Congenital Structural Heart Disease Panel

Updated
Summary
  • Is a 114 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
Availability

4 weeks

Number of genes

114

Test code

CA1501

Panel size

Small

CPT codes
81479

Summary

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

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

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

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. Read more about our sample requirements here.

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 5
ACTA2 Aortic aneurysm, familial thoracic, Moyamoya disease, Multisystemic smooth muscle dysfunction syndrome AD 20 76
ACTB* Baraitser-Winter syndrome AD 55 60
ACTC1 Left ventricular noncompaction, Hypertrophic cardiomyopathy (HCM), Cardiomyopathy, restrictive, Atrial septal defect, Dilated cardiomyopathy (DCM) AD 23 63
ACTG1* Deafness, Baraitser-Winter syndrome AD 27 47
ACVR1 Fibrodysplasia ossificans progressiva AD 14 19
ACVR2B Heterotaxy, visceral, 4, autosomal AD 1 2
ADAMTS10 Weill-Marchesani syndrome AR 8 14
ADAMTS17 Weill-Marchesani-like syndrome AR 6 7
AFF4 Cognitive impairment, coarse facies, Heart defects, Obesity, Pulmonary involvement, Short stature, and skeletal dysplasia (CHOPS syndrome) AD 3 3
AMMECR1 Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis XL 4 5
ARHGAP31 Adams-Oliver syndrome AD 3 6
ARID1A Coffin-Siris syndrome, Mental retardation AD 27 35
ARID1B Coffin-Siris syndrome, Mental retardation AD 153 185
B3GAT3#* Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects AR 6 13
BCOR Microphthalmia, syndromic, Oculofaciocardiodental syndrome XL 40 53
BMPR2 Pulmonary hypertension, primary, Pulmonary venoocclusive disease AD 391 572
BRAF* LEOPARD syndrome, Noonan syndrome, Cardiofaciocutaneous syndrome AD 134 65
C12ORF57 Corpus callosum hypoplasia, recessive, Temtamy syndrome AR 7 6
CBL Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia AD 24 43
CDK13 Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder AD 13 20
CDK9 AR 1
CFAP53 Heterotaxy, visceral, 6, autosomal recessive AR 4 4
CHD4 Sifrim-Hitz-Weiss syndrome AD 14 21
CHD7 Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome AD 276 860
CHRM2 Dilated cardiomyopathy (DCM) AD/AR 1
CREBBP Rubinstein-Taybi syndrome AD 175 362
CRELD1 Atrioventricular septal defect, partial, with or without heterotaxy AD 2 16
CTC1 Cerebroretinal microangiopathy with calcifications and cysts AR 21 33
DHCR7 Smith-Lemli-Opitz syndrome AR 88 217
DLL4 Adams-Oliver syndrome AD 13 14
DOCK6 Adams-Oliver syndrome AR 21 21
EFTUD2 Mandibulofacial dysostosis with microcephaly, Esophageal atresia, syndromic AD 45 99
EHMT1 Kleefstra syndrome AD 86 89
EIF2AK4 Pulmonary venoocclusive disease AR 27 84
ELN Cutis laxa, Supravalvular aortic stenosis AD 78 113
ENG Juvenile polyposis syndrome, Hereditary hemorrhagic telangiectasia AD 158 491
EOGT Adams-Oliver syndrome AR 8 5
EP300 Rubinstein-Taybi syndrome AD 63 101
EVC Weyers acrofacial dysostosis, Ellis-van Creveld syndrome AD/AR 58 83
EVC2 Ellis-van Creveld syndrome, Weyers acrodental dysostosis AD/AR 78 75
FLNA Frontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defects XL 133 257
FOXC1 Axenfeld-Rieger syndrome, Iridogoniodysgenesis, Peters anomaly AD 46 135
FOXF1 Alveolar capillary dysplasia with misalignment of pulmonary veins AD 10 102
FOXH1 Congenital heart malformations, Holoprosencephaly AD 33
FOXP1 Mental retardation with language impairment and autistic features, Congenital heart malformations AD 48 76
GATA4* Tetralogy of Fallot, Atrioventricular septal defect, Testicular anomalies with or without congenital heart disease, Ventricular septal defect, Atrial septal defect AD 37 140
GATA5 Familial atrial fibrillation, Tetralogy of Fallot, Single ventricular septal defect AD 5 32
GATA6 Heart defects, congenital, and other congenital anomalies, Atrial septal defect 9, atrioventricular septal defect 5, Persistent truncus arteriosus, Tetralogy of Fallot AD 16 82
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 31 107
GJA5 Progressive familial heart block, Atrial standstill, digenic, Atrial fibrillation AD/Digenic 8 34
GPC3 Simpson-Golabi-Behmel syndrome XL 33 75
HAND1 Congenital heart defects, Dilated cardiomyopathy AD 9
HAND2 Dilated cardiomyopathy (DCM), Congenital heart malformations AD 2 5
HDAC8 Cornelia de Lange syndrome XL 41 50
HNRNPK* Au-Kline syndrome AD 14 10
HOXA1 Athabaskan brainstem dysgenesis syndrome, Bosley-Salih-Alorainy syndrome AR 4 7
HRAS Costello syndrome, Congenital myopathy with excess of muscle spindles AD 43 31
JAG1 Alagille syndrome AD 131 610
KDM6A Kabuki syndrome XL 40 69
KMT2D Kabuki syndrome AD 350 670
KRAS* Noonan syndrome, Cardiofaciocutaneous syndrome AD 63 35
KYNU Hydroxykynureninuria, Vertebral, cardiac, renal, and limb defects syndrome 2 AR 4 7
LEFTY2* Left-right axis malformations AD 1 3
MED12 Ohdo syndrome, Mental retardation, with Marfanoid habitus, FG syndrome, Opitz-Kaveggia syndrome, Lujan-Fryns syndrome XL 29 30
MED13L Transposition of the great arteries, dextro-looped 1, Mental retardation and distinctive facial features with or without cardiac defects, Congenital heart defects and intellectual disability, Intellectual disability, autosomal recessive AD/AR 92 78
MEIS2 Cleft palate, cardiac defects, and mental retardation (CPCMR) AD 10 18
MMP21 Heterotaxy, visceral, 7 AR 4 18
MYCN Feingold syndrome AD 27 41
MYO18B Klippel-Feil syndrome 4, autosomal recessive, with myopathy and facial dysmorphism AR 2 4
MYRF Congenital heart malformations, Congenital abnormalities of the kidney and urinary tract AD 1 1
NAA15 Congenital heart malformations AD 10 32
NF1* Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndrome AD 1157 2901
NIPBL Cornelia de Lange syndrome AD 311 425
NKX2-5 Conotruncal heart malformations, Hypothyroidism, congenital nongoitrous,, Atrial septal defect, Ventricular septal defect 3, Conotruncal heart malformations, variable, Tetralogy of Fallot AD 45 108
NKX2-6 Persistent truncus arteriosus, Conotruncal heart malformations AD/AR 2 9
NODAL Heterotaxy, visceral AD 4 15
NONO Mental retardation, X-linked, syndrome 34, Left ventricular non-compaction cardiomyopathy (LVNC) XL 10 4
NOTCH1 Aortic valve disease, Adams-Oliver syndrome AD 56 96
NOTCH2* Alagille syndrome, Hajdu-Cheney syndrome AD 37 70
NR2F2 Congenital heart defects, multiple types, 4 AD 12 16
NSD1 Sotos syndrome, Weaver syndrome, Beckwith-Wiedemann syndrome AD 329 517
PITX2 Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomaly AD 23 101
PKD1L1 Heterotaxy, visceral, 8, autosomal AR 2 6
PPP1CB Noonan syndrome-like disorder with loose anagen hair 2 AD 8 11
PRDM6 Patent ductus arteriosus 3, Congenital heart malformations 4 3
PRKD1 Congenital heart defects and ectodermal dysplasia AD 2 7
PTPN11 Noonan syndrome, Metachondromatosis AD 135 140
PUF60 Short stature, Microcephaly AD 24 30
RAB23 Carpenter syndrome 1 AR 5 15
RAF1 LEOPARD syndrome, Noonan syndrome, Dilated cardiomyopathy (DCM) AD 45 53
RBM10 TARP syndrome XL 12 10
RERE* Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH) 24 24
RIT1 Noonan syndrome AD 23 26
SALL4 Acro-renal-ocular syndrome, Duane-radial ray/Okohiro syndrome AD 21 56
SMARCB1 Schwannomatosis, Rhabdoid tumor predisposition syndrome, Coffin-Siris syndrome 3 AD 36 118
SMC1A Cornelia de Lange syndrome XL 73 87
SMC3 Cornelia de Lange syndrome AD 25 21
SOS1 Noonan syndrome AD 44 71
SOS2 Noonan syndrome 9 AD 4 6
STAG2 Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder XL 6 14
STRA6 Microphthalmia, syndromic, Microphthalmia, isolated, with coloboma AR 22 33
TAB2 Congenital heart defects, multiple types, 2 AD 13 31
TBX1 Conotruncal anomaly face syndrome AD 17 72
TBX20* Atrial septal defect 4 AD 4 28
TBX5 Holt-Oram syndrome AD 61 127
TFAP2B Patent ductus arteriosus, nonsyndromic, Char syndrome AD 10 12
TGDS Catel-Manzke syndrome AR 6 7
TLL1 Atrial septal defect AD 3 7
TMEM94 Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH) AR 3
ZEB2* Mowat-Wilson syndrome AD 154 287
ZFPM2 46,XY sex reversal, Diaphragmatic hernia 3, Tetralogy of Fallot AD/AR 9 50
ZIC3 Heterotaxy, visceral, VACTERL association, Congenital heart defects, nonsyndromic XL 15 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 Congenital Structural Heart Disease Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ACTC1 Chr15:35080829 c.*1784T>C NM_005159.4
BMPR2 Chr2:203241251 c.-947_-946delGCinsAT NM_001204.6 rs1085307144
BMPR2 Chr2:203241851 c.-347C>T NM_001204.6
BMPR2 Chr2:203241919 c.-279C>A NM_001204.6
BMPR2 Chr2:203242106 c.-92C>A NM_001204.6
BMPR2 Chr2:203395505 c.968-12T>G NM_001204.6
CHD7 Chr8:61734568 c.2836-15C>G NM_017780.3
CHD7 Chr8:61757794 c.5051-15T>A NM_017780.3
CHD7 Chr8:61763034 c.5405-18C>A NM_017780.3 rs199981784
CHD7 Chr8:61763035 c.5405-17G>A NM_017780.3 rs794727423
CHD7 Chr8:61763039 c.5405-13G>A NM_017780.3 rs1131690787
CREBBP Chr16:3788684 c.4281-11C>G NM_004380.2 rs587783493
EHMT1 Chr9:140678546 c.2382+1697T>G NM_024757.4 rs786205602
ELN Chr7:73480347 c.2272+20C>G NM_001278939.1
ENG Chr9:130578354 c.1742-22T>C NM_001114753.2
ENG Chr9:130588962 c.361-11T>A NM_001114753.2
ENG Chr9:130616692 c.-58G>A NM_001114753.2 rs971268057
ENG Chr9:130616761 c.-127C>T NM_001114753.2
ENG Chr9:130616776 c.-142A>T NM_001114753.2
EP300 Chr22:41537040 c.1879-12A>G NM_001429.3
EVC Chr4:5749725 c.940-150T>G NM_153717.2
FLNA ChrX:153581587 c.6023-27_6023-16delTGACTGACAGCC NM_001110556.1
FOXC1 Chr6:1610252 NM_001453.2
GATA4 Chr8:11561282 c.-989C>T NM_002052.3
GATA4 Chr8:11561369 c.-902G>T NM_002052.3
GATA4 Chr8:11561399 NM_002052.3 rs1195641788
GATA4 Chr8:11612500 c.910-55T>C NM_002052.3
GATA4 Chr8:11612745 c.997+103G>T NM_002052.3 rs113049875
GATA4 Chr8:11614418 c.998-26G>A NM_002052.3
GATA5 Chr20:61051165 c.-201A>G NM_080473.4
GATA5 Chr20:61051462 NM_080473.4 rs1193866928
GATA6 Chr18:19749151 c.-530A>T NM_005257.4
GATA6 Chr18:19749272 c.-409C>G NM_005257.4
HNRNPK Chr9:86590455 c.214-35A>G NM_002140.3
JAG1 Chr20:10629767 c.1349-12T>G NM_000214.2
KMT2D Chr12:49428461 c.10356-12G>A NM_003482.3
NF1 Chr17:29422055 c.-273A>C NM_001042492.2
NF1 Chr17:29422056 c.-272G>A NM_001042492.2
NF1 Chr17:29431417 c.60+9031_60+9035delAAGTT NM_001042492.2
NF1 Chr17:29475515 c.61-7486G>T NM_001042492.2
NF1 Chr17:29488136 c.288+2025T>G NM_001042492.2
NF1 Chr17:29508426 c.587-14T>A NM_001042492.2
NF1 Chr17:29508428 c.587-12T>A 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
NF1 Chr17:29527428 c.889-12T>A 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 Chr17:29540877 c.1393-592A>G NM_001042492.2
NF1 Chr17:29542762 c.1527+1159C>T NM_001042492.2 rs878853868
NF1 Chr17:29548419 c.1642-449A>G NM_001042492.2
NF1 Chr17:29549489 c.*481A>G NM_001128147.2
NF1 Chr17:29553439 c.2002-14C>G NM_001042492.2
NF1 Chr17:29554225 c.2252-11T>G NM_001042492.2
NF1 Chr17:29556025 c.2410-18C>G NM_001042492.2
NF1 Chr17:29556027 c.2410-16A>G NM_001042492.2
NF1 Chr17:29556028 c.2410-15A>G NM_001042492.2
NF1 Chr17:29556031 c.2410-12T>G NM_001042492.2
NF1 Chr17:29556839 c.2851-14_2851-13insA NM_001042492.2
NF1 Chr17:29557267 c.2991-11T>G NM_001042492.2
NF1 Chr17:29558777 c.3198-314G>A NM_001042492.2
NF1 Chr17:29563299 c.3974+260T>G NM_001042492.2
NF1 Chr17:29577082 c.4110+945A>G NM_001042492.2
NF1 Chr17:29580296 c.4173+278A>G NM_001042492.2
NF1 Chr17:29588708 c.4578-20_4578-18delAAG NM_001042492.2
NF1 Chr17:29588715 c.4578-14T>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 Chr17:29661577 c.5813-279A>G 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 Chr17:29676127 c.7190-11_7190-10insGTTT NM_001042492.2
NF1 Chr17:29685177 c.7971-321C>G NM_001042492.2
NF1 Chr17:29685481 c.7971-17C>G NM_001042492.2
NF1 Chr17:29685665 c.8113+25A>T NM_001042492.2
NIPBL Chr5:36877039 c.-321_-320delCCinsA NM_133433.3 rs724159980
NIPBL Chr5:36877266 c.-94C>T NM_133433.3
NIPBL Chr5:36953718 c.-79-2A>G NM_133433.3
NIPBL Chr5:37022138 c.5329-15A>G NM_133433.3 rs587783968
NIPBL Chr5:37026318 c.5710-13_5710-12delCTinsAA NM_133433.3
NKX2-5 Chr5:172662741 NM_004387.3
NKX2-5 Chr5:172672291 c.-10205G>A .
NKX2-5 Chr5:172672303 c.-10217G>C .
NR2F2 Chr15:96869479 c.-60C>T NM_001145155.1
PITX2 Chr4:111538758 c.*520_*522delTAT NM_000325.5 rs561702585,rs775662096
PITX2 Chr4:111539855 c.412-11A>G NM_000325.5
PITX2 Chr4:111559138 c.-1214_-1213delAT NM_153426.2
PTPN11 Chr12:112915602 c.934-59T>A NM_002834.3
SMARCB1 Chr22:24130008 c.93+559A>G NM_003073.3
SMARCB1 Chr22:24176316 c.1119-12C>G NM_003073.3
SMARCB1 Chr22:24176437 c.*70C>T NM_003073.3
SMARCB1 Chr22:24176449 c.*82C>T NM_003073.3
TBX1 Chr22:19743578 c.-777C>T NM_080647.1
TBX1 Chr22:19743735 c.-620A>C NM_080647.1 rs536892777
TBX20 Chr7:35293780 c.-549G>A NM_001077653.2 rs571512677
TBX5 Chr12:114704515 c.*88822C>A NM_000192.3 rs141875471
ZEB2 Chr2:145274987 c.-69-1G>A NM_014795.3
ZEB2 Chr2:145274988 c.-69-2A>C NM_014795.3

Added and removed genes from the panel

Genes added Genes removed
AFF4
AMMECR1
ARHGAP31
ARID1A
ARID1B
BRAF
C12ORF57
CDK9
CFAP53
CHRM2
CREBBP
DLL4
DOCK6
EHMT1
EOGT
EP300
EVC
EVC2
FOXC1
FOXF1
FOXH1
FOXP1
HAND2
HDAC8
HNRNPK
KDM6A
KMT2D
KRAS
KYNU
MED12
MED13L
MMP21
MYO18B
MYRF
NIPBL
NONO
PKD1L1
PRDM6
PTPN11
PUF60
RAB23
RAF1
RERE
RIT1
SMARCB1
SMC1A
SMC3
SOS1
STAG2
STRA6
TMEM94
ZEB2

Test Strengths

The strengths of this test include:
  • CAP and ISO-15189 accredited laboratory
  • 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 publicly available analytic validation demonstrating complete details of test performance
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous 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: B3GAT3 (NM_001288722:5). 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 (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • 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 high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999
Insertions, deletions and indels by sequence analysis
1-10 bps 96.9% (7,563/7,806) >99.9999
11-50 bps 99.13% (2,524/2,546) >99.9999
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

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 and regulatory 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 including, 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, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the 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 is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call.
Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed 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, abstracts and variant databases used to help ordering providers 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. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. 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.

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