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Glaucoma Sequencing Panel
- Summary and Pricing
- Clinical Features and Genetics
- Citations
- Methods
- Ordering/Specimens
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TEST METHODS
- NextGen Sequencing using PG-Select Capture Probes
- Deletion/Duplication Testing via Array Comparative Genomic Hybridization
NGS Sequencing
| Test Code | Test Copy Genes | CPT Code Copy CPT Codes | |
|---|---|---|---|
| 1993 | ATOH7 | 81479 | Add |
| COL4A1 | 81408 | ||
| COL8A1 | 81479 | ||
| COL8A2 | 81479 | ||
| CYP1B1 | 81404 | ||
| FOXC1 | 81479 | ||
| LMX1B | 81479 | ||
| LTBP2 | 81479 | ||
| MFRP | 81479 | ||
| MYOC | 81479 | ||
| OPTC | 81479 | ||
| OPTN | 81406 | ||
| PAX6 | 81479 | ||
| PITX2 | 81479 | ||
| SH3PXD2B | 81479 | ||
| SLC4A4 | 81479 | ||
| WDR36 | 81479 | ||
| Full Panel Price* | $640.00 | ||
| Test Code | Test Copy Genes | Total Price | CPT Codes Copy CPT Codes | |
|---|---|---|---|---|
| 1993 | Genes x (17) |
$640.00 | 81404, 81406, 81408, 81479(x14) | Add |
Pricing Comment
We are happy to accommodate requests for single genes or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered on our PGxome Custom Panel.
Targeted Testing
For ordering targeted known variants, please proceed to our Targeted Variants landing page.
Turnaround Time
The great majority of tests are completed within 26 days.
Clinical Sensitivity
Approximately 10%–20% of adult-onset primary open-angle glaucoma (POAG) cases are due to pathogenic variants in the MYOC gene (Khan. 2011. PubMed ID: 21730848; Wiggs et al. 2004. PubMed ID: 15108121). Abu-Amero et al. detected CYP1B1 pathogenic variants in 76% of families (41 out of 54) with at least one affected member with primary congenital glaucoma (PCG) (Abu-Amero. 2011. PubMed ID: 22128238). Another molecular analysis of CYP1B1 identified three pathogenic variants in 78% (7/9) of the unrelated PCG index cases (El-Gayar et al. 2009. PubMed ID: 19597567). Another study reported that 3.6% (9/251) of the POAG patients had pathogenic variants in the CYP1B1, MYOC, and OPTN genes (Kumar et al. 2007. PubMed ID: 17563717).
Deletion/Duplication Testing via aCGH
| Test Code | Test Copy Genes | Individual Gene Price | CPT Code Copy CPT Codes | |
|---|---|---|---|---|
| 600 | CYP1B1 | $990.00 | 81479 | Add |
| FOXC1 | $990.00 | 81479 | ||
| LMX1B | $990.00 | 81479 | ||
| LTBP2 | $990.00 | 81479 | ||
| MFRP | $990.00 | 81479 | ||
| MYOC | $990.00 | 81479 | ||
| OPTN | $990.00 | 81479 | ||
| PAX6 | $990.00 | 81479 | ||
| PITX2 | $990.00 | 81479 | ||
| Full Panel Price* | $1290.00 | |||
| Test Code | Test Copy Genes | Total Price | CPT Codes Copy CPT Codes | |
|---|---|---|---|---|
| 600 | Genes x (9) |
$1290.00 | 81479(x9) | Add |
Pricing Comment
|
# of Genes Ordered |
Total Price |
|
1 |
$990 |
|
2-5 |
$1190 |
|
6-10 |
$1290 |
|
11-100 |
$1490 |
|
Over 100 |
Call for quote |
Turnaround Time
The great majority of tests are completed within 20 days.
Clinical Sensitivity
Copy number variants in FOXC1, PAX6, CYP1B1, PITX2, LMX1B and ATOH7 genes have been reported to date. All documented large deletions in OPTN have been reported in amyotrophic lateral sclerosis patients, while none have been reported in glaucoma patients (Human Gene Mutation Database).
Clinical Features
Glaucoma is a major cause of blindness worldwide. Glaucoma is characterized by elevated intraocular pressure (IOP), increased corneal diameter (megalocornea), enlarged globe (buphthalmos), Haab’s striae (opacification of the cornea with ruptures involving Descemet’s membrane), corneal edema and optic nerve head cupping, thinning of the anterior sclera and atrophy of the iris. Symptoms include photophobia, blepharospasm (abnormal contraction of the eyelid), and hyperlacrimation (excessive tearing). Abnormal development of the anterior segment angle or goniodysgenesis are the hallmarks of congenital glaucoma. It is a chronic disease and a major cause of blindness. Early detection is needed in order to prevent vision loss (Martin et al. 2000. PubMed ID: 10851252; Abu-Amero. 2011. PubMed ID: 22128238). Adult-onset primary open-angle glaucoma (POAG) is the most prevalent form of glaucoma affecting all ages and is genetically complex (Ray and Mookherjee. 2009. PubMed ID: 20090207). Primary congenital glaucoma (PCG) or Trabeculodysgenesis presents in neonates and during the infantile period with a varying prevalence rate ranging from 1 in 1,250 to 20,000 among different geographic locations and ethnic groups. The highest prevalence is found in the Gypsy population of Slovakia (1 in 1,250) followed by Saudi Arabians (1:2,500), Southern India (1:3,300), and the Western nations (1:5000-22,000) (Gencik et al. 1982. PubMed ID: 7173860; Azmanov et al. 2011. PubMed ID: 21081970; Abu-Amero. 2011. PubMed ID: 22128238).
Genetics
Adult-onset POAG is generally inherited as a complex trait, whereas juvenile-onset POAG exhibits autosomal dominant inheritance and is due to heterozygous pathogenic variants in MYOC, OPTN, or WDR36. Approximately 10%–20% of adult-onset POAG cases are due to monoallelic pathogenic variants in the MYOC gene (Khan. 2011. PubMed ID: 21730848; Wiggs et al. 2004. PubMed ID: 15108121). Pathogenic variants in CYP1B1 and LTBP2 have been reported to cause congenital glaucoma with autosomal recessive inheritance (Abu-Amero. 2011. PubMed ID: 22128238). Glaucoma is manifested in several syndromic and other disorders associated with anterior segment dysgenesis. For example, Nail-patella syndrome, Axenfeld-Rieger syndrome, Aniridia, nanophthalmos, and Frank-ter Haar syndrome. Causative variants in LMX1B (Vollrath et al. 1998. PubMed ID: 9618165), PITX2 (Strungaru et al. 2007. PubMed ID: 17197537), FOXC1 also known as FKHL7 (Ito et al. 2014. PubMed ID: 24556684; Paylakhi et al. 2013. PubMed ID: 23541832), PAX6 (Tzoulaki et al. 2005. PubMed ID: 15918896) and COL4A1 (Sibon et al. 2007. PubMed ID: 17696175) are inherited in an autosomal dominant manner.
Causative variants in MFRP (Ayala-Ramirez et al. 2006. PubMed ID: 17167404), SH3PXD2B (Iqbal. 2010. PubMed ID: 20137777), SLC4A4 (Igarashi et al. 1999. PubMed ID: 10545938) and ATOH7 (Prasov et al. 2012. PubMed ID: 22645276) are inherited in an autosomal recessive manner.
The mode of inheritance for OPTC (Acharya et al. 2007. PubMed ID: 17359525), COL8A2 and COL8A1 (Desronvil et al. 2010. PubMed ID: 21139683) is currently unknown.
A wide variety of causative variants (missense, nonsense, splicing, small deletions and insertions) have been reported in these glaucoma-associated genes, including large deletions/duplications and complex genomic rearrangements in a few genes (FOXC1, PAX6, CYP1B1, PITX2, LMX1B and ATOH7) (Human Gene Mutation Database).
See individual gene test descriptions for information on molecular biology of gene products and spectra of pathogenic variants.
Testing Strategy
For this Next Generation Sequencing (NGS) test, sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for regions not captured or with insufficient number of sequence reads. All reported pathogenic, likely pathogenic, and variants of uncertain significance are confirmed by Sanger sequencing.
For Sanger sequencing, polymerase chain reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.
This panel typically provides >99.8% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.
A full list of regions not covered by NGS or Sanger sequencing is available upon request.
Indications for Test
All patients with symptoms suggestive of primary open angle, congenital, juvenile, or adult-onset glaucoma are candidates.
Genes
| Official Gene Symbol | OMIM ID |
|---|---|
| ATOH7 | 609875 |
| COL4A1 | 120130 |
| COL8A1 | 120251 |
| COL8A2 | 120252 |
| CYP1B1 | 601771 |
| FOXC1 | 601090 |
| LMX1B | 602575 |
| LTBP2 | 602091 |
| MFRP | 606227 |
| MYOC | 601652 |
| OPTC | 605127 |
| OPTN | 602432 |
| PAX6 | 607108 |
| PITX2 | 601542 |
| SH3PXD2B | 613293 |
| SLC4A4 | 603345 |
| WDR36 | 609669 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
Related Tests
CONTACTS
Genetic Counselors
- Genetic Counselor Team - clinicaldnatesting@preventiongenetics.com
Geneticist
- Madhulatha Pantrangi, PhD - madhu.pantrangi@preventiongenetics.com
Citations
- Abu-Amero. 2011. PubMed ID: 22128238
- Acharya et al. 2007. PubMed ID: 17359525
- Ayala-Ramirez et al. 2006. PubMed ID: 17167404
- Azmanov et al. 2011. PubMed ID: 21081970
- Desronvil et al. 2010. PubMed ID: 21139683
- El-Gayar et al. 2009. PubMed ID: 19597567
- Gencik et al. 1982. PubMed ID: 7173860
- Human Gene Mutation Database (Bio-base).
- Igarashi. 1999. PubMed ID: 10545938
- Iqbal. 2010. PubMed ID: 20137777
- Ito et al. 2014. PubMed ID: 24556684
- Khan. 2011. PubMed ID: 21730848
- Kumar et al. 2007. PubMed ID: 17563717
- Martin et al. 2000. PubMed ID: 10851252
- Paylakhi et al. 2013. PubMed ID: 23541832
- Prasov et al. 2012. PubMed ID: 22645276
- Ray and Mookherjee. 2009. PubMed ID: 20090207
- Sibon et al. 2007. PubMed ID: 17696175
- Strungaru et al. 2007. PubMed ID: 17197537
- Tzoulaki et al. 2005. PubMed ID: 15918896
- Vollrath et al. 1998. PubMed ID: 9618165
- Wiggs et al. 2004. PubMed ID: 15108121
Order Kits
TEST METHODS
- NextGen Sequencing using PG-Select Capture Probes
- Deletion/Duplication Testing via Array Comparative Genomic Hybridization
NextGen Sequencing using PG-Select Capture Probes
Test Procedure
We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from the patient specimen. For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes. Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA). Regions with insufficient coverage by NGS are covered by Sanger sequencing. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.
For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.
Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).
(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants
Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org). Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.
Analytical Validity
As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.
In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.
Analytical Limitations
Interpretation of the test results is limited by the information that is currently available. Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.
When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles. Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion. In these cases, the report will contain no information about the second allele. Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).
We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon. Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.
In most cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.
Our ability to detect minor sequence variants due to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.
Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.
Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood). Test reports contain no information about the DNA sequence in other cell-types.
We cannot be certain that the reference sequences are correct.
Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.
We have confidence in our ability to track a specimen once it has been received by PreventionGenetics. However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.
Deletion/Duplication Testing via Array Comparative Genomic Hybridization
Test Procedure
Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.
Analytical Validity
PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.
Analytical Limitations
Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.
This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.
aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.
Breakpoints, if occurring outside the targeted gene, may be hard to define.
The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.
Order Kits
Ordering Options
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
SPECIMEN TYPES
WHOLE BLOOD
(Delivery accepted Monday - Saturday)
- Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
- For small babies, we require a minimum of 1 ml of blood.
- Only one blood tube is required for multiple tests.
- Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
- During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
- In cold weather, include an unfrozen ice pack in the shipping container as insulation.
- At room temperature, blood specimen is stable for up to 48 hours.
- If refrigerated, blood specimen is stable for up to one week.
- Label the tube with the patient name, date of birth and/or ID number.
DNA
(Delivery accepted Monday - Saturday)
- Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
- For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
- DNA may be shipped at room temperature.
- Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
- We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.
CELL CULTURE
(Delivery preferred Monday - Thursday)
- PreventionGenetics should be notified in advance of arrival of a cell culture.
- Culture and send at least two T25 flasks of confluent cells.
- Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
- Send specimens in insulated, shatterproof container overnight.
- Cell cultures may be shipped at room temperature or refrigerated.
- Label the flasks with the patient name, date of birth, and/or ID number.
- We strongly recommend maintaining a local back-up culture. We do not culture cells.
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