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Best Vitelliform Macular Dystrophy (BVMD) and Bestrophinopathies via the BEST1 gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
671 BEST1$840.00 81406 Add to Order
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 18 days.

Clinical Sensitivity
Krämer et al detected 23 unique BEST1 mutations in 34 of 41 BVMD affected patients. Out of 25 probands who had positive family history, 96% (24/25) had BEST1 mutations, whereas with unknown family history the detection rate was significantly reduced to 69% (11/16) (Krämer et al. Eur J Hum Genet 8(4):286-292, 2000). Marchant et al also reports high detection rate for BEST1 mutations in BVMD patients (at least one mutation in each patient) (Marchant et al. J Med Genet 44(3):e70).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 BEST1$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity
Thus far, no gross insertions/deletions have been identified in BEST1 (Human Gene Mutation Database).

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Clinical Features
Visual acuity in humans and other higher primates is mediated by the central (or macular) region of the retina called the fovea, which has the highest density of cone photoreceptor cells (Sun et al. Proc Natl Acad Sci USA 99(6):4008-4013, 2002).  Age related-Macular degeneration (AMD) is the most common cause of irreversible vision loss that usually affects older adults due to progressive changes in the retina and/or the underlying retinal pigment epithelium (RPE). Both genetic and environmental factors influence AMD, but juvenile-onset macular degeneration (MD) or Best vitelliform macular dystrophy (BVMD/Best disease, OMIM 153700) is exclusively a genetic disorder (Hartzell et al. Physiology 20:292-302, 2005). Autosomal dominant (AD) BVMD is one of the most common retinal degeneration disorders, with an estimated prevalence of 1.5 per 100 000 individuals in Denmark (Bitner, H. et al. Am J Ophthalmol 154(2):403-412, 2012). BVMD is clinically characterized by large deposits of lipofuscin-like material in the RPE, which forms the characteristic macular lesions resembling the egg yolk ('vitelliform'), a normal electoretinogram (ERG) and an unusual electrooculogram (EOG) light rise and risk of angle-closure glaucoma (Low et al. Mol Vis 17:2272-2282, 2011). The BEST1 gene (Gene/Locus OMIM 607854; previously known as VMD2) has been linked to BVMD. Over 250 causative mutations have been identified in this gene and are associated with clinically distinct ocular phenotypes that are collectively referred as bestrophinopathies (Piñeiro-Gallego et al. Mol Vis 17:1607-1617, 2011). The other clinical phenotypes associated with BEST1 mutations are AD Vitreo-retino-choroidopathy (ADVIRC, OMIM 193220) (Kaufman et al. Arch Ophthalmol 100(2):272-278, 1982), Vitelliform macular dystrophy, adult-onset (AVMD, OMIM 608161)(Do and Ferrucci. Optometry 77(4):156-166, 2006), Autosomal recessive (AR) Bestrophinopathy (ARB, OMIM 611809) (Burgess et al. Am J Hum Genet 82(1):19-31, 2008) and AD/AR Retinitis pigmentosa-50 (RP50, OMIM 613194) (Davidson et al. Am J Hum Genet 85(5):581-592, 2009).
Genetics
While BEST1 mutations typically cause AD inheritance, AR inheritance has also been reported (Bitner, H. et al. Invest Ophthalmol Vis Sci 52(8):5332-5338, 2011). BEST1, located on the long arm (q13) of chromosome 11, encodes Bestrophin, a transmembrane protein that is located in the basolateral portion of the RPE and is responsible for the basolateral Cl- conductance that regulates voltage-dependent Ca2+ channels and generates the light peak. Dysfunction of this transport due to mutations in BEST1 might result in significant accumulation of lipofuscin, ion imbalance in the space around the photoreceptor outer segments and characteristically reduced light peak, which is a pathological hallmark of Best disease. BEST1 is predominantly expressed in RPE and is comprised of 11 exons coding 585 amino acids (aa). Causative mutations in BEST1 are distributed throughout the first 312 aa, and it has been reported that aa 293–311 are especially highly conserved and have functional importance. Mutations in 16 of these 18 aa are linked to Best disease (Hartzell et al. 2005; White et al Hum Mutat 15(4):301-308, 2000).

BVMD, AVMD and AMD share some phenotypic features, though AVMD and AMD differ from BVMD by later onset. Along with BEST1 (responsible for 25% of AVMD cases), PRPH2 (periperin/RDS) mutations are linked to AVMD (~36% of cases), indicating genetic heterogeneity of the disorder (Zhuk and Edwards. Mol Vis 12:811-815, 2006). BEST1 pre-mRNA splicing mutations that lead to in-frame deletions are reported in ADVIRC (Yardley et al Invest Ophthalmol Vis Sci 45(10):3683-3689, 2004), whereas missense mutations were associated with AD/AR Retinitis Pigmentosa (Davidson et al. 2009) . The vast majority of identified BEST1 mutations (90/93) in patients with classical Best disease are missense mutations or small in-frame deletions (MacDonald, I.M. and Lee, T., GeneReviews, 2009 ; Bitner, H. et al. Am J Ophthalmol 154(2):403-412, 2012). There are a few reports of de novo mutations in BVMD patients whose parents were phenotypically and genetically unaffected (Apushkin et al. Arch Ophthalmol 124(6):887-889, 2006; Palomba et al. Am J Ophthalmol 129(2):260-262, 2000)
Testing Strategy
Full gene sequencing of BEST1 involves bidirectional Sanger sequencing of exons 2 to 11 plus ~20bp of adjacent noncoding sequences.  We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
Ideal BEST1 test candidates are BVMD, AVMD, ADVIRC, ARB and AD/AR RP patients.

Gene

Official Gene Symbol OMIM ID
BEST1 607854
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Apushkin, M.A. et al. (2006). "Novel de novo mutation in a patient with Best macular dystrophy." Arch Ophthalmol 124(6):887-889. PubMed ID: 16769844
  • Bitner, H. et al. (2011). “A homozygous frameshift mutation in BEST1 causes the classical form of Best disease in an autosomal recessive mode.” Invest Ophthalmol Vis Sci 52(8):5332-5338. PubMed ID: 21467170
  • Bitner, H. et al. (2012). “Frequency, genotype, and clinical spectrum of best vitelliform macular dystrophy: data from a national center in Denmark.” Am J Ophthalmol 154(2):403-412. PubMed ID: 22633354
  • Burgess, R. (2008). “Biallelic mutation of BEST1 causes a distinct retinopathy in humans.” Am J Hum Genet 82(1):19-31. PubMed ID: 18179881
  • Davidson, A.E. et al. (2009). “Missense mutations in a retinal pigment epithelium protein, bestrophin-1, cause retinitis pigmentosa.”  Am J Hum Genet 85(5):581-592. PubMed ID: 19853238
  • Do, P and Ferrucci, S. (2006).  "Adult-onset foveomacular vitelliform dystrophy." Optometry 77(4):156-166. PubMed ID: 16567277
  • Hartzell, C. et al. (2005). “Looking chloride channels straight in the eye: bestrophins, lipofuscinosis, and retinal degeneration.”  Physiology (Bethesda) 20:292-302. PubMed ID: 16174869
  • Human Gene Mutation Database (Bio-base).
  • Kaufman, S.J. et al. (1982). “Autosomal dominant vitreoretinochoroidopathy.” Arch Ophthalmol 100(2):272-278. PubMed ID: 7065944
  • Krämer, F. et al. (2000). “Mutations in the VMD2 gene are associated with juvenile-onset vitelliform macular dystrophy (Best disease) and adult vitelliform macular dystrophy but not age-related macular degeneration.” Eur J Hum Genet 8(4):286-292. PubMed ID: 10854112
  • Low, S. et al. (2011). "Autosomal dominant Best disease with an unusual electrooculographic light rise and risk of angle-closure glaucoma: a clinical and molecular genetic study." Mol Vis 17:2272-2282. PubMed ID: 21921978
  • MacDonald, I.M. and Lee, T. (2009). "Best Vitelliform Macular Dystrophy." GeneReviews. PubMed ID: 20301346
  • Marchant, D. et al. (2007). “New VMD2 gene mutations identified in patients affected by Best vitelliform macular dystrophy.” J Med Genet 44(3):e70. PubMed ID: 17287362
  • Palomba, G. et al. (2000). “A novel spontaneous missense mutation in VMD2 gene is a cause of a best macular dystrophy sporadic case.” Am J Ophthalmol 129(2):260-262. PubMed ID: 10682987
  • Piñeiro-Gallego, T. et al. (2011). “Clinical evaluation of two consanguineous families with homozygous mutations in BEST1.” Mol Vis 17:1607-1617. PubMed ID: 21738390
  • Sun, H. et al. (2002). "The vitelliform macular dystrophy protein defines a new family of chloride channels." Proc Natl Acad Sci USA 99(6):4008-4013. PubMed ID: 11904445
  • White, K. et al. (2000). “VMD2 mutations in vitelliform macular dystrophy (Best disease) and other maculopathies.” Hum Mutat 15(4):301-308. PubMed ID: 10737974
  • Yardley, J. et al. (2004). “Mutations of VMD2 splicing regulators cause nanophthalmos and autosomal dominant vitreoretinochoroidopathy (ADVIRC).” Invest Ophthalmol Vis Sci 45(10):3683-3689. PubMed ID: 15452077
  • Zhuk and Edwards. (2006). "Peripherin/RDS and VMD2 mutations in macular dystrophies with adult-onset vitelliform lesion." Mol Vis 12:811-815. PubMed ID: 16885924
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all 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 for example 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 and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

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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