Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Panel

Updated
Summary
  • Is a 61 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion / diagnosis of microphthalmia, anophthalmia or an anterior segment dysgenesis disorder.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

61

Test code

OP0601

Panel size

Large

CPT codes
81479

Summary

The Blueprint Genetics Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Panel (test code OP0601):

Test Specific Strength

Assesses for non-coding disease-causing variants in one or more genes. For additional information, see the list of genes included in this panel.

ICD codes

Commonly used ICD-10 code(s) when ordering the Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Panel

ICD-10 Disease
Q87.1 COFS syndrome
Q89.8 CHARGE syndrome
Q13.9 Axenfeld-Rieger syndrome
Q11.0 Anophthalmia
Q11.0 Isolated anophthalmia - microphthalmia
Q11.2 Microphthalmia
Q13.4 Peters anomaly
Q04.8 Septo-optic dysplasia

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.

Anophthalmia and microphthalmia are rare developmental defects of the globe. Microphthalmia refers to an eye with reduced volume and may be associated with coloboma or with an orbital cyst. Anophthalmia is the absence of one or both eyes. Anophthalmia and microphthalmia may be unilateral or bilateral, and over 50% are associated with systemic abnormalities. Anophthalmia and microphthalmia may be inherited as an autosomal dominant, autosomal recessive, or X-linked manner. The major causative gene is SOX2 in which heterozygous loss-of-function variants account for 25% of cases. Examples of syndromes associated with anophthalmia/microphthalmia are CHARGE syndrome (CDH7) and COFS syndrome (ERCC2ERCC5ERCC6). Anterior segment dysgenesis (ASD) disorders encompass a wide variety of developmental conditions affecting the cornea, iris, and lens. It can be an isolated ocular anomaly or accompanied by systemic defects. Anterior segment anomalies are associated with an approximate 50% risk of glaucoma. The majority of genes associated with ASD show autosomal dominant inheritance. Axenfeld-Rieger syndrome is caused by variants in PITX2 and FOXC1 with an estimated prevalence of 1:200,000.

Genes in the Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ABCB6 Blood group, Langereis system, Pseudohyperkalemia, Dyschromatosis universalis hereditaria, Microphthalmia, isolated, with coloboma 7 AD/BG 9 20
ADAMTS18 Knobloch syndrome 2, Microcornea, myopic chorioretinal atrophy, and telecanthus, Retinal dystrophy, early onset, autosomal recessive AR 4 14
ALDH1A3 Microphthalmia, isolated 8 AR 8 23
BCOR Microphthalmia, syndromic, Oculofaciocardiodental syndrome XL 40 53
BMP4 Microphthalmia, syndromic, Orofacial cleft AD 8 39
BMP7 Anophthalmia, microphthalmia, and variable brain, ear, palate, and skeletal anomalies AD 2 6
CDK9 AR 1
CHD7 Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome AD 276 860
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 58 107
COX7B Linear skin defects with multiple congenital anomalies 2 XL 5 5
CPAMD8* Anterior segement dysgenesis 8 4 6
CYP1B1 Glaucoma, primary open angle glaucoma, juvenile-onset, Glaucoma, primary open angle, adult-onset, Glaucoma, primary congenital, Peters anomaly AR 24 237
ERCC2 Xeroderma pigmentosum, Trichothiodystrophy, photosensitive, Cerebrooculofacioskeletal syndrome 2 AR 26 98
ERCC5 Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne syndrome AR 21 54
ERCC6* Xeroderma Pigmentosum-Cockayne Syndrome, De Sanctis-Cacchione syndrome AD/AR 87 135
FOXC1 Axenfeld-Rieger syndrome, Iridogoniodysgenesis, Peters anomaly AD 46 135
FOXE3 Aphakia, congenital primary, Anterior segment mesenchymal dysgenesis, Cataract 34, Aortic aneurysm, familial thoracic AR/AD 9 29
FOXL2 Premature ovarian failure, Blepharophimosis, epicanthus inversus, and ptosis AD 74 215
FRAS1 Fraser syndrome AR 27 58
FREM1 Bifid nose, Manitoba oculotrichoanal syndrome, Trigonocephaly AD/AR 14 35
FREM2 Fraser syndrome 2 AR 11 23
GJA1* Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3 AD/AR 31 107
GRIP1 Fraser syndrome AR 5 17
HCCS Linear skin defects with multiple congenital anomalies 1 (MIDAS syndrome) XL 7 13
HESX1 Septooptic dysplasia, Pituitary hormone deficiency, combined AR/AD 15 26
HMX1 Oculoauricular syndrome AR 3 4
MAB21L2 Microphthalmia/coloboma and skeletal dysplasia syndrome AR 6 9
MFRP Microphthalmia, isolated 5, Nanophthalmos 2, Retinitis pigmentosa, autosomal recessive AR 27 30
MITF Tietz albinism-deafness syndrome, Waardenburg syndrome, Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD) AD/AR 32 58
NAA10 Microphthalmia, syndromic 1 (Lenz microphthalmia) XL 16 10
NDP Exudative vitreoretinopathy, Norrie disease XL 31 167
OCRL Lowe syndrome, Dent disease XL 47 264
OTX2 Microphthalmia, syndromic, Pituitary hormone deficiency, combined, Retinal dystrophy, early-onset, and pituitary dysfunction AD 23 73
PAX2 Isolated renal hypoplasia, Papillorenal syndrome, Focal segmental glomerulosclerosis 7 AD 30 96
PAX6 Aniridia, cerebellar ataxia, and mental retardation (Gillespie syndrome), Keratitis, Coloboma, ocular, Cataract with late-onset corneal dystrophy, Morning glory disc anomaly, Foveal hypoplasia, Aniridia, Optic nerve hypoplasia, Peters anomaly AD 144 550
PITX2 Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomaly AD 23 101
PQBP1 Renpenning syndrome XL 14 18
PRSS56 Microphthalmia, isolated 6 AR 10 24
PXDN Anterior segment dysgenesis 7 AR 7 14
RAB18 Warburg micro syndrome 3 AR 5 5
RAB3GAP1 Warburg micro syndrome AR 29 66
RAB3GAP2 Warburg micro syndrome, Martsolf syndrome AR 11 15
RARB Microphthalmia, syndromic 12 AD/AR 9 6
RAX Microphthalmia, isolated 3 AR 5 14
RBP4 Retinal dystrophy, iris coloboma, and comedogenic acne syndrome, Microphthalmia, isolated, with coloboma 10 AD/AR 8 7
SHH Holoprosencephaly, Microphthalmia with coloboma AD 42 218
SIPA1L3 Cataract 45 AR 2 4
SIX3 Holoprosencephaly AD 17 87
SIX6 Microphthalmia, isolated, with cataract 2, Optic disc anomalies with retinal and/or macular dystrophy AD 2 8
SLC38A8 Foveal hypoplasia 2 AR 11 18
SMCHD1 Facioscapulohumeral muscular dystrophy, Facioscapulohumeral muscular dystrophy, type 2 AD 51 79
SMOC1 Microphthalmia with limb anomalies AR 9 15
SOX2* Microphthalmia, syndromic AD 34 104
STRA6 Microphthalmia, syndromic, Microphthalmia, isolated, with coloboma AR 22 33
TBC1D20 Warburg micro syndrome 4 AR 6 6
TENM3 Microphthalmia, isolated, with coloboma 10 AR 9 2
TFAP2A Branchiooculofacial sydrome AD 23 42
VPS13B Cohen syndrome AR 351 203
VSX2 Microphthalmia, isolated 2, Microphthalmia, isolated, with coloboma 3 AR 9 13
YAP1 Ocular coloboma with or without hearing impairment, cleft lip/palate, and/or mental retardation AD 2 10
ZIC2 Holoprosencephaly AD 22 114

* 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), 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.

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 Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
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
COL4A1 Chr13:110802675 c.*35C>A NM_001845.4
COL4A1 Chr13:110802678 c.*32G>A/T NM_001845.4
COL4A1 Chr13:110802679 c.*31G>T NM_001845.4
CYP1B1 Chr2:38303243 c.-322A>C NM_000104.3
CYP1B1 Chr2:38303258 c.-337G>T NM_000104.3 rs552932800
ERCC5 Chr13:103514354 c.881-26T>G NM_000123.3
ERCC6 Chr10:50681659 c.2599-26A>G NM_000124.3 rs4253196
FOXC1 Chr6:1610252 NM_001453.2
NAA10 ChrX:153195397 c.*43A>G NM_003491.3
NAA10 ChrX:153195400 c.*40A>G NM_003491.3
NAA10 ChrX:153195401 c.*39A>G NM_003491.3
NDP ChrX:43818099 c.-207-1G>A NM_000266.3
NDP ChrX:43832545 c.-208+5G>A NM_000266.3
NDP ChrX:43832548 c.-208+2T>G NM_000266.3
NDP ChrX:43832549 c.-208+1G>A NM_000266.3
NDP ChrX:43832685 c.-343A>G NM_000266.3 rs895911086
NDP ChrX:43832722 c.-391_-380delCTCTCTCTCCCTinsGTCTCTC NM_000266.3
NDP ChrX:43832724 c.-396_-383delTCCCTCTCTCTCTC NM_000266.3 rs770996360
OCRL ChrX:128674707 c.40-14A>G NM_000276.3
OCRL ChrX:128687279 c.239-4023A>G NM_000276.3
OCRL ChrX:128696350 c.940-11G>A NM_000276.3
PAX6 Chr11:31685945 c.*125537G>T NM_000280.4 rs606231388
PAX6 Chr11:31812434 c.1033-42_1033-26delATGTGTTCCTCAGTAACinsG NM_000280.4
PAX6 Chr11:31816377 c.524-41T>G NM_000280.4
PAX6 Chr11:31823338 c.142-14C>G NM_000280.4 rs1131692291
PAX6 Chr11:31828391 c.-52+5delG NM_000280.4
PAX6 Chr11:31828391 c.-52+3_-52+6delAAGTinsTG NM_000280.4
PAX6 Chr11:31828392 c.-52+3_-52+4delAA NM_000280.4
PAX6 Chr11:31828395 c.-52+1delG NM_000280.4
PAX6 Chr11:31828396 c.-52+1G>A NM_000280.4
PAX6 Chr11:31828456 c.-115_-112delACTA NM_000280.4 rs1011844558
PAX6 Chr11:31828461 c.-118_-117delTT NM_000280.4
PAX6 Chr11:31828469 c.-125dupG NM_000280.4
PAX6 Chr11:31828474 c.-128-1G>T NM_000280.4
PAX6 Chr11:31828474 c.-128-2delA NM_000280.4 rs1131692282
PAX6 Chr11:31832372 c.-138_-129+3delCCTCATAAAGGTG NM_000280.4
PAX6 Chr11:31832374 c.-129+2T>A NM_000280.4
PAX6 Chr11:31832375 c.-129+1G>A NM_000280.4
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
SHH Chr7:155599270 c.301-19G>A NM_000193.2
SHH Chr7:156061506 c.-456690G>A NM_000193.2
SHH Chr7:156583831 c.-979015A>G NM_000193.2 rs606231150
SHH Chr7:156583949 c.-979133C>G NM_000193.2 rs606231151
SHH Chr7:156583951 c.-979135C>T NM_000193.2
SHH Chr7:156584107 c.-979291T>G NM_000193.2
SHH Chr7:156584153 c.-979337A>G NM_000193.2
SHH Chr7:156584164 c.-979348A>G NM_000193.2
SHH Chr7:156584166 c.-979350G>C/T NM_000193.2
SHH Chr7:156584166 c.-979350G>A NM_000193.2 rs606231147
SHH Chr7:156584168 c.-979352C>T NM_000193.2 rs587779752
SHH Chr7:156584241 c.-979425T>C NM_000193.2 rs606231149
SHH Chr7:156584265 c.-979449A>T NM_000193.2 rs606231148
SHH Chr7:156584275 c.-979459T>C NM_000193.2 rs606231152
SHH Chr7:156584283 c.-979467C>A NM_000193.2
SHH Chr7:156584465 c.-979649C>G NM_000193.2 rs606231146
SHH Chr7:156584863 c.-980047C>T NM_000193.2
SMCHD1 Chr18:2701019 c.1647+103A>G NM_015295.2
SMCHD1 Chr18:2705677 c.1843-15A>G NM_015295.2
SMCHD1 Chr18:2743740 c.3634-19A>G NM_015295.2
ZIC2 Chr13:100634295 c.-24C>T NM_007129.3

Added and removed genes from the panel

Genes added Genes removed
CDK9
CPAMD8
RAB18
RAB3GAP2
SIPA1L3
TBC1D20
YAP1

Test Strengths

Assesses for non-coding disease-causing variants in one or more genes. For additional information, see the list of genes included in this panel.

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
  • 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 ‘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

Due to one or more regions of segmental duplication, this panel has reduced sensitivity to detect variants in exon 1 of GJA1 and exon 1 of SOX2. 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 (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 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.

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 99.2% (7,745/7,806) >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%
     
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 depth 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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