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Retinitis Pigmentosa via the PRPF31 Gene

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

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
666 PRPF31$810.00 81479 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
Mutations in the PRPF31 gene account for ~ 8% of RP (Daiger et al. Adv Exp Med Bio 613:203-209, 2008).  PreventionGenetics plans to offer tests for all genes known to cause RP and is committed to add new tests as the remaining RP genes are discovered.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 PRPF31$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 Features

Nonsyndromic Retinitis Pigmentosa (RP, OMIM 268000) is a large group of inherited degenerative diseases of the retina characterized by abnormalities of the photoreceptors or the retinal pigment epithelium. It is a progressive disease. Symptoms usually begin with night blindness, progressing to constriction of the peripheral visual field and, eventually, to loss of central vision. The age of onset varies from childhood to middle age (Gu et al. J Med Genet 36:705-707, 1999). The clinical hallmarks are abnormal fundus with bone-spicule deposits and attenuated retinal vessels, abnormal electroretinographic findings and reduced visual fields (Daiger et al. Arch Ophthalmol 125:151-158, 2007). RP affects 1 in 3,000 people worldwide (Farrar et al. EMBO J 21:857-864, 2002). Genetic abnormalities are the primary cause of RP.

Genetics

Retinitis Pigmentosa (RP) is genetically and clinically heterogeneous. At least four distinct subgroups are recognized on the basis of the mode of inheritance and age of onset. These include autosomal dominant (AD-RP), autosomal recessive (AR-RP), X-linked, and digenic (Kajiwara et al. Science 264:1604-1608, 1994). In addition, RP can be inherited as a mitochondrial trait (Mansergh et al. Am J Hum Genet 64:971-985, 1999). About 50% of patients with RP are isolated cases with no known affected relatives. It is unclear how many of these are real isolated cases caused by de novo mutations or inherited with low penetrance. RP affects all ethnic groups. Currently, mutations in 18 genes are known to cause AD-RP. These include the PRPF31 gene. At least 40 heterozygous mutations in the PRPF31 gene have been identified in patients with RP (Rio Frio et al. J Clin Invest 118:1519-1531, 2008), including familial and sporadic cases (Vithana et al. Mol Cell 8:375-381, 2001; Martínez-Gimeno et al. Invest Ophthalmol Vis Sci 44:2171-2177, 2003; Wang et al. Am J Med Genet 121A:235-239, 2003). The PRPF31 mutations, most of which are novel, are distributed throughout the gene and are of various types. These mutations are associated with a wide clinical variability in terms of age of onset, disease severity and progression. PRPF31 mutations have been detected in patients of various ethnic groups; however, the c.1142delG mutation has been found only in Japanese patients and accounts for the majority of Japanese RP (Taira et al. Jpn J Opthalmol 51:45-48, 2007).

PRPF31 encodes the pre-mRNA-processing factor 31 protein, which participates in the removal of introns from mRNA. Mutations in such proteins are expected to affect the splicing process of photoreceptor-specific genes resulting in abnormal gene products and ultimately retinal degeneration.

Testing Strategy

This test involves bidirectional sequencing using genomic DNA of all 13 coding exons and splice sites of PRPF31. The full coding sequence of each exon plus ~ 20 bp of flanking-coding DNA on either side are sequenced. We will also sequence and single exon (Test #100) in family members of patients with a known mutation or to confirm research results.

This test will also sequence the region encompassing the deep intronic variant c.1374+654C>G.

Indications for Test

The PRPF31 gene is a candidate for RP patients with autosomal dominant or sporadic RP.

Gene

Official Gene Symbol OMIM ID
PRPF31 606419
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Retinitis Pigmentosa 11 600138

Related Tests

Name
Autosomal Dominant Retinitis Pigmentosa Sequencing Panel
Autosomal Recessive Retinitis Pigmentosa Sequencing Panel
Retinitis Pigmentosa (includes RPGR ORF15) Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Daiger SP, Bowne SJ, Sullivan LS. 2007. Perspective on genes and mutations causing retinitis pigmentosa. Archives of ophthalmology 125: 151-158. PubMed ID: 17296890
  • Daiger, S. P., et.al. (2008). "Mutations in known genes account for 58% of autosomal dominant retinitis pigmentosa (adRP)." Adv Exp Med Biol 613: 203-9. PubMed ID: 18188946
  • Farrar, G. J., et.al. (2002). "On the genetics of retinitis pigmentosa and on mutation-independent approaches to therapeutic intervention." Embo J 21(5): 857-64. PubMed ID: 11867514
  • Gu S. et al. 1999. Journal of Medical Genetics. 36: 705-7. PubMed ID: 10507729
  • Kajiwara, K. et.al. (1994). "Digenic retinitis pigmentosa due to mutations at the unlinked peripherin/RDS and ROM1 loci." Science 264(5165): 1604-1608. PubMed ID: 8202715
  • Mansergh, F. C., et.al. (1999). "Retinitis pigmentosa and progressive sensorineural hearing loss caused by a C12258A mutation in the mitochondrial MTTS2 gene." Am J Hum Genet 64(4): 971-85. PubMed ID: 10090882
  • Martinez-Gimeno, M., et.al. (2003). "Mutations in the pre-mRNA splicing-factor genes PRPF3, PRPF8, and PRPF31 in Spanish families with autosomal dominant retinitis pigmentosa." Invest Ophthalmol Vis Sci 44(5): 2171-7. PubMed ID: 12714658
  • Rio Frio, T., et.al. (2008). "Premature termination codons in PRPF31 cause retinitis pigmentosa via haploinsufficiency due to nonsense-mediated mRNA decay." J Clin Invest 118(4): 1519-31. PubMed ID: 18317597
  • Taira, K., et.al. (2007). "Mutation c. 1142 del G in the PRPF31 gene in a family with autosomal dominant retinitis pigmentosa (RP11) and its implications." Jpn J Ophthalmol 51(1): 45-8. PubMed ID: 17295140
  • Vithana, E. N., et.al. (2001). "A human homolog of yeast pre-mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11)." Mol Cell 8(2): 375-81. PubMed ID: 11545739
  • Wang, L., et.al. (2003). "Novel deletion in the pre-mRNA splicing gene PRPF31 causes autosomal dominant retinitis pigmentosa in a large Chinese family." Am J Med Genet A 121A(3): 235-9. PubMed ID: 12923864
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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