GeneSeq®: Cardio Familial Congenital Heart Disease Profile

CPT: 81405; 81407; 81479
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Test Details

Test Includes

This test covers all coding nucleotides of 4 genes: GATA4, NKX2.5, TBX5, and CHD7; plus at least two and typically 10 flanking intronic nucleotides upstream and downstream of each coding exon, covering the conserved donor and acceptor splice sites, as well as typically 10 flanking nucleotides in the 5′ and 3′ UTR.

Use

Confirm a clinical diagnosis of Congenital Heart Disease and identify presymptomatic family members, guiding prophylactic measures.

Limitations

This analysis does not rule out germline mosaicism, the presence of large chromosomal aberrations (including deletions, insertions, and rearrangements), mutations in regions or genes not included in this test, and possible inter/intragenic interactions between sequence variants. False-positive or false-negative results may occur for reasons that include genetic variants, blood transfusions, bone marrow transplantation, mislabeled specimens, or erroneous representation of family relationships.

Methodology

Mutation analysis is performed using the Agilent Sure Select XT® enrichment method and the Illumina® next-generation sequencing platform. Regions of interest include all exons and splice junctions for each gene and limited regions for the following: SHOC2 (exon 2), APOB (556bp of exon 26), and AKAP9 (exon 18). Sequencing reads are aligned with the hg19 build of the human genome reference sequence. Analytical sensitivity is based on the depth of coverage across the regions of the interest and is provided separately for each gene. Greater than 98% of target bases are synonymous variants not previously recorded at ≥20x coverage. Sanger sequencing is used to confirm mutation identity and analyze regions with low coverage. Variants are reported using numbering and nomenclature recommended by the Human Genome Variation Society (HGVS). Variants known to be benign and synonymous variants not previously recorded in our internal variant data bases are not reported.

Additional Information

Affecting more than 1 in 1000 live births, atrial septal defects (ASDs) account for about 10% of cases of congenital heart disease. In some individuals with ASDs, a positive family history for that disorder or other congenital heart malformations exists. Genetic mutations associated with ASDs could be a major cause of familial cases.

Genetic testing for the presence of a germline mutation in the genes known to be associated with ASDs may:

• Confirm a diagnosis of familial ASDs

• Assist with clinical management of ASDs

• Facilitate identification of at-risk individuals in affected families

CHARGE is an acronym for the hallmark characteristics of a congenital syndrome that affects about 1 in 10,000 births worldwide. Given the complexities of CHARGE syndrome, genetic testing may help to:

• Confirm a diagnosis

• Differentiate CHARGE syndrome from other multiple malformation syndromes such as 22q11.2 deletion syndrome and VACTERL association.

Specimen Requirements

Specimen

Whole blood

Volume

10 mL whole blood or 30 mL if ordering multiple tests

Container

Yellow-top (ACD) tube or lavender-top (EDTA) tube

Storage Instructions

Maintain specimen at room temperature.

Causes for Rejection

Frozen specimen; container broken or leaking; container not labeled or label not legible; improper anticoagulant

Clinical Information

Special Instructions

Test orders must include an attestation that the provider has the patient's informed consent for genetic testing. See sample physician office consent form: Consent for Genetic Testing. Please call customer service at 866-647-0735 before submitting specimens for family testing.

References

Atrial Septal Defects
Benson DW, Sharkey A, Fatkin D, et al. Reduced penetrance, variable expressivity, and genetic heterogeneity of familial atrial septal defects. Circulation. 1998 May 26; 97(20):2043-2048. 9610535
Elliot DA, Kirk EP, Yeoh T. Cardiac homeobox gene NKX2-5 mutations and congenital heart disease: associations with atrial septal defect and hypoplastic left heart syndrome. J Am Coll Cardiol. 2003 Jun 4; 41(11):2072-2076. 12798584
Epstein JA, Parmacek MS. Recent advances in cardiac development with therapeutic implications for adult cardiovascular disease. Circulation. 2005 Jul 26; 112(4);592-597. 16043659
Gruber PJ, Epstein JA. Development gone awry: Congenital heart disease. Circ Res. 2004 Feb 20; 94(3): 273-283. 14976138
Sarkozy A, Conti E, Neri C, et al. Spectrum of atrial septal defects associated with mutations of NKX2.5 and GATA4 transcription factor. J Med Genet. 2005 Feb; 42(2); e16. 15689439
Webb G, Gatzoulis MA. Atrial septal defects in the adult: Recent progress and overview. Circulation. 2006 Oct 10; 114(15):1645-1653. 17030704
CHARGE Syndrome
Blake KD, Davenport SL, Hall BD, et al. CHARGE association: an update and review for the primary pediatrician. Clin Pediatr (Phila). 1998 Mar; 37(3):159-173. 9545604
Lalani SR, Hefner MA, Belmont JW, Davenport SLH. CHARGE syndrome. [GeneReviews Web site]. February 2, 2012. Available at: http://www.genetests.org. Accessed December 18, 2009. 20301296
Pauli S, Pieper L, Haberle J, et al. Proven germline mosaicism in a father of two children with CHARGE syndrome. Clin Genet. 2009 May; 75(5):473-479. 19475719

LOINC® Map

Order Code Order Code Name Order Loinc Result Code Result Code Name UofM Result LOINC
451402 GeneSeq: Congenital Heart Dise 451331 Specimen Type: 31208-2
451402 GeneSeq: Congenital Heart Dise 451421 Results: 48003-8
451402 GeneSeq: Congenital Heart Dise 451776 Key Findings 53037-8
451402 GeneSeq: Congenital Heart Dise 451777 Additional Information 49549-9
451402 GeneSeq: Congenital Heart Dise 451778 Gene Information 51968-6
451402 GeneSeq: Congenital Heart Dise 451779 Tech Spec Results 51958-7
451402 GeneSeq: Congenital Heart Dise 451781 Seq Variants Detected 69548-6
451402 GeneSeq: Congenital Heart Dise 451409 Disclaimer N/A
451402 GeneSeq: Congenital Heart Dise 451782 Director Review: 48672-0
451402 GeneSeq: Congenital Heart Dise 451783 PDF 51969-4
451402 GeneSeq: Congenital Heart Dise 451423 GeneSeq:Congenital Heart Dises N/A

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The LOINC® codes are copyright © 1994-2017, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee. Permission is granted in perpetuity, without payment of license fees or royalties, to use, copy, or distribute the LOINC® codes for any commercial or non-commercial purpose, subject to the terms under the license agreement found at https://loinc.org/license/. Additional information regarding LOINC® codes can be found at LOINC.org, including the LOINC Manual, which can be downloaded at LOINC.org/downloads/files/LOINCManual.pdf