Congenital Structural Heart Disease Panel

Last modified: Jun 12, 2018

Summary

  • Is a 62 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with congenital heart disease, particularly those with features of hereditary disorders.

    Is not ideal for patients suspected to have a ciliopathy or a rasopathy. For those patients, please consider our Primary Ciliary Dyskinesia Panel and our Noonan Syndrome Panel, respectively.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

3-4 weeks

Number of genes

62

Test code

CA1501

CPT codes

SEQ 81405
SEQ 81406
SEQ 81407
DEL/DUP 81479

Summary

The Blueprint Genetics Congenital Structural Heart Disease Panel (test code CA1501):

  • Is a 62 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Congenital Structural Heart Disease Panel

ICD-10 Disease
Q21.3 Tetralogy of Fallot
Q87.2 Holt-Oram syndrome
Q25.3 Supravalvular aortic stenosis
Q44.7 Alagille syndrome

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

There are many types of congenital heart disease (CHD) ranging from simple asymptomatic defects to complex defects with severe, life-threatening symptoms. CHDs are the most common type of birth defect and affect at least 8 out of every 1,000 newborns. Annually, more than 35,000 babies in the United States are born with CHDs. Many of these CHDs are simple conditions and need no treatment or are easily repaired. Some babies are born with complex CHD requiring special medical care. The diagnosis and treatment of complex CHDs has greatly improved over the past few decades. As a result, almost all children who have complex heart defects survive to adulthood and can live active, productive lives. However, many patients who have complex CHDs continue to need special heart care throughout their lives. In the United States, more than 1 million adults are living with congenital heart disease.

Genes in the Congenital Structural Heart Disease Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ABL1 Congenital heart defects and skeletal malformations syndrome (CHDSKM) AD 30 3
ACTA2 Aortic aneurysm, familial thoracic, Moyamoya disease, Multisystemic smooth muscle dysfunction syndrome AD 20 72
ACTB* Baraitser-Winter syndrome AD 46 54
ACTC1 Left ventricular noncompaction, Hypertrophic cardiomyopathy (HCM), Cardiomyopathy, restrictive, Atrial septal defect, Dilated cardiomyopathy (DCM) AD 23 60
ACTG1* Deafness, Baraitser-Winter syndrome AD 25 43
ACVR1 Fibrodysplasia ossificans progressiva AD 14 19
ACVR2B Heterotaxy, visceral, 4, autosomal AD 1 2
ADAMTS10 Weill-Marchesani syndrome AR 8 13
ADAMTS17 Weill-Marchesani-like syndrome AR 6 7
B3GAT3* Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects AR 5 13
BCOR Microphthalmia, syndromic, Oculofaciocardiodental syndrome XL 38 50
BMPR2 Pulmonary hypertension, primary, Pulmonary venoocclusive disease AD 386 417
CBL Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia AD 23 38
CDK13 Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder AD 13 13
CHD4 Epilepsy, hearing loss, and mental retardation syndrome; EHLMRS AD 14 16
CHD7 Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome AD 244 813
CRELD1 Atrioventricular septal defect, partial, with or without heterotaxy AD 16
CTC1 Cerebroretinal microangiopathy with calcifications and cysts AR 16 30
DHCR7 Smith-Lemli-Opitz syndrome AR 67 216
EFTUD2 Mandibulofacial dysostosis with microcephaly, Esophageal atresia, syndromic AD 43 93
EIF2AK4 Pulmonary venoocclusive disease AR 27 68
ELN Cutis laxa, Supravalvular aortic stenosis AD 72 105
ENG Juvenile polyposis syndrome, Hereditary hemorrhagic telangiectasia AD 120 478
FLNA Frontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defects XL 119 235
GATA4 Tetralogy of Fallot, Atrioventricular septal defect, Testicular anomalies with or without congenital heart disease, Ventricular septal defect, Atrial septal defect AD 36 126
GATA5 Familial atrial fibrillation, Tetralogy of Fallot, Single ventricular septal defect AD/AR 5 31
GATA6 Heart defects, congenital, and other congenital anomalies, Atrial septal defect 9, atrioventricular septal defect 5, Persistent truncus arteriosus, Tetralogy of Fallot AD 16 79
GDF1 Transposition of the great arteries, dextro-looped 3, Double-outlet right ventricle AD 11 15
GJA1* Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3 AD/AR 32 106
GJA5 Progressive familial heart block, Atrial standstill, digenic, Atrial fibrillation AD/Digenic 8 34
GPC3 Simpson-Golabi-Behmel syndrome XL 29 72
HAND1 Congenital heart defects, Dilated cardiomyopathy AD 8
HOXA1 Athabaskan brainstem dysgenesis syndrome, Bosley-Salih-Alorainy syndrome AR 4 7
HRAS Costello syndrome, Congenital myopathy with excess of muscle spindles AD 41 29
JAG1 Alagille syndrome AD 121 569
LEFTY2* Left-right axis malformations AD 3 3
MEIS2 Cleft palate, cardiac defects, and mental retardation (CPCMR) AD 8 17
MYCN Feingold syndrome AD 25 40
NAA15 Congenital heart malformations AD 6 8
NF1* Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndrome AD 810 2703
NKX2-5 Conotruncal heart malformations, Hypothyroidism, congenital nongoitrous,, Atrial septal defect, Ventricular septal defect 3, Conotruncal heart malformations, variable, Tetralogy of Fallot AD 43 102
NKX2-6 Persistent truncus arteriosus, Conotruncal heart malformations AR 2 9
NODAL Heterotaxy, visceral AD 4 13
NOTCH1 Aortic valve disease AD 44 91
NOTCH2* Alagille syndrome, Hajdu-Cheney syndrome AD 35 63
NR2F2 Congenital heart defects, multiple types, 4 AD 10 14
NSD1 Sotos syndrome, Weaver syndrome, Beckwith-Wiedemann syndrome AD 303 515
PITX2 Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomaly AD 23 96
PPP1CB# Noonan syndrome-like disorder with loose anagen hair 2 AD 7 7
PRKD1 Congenital heart defects and ectodermal dysplasia AD 2 6
RBM10 TARP syndrome XL 12 10
SALL4 Acro-renal-ocular syndrome, Duane-radial ray/Okohiro syndrome AD 19 55
SOS2 Noonan syndrome 9 AD 3 6
TAB2 Congenital heart defects, multiple types, 2 AD 11 27
TBX1 Conotruncal anomaly face syndrome AD 15 65
TBX5 Holt-Oram syndrome AD 55 126
TBX20* Atrial septal defect 4 AD 3 27
TFAP2B Patent ductus arteriosus, nonsyndromic, Char syndrome AD 10 12
TGDS Catel-Manzke syndrome AR 6 7
TLL1 Atrial septal defect AD 3 7
ZFPM2 46,XY sex reversal, Diaphragmatic hernia 3, Tetralogy of Fallot AD 9 44
ZIC3 Heterotaxy, visceral, VACTERL association, Congenital heart defects, nonsyndromic XL 14 41

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ACTC1 Chr15:35080829 c.*1784T>C NM_005159.4
BMPR2 Chr2:203419960 c.1587-7_1587-4delCTTT NM_001204.6 rs769408722
CHD7 Chr8:61734568 c.2836-15C>G NM_017780.3
CHD7 Chr8:61757794 c.5051-15T>A NM_017780.3
CHD7 Chr8:61763035 c.5405-17G>A NM_017780.3 rs794727423
ELN Chr7:73480347 c.2272+20C>G NM_001278939.1
ENG Chr9:130616761 c.-127C>T NM_001114753.2
ENG Chr9:130578354 c.1742-22T>C NM_001114753.2
ENG Chr9:130588962 c.361-11T>A NM_001114753.2
GATA4 Chr8:11560864 c.-1407C>A NM_002052.3 rs769262495
GATA4 Chr8:11560787 c.-1484T>C NM_002052.3 rs372004083
GATA4 Chr8:11561369 c.-902G>T NM_002052.3
GATA4 Chr8:11561282 c.-989C>T NM_002052.3
GATA5 Chr20:61051165 c.-201A>G NM_080473.4
GATA6 Chr18:19749272 c.-409C>G NM_005257.4
GATA6 Chr18:19749151 c.-530A>T NM_005257.4
JAG1 Chr20:10629767 c.1349-12T>G NM_000214.2
NF1 Chr17:29422056 c.-272G>A NM_001042492.2
NF1 Chr17:29422055 c.-273A>C NM_001042492.2
NF1 Chr17:29530107 c.1260+1604A>G NM_001042492.2
NF1 Chr17:29533239 c.1261-19G>A NM_001042492.2
NF1 Chr17:29534143 c.1392+754T>G NM_001042492.2
NF1 Chr17:29488136 c.288+2025T>G NM_001042492.2
NF1 Chr17:29577934 c.4110+1802delA NM_001042492.2 rs863224944
NF1 Chr17:29577082 c.4110+945A>G NM_001042492.2
NF1 Chr17:29580296 c.4173+278A>G NM_001042492.2
NF1 Chr17:29654479 c.5269-38A>G NM_001042492.2
NF1 Chr17:29656858 c.5610-456G>T NM_001042492.2
NF1 Chr17:29657848 c.5812+332A>G NM_001042492.2 rs863224491
NF1 Chr17:29508428 c.587-12T>A NM_001042492.2
NF1 Chr17:29508426 c.587-14T>A NM_001042492.2
NF1 Chr17:29664375 c.6428-11T>G NM_001042492.2
NF1 Chr17:29664618 c.6642+18A>G NM_001042492.2
NF1 Chr17:29676126 c.7190-12T>A NM_001042492.2
NF1 Chr17:29685481 c.7971-17C>G NM_001042492.2
NF1 Chr17:29685177 c.7971-321C>G NM_001042492.2
NF1 Chr17:29685665 c.8113+25A>T NM_001042492.2
NF1 Chr17:29510334 c.888+651T>A NM_001042492.2
NF1 Chr17:29510427 c.888+744A>G NM_001042492.2
NF1 Chr17:29510472 c.888+789A>G NM_001042492.2
NKX2-5 Chr5:172672291 c.-10205G>A .
NKX2-5 Chr5:172672303 c.-10217G>C .
NR2F2 Chr15:96869479 c.-60C>T NM_001145155.1
PITX2 Chr4:111539855 c.412-11A>G NM_000325.5
TBX1 Chr22:19743735 c.-620A>C NM_080647.1 rs536892777
TBX1 Chr22:19743578 c.-777C>T NM_080647.1
TBX20 Chr7:35293780 c.-549G>A NM_001077653.2 rs571512677
TBX5 Chr12:114704515 c.*88822C>A NM_000192.3 rs141875471

Added and removed genes from the panel

Genes added Genes removed
ABL1
ACTB
ACTG1
ACVR1
ACVR2B
ADAMTS10
ADAMTS17
B3GAT3
BCOR
CBL
CDK13
CHD4
CRELD1
DHCR7
EFTUD2
EIF2AK4
ENG
GDF1
GPC3
HAND1
HOXA1
LEFTY2
MEIS2
MYCN
NAA15
NKX2-6
NR2F2
NSD1
PITX2
PPP1CB
PRKD1
RBM10
SALL4
SOS2
TAB2
TBX20
TGDS
FOXC1
FOXH1
G6PC3

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene’s target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics congenital structural heart disease panel covers classical genes associated with tetralogy of Fallot, Holt-Oram syndrome, supravalvular aortic stenosis, Alagille syndrome, atrial septal defect, ventricular septal defect, aorta stenosis, ebstein anomaly, Hypoplastic left heart syndrome and pulmonary artery stenosis. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient’s phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.