Comprehensive Cardiology Panel

184 gene panel that includes assessment of non-coding variants

The Comprehensive Cardiology Panel covers known genetic causes of channelopathies and cardiomyopathies. It is ideal for patients in whom the phenotype is complex including features of both channelopathy and cardiomyopathy and for the investigation of sudden cardiac death as this panel includes all of our channelopathy and cardiomyopathy genes.

Analysis methods Availability Number of genes Test code CPT codes
4 weeks 184 GHC0008 SEQ 81410
SEQ 81413
DEL/DUP 81414
SEQ 81439


ICD codes
Commonly used ICD-10 code(s) when ordering the Comprehensive Cardiology Panel

I46.2 Cardiac arrest
Q24.8 Brugada syndrome
I42.5 RCM
I42.9 Cardiomyopathy NAS
Q87.1 Noonan syndrome
I49.9 Catecholaminergic polymorphic ventricular tachycardia (CPVT)
I46.2 Cardiac arrest underlying cardiac condition
I46.9 Cardiac arrest cause unspecified
I45.81 Long QT syndrome
I42.2 Hypertrophic cardiomyopathy (HCM)
I42.0 Dilated cardiomyopathy (DCM)
I42.8 Arrhythmogenic right ventricular cardiomyopathy (ARVC)
I42.8 Left ventricular non-compaction cardiomyopathy (LVNC)
I49.9 Short QT 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.


When a person dies suddenly and unexpectedly from a suspected cardiovascular cause, the term sudden cardiac death (SCD) is used. SCD is frequently caused by an abrupt change in heart rhythm (arrhythmia), most often ventricular tachycardia or ventricular fibrillation that impairs cardiac pumping, thereby depriving vital organs of oxygenated blood. A brief episode of VT or VF may cause only momentary loss of consciousness (syncope), but death is the inevitable result of sustained VF in the absence of emergent medical care. The differential diagnosis between ion channel disease and cardiomyopathies can be challenging on occasion as severe ventricular arrhythmias can manifest in cardiomyopathy patients with subclinical or no morphological cardiomyopathy.

Panel Content

Genes in the Comprehensive Cardiology Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
AARS2Leukoencephalopathy, progressive, with ovarian failure, Combined oxidative phosphorylation deficiency 8AR1726
ABCC6Pseudoxanthoma elasticumAR368374
ABCC9Atrial fibrillation, Cantu syndrome, Dilated cardiomyopathy (DCM)AD2540
ACAD9Acyl-CoA dehydrogenase family, deficiencyAR2544
ACADVLAcyl-CoA dehydrogenase, very long chain, deficiencyAR94270
ACTA2Aortic aneurysm, familial thoracic, Moyamoya disease, Multisystemic smooth muscle dysfunction syndromeAD2072
ACTC1Left ventricular noncompaction, Hypertrophic cardiomyopathy (HCM), Cardiomyopathy, restrictive, Atrial septal defect, Dilated cardiomyopathy (DCM)AD2360
ACTN2Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD1041
AGKSengers syndrome, Cataract 38AR1827
AGLGlycogen storage diseaseAR90243
AKAP9Long QT syndromeAD433
ALMS1Alstrm syndromeAR64295
ALPK3Pediatric cardiomyopathyAR95
ANK2Cardiac arrhythmia, Long QT syndromeAD770
ANO5Gnathodiaphyseal dysplasia, LGMD2L and distal MMD3 muscular dystrophiesAD/AR60115
APOA1Amyloidosis, systemic nonneuronopathic, HypoalphalipoproteinemiaAD/AR2769
BAG3Dilated cardiomyopathy (DCM), Myopathy, myofibrillarAD3660
BRAFLEOPARD syndrome, Noonan syndrome, Cardiofaciocutaneous syndromeAD13565
CACNA1CBrugada syndrome, Timothy syndromeAD2062
CACNB2Brugada syndromeAD322
CALM1Ventricular tachycardia, catecholaminergic polymorphic, Recurrent cardiac arrest, infantile, Long QT syndromeAD910
CALM2Long QT syndromeAD710
CALM3Catecholaminergic polymorphic ventricular tachycardiaAD/AR44
CALR3Cardiomyopathy, familial hypertrophic, 19AD3
CAPN3Muscular dystrophy, limb-girdle, Eosinophilic myositisAR134428
CASQ2Ventricular tachycardia, catecholaminergic, polymorphicAR2433
CAV3Creatine phosphokinase, elevated serum, Hypertrophic cardiomyopathy (HCM), Long QT syndrome, Muscular dystrophy, limb-girdle, type IC, Myopathy, distal, Tateyama type, Rippling muscle disease 2AD/Digenic2149
CBLNoonan syndrome-like disorder with or without juvenile myelomonocytic leukemiaAD2338
CDH2Arrhythmogenic right ventricular cardiomyopathy (ARVC)AD5
COX15Leigh syndrome, Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiencyAR75
CPT2Carnitine palmitoyltransferase II deficiencyAR48107
CRYABCataract, myofibrillar myopathy and cardiomyopathy, Congenital cataract and cardiomyopathy, Dilated cardiomyopathy (DCM), Myopathy, myofibrillar, Cataract 16, multiple types, Myopathy, myofibrillar, fatal infantile hypertonic, alpha-B crystallin-relatedAD1528
CSRP3Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD529
CTNNA3Arrhythmogenic right ventricular dysplasiaAD641
DBHDopamine beta-hydroxylase deficiencyAR1013
DESDilated cardiomyopathy (DCM), Myopathy, myofibrillar, Scapuloperoneal syndrome, neurogenic, Kaeser typeAD/AR61117
DMDBecker muscular dystrophy, Duchenne muscular dystrophy, Dilated cardiomyopathy (DCM)XL6823818
DNAJC193-methylglutaconic aciduriaAR35
DOLKCongenital disorder of glycosylationAR811
DSC2Arrhythmogenic right ventricular dysplasia with palmoplantar keratoderma and woolly hair, Arrhythmogenic right ventricular dysplasiaAD/AR2585
DSG2Arrhythmogenic right ventricular dysplasia, Dilated cardiomyopathy (DCM)AD40125
DSPCardiomyopathy, dilated, with wooly hair, keratoderma, and tooth agenesis, Arrhythmogenic right ventricular dysplasia, familial, Cardiomyopathy, dilated, with wooly hair and keratoderma, Keratosis palmoplantaris striata II, Epidermolysis bullosa, lethal acantholyticAD/AR155281
DTNALeft ventricular noncompaction 1AD36
DYSFMiyoshi muscular dystrophy, Muscular dystrophy, limb-girdle, Myopathy, distal, with anterior tibial onsetAR188517
EEF1A2Epileptic encephalopathy, early infantile, Mental retardationAD1211
ELAC2Combined oxidative phosphorylation deficiency 17AR1115
EMDEmery-Dreifuss muscular dystrophyXL44112
ENPP1Arterial calcification, Hypophosphatemic ricketsAR2068
EPG5Vici syndromeAR2950
ETFAGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR929
ETFBGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR614
ETFDHGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR41173
FBXO32Dilated cardiomyopathy (DCM)AD/AR2
FHL1Myopathy with postural muscle atrophy, Emery-Dreifuss muscular dystrophy, Reducing bod myopathyXL2260
FKRPMuscular dystrophy-dystroglycanopathyAR41137
FKTNMuscular dystrophy-dystroglycanopathy, Dilated cardiomyopathy (DCM), Muscular dystrophy-dystroglycanopathy (limb-girdle)AD/AR3457
FOXD4Dilated cardiomyopathy (DCM)AD1
FOXRED1Leigh syndrome, Mitochondrial complex I deficiencyAR158
FXNFriedreich ataxiaAR1263
GAAGlycogen storage diseaseAR147558
GATA5Familial atrial fibrillation, Tetralogy of Fallot, Single ventricular septal defectAD/AR531
GATA6Heart defects, congenital, and other congenital anomalies, Atrial septal defect 9, atrioventricular septal defect 5, Persistent truncus arteriosus, Tetralogy of FallotAD1679
GATAD1Dilated cardiomyopathy (DCM)AR231
GBE1Glycogen storage diseaseAR3470
GFM1Combined oxidative phosphorylation deficiencyAR1818
GLAFabry diseaseXL215919
GLB1GM1-gangliosidosis, Mucopolysaccharidosis (Morquio syndrome)AR65212
GMPPBMuscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), Limb-girdle muscular dystrophy-dystroglycanopathyAR1435
GTPBP3Combined oxidative phosphorylation deficiency 23AR1415
HADHATrifunctional protein deficiency, Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiencyAR5070
HAND1Congenital heart defects, Dilated cardiomyopathyAD8
HCN4Sick sinus syndrome, Brugada syndromeAD928
HRASCostello syndrome, Congenital myopathy with excess of muscle spindlesAD4129
ISPDMuscular dystrophy-dystroglycanopathyAR3049
JPH2Hypertrophic cardiomyopathy (HCM)AD312
JUPArrhythmogenic right ventricular dysplasia, Naxos diseaseAD/AR843
KCNA5Atrial fibrillationAD423
KCNE1Long QT syndrome, Jervell and Lange-Nielsen syndromeAD/AR/Digenic745
KCNE2Long QT syndrome, Atrial fibrillation, familialAD623
KCNH2Short QT syndrome, Long QT syndromeAD346925
KCNJ2Short QT syndrome, Andersen syndrome, Long QT syndrome, Atrial fibrillationAD4187
KCNJ5Long QT syndrome, Hyperaldosteronism, familialAD715
KCNQ1Short QT syndrome, Long QT syndrome, Atrial fibrillation, Jervell and Lange-Nielsen syndromeAD/AR/Digenic285604
KRASNoonan syndrome, Cardiofaciocutaneous syndromeAD6134
LAMA2Muscular dystrophy, congenital merosin-deficientAR125294
LAMP2Danon diseaseXL5797
LARGEMuscular dystrophy-dystroglycanopathyAR1625
LDB3Dilated cardiomyopathy (DCM), Myopathy, myofibrillarAD914
LMNAHeart-hand syndrome, Slovenian, Limb-girdle muscular dystrophy, Muscular dystrophy, congenital, LMNA-related, Lipodystrophy (Dunnigan), Emery-Dreiffus muscular dystrophy, Malouf syndrome, Dilated cardiomyopathy (DCM), Mandibuloacral dysplasia type A, Progeria Hutchinson-Gilford typeAD/AR231553
LRRC10Dilated cardiomyopathy (DCM)AD/AR4
LZTR1Schwannomatosis, Noonan syndromeAD2764
MAP2K1Cardiofaciocutaneous syndromeAD4521
MAP2K2Cardiofaciocutaneous syndromeAD2135
MLYCDMalonyl-CoA decarboxylase deficiencyAR1338
MTO1Combined oxidative phosphorylation deficiencyAR1524
MYBPC3Left ventricular noncompaction, Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD4601022
MYBPHLDilated cardiomyopathy (DCM)AD2
MYH6Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM), Atrial septal defect 3AD13114
MYH7Hypertrophic cardiomyopathy (HCM), Myopathy, myosin storage, Myopathy, distal, Dilated cardiomyopathy (DCM)AD285950
MYL2Hypertrophic cardiomyopathy (HCM), Infantile type I muscle fibre disease and cardiomyopathyAD2066
MYL3Hypertrophic cardiomyopathy (HCM)AD/AR1340
MYL4Atrial fibrillation, familial, 18AD22
MYOTMyopathy, myofibrillar, Muscular dystrophy, limb-girdle, 1A, Myopathy, spheroid bodyAD716
MYPNHypertrophic cardiomyopathy (HCM), Cardiomyopathy, restrictive, Dilated cardiomyopathy (DCM), Nemaline myopathy 11, autosomal recessiveAD543
NDUFAF2Mitochondrial complex I deficiency, Leigh syndromeAR108
NEXNHypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD542
NF1Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndromeAD8102703
NKX2-5Conotruncal heart malformations, Hypothyroidism, congenital nongoitrous,, Atrial septal defect, Ventricular septal defect 3, Conotruncal heart malformations, variable, Tetralogy of FallotAD43102
NOS1APRomano-Ward syndromeAD/AR4
NRASNoonan syndromeAD3114
NUP155Atrial fibrillation 15AR21
PCCAPropionic acidemiaAR48123
PCCBPropionic acidemiaAR41114
PKP2Arrhythmogenic right ventricular dysplasiaAD141275
PLECMuscular dystrophy, limb-girdle, Epidermolysis bullosaAR3398
PLEKHM2Dilated cardiomyopathy (DCM), left ventricular noncompactionAR11
PLNHypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD/AR829
PNPLA2Neutral lipid storage disease with myopathyAR1236
POMT1Muscular dystrophy-dystroglycanopathyAR4194
PPA2Sudden cardiac failure, infantileAR88
PPP1CBNoonan syndrome-like disorder with loose anagen hair 2AD77
PRDM16Left ventricular noncompaction, Dilated cardiomyopathy (DCM)AD1615
PRKAG2Hypertrophic cardiomyopathy (HCM), Wolff-Parkinson-White syndrome, Glycogen storage disease of heart, lethal congenitalAD1756
PTPN11Noonan syndrome, MetachondromatosisAD128139
RAF1LEOPARD syndrome, Noonan syndrome, Dilated cardiomyopathy (DCM)AD4448
RASA2Noonan syndromeAD13
RBCK1Polyglucosan body myopathyAR1014
RBM20Dilated cardiomyopathy (DCM)AD1943
RIT1Noonan syndromeAD2025
RMND1Combined oxidative phosphorylation deficiencyAR1815
RRASNoonan-syndrome like phenotypeAD/AR2
RYR2Ventricular tachycardia, catecholaminergic polymorphic, Arrhythmogenic right ventricular dysplasiaAD113353
SALL4Acro-renal-ocular syndrome, Duane-radial ray/Okohiro syndromeAD1955
SCN1BAtrial fibrillation, Brugada syndrome, Generalized epilepsy with febrile seizures plus, Epilepsy, generalized, with febrile seizures plus, type 1, Epileptic encephalopathy, early infantile, 52AD1529
SCN3BAtrial fibrillation, familial, Brugada syndromeAD37
SCN5AHeart block, nonprogressive, Heart block, progressive, Long QT syndrome, Ventricular fibrillation, Atrial fibrillation, Sick sinus syndrome, Brugada syndrome, Dilated cardiomyopathy (DCM)AD/AR/Digenic225829
SCN10AParoxysmal extreme pain disorder, Channelopathy-associated congenital insensitivity to pain, Primary erythermalgia, Sodium channelopathy-related small fiber neuropathy, Brugada syndromeAD/AR170
SCNN1BLiddle syndrome, Pseudohypoaldosteronism, Bronchiectasis with or without elevated sweat chlorideAD/AR1846
SCNN1GLiddle syndrome, Pseudohypoaldosteronism, Bronchiectasis with or without elevated sweat chlorideAD/AR518
SCO2Leigh syndrome, Hypertrophic cardiomyopathy (HCM), Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency, MyopiaAR4233
SDHALeigh syndrome/Mitochondrial respiratory chain complex II deficiency, Gastrointestinal stromal tumor, Paragangliomas, Dilated cardiomyopathy (DCM), Cardiomyopathy, dilated, 1GGAD/AR4258
SELENONMuscular dystrophy, rigid spine, Myopathy, congenital, with fiber- disproportionAR3262
SGCAMuscular dystrophy, limb-girdleAR4799
SGCBMuscular dystrophy, limb-girdleAR2962
SGCDMuscular dystrophy, limb-girdle, Dilated cardiomyopathy (DCM)AR1326
SGCGMuscular dystrophy, limb-girdleAR2063
SHOC2Noonan-like syndrome with loose anagen hairAD24
SLC22A5Carnitine deficiency, systemic primaryAR84150
SLC25A4Progressive external ophthalmoplegia with mitochondrial DNA deletions, Mitochondrial DNA depletion syndromeAD/AR1215
SLC25A20Carnitine-acylcarnitine translocase deficiencyAR1442
SMCHD1Facioscapulohumeral muscular dystrophy, Facioscapulohumeral muscular dystrophy, type 2Digenic (involving a SMCHD1 mutation and permissive D4Z4 haplotype)4676
SOS1Noonan syndromeAD4567
SOS2Noonan syndrome 9AD36
SPEGCentronuclear myopathy 5AR58
SPRED1Legius syndromeAD2371
TAB2Congenital heart defects, multiple types, 2AD1127
TAZ3-Methylglutaconic aciduria, (Barth syndrome)XL42153
TBX5Holt-Oram syndromeAD55126
TBX20Atrial septal defect 4AD327
TCAPMuscular dystrophy, limb-girdle, Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD/AR1227
TECRLVentricular tachycardia, catecholaminergic polymorphic, 3AR22
TGFB3Loeys-Dietz syndrome (Reinhoff syndrome), Arrhythmogenic right ventricular dysplasiaAD1722
TMEM43Arrhythmogenic right ventricular dysplasia, Emery-Dreifuss muscular dystrophyAD524
TMEM70Mitochondrial complex V (ATP synthase) deficiencyAR1118
TNNC1Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD923
TNNI3Hypertrophic cardiomyopathy (HCM), Cardiomyopathy, restrictive, Dilated cardiomyopathy (DCM)AD/AR54127
TNNI3KCardiac conduction disease with or without dilated cardiomyopathyAD12
TNNT2Left ventricular noncompaction, Hypertrophic cardiomyopathy (HCM), Cardiomyopathy, restrictive, Dilated cardiomyopathy (DCM)AD57140
TOR1AIP1Muscular dystrophy with progressive weakness, distal contractures and rigid spineAD/AR25
TPM1Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD3395
TRDNVentricular tachycardia, catecholaminergic polymorphicAR106
TRIM32Bardet-Biedl syndrome, Muscular dystrophy, limb-girdleAR1316
TRPM4Progressive familial heart blockAD529
TSFMCombined oxidative phosphorylation deficiencyAR76
TTNDilated cardiomyopathy (DCM), Tibial muscular dystrophy, Limb-girdle muscular dystrophy, Hereditary myopathy with early respiratory failure, Myopathy, early-onset, with fatal cardiomyopathy (Salih myopathy), Muscular dystrophy, limb-girdle, type 2JAD725304
TTRDystransthyretinemic hyperthyroxinemia, Amyloidosis, hereditary, transthyretin-relatedAD49146
VCLHypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD829
VCPAmyotrophic lateral sclerosis, Inclusion body myopathy with early-onset Paget disease, Charcot-Marie-Tooth diseaseAD1857
XKMcLeod syndromeXL1039

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number

Panel Update

Genes added

  • ABCC6
  • ALMS1
  • CALR3
  • CDH2
  • DOLK
  • DTNA
  • EEF1A2
  • ELAC2
  • EPG5
  • FOXD4
  • GATA6
  • GTPBP3
  • HAND1
  • LRRC10
  • MYL4
  • NUP155
  • PCCA
  • PCCB
  • PPA2
  • PPP1CB
  • RBCK1
  • RMND1
  • SALL4
  • SOS2
  • SPEG
  • TAB2
  • TBX20
  • TNNI3K
  • TOR1AIP1
  • VPS13A

Genes removed

  • A2ML1
  • ABCB4
  • ANKRD1
  • APOB
  • CACNA2D4
  • CHKB
  • CPT1A
  • DAG1
  • EYA4
  • GJA5
  • GNE
  • KCND3
  • KCNE3
  • NSUN2
  • POMT2

Test strength and Limitations

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 The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: *PPA2* (11, 12). 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. 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 GHC Genetics.

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

Test Performance

The GHC Genetics panel covers classical genes associated with Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia (CPVT), cardiac arrest underlying cardiac condition, cardiac arrest cause unspecified, syncope and collapse, abnormal ECG, Long QT syndrome, arrhythmogenic right ventricular cardiomyopathy (ARVC) and Short QT syndrome. 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 GHC 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%

Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Detection of Del/Dup of several genes is by MLPA analysis (MS Holland). All genes are performed by CNV analysis through the genome depending on exon size, sequencing coverage and sequence content. We have validated the assays for different starting materials including isolated DNA from EDTA blood that provide high-quality results.

Bioinformatics & clinical interpretation

The sequencing data generated in our laboratory is analysed by our bioinformatic pipeline, integrating state-of-the art algorithms and industry-standard software solutions. We use also JSI medical systems software for sequencing data analysis. JSI medical systems is a certified system offering sophisticated bioinformatic software solutions covering a wide field of sequencing techniques.

Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results.

Every pathogenic or probably pathogenic variant is confirmed by the Sanger sequencing method. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. The analysis of detected variants was performed on the basis of the reference database of polymorphisms and international mutation databases: UMD, LOVD and ClinVar.

The consequence of variants in coding and splice regions are estimated using Alamut software. The Alamut database contains more than 28000 coding genes, non-protein coding genes and pseudogenes. This database (shared with the high throughput annotation engine for NGS data, Alamut Batch) is frequently updated. Information comes from different public databases such as NCBI, EBI, and UCSC, as well as other sources including gnomAD, ESP, Cosmic, ClinVar, or HGMD and CentoMD (for those a separate subscription from Qiagen/Biobase and Centogene respectively is required). Alamut Visual finds information about nucleotide conservation data through many vertebrates’ species, with the phastCons and phyloP scores, amino acid conservation data through orthologue alignments and information on protein domains.

Moreover, we integrate several missense variant pathogenicity prediction tools and algorithms such as SIFT, PolyPhen, AlignGVGD or MutationTaster. It also offers a window dedicated to the in silico study of variants’ effect on RNA splicing, allowing the assessment of their potential impact on splice junctions and visualization of cryptic or de novo splice sites. Impact on splicing regulation is also assessed.

Clinical interpretation

At GHC Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical report. We recommend an interpretation of the findings of this molecular genetic analysis, including subsequent oncological consultation for the patient in the context of genetic counselling for the patient.

We strive to continuously monitor current genetic literature identifying new relevant information and findings and adapting them to our diagnostics. This enables relevant novel discoveries to be rapidly translated and adopted into our ongoing diagnostics development without delay. The undertaking of such comprehensive due diligence ensures that our diagnostic panels and clinical statements are the most up-to-date on the market.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. 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 analysed at our laboratories enables 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 three times at GHC Genetics. Reported variants of uncertain significance (VUS) 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 GHC 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, 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 counselling.

Our Clinical interpretation team analyses 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 laboratories are therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by GHC Genetics is re-classified, our laboratories will issue a follow-up statement to the original ordering health care provider at no additional cost.