81479
Full Panel Price* $680
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1212 Genes x (30) $680 81405(x4), 81406(x2), 81407, 81408(x2), 81479(x51) Add to Order

New York State Approved Test

Pricing Comments

CPT codes 81410 and 81411 can be used if analysis includes FBN1, TGFBR1, TGFBR2, COL3A1, MYH11, ACTA2, SLC2A10, SMAD3, and MYLK.

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available.

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

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 20 days.

Clinical Sensitivity

This test is predicted to detect a disease-causing variant in approximately 30% of individuals with familial thoracic aortic aneurysm and dissection (TAAD) (Milewicz and Regalado 2012. PubMed ID: 20301299). FBN1 pathogenic variants have been identified in up to 90% of patients with a clinical diagnosis of Marfan syndrome based on the Ghent nosology (Dietz 2011. PubMed ID: 20301510; Mátyás et al. 2007. PubMed ID: 17492313). FBN2 pathogenic variants have been identified in up to 75% of individuals diagnosed with congenital contractural arachnodactyly (CCA) (Nishimura et al. 2007. PubMed ID: 17345643). More than 95% of patients with clinical findings consistent with Loeys-Dietz have a pathogenic variant in TGFBR1 or TGFBR2 (Loeys and Dietz. 2013. PubMed ID: 20301312). COL3A1 pathogenic variants have been identified in approximately 95% of individuals with Ehlers-Danlos syndrome (EDS) IV (Pepin and Byers. 2011. PubMed ID: 20301667). COL5A1 and COL5A2 pathogenic variants have been identified in at least 50% of affected individuals with classic EDS (Malfait et al. 2011). Twenty-eight out of 29 individuals with Shprintzen-Goldberg syndrome were found to have a pathogenic variant in SKI (Carmignac et al. 2012. PubMed ID: 23103230; Doyle et al. 2012. PubMed ID: 23023332). FLNA pathogenic variants were identified in 26 out of 41 patients with FLNA-related disorders (OPD1, OPD2, FMD, MNS) (Robertson et al. 2003. PubMed ID: 12612583). 95-98% of patients with homocystinuria are found to harbor two pathogenic variants (Gaustadnes et al. 2002. PubMed ID: 12124992; Kruger et al. 2003. PubMed ID: 14635102; Cozar et al. 2011. PubMed ID: 21520339; Karaca et al. 2014. PubMed ID: 24211323). Nine out of 12 individuals with EDS type VIA were found to have a pathogenic variant in PLOD1 (Rohrbach et al. 2011. PubMed ID: 21699693). This test is predicted to detect pathogenic variants in 22%-35% of Supravalvar aortic stenosis patients that do not have gross deletions in the ELN gene (Metcalfe et al. 2000. PubMed ID: 11175284; Micale et al. 2010. PubMed ID: 19844261). Deletions of 7q11.23 which encompasses the ELN gene are commonly found in individuals with Williams syndrome. This NGS test will only detect copy number changes in the ELN gene, therefore we will not be able to determine how many additional genes are deleted in patients with Williams syndrome.

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Clinical Features

This panel tests for syndromic and non-syndromic causes of thoracic aortic aneurysm and dissection (TAAD). TAAD is a life-threatening disease affecting the aorta and is the 15th leading cause of death in the United States (Hoyert et al. 2001. PubMed ID: 11591077). Aortic dissections most commonly originate in the ascending aorta above the aortic valve (Stanford type A), but also can occur in the descending aorta (Stanford type B). Aneurysms in the cerebral and peripheral artery and abdominal aorta have also been observed (Milewicz and Regalado. 2012. PubMed ID: 20301299). An intense sharp pain in the chest is the most common symptom of aortic dissection. Familial TAAD is diagnosed based on the presence of dilatation and/or dissection of the thoracic aorta using imaging studies (MRI, echocardiography, CT), the absence of syndromic conditions that have clinical features that overlap with familial TAAD, and a positive family history. Syndromic forms of TAAD include Marfan syndrome, Loeys-Dietz syndrome, arterial tortuosity syndrome, Shprintzen-Golberg syndrome, congenital contractural arachnodactyly, aneurysms-osteoarthritis syndrome, multisystemic smooth muscle dysfunction syndrome, Ehlers-Danlos syndrome (vascular type, classic type, and kyphoscoliosis form), and periventricular nodular heterotopia.

Lujan syndrome, homocystinuria, and Snyder-Robinson syndrome have phenotypic overlap with Marfan syndrome. Patients with Lujan syndrome have cognitive impairment and marfanoid habitus, and craniofacial dysmorphisms (Lujan et al. 1984. PubMed ID: 6711603; Schwartz et al. 2007. PubMed ID: 17369503). Classic homocystinuria symptoms include developmental delay or intellectual disability, ectopia lentis and/or severe myopia, skeletal abnormalities, osteoporosis, and vascular disease, including potentially fatal thromboembolisms (Kraus et al. 1999. PubMed ID: 10338090; Picker and Levy. 2014. PubMed ID:20301697; Mudd et al. 2014). Snyder-Robinson syndrome is characterized by mild to moderate X-linked intellectual disability, seizures, speech and gait abnormalities, marfanoid habitus, hypotonia and movement disorders, skeletal changes caused by osteoporosis, and facial dysmorphism (Cason et al. 2003. PubMed ID: 14508504; Becerra-Solano et al. 2009. PubMed ID: 19206178; Albert et al. 2015. PubMed ID: 25888122).

Supravalvular aortic stenosis is a congenital narrowing of the ascending aorta. The narrowing of the aorta can lead to shortness of breath, chest pain and heart failure. Supravalvular aortic stenosis can occur as an isolated condition or as one feature of Williams-Beuren syndrome (Metcalfe et al. 2000. PubMed ID: 11175284).

Cutis laxa is characterized by loose, sagging skin. Occasionally, aortic aneurysms and obstructive pulmonary disease are present (Callewaert et al. 2011. PubMed ID: 21309044). Aortic imaging is recommended in first degree relatives of individuals with TAAD. Age of onset of dilatation is variable within families.

Genetics

Marfan syndrome, Loeys-Dietz syndrome, congenital contractural arachnodactyly, Shprintzen-Golberg syndrome, aneurysms-osteoarthritis syndrome, multisystemic smooth muscle dysfunction syndrome, supravalvar aortic stenosis, cutis laxa, Ehlers-Danlos vascular and classic type, and familial TAAD are inherited in an autosomal dominant manner due to pathogenic variants in the FBN1, TGFBR1, TGFBR2, TGFB2, TGB3, FBN2, SKI, ELN, FBLN5, COL5A1, COL5A2, COL3A1, MYLK, MYH11, ACTA2, FOXE3, LOX, MAT2A, MFAP5, NOTCH1, PRKG1, SMAD3, and SMAD4 genes. Arterial tortuosity syndrome, cutis laxa, homocystinuria, and Ehlers-Danlos syndrome, type VI are inherited in an autosomal recessive manner due to pathogenic variants in SLC2A10, EFEMP2, FBLN5, CBS, and PLOD1, respectively. FG syndrome, Lujan syndrome, and Snyder Robinson syndrome are inherited in an X-linked manner due to FLNA, MED12, and SMS genes.

See individual test descriptions for information on molecular biology of gene products and mutation spectra.

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.

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 panel typically provides ≥98% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients with non-syndromic and syndromic forms of thoracic aortic aneurysm and dissection. Syndromic forms include Marfan syndrome, Loeys-Dietz syndrome, arterial tortuosity syndrome, Shprintzen-Golberg syndrome, aneurysms-osteoarthritis syndrome, multisystemic smooth muscle dysfunction syndrome, congenital contractural arachnodactyly, cutis laxa, Ehlers-Danlos vascular type, Ehlers-Danlos classic type, and Ehlers-Danlos kyphoscoliosis form. Lujan syndrome, homocystinuria, and Snyder-Robinson syndrome are included in this panel as a differential for Marfan syndrome.

Diseases

Name Inheritance OMIM ID
Aortic Aneurysm, Familial Thoracic 10 AD 617168
Aortic Aneurysm, Familial Thoracic 11, susceptibility to AD 617349
Aortic Aneurysm, Familial Thoracic 4 AD 132900
Aortic Aneurysm, Familial Thoracic 6 AD 611788
Aortic Aneurysm, Familial Thoracic 7 AD 613780
Aortic Aneurysm, Familial Thoracic 8 AD 615436
Aortic Aneurysm, Familial Thoracic 9 AD 616166
Aortic Valve Disorder AD 109730
Arterial Tortuosity Syndrome AR 208050
Congenital Contractural Arachnodactyly AD 121050
Cutis Laxa, Autosomal Dominant AD 123700
Cutis Laxa, Autosomal Dominant 2 AD 614434
Cutis Laxa, Autosomal Recessive, Type IA AR 219100
Cutis Laxa, Autosomal Recessive, Type IB AR 614437
Ehlers-Danlos Syndrome, Hydroxylysine-Deficient AR 225400
Ehlers-Danlos Syndrome, Type 1 AD 130000
Ehlers-Danlos Syndrome, Type 2 AD 130010
Ehlers-Danlos Syndrome, Type 3 AD 130020
Ehlers-Danlos Syndrome, Type 4 AD 130050
FG Syndrome 2 XL 300321
Homocystinuria Due To Cbs Deficiency AR 236200
Loeys-Dietz Syndrome 1 AD 609192
Loeys-Dietz Syndrome 2 AD 610168
Loeys-Dietz Syndrome 3 AD 613795
Loeys-Dietz Syndrome 4 AD 614816
Loeys-Dietz Syndrome 5 AD 615582
Lujan-Fryns Syndrome XL 309520
Marfan Syndrome AD 154700
Moyamoya Disease 5 AD 614042
Multisystemic Smooth Muscle Dysfunction Syndrome AD 613834
Shprintzen-Goldberg Syndrome AD 182212
Snyder Robinson Syndrome XL 309583

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CONTACTS

Genetic Counselors
Geneticist
Citations
  • Albert et al. 2015. PubMed ID: 25888122
  • Becerra-Solano et al. 2009. PubMed ID: 19206178
  • Callewaert et al. 2011. PubMed ID: 21309044
  • Cason et al. 2003. PubMed ID: 14508504
  • Cozar et al. 2011. PubMed ID: 21520339
  • Dietz. 2011. PubMed ID: 20301510
  • Doyle et al. 2012. PubMed ID: 23023332
  • Gaustadnes et al. 2002. PubMed ID: 12124992
  • Hoyert et al. 2001. PubMed ID: 11591077
  • Karaca et al. 2014. PubMed ID: 24211323
  • Kraus et al. 1999. PubMed ID: 10338090
  • Kruger et al. 2003. PubMed ID: 14635102
  • Loeys and Dietz. 2013. PubMed ID: 20301312
  • Lujan et al. 1984. PubMed ID: 6711603
  • Malfait et al. 2011. PubMed ID: 20301422
  • Mátyás et al. 2007. PubMed ID: 17492313
  • Metcalfe et al. 2000. PubMed ID: 11175284
  • Micale et al. 2010. PubMed ID: 19844261
  • Milewicz and Regalado. 2012. PubMed ID: 20301299
  • Mudd et al. 2014. Disorders of Transsulfuration. In: Valle D, Beaudet AL, Vogelstein B, et al., editors.New York, NY: McGraw-Hill. OMMBID. 
  • Nishimura et al. 2007. PubMed ID: 17345643
  • Pepin and Byers. 2011. PubMed ID: 20301667
  • Picker and Levy. 2014. PubMed ID: 20301697
  • Robertson et al. 2003. PubMed ID: 12612583
  • Rohrbach et al. 2011. PubMed ID: 21699693
  • Schwartz et al. 2007. PubMed ID: 17369503
  • Zhu et al. 2006. PubMed ID: 16444274
Order Kits
TEST METHODS

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes

Test Procedure

NextGen Sequencing

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~10 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.

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 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.

Deletion and Duplication Testing via NGS

Copy number variants (CNVs) such as deletions and duplications are detected from next generation sequencing 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 PCR, aCGH or MLPA 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.

Deletion and Duplication Testing via NGS
 
In general, sensitivity for single, double, or triple exon CNVs is ~80% and for CNVs of four exon size or larger is close to 100%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region.
Analytical Limitations

NextGen Sequencing

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 ~10 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.

Deletion and Duplication Testing via NGS
 
This CNV calling algorithm used in this test detects most deletions and duplications; 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. single vs. two or more exons), and inadequate coverage. 
 
Balanced translocations or inversions within a targeted gene, or large unbalanced translocations or inversions that extend beyond the genomic location of a targeted gene are not detected.
 
In nearly all cases, our ability to determine the exact copy number change within a targeted gene is limited. In particular, when we find copy excess within a targeted gene, we cannot be certain that the region is duplicated, triplicated etc. In many duplication cases, we are unable to determine the genomic location or the orientation of the duplicated segment with respect to the gene. In particular, we often cannot determine if the duplicated segment is inserted in tandem within the gene or inserted elsewhere in the genome. Similarly, we may not be able to determine the orientation of the duplicated segment (direct or inverted), and whether it will disrupt the open reading frame of the given gene.
 
Our ability to detect CNVs due to somatic mosaicism is limited.
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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