Comprehensive Epilepsy Panel

  • bpg-method PLUS
  • bpg-method SEQ
  • bpg-method DEL/DUP

Test code: NE1001

The Blueprint Genetics Comprehensive Epilepsy Panel is a 194 gene test for genetic diagnostics of patients with clinical suspicion of epilepsy.

For patients aged between 24 and 60 months, please check the no cost Europe and Middle-East program: Paediatric Epilepsy? Look Beyond…

The panel covers generalized and focal genetic epilepsies, epileptic encephalopathies, progressive myoclonic epilepsies and epilepsies associated with X-linked mental retardation. Also other syndromes that include epileptic seizures as one of the main manifestation are included as well as hereditary metabolic diseases that manifest as epilepsy. We recommend the panel also to patients with sudden unexplained death. New genomic technologies have led to advances in understanding of the different genomic and genetic architectures across all the major classes of epilepsy, including uncovering a surprising overlap among seemingly different disorders (PMID: 26302787). There is an increasingly wide phenotypic spectrum associated with mutations in several eplepsy genes such as GABRA1, KCNQ2, KCNT1, SCN8A, TBC1D24, and DEPDC5. Thus using a comprehensive epilepsy panel is justifyed. Few studies have applied next generation sequencing technologies to analyze gene panels in unselected epilepsy patient cohorts (PMID: 22612257, 24848745). The reported total diagnostic yield has been 47-48% but the diagnostic yield per gene cannot be estimated from these studies due to small patient cohorts and variable number of genes tested (67 to 265). Recently, it was shown that 25% of sudden unexpected death in epilepsy (SUDEP) patients have mutations in epilepsy genes (PMID: 26704558). This Comprehensive Epilepsy Panel covers the following smaller panels: Idiopathic Generalized and Focal Epilepsy Panel, Epileptic Encephalopathy Panel, NCL and Progressive Myoclonic Epilepsy Panel, Leukodystrophy and Leukoencephalopathy Panel, Epilepsy and X-linked Mental Retardation Panel and Metabolic Epilepsy Panel.

About Epilepsy

Epilepsy is defined by recurrent, unprovoked seizures due to abnormal, synchronized neuronal firing in the brain. The condition is one of the most common neurological conditions. Approximately 20-30 % of epilepsy cases are caused by acquired conditions, but the remaining 70-80 % of cases are believed to be due to one or more genetic factors. The epilepsies can be broadly grouped into three classes: genetic generalized epilepsy (formerly idiopathic generalized epilepsy); focal epilepsy; and epileptic encephalopathy. There are then several specific syndromes within each class defined by differences in specific seizure types, electroencephalogram (EEG) patterns, age of onset and disease progression. Epilepsy is also one of the manifestations of many dysmorphology and multisystemic genetic syndromes and often occurs in neurodegenerative diseases.

Availability

Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more: http://blueprintgenetics.com/faqs/#prenatal

Genes in the Comprehensive Epilepsy Panel and their clinical significance
Gene Associated phenotypes Inheritance ClinVar HGMD
ABCD1* Adrenoleukodystrophy XL 58 654
ADAR Dyschromatosis symmetrica hereditaria, Aicardi-Goutières syndrome AD/AR 16 202
ADSL Adenylosuccinase deficiency AR 22 53
AFG3L2* Spastic ataxia, Spinocerebellar ataxia AD/AR 19 25
AGA Aspartylglucosaminuria AR 29 35
AIMP1 Leukodystrophy, hypomyelinating AR 3 5
ALDH5A1 Succinic semialdehyde dehydrogenase deficiency AR 8 67
ALDH7A1 Epilepsy, pyridoxine-dependent AR 29 110
ALG13 Congenital disorder of glycosylation XL 3 6
AMACR Alpha-methylacyl-CoA racemase deficiency, Bile acid synthesis defect AR 3 13
AMT Glycine encephalopathy AR 26 51
ARG1 Hyperargininemia AR 13 52
ARHGEF9 Epileptic encephalopathy, early infantile XL 3 11
ARSA Metachromatic leukodystrophy AR 61 212
ARX Lissencephaly, Epileptic encephalopathy, Corpus callosum, agenesis of, with abnormal genitalia, Partington syndrome, Proud syndrome, Hydranencephaly with abnormal genitalia, Mental retardation XL 56 80
ASAH1 Spinal muscular atrophy with progressive myoclonic epilepsy, Farber lipogranulomatosis AR 11 53
ASPA Aspartoacylase deficiency (Canavan disease) AR 19 90
ATP13A2 Parkinson disease (Kufor-Rakeb syndrome) AR 11 35
ATRX Carpenter-Waziri syndrome, Alpha-thalassemia/mental retardation syndrome, Holmes-Gang syndrome, Juberg-Marsidi syndrome, Smith-Fineman-Myers syndrome, Mental retardation-hypotonic facies syndrome XL 42 149
BTD Biotinidase deficiency AR 165 231
CACNA1A Migraine, familial hemiplegic, Episodic ataxia AD 55 181
CACNA1H Childhood absence epilepsy AD 4 49
CACNB4 Episodic ataxia AD 1 6
CASK Mental retardation and microcephaly with pontine and cerebellar hypoplasia, FG syndrome, Mental retardation XL 43 80
CASR Hypocalcemia, Neonatal hyperparathyroidism, Familial Hypocalciuric hypercalcemia with transient Neonatal hyperparathyroidism AD/AR 78 392
CDKL5 Epileptic encephalopathy, early infantile, Rett syndrome, atypical, Angelman-like syndrome XL 222 254
CERS1 Epilepsy, progressive myoclonic AR 4 1
CHD2 Epileptic encephalopathy, childhood-onset AD 42 35
CHRNA2 Epilepsy, nocturnal frontal lobe AD 1 11
CHRNA4 Epilepsy, nocturnal frontal lobe AD 8 23
CHRNB2 Epilepsy, nocturnal frontal lobe AD 8 12
CLCN2 Leukoencephalopathy with ataxia, Epilepsy AD/AR 18 29
CLN3 Ceroid lipofuscinosis, neuronal AR 69 64
CLN5 Ceroid lipofuscinosis, neuronal AR 40 42
CLN6 Ceroid lipofuscinosis, neuronal AR 21 80
CLN8 Ceroid lipofuscinosis, neuronal AR 31 35
CNTNAP2 Pitt-Hopkins like syndrome, Cortical dysplasia-focal epilepsy syndrome AR 22 60
COL4A1 Schizencephaly, Anterior segment dysgenesis with cerebral involvement, Retinal artery tortuosity, Porencephaly, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Brain small vessel disease AD 27 88
COX15 Leigh syndrome, Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency AR 6 5
CPT2 Carnitine palmitoyltransferase II deficiency AR 36 102
CSF1R Leukoencephalopathy, diffuse hereditary, with spheroids AD 44 70
CSTB Epilepsy, progressive myoclonic AR 16 13
CTSD Ceroid lipofuscinosis, neuronal AR 11 15
CTSF Neuronal ceroid lipofuscinosis AR 7 9
CUL4B Mental retardation, syndromic, Cabezas XL 9 34
DARS2 Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation AR 15 56
DCX Lissencephaly, Subcortical laminal heterotopia XL 117 138
DEPDC5 Epilepsy, familial focal, with variable foci AD 50 68
DNAJC5 Kufs disease,, Ceroid lipofuscinosis, neuronal 4, Parry AD 2 2
DNM1* Epileptic encephalopathy, early infantile AD 8 15
DOCK7 Epilepitic encephalopathy AR 11 4
DPYD 5-fluorouracil toxicity AD/AR 10 96
EARS2 Combined oxidative phosphorylation deficiency AR 8 26
EEF1A2 Epileptic encephalopathy, early infantile, Mental retardation AD 6 10
EFHC1 Epilepsy, myoclonic juvenile, Epilepsy, severe intractable, Epilepsy, juvenile absence AD/AR 3 17
EIF2B1 Leukoencephalopathy with vanishing white matter, Ovarioleukodystrophy AR 7 9
EIF2B2 Leukoencephalopathy with vanishing white matter, Ovarioleukodystrophy AR 8 25
EIF2B3 Leukoencephalopathy with vanishing white matter, Ovarioleukodystrophy AR 5 20
EIF2B4 Leukoencephalopathy with vanishing white matter, Ovarioleukodystrophy AR 6 29
EIF2B5 Leukoencephalopathy with vanishing white matter, Ovarioleukodystrophy AR 14 95
EPM2A Epilepsy, progressive myoclonic AR 12 74
ETFA Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 7 28
ETFB Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 7 13
ETFDH Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 36 168
FAM126A Leukodystrophy, hypomyelinating AR 6 12
FH Hereditary leiomyomatosis and renal cell cancer AD/AR 89 161
FLNA Frontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defects XL 86 209
FOLR1 Cerebral folate deficiency AR 4 24
FOXG1 Rett syndrome, congenital variant AD 68 115
FOXRED1 Leigh syndrome, Mitochondrial complex I deficiency AR 10 7
GABRA1 Epileptic encephalopathy, early infantile, Epilepsy, childhood absence, Epilepsy, juvenile myoclonic AD 15 35
GABRB3 Epilepsy, childhood absence AD 5 46
GABRG2 Generalized epilepsy with febrile seizures plus, Familial febrile seizures, Dravet syndrome, Epilepsy, childhood absence AD 21 23
GALC Krabbe disease AR 35 210
GAMT Guanidinoacetate methyltransferase deficiency AR 12 53
GCDH Glutaric aciduria AR 36 198
GCH1 Dopa-Responsive Dystonia Hyperphenylalaninemia, BH4-deficient, GTP Cyclohydrolase 1-Deficient Dopa-Responsive Dystonia AD/AR 25 229
GFAP Alexander disease AD 110 112
GJC2 Spastic paraplegia, Lymphedema, hereditary, Leukodystrophy, hypomyelinating AD/AR 15 53
GLDC Glycine encephalopathy AR 89 214
GNAO1 Epileptic encephalopathy, early infantile AD 12 20
GNE Inclusion body myopathy, Nonaka myopathy, Sialuria AD/AR 32 193
GOSR2* Epilepsy, progessive myoclonic AR 5 3
GPHN Hyperekplexia, Molybdenum cofactor deficiency AD/AR 25 20
GRIA3 Mental retardation XL 9 17
GRIN2A Epilepsy, focal, with speech disorder AD 37 75
GRIN2B Epileptic encephalopathy, early infantile, Mental retardation AD 38 41
GRN Frontotemporal lobar degeneration with TDP43 inclusions, GRN-related, Neuronal ceroid lipofuscinosis AD/AR 24 165
HCN1 Epileptic encephalopathy, early infantile AD 7 8
HEPACAM Megalencephalic leukoencephalopathy with subcortical cysts, remitting AD/AR 9 23
HNRNPU Intellectual disability and seizures AD 4 34
HSD17B10 17-beta-hydroxysteroid dehydrogenase X deficiency, Mental retardation, syndromic XL 8 12
HSPD1* Spastic paraplegia, Leukodystrophy, hypomyelinating AD/AR 4 4
IQSEC2 Mental retardation XL 16 36
KCNA1 Episodic ataxia/myokymia syndrome AD 20 37
KCNA2 Epileptic encephalopathy, early infantile AD 5 10
KCNB1 Early infantile epileptic encephalopathy AD 6 9
KCNC1 Epilepsy, progressive myoclonic AD 1 1
KCNQ2 Epileptic encephalopathy, early infantile, Benign familial neonatal seizures, Myokymia AD 240 205
KCNQ3 Seizures, benign neonatal AD 11 17
KCNT1 Epilepsy, nocturnal frontal lobe AD 16 28
KCTD7* Epilepsy, progressive myoclonic AR 12 13
KDM5C Mental retardation, syndromic, Claes-Jensen XL 21 44
KIF1A Spastic paraplegia, Neuropathy, hereditary sensory, Mental retardation AD/AR 35 27
L2HGDH L-2-hydroxyglutaric aciduria AR 8 75
LGI1 Epilepsy, familial temporal lobe AD 19 48
MARS2 Combined oxidative phosphorylation deficiency AR 6 5
MBD5 Mental retardation AD 21 72
MECP2 Angelman-like syndrome, Autism, Rett syndrome, Encephalopathy, Mental retardation XL 429 937
MED12 Ohdo syndrome, Mental retardation, with Marfanoid habitus, FG syndrome, Opitz-Kaveggia syndrome, Lujan-Fryns syndrome XL 17 19
MEF2C Mental retardation AD 25 66
MFSD8 Ceroid lipofuscinosis, neuronal AR 19 41
MLC1 Megalencephalic leukoencephalopathy with subcortical cysts AR 17 111
MOCS1 Molybdenum cofactor deficiency AR 7 32
MTHFR Homocystinuria due to MTHFR deficiency AR 51 127
MTOR Smith-Kingsmore syndrome AD 7 10
NDUFAF5 Mitochondrial complex I deficiency AR 8 10
NECAP1* Epileptic encephalopathy, early infantile AR 1 1
NEU1 Sialidosis AR 19 56
NHLRC1 Epilepsy, progressive myoclonic AR 14 70
NOTCH3 Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) AD 22 313
NRXN1 Pitt-Hopkins like syndrome, Schizophrenia AD/AR 51 290
OFD1 Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome XL 129 148
OPHN1 Mental retardation, with cerebellar hypoplasia and distinctive facial appearance XL 13 34
PCDH19 Epileptic encephalopathy, early infantile XL 62 141
PGK1 Phosphoglycerate kinase 1 deficiency XL 14 26
PHF6 Borjeson-Forssman-Lehmann syndrome XL 15 27
PIGA* Multiple congenital anomalies-hypotonia-seizures syndrome XL 19 14
PLCB1 Epileptic encephalopathy, early infantile AR 5 10
PLP1 Spastic paraplegia, Pelizaeus-Merzbacher disease XL 41 266
PNKP Epileptic encephalopathy, early infantile, Ataxia-oculomotor AR 21 16
PNPO Pyridoxamine 5'-phosphate oxidase deficiency AR 14 28
POLR3A Leukodystrophy, hypomyelinating AR 21 67
POLR3B Leukodystrophy, hypomyelinating AR 11 54
PPT1 Ceroid lipofuscinosis, neuronal AR 72 77
PRICKLE1 Epilepsy, progressive myoclonic AD/AR 4 14
PRICKLE2 Epilepsy, progessive myoclonic AD 1 6
PRODH* Hyperprolinemia AR 19 26
PRRT2 Episodic kinesigenic dyskinesia AD 32 91
PSAP Krabbe disease, atypical, Metachromatic leukodystrophy due to saposin-b deficiency, Combined saposin deficiency, Gaucher disease, atypical, due to saposin C deficiency AR 15 24
PTS Hyperphenylalaninemia, BH4-deficient AR 11 84
PURA Mental retardation AD 36 23
QDPR Hyperphenylalaninemia, BH4-deficient AR 8 55
RAB39B Waisman parkinsonism-mental retardation syndrome, Mental retardation XL 4 11
RELN Lissencephaly, Epilepsy, familial temporal lobe AD/AR 17 31
RNASEH2A Aicardi-Goutières syndrome AR 12 21
RNASEH2B Aicardi-Goutières syndrome AR 5 39
RNASEH2C Aicardi-Goutières syndrome AR 4 14
RNASET2 Leukoencephalopathy, cystic, without megalencephaly AR 6 11
SAMHD1 Aicardi-Goutières syndrome AR 22 48
SCARB2 Epilepsy, progressive myoclonic AR 22 22
SCN1A Migraine, familial hemiplegic, Epileptic encephalopathy, early infantile, Generalized epilepsy with febrile seizures plus AD 476 1282
SCN1B Atrial fibrillation, Brugada syndrome, Generalized epilepsy with febrile seizures plus AD 11 18
SCN2A Epileptic encephalopathy, early infantile, Seizures, benign familial infantile AD 86 131
SCN8A Cognitive impairment, Epileptic encephalopathy, early infantile AD 56 55
SCN9A Paroxysmal extreme pain disorder AD/AR 34 102
SERPINI1 Encephalopathy, familial, with neuroserpin inclusion bodies AD 5 7
SIK1 Epileptic encephalopathy, early infantile AD 5 6
SLC2A1 Stomatin-deficient cryohydrocytosis with neurologic defects, Epilepsy, idiopathic generalized, GLUT1 deficiency syndrome AD/AR 65 253
SLC6A1 Myoclonic-astastic epilepsy AD 6 12
SLC6A8* Creatine deficiency syndrome XL 19 127
SLC9A6 Mental retardation, syndromic, Christianson XL 21 18
SLC12A5 Epileptic encephalopathy, early infantile AR 3 12
SLC13A5 Epileptic encephalopathy, early infantile AR 10 14
SLC19A3 Thiamine metabolism dysfunction syndrome AR 14 24
SLC25A15* Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome AR 18 35
SLC25A22 Epileptic encephalopathy, early infantile AR 6 4
SLC35A2 Congenital disorder of glycosylation XL 7 13
SLC46A1 Folate malabsorption AR 17 19
SMS Mental retardation, Snyder-Robinson XL 9 10
SNAP25 Myasthenic syndrome, congenital AD 2 3
SOX10 Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease AD 31 119
SPTAN1 Epileptic encephalopathy, early infantile AD 15 15
ST3GAL3 Epileptic encephalopathy, early infantile, Mental retardation AR 3 3
ST3GAL5 Ganglioside GM3 synthase deficiency AR 4 4
STX1B Generalized epilepsy with febrile seizures plus AD 7 9
STXBP1 Epileptic encephalopathy, early infantile AD 63 156
SUMF1 Multiple sulfatase deficiency AR 18 51
SUOX Sulfocysteinuria AR 6 26
SYN1 Epilepsy, with variable learning disabilities and behavior disorders XL 7 5
SYNGAP1 Mental retardation AD 23 57
SZT2 Epileptic encephalopathy, early infantile AR 5 6
TBC1D24 Deafness, Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome AD/AR 27 41
TCF4 Corneal dystrophy, Fuchs endothelial, Pitt-Hopkins syndrome AD 51 129
TPP1 Spinocerebellar ataxia, Neuronal ceroid lipofuscinosis type 2 AR 33 109
TREX1 Vasculopathy, retinal, with cerebral leukodystrophy, Chilblain lupus, Aicardi-Goutières syndrome AD/AR 24 65
TSC1 Lymphangioleiomyomatosis, Tuberous sclerosis AD 61 306
TSC2 Lymphangioleiomyomatosis, Tuberous sclerosis AD 141 977
TUBB4A* Leukodystrophy, hypomyelinating, Dystonia AD 35 36
UBE2A Mental retardation, syndromic, Nascimento XL 4 21
UBE3A* Angelman syndrome AD 143 170
WDR45 Neurodegeneration with brain iron accumulation XL 20 56
WWOX Epileptic encephalopathy, early infantile, Spinocerebellar ataxia AR 19 35
ZEB2* Mowat-Wilson syndrome AD 104 247

*Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Gene Genomic location HG19 HGVS RefSeq RS-number Comment Reference
AMT Chr3:49459938 c.-55C>T NM_000481.3 rs386833677
CDKL5 ChrX:18525053 c.-162-2A>G NM_003159.2 rs786204973
DARS2 Chr1:173797450 c.228-21_228-20insC NM_018122.4 rs367543010
GJC2 Chr1:228337561 c.-167A>G NM_020435.3
GJC2 Chr1:228337558 c.-170A>G NM_020435.3
MOCS1 Chr6:39874534 c.*365_*366delAG NM_005943.5 rs397518419
MTHFR Chr1:11863212 c.-13-28_-13-27delCT NM_005957.4 rs786204005
MTHFR Chr1:11850973 c.1753-18G>A NM_005957.4 rs777661576
OFD1 ChrX:13773245 c.1130-22_1130-19delAATT NM_003611.2 rs312262865
OFD1 ChrX:13768358 c.935+706A>G NM_003611.2 rs730880283
PNKP Chr19:50364799 c.1387-33_1386+49delCCTCCTCCCCTGACCCC NM_007254.3 rs752902474
POLR3A Chr10:79769277 c.1909+18G>A NM_007055.3 rs267608677
PPT1 Chr1:40539203 c.*526_*529delATCA NM_000310.3 rs386833624
PTS Chr11:112098994 c.84-323A>T NM_000317.2 rs794726657
TSC2 Chr16:2098067 c.-30+1G>C NM_000548.3 rs587778004

The strengths of this test include:

  • Blueprint Genetics is one of the few laboratories worldwide with CAP and ISO-15189 accreditation for NGS panels and CLIA certification
  • Superior sequencing quality
  • Careful selection of genes based on current literature, our experience and the most current mutation databases
  • Transparent and easy access to quality and performance data at the patient level that are accessible via our Nucleus portal
  • Transparent and reproducible analytical validation for each panel (see Test performance section; for complete details, see our Analytic Validation)
  • Sequencing and high resolution del/dup analysis available in one test
  • Inclusion of non-coding disease causing variants where clinically indicated (please see individual Panel descriptions)
  • Interpretation of variants following ACMG variant classification guidelines
  • Comprehensive clinical statement co-written by a PhD geneticist and a clinician specialist

 

This test does not detect the following:

  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Variants in regulatory or non-coding regions of the gene unless otherwise indicated (please see Non-coding disease causing variants covered by the panel). This mean for instance intronic variants locating deeper than 15 nucleotides from the exon-intron boundary.

 

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
  • Disorders caused by long repetitive sequences (e.g. trinucleotide repeat expansions)

 

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.

Blueprint Genetics offers a Comprehensive Epilepsy Panel that covers classical genes associated with epilepsy, leukoencephalopathy, metabolic epilepsy, neuronal ceroid lipofuscinosis and sudden unexpected death. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.

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. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint 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 statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. 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. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ 81479
DEL/DUP 81479


ICD codes

Commonly used ICD-10 codes when ordering the Comprehensive Epilepsy Panel

ICD-10 Disease
G40.9 Epilepsy

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • 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.

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