Cataract Panel

Summary
Is a 113 gene panel that includes assessment of non-coding variants.

In addition, it also includes the maternally inherited mitochondrial genome.
Is ideal for patients with a clinical suspicion / diagnosis of congenital cataracts or a syndrome with cataracts as a feature.

Analysis methods
  • PLUS
Availability
4 weeks
Number of genes
113
Test code
OP0201
Panel tier
Tier 1
CPT Code *
81403, 81404, 81405 x3, 81406 x3, 81408, 81479, 81460, 81465
* The CPT codes provided are based on AMA guidelines and are for informational purposes only. CPT coding is the sole responsibility of the billing party. Please direct any questions regarding coding to the payer being billed.

Summary

The Blueprint Genetics Cataract Panel (test code OP0201):

Read about our accreditations, certifications and CE-marked IVD medical devices here.

ICD Codes

Refer to the most current version of ICD-10-CM manual for a complete list of ICD-10 codes.

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Please see Sample Requirements for accepted saliva kits)

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

We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.

Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.

Read more about our sample requirements here.

Cataract is defined as opacification of the normally transparent crystalline lens. Cataract can be classified as congenital, infantile, juvenile, presenile, and senile. Congenital cataract (CC) is present at birth or during early childhood and is one of the most common ocular diseases causing visual impairment or blindness in children worldwide. Nuclear cataract is the most common type of hereditary CC and is characterized by the opacification limited to the embryonic and/or fetal nuclei of the lens (PMID: 24384146). It can be inherited in an autosomal dominant, autosomal recessive, or X-linked manner, of which the autosomal dominant mode is the most common. Nuclear CC is genetically highly heterogeneous. Mutations in lens crystallins (CRYAACRYABCRYBB1CRYBB2CRYBB3CRYGCCRYGD) explain approximately half of the cases, followed by connexins (GJA3GJA8). Congenital nuclear cataract can be isolated (70%) or associated with other ocular disorders, such as microphthalmia or aniridia. It may also be part of multisystem genetic disorders such as Nance-Horan syndrome (NHS), Lowe syndrome (OCRL) or neurofibromatosis type 2 (NF2). The prevalence of cataract in children has been estimated between 1-15:10,000.

Genes in the Cataract Panel and their clinical significance

To view complete table content, scroll horizontally.

GeneAssociated phenotypesInheritanceClinVarHGMD
ABCB6Blood group, Langereis system, Pseudohyperkalemia, Dyschromatosis universalis hereditaria, Microphthalmia, isolated, with coloboma 7AD/BG920
ADAMTS18Knobloch syndrome 2, Microcornea, myopic chorioretinal atrophy, and telecanthus, Retinal dystrophy, early onset, autosomal recessiveAR414
ADAMTSL4Ectopia lentis, isolatedAR1127
AGK*Sengers syndrome, Cataract 38AR1827
ALDH18A1Spastic paraplegia, Cutis laxaAD/AR2230
BCORMicrophthalmia, syndromic, Oculofaciocardiodental syndromeXL4053
BFSP1Cataract 33AR47
BFSP2CataractAD27
CHMP4BCataract 31, multiple typesAD22
COL11A1Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2, DeafnessAD/AR3494
COL18A1Knobloch syndromeAR2731
COL2A1Avascular necrosis of femoral head, Rhegmatogenous retinal detachment, Epiphyseal dysplasia, with myopia and deafness, Czech dysplasia, Achondrogenesis type 2, Platyspondylic dysplasia Torrance type, Hypochondrogenesis, Spondyloepiphyseal dysplasia congenital (SEDC), Spondyloepimetaphyseal dysplasia (SEMD) Strudwick type, Kniest dysplasia, Spondyloperipheral dysplasia, Mild SED with premature onset arthrosis, SED with metatarsal shortening, Stickler syndrome type 1AD/AR180561
COL4A1Schizencephaly, Anterior segment dysgenesis with cerebral involvement, Retinal artery tortuosity, Porencephaly, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Brain small vessel diseaseAD58107
CRYAACataractAD/AR1224
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-relatedAD1428
CRYBA1Cataract 10, multiple typesAD913
CRYBA4Cataract 23AD410
CRYBB1CataractAD/AR718
CRYBB2*CataractAD1027
CRYBB3CataractAR37
CRYGCCataractAD1028
CRYGDCataractAD1026
CRYGSCataract, progressive polymorphic corticalAD38
CTDP1Congenital cataracts, facial dysmorphism, and neuropathyAR11
CYP27A1Cerebrotendinous xanthomatosisAR69110
DNMBPCataractAR
EPHA2Cataract 6, multiple typesAD/AR720
ERCC2Xeroderma pigmentosum, Trichothiodystrophy, photosensitive, Cerebrooculofacioskeletal syndrome 2AR2698
ERCC5Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne syndromeAR2154
ERCC6*Xeroderma Pigmentosum-Cockayne Syndrome, De Sanctis-Cacchione syndromeAD/AR87135
ERCC8UV-sensitive syndrome, Cockayne syndromeAR3464
EYA1Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndromeAD56218
FAM126ALeukodystrophy, hypomyelinatingAR812
FOXE3Aphakia, congenital primary, Anterior segment mesenchymal dysgenesis, Cataract 34, Aortic aneurysm, familial thoracicAR/AD929
FTLHyperferritinemia-cataract syndrome, L-ferritin deficiency, Neurodegeneration with brain iron accumulationAD/AR2163
FYCO1CataractAR1020
FZD4Retinopathy of prematurity, Exudative vitreoretinopathyAD/Digenic1490
GALEGalactose epimerase deficiencyAR1226
GALK1Galactokinase deficiencyAR1544
GALTGalactosemiaAR238330
GCNT2Blood group, Ii, Adult i pheno without cataract, Cataract 13 with adult i phenoBG/AR1111
GJA1*Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3AD/AR31107
GJA3CataractAD1443
GJA8CataractAD/AR2061
HSF4CataractAD/AR818
LEMD2Cataract 46, juvenile onset, Arrhythmogenic right ventricular cardiomyopathy (ARVC), Dilated cardiomyopathy (DCM)AR11
LIM2CataractAD/AR24
MAF#Ayme-Gripp syndrome, Cataract 21, multiple typesAD2122
MIPCataract 15, multiple typesAD1127
MT-ATP6Neuropathy, ataxia, and retinitis pigmentosa, Leber hereditary optic neuropathy, Ataxia and polyneuropathy, adult-onset, Cardiomyopathy, infantile hypertrophic, Leigh syndrome, Striatonigral degeneration, infantile, mitochondrialMitochondrial19
MT-ATP8Cardiomyopathy, apical hypertrophic, and neuropathy, Cardiomyopathy, infantile hypertrophicMitochondrial4
MT-CO1Myoglobinuria, recurrent, Leber hereditary optic neuropathy, Sideroblastic anemia, Cytochrome C oxidase deficiency, Deafness, mitochondrialMitochondrial17
MT-CO2Cytochrome c oxidase deficiencyMitochondrial8
MT-CO3Cytochrome c oxidase deficiency, Leber hereditary optic neuropathyMitochondrial9
MT-CYBMitochondrial69
MT-ND1Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Leber hereditary optic neuropathy, Leber optic atrophy and dystoniaMitochondrial21
MT-ND2Leber hereditary optic neuropathy, Mitochondrial complex I deficiencyMitochondrial6
MT-ND3Leber optic atrophy and dystonia, Mitochondrial complex I deficiencyMitochondrial7
MT-ND4Leber hereditary optic neuropathy, Leber optic atrophy and dystonia, Mitochondrial complex I deficiencyMitochondrial11
MT-ND4LLeber hereditary optic neuropathyMitochondrial2
MT-ND5Myoclonic epilepsy with ragged red fibers, Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Leber hereditary optic neuropathy, Mitochondrial complex I deficiencyMitochondrial19
MT-ND6Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Oncocytoma, Leber hereditary optic neuropathy, Leber optic atrophy and dystonia, Mitochondrial complex I deficiencyMitochondrial16
MT-RNR1Deafness, mitochondrialMitochondrial3
MT-RNR2Chloramphenicol toxicity/resistanceMitochondrial2
MT-TAMitochondrial4
MT-TCMitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodesMitochondrial3
MT-TDMitochondrial1
MT-TEDiabetes-deafness syndrome, Mitochondrial myopathy, infantile, transient, Mitochondrial myopathy with diabetesMitochondrial5
MT-TFMyoclonic epilepsy with ragged red fibers, Nephropathy, tubulointerstitial, Encephalopathy, mitochondrial, Epilepsy, mitochondrial, Myopathy, mitochondrial, Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodesMitochondrial7
MT-TGMitochondrial3
MT-THMitochondrial4
MT-TIMitochondrial7
MT-TKMyoclonic epilepsy with ragged red fibers, Leigh syndromeMitochondrial5
MT-TL1Cytochrome c oxidase deficiency, Myoclonic epilepsy with ragged red fibers, Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Diabetes-deafness syndrome, Cyclic vomiting syndrome, SIDS, susceptibility toMitochondrial14
MT-TL2Mitochondrial multisystemic disorder, Progressive external ophthalmoplegia, Mitochondrial Myopathy, Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodesMitochondrial5
MT-TMLeigh syndrome, Mitochondrial multisystemic disorderMitochondrial1
MT-TNProgressive external ophthalmoplegia, Mitochondrial multisystemic disorderMitochondrial3
MT-TPMitochondrial2
MT-TQMitochondrial multisystemic disorderMitochondrial2
MT-TREncephalopathy, mitochondrialMitochondrial2
MT-TS1Myoclonic epilepsy with ragged red fibers, Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodesMitochondrial10
MT-TS2Mitochondrial multisystemic disorderMitochondrial2
MT-TTMitochondrial5
MT-TVHypertrophic cardiomyopathy (HCM), Leigh syndrome, Mitochondrial multisystemic disorder, Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodesMitochondrial3
MT-TWLeigh syndrome, Myopathy, mitochondrialMitochondrial8
MT-TYMitochondrial multisystemic disorderMitochondrial4
MYH9Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness, Deafness, autosomal dominant 17AD25117
NDPExudative vitreoretinopathy, Norrie diseaseXL31167
NF2Schwannomatosis, NeurofibromatosisAD66433
NHSNance-Horan syndrome, CataractXL3652
OCRLLowe syndrome, Dent diseaseXL47264
OPA3Optic atrophy, 3-methylglutaconic aciduriaAD/AR1315
P3H2Myopia, high, with cataract and vitreoretinal degenerationAR77
PAX6Aniridia, cerebellar ataxia, and intellectual disability (Gillespie syndrome), Keratitis, Coloboma, ocular, Cataract with late-onset corneal dystrophy, Morning glory disc anomaly, Foveal hypoplasia, Aniridia, Optic nerve hypoplasia, Peters anomalyAD144550
PITX3Cataract, Anterior segment mesenchymal dysgenesisAD511
PXDNAnterior segment dysgenesis 7AR714
RAB18Warburg micro syndrome 3AR55
RAB3GAP1Warburg micro syndromeAR2966
RAB3GAP2Warburg micro syndrome, Martsolf syndromeAR1115
RECQL4Baller-Gerold syndrome, RAPADILINO syndrome, Rothmund-Thomson syndromeAR82114
SIL1Marinesco-Sjogren syndromeAR1449
SIPA1L3Cataract 45AR24
SLC16A12Cataract 47AD318
SLC33A1*Congenital cataracts, hearing loss, and neurodegeneration, Spastic paraplegia 42, autosomal dominantAD/AR67
TBC1D20Warburg micro syndrome 4AR66
TDRD7CataractAR55
TFAP2ABranchiooculofacial syndromeAD2342
TMEM70Mitochondrial complex V (ATP synthase) deficiencyAR1218
VIMCataract 30, multiple typesAD23
VSX2Microphthalmia, isolated 2, Microphthalmia, isolated, with coloboma 3AR913
WFS1Wolfram syndrome, Wolfram-like syndrome, autosomal dominant, Deafness, autosomal dominant 6/14/38, Cataract 41AD/AR69362
WRN*Werner syndromeAR64107
XYLT2Spondyloocular syndromeAR210
#

The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads.

*

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

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#). Due to possible limitations these genes may not be available as single gene tests.

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), 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 Mitomap databases.

Non-coding variants covered by Cataract Panel

To view complete table content, scroll horizontally.

GeneGenomic location HG19HGVSRefSeqRS-number
COL11A1Chr1:103386637c.3744+437T>GNM_080629.2
COL11A1Chr1:103488576c.1027-24A>GNM_080629.2
COL11A1Chr1:103491958c.781-450T>GNM_080629.2rs587782990
COL2A1Chr12:48379984c.1527+135G>ANM_001844.4
COL4A1Chr13:110802675c.*35C>ANM_001845.4
COL4A1Chr13:110802678c.*32G>A/TNM_001845.4
COL4A1Chr13:110802679c.*31G>TNM_001845.4
ERCC5Chr13:103514354c.881-26T>GNM_000123.3
ERCC6Chr10:50681659c.2599-26A>GNM_000124.3rs4253196
ERCC8Chr5:60223572c.173+1119G>CNM_000082.3
ERCC8Chr5:60223645c.173+1046A>GNM_000082.3
EYA1Chr8:72156939c.1051-12T>GNM_000503.4
EYA1Chr8:72211483c.640-15G>ANM_000503.4
FTLChr19:49468350c.-415C>ANM_000146.3
FTLChr19:49468574c.-189_-161delGGTCCCGCGGGTCTGTCTCTTGCTTCAACNM_000146.3
FTLChr19:49468575c.-190C>TNM_000146.3
FTLChr19:49468579c.-186C>GNM_000146.3
FTLChr19:49468581c.-184C>TNM_000146.3
FTLChr19:49468583c.-182C>TNM_000146.3
FTLChr19:49468583c.-182_-178delCGGGTinsTGGGGNM_000146.3
FTLChr19:49468586c.-175_-170delGTCTCTNM_000146.3rs398124639
FTLChr19:49468587c.-178T>GNM_000146.3
FTLChr19:49468589c.-176T>CNM_000146.3
FTLChr19:49468593c.-168_-165delGCTTNM_000146.3
FTLChr19:49468594c.-171C>GNM_000146.3
FTLChr19:49468597c.-168G>A/C/TNM_000146.3rs398124635
FTLChr19:49468597c.-168G>TNM_000146.3
FTLChr19:49468597c.-168G>CNM_000146.3
FTLChr19:49468597c.-168G>ANM_000146.3
FTLChr19:49468598c.-167C>A/TNM_000146.3
FTLChr19:49468598c.-167C>ANM_000146.3
FTLChr19:49468598c.-167C>TNM_000146.3
FTLChr19:49468599c.-166T>CNM_000146.3
FTLChr19:49468601c.-158_-143delTGTTTGGACGGAACAGNM_000146.3
FTLChr19:49468601c.-164C>GNM_000146.3
FTLChr19:49468601c.-164C>A/TNM_000146.3rs398124637
FTLChr19:49468602c.-163A>C/G/TNM_000146.3
FTLChr19:49468602c.-161_-160delCANM_000146.3
FTLChr19:49468602c.-163A>CNM_000146.3
FTLChr19:49468602c.-163A>TNM_000146.3
FTLChr19:49468602c.-163A>GNM_000146.3
FTLChr19:49468603c.-161delCNM_000146.3
FTLChr19:49468604c.-161C>TNM_000146.3rs398124636
FTLChr19:49468604c.-161C>A/GNM_000146.3
FTLChr19:49468605c.-160A>GNM_000146.3rs398124633
FTLChr19:49468606c.-159G>CNM_000146.3rs398124634
FTLChr19:49468608c.-157G>ANM_000146.3
FTLChr19:49468611c.-154T>GNM_000146.3
FTLChr19:49468612c.-153_-152delGGinsCTNM_000146.3
FTLChr19:49468612c.-153G>ANM_000146.3
FTLChr19:49468614c.-151A>CNM_000146.3
FTLChr19:49468614c.-151A>GNM_000146.3
FTLChr19:49468615c.-150C>ANM_000146.3
FTLChr19:49468616c.-149G>CNM_000146.3rs398124638
FTLChr19:49468617c.-148G>CNM_000146.3
FTLChr19:49468621c.-144A>TNM_000146.3
FTLChr19:49468655c.-110C>TNM_000146.3
FTLChr19:49468720c.-44delTNM_000146.3rs772029022
GALK1Chr17:73761239c.-22T>CNM_000154.1rs545362817
GALTChr9:34646606c.-96T>GNM_000155.3
GALTChr9:34647075c.83-11T>GNM_000155.3
GALTChr9:34648082c.508-29delTNM_000155.3rs111033711
GALTChr9:34648519c.687+66T>ANM_000155.3
GALTChr9:34648904c.820+13A>GNM_000155.3rs111033768
GALTChr9:34649617c.1059+56C>TNM_000155.3rs111033821
NDPChrX:43818099c.-207-1G>ANM_000266.3
NDPChrX:43832545c.-208+5G>ANM_000266.3
NDPChrX:43832548c.-208+2T>GNM_000266.3
NDPChrX:43832549c.-208+1G>ANM_000266.3
NDPChrX:43832685c.-343A>GNM_000266.3rs895911086
NDPChrX:43832722c.-391_-380delCTCTCTCTCCCTinsGTCTCTCNM_000266.3
NDPChrX:43832724c.-396_-383delTCCCTCTCTCTCTCNM_000266.3rs770996360
NF2Chr22:30050946c.516+232G>ANM_000268.3
OCRLChrX:128674707c.40-14A>GNM_000276.3
OCRLChrX:128687279c.239-4023A>GNM_000276.3
OCRLChrX:128696350c.940-11G>ANM_000276.3
PAX6Chr11:31685945c.*125537G>TNM_000280.4rs606231388
PAX6Chr11:31812434c.1033-42_1033-26delATGTGTTCCTCAGTAACinsGNM_000280.4
PAX6Chr11:31816377c.524-41T>GNM_000280.4
PAX6Chr11:31823338c.142-14C>GNM_000280.4rs1131692291
PAX6Chr11:31828391c.-52+5delGNM_000280.4
PAX6Chr11:31828391c.-52+3_-52+6delAAGTinsTGNM_000280.4
PAX6Chr11:31828392c.-52+3_-52+4delAANM_000280.4
PAX6Chr11:31828395c.-52+1delGNM_000280.4
PAX6Chr11:31828396c.-52+1G>ANM_000280.4
PAX6Chr11:31828456c.-115_-112delACTANM_000280.4rs1011844558
PAX6Chr11:31828461c.-118_-117delTTNM_000280.4
PAX6Chr11:31828469c.-125dupGNM_000280.4
PAX6Chr11:31828474c.-128-1G>TNM_000280.4
PAX6Chr11:31828474c.-128-2delANM_000280.4rs1131692282
PAX6Chr11:31832372c.-138_-129+3delCCTCATAAAGGTGNM_000280.4
PAX6Chr11:31832374c.-129+2T>ANM_000280.4
PAX6Chr11:31832375c.-129+1G>ANM_000280.4
SIL1Chr5:138283180c.1030-18G>ANM_022464.4rs769052639
WFS1Chr4:6271704c.-43G>TNM_006005.3
WRNChr8:30966107c.2089-3024A>GNM_000553.4rs281865157
WRNChr8:30999982c.3234-160A>GNM_000553.4

Test Strengths

The strengths of this test include:

  • CAP 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
  • Some of the panels include the whole mitochondrial genome (please see the Panel Content section)
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
  • 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

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
  • Some of the panels include the whole mitochondrial genome but not all (please see the Panel Content section)
  • 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 in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Low level heteroplasmy in mtDNA (>90% are detected at 5% level)
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments
  • Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis.

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.

The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

The performance metrics listed below are from an initial validation performed at our main laboratory in Finland. The performance metrics of our laboratory in Marlborough, MA, are equivalent.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN)Specificity %
Single nucleotide variants99.89% (99,153/99,266)>99.9999%
Insertions, deletions and indels by sequence analysis
1-10 bps99.2% (7,745/7,806)>99.9999%
11-50 bps99.13% (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/duplication98.7%100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb)100% (25/25)
   
The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics
   
Mean sequencing depth143X
Nucleotides with >20x sequencing coverage (%)99.86%

Performance of Blueprint Genetics Mitochondrial Sequencing Assay.

Sensitivity %Specificity %
ANALYTIC VALIDATION (NA samples; n=4)
Single nucleotide variants
Heteroplasmic (45-100%)100.0% (50/50)100.0%
Heteroplasmic (35-45%)100.0% (87/87)100.0%
Heteroplasmic (25-35%)100.0% (73/73)100.0%
Heteroplasmic (15-25%)100.0% (77/77)100.0%
Heteroplasmic (10-15%)100.0% (74/74)100.0%
Heteroplasmic (5-10%)100.0% (3/3)100.0%
Heteroplasmic (<5%)50.0% (2/4)100.0%
CLINICAL VALIDATION (n=76 samples)
All types
Single nucleotide variants n=2026 SNVs
Heteroplasmic (45-100%)100.0% (1940/1940)100.0%
Heteroplasmic (35-45%)100.0% (4/4)100.0%
Heteroplasmic (25-35%)100.0% (3/3)100.0%
Heteroplasmic (15-25%)100.0% (3/3)100.0%
Heteroplasmic (10-15%)100.0% (9/9)100.0%
Heteroplasmic (5-10%)92.3% (12/13)99.98%
Heteroplasmic (<5%)88.9% (48/54)99.93%
Insertions and deletions by sequence analysis n=40 indels
Heteroplasmic (45-100%) 1-10bp100.0% (32/32)100.0%
Heteroplasmic (5-45%) 1-10bp100.0% (3/3)100.0%
Heteroplasmic (<5%) 1-10bp100.0% (5/5)99,997%
SIMULATION DATA /(mitomap mutations)
Insertions, and deletions 1-24 bps by sequence analysis; n=17
Homoplasmic (100%) 1-24bp100.0% (17/17)99.98%
Heteroplasmic (50%)100.0% (17/17)99.99%
Heteroplasmic (25%)100.0% (17/17)100.0%
Heteroplasmic (20%)100.0% (17/17)100.0%
Heteroplasmic (15%)100.0% (17/17)100.0%
Heteroplasmic (10%)94.1% (16/17)100.0%
Heteroplasmic (5%)94.1% (16/17)100.0%
Copy number variants (separate artifical mutations; n=1500)
Homoplasmic (100%) 500 bp, 1kb, 5 kb100.0%100.0%
Heteroplasmic (50%) 500 bp, 1kb, 5 kb100.0%100.0%
Heteroplasmic (30%) 500 bp, 1kb, 5 kb100.0%100.0%
Heteroplasmic (20%) 500 bp, 1kb, 5 kb99.7%100.0%
Heteroplasmic (10%) 500 bp, 1kb, 5 kb99.0%100.0%
The performance presented above reached by following coverage metrics at assay level (n=66)
Mean of mediansMedian of medians
Mean sequencing depth MQ0 (clinical)18224X17366X
Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical)100%
rho zero cell line (=no mtDNA), mean sequencing depth12X

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. If the test includes the mitochondrial genome the target region gene list contains the mitochondrial genes. 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 suboptimal coverage (<20X for nuclear genes and <1000X for mtDNA) if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

We provide customers with comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our Ph.D. molecular geneticists, medical professionals, and other highly experienced experts prepare clinical reports by evaluating the identified variants in the context of the phenotypic information provided in the requisition form.

Our goal is to provide clinically meaningful reports that are understandable for all medical professionals regardless of whether they have formal training in genetics. Variant classification is the cornerstone of clinical interpretation and resulting patient management decisions. Our classifications follow the ACMG guideline 2015. Sequence and copy number variants classified as pathogenic, likely pathogenic, and variants of uncertain significance (VUS) are confirmed using bidirectional Sanger sequencing or by orthogonal methods such as qPCR/ddPCR when they do not meet our stringent NGS quality metrics for a true positive call.

Our clinical report includes tables for sequence and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, 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 panel report is divided into primary findings and additional findings sections. Variants reported as primary findings are known disease-causing variants or rare variants that could potentially explain the patient’s phenotype as described to the laboratory at the time of interpretation. The conclusion summarizes all the existing information and provides our rationale for the classification of the variant.

Variants reported as additional findings are variants that are not likely or sufficient to cause the tested patient’s phenotype, based on the current knowledge. Additional findings in panel reports include variants that are, for example, carrierships of single heterozygous variants in genes associated with autosomal recessive disorders, variants of uncertain significance in genes associated with autosomal dominant disorders (if pathogenic or likely pathogenic variants considered sufficient to explain the patient’s phenotype are reported as primary findings), or risk alleles identified in genes included in the panel.

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 reclassify previously reported variants as new information becomes available. If a variant previously reported as a primary or secondary finding by Blueprint Genetics is reclassified so that it becomes diagnostic (VUS to P/LP) or earlier molecular diagnosis is removed (P/LP to VUS, LB, B), our laboratory will issue a follow-up statement to the original ordering healthcare provider at no additional cost.