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Joubert and Meckel-Gruber Syndromes Sequencing Panel

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

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
1057 AHI1 81407 Add to Order
ARL13B 81479
B9D1 81479
B9D2 81479
C5orf42 81479
CC2D2A 81479
CEP290 81408
CEP41 81479
CSPP1 81479
INPP5E 81479
KIF14 81479
KIF7 81479
MKS1 81479
NPHP1 81406
NPHP3 81479
OFD1 81479
PDE6D 81479
RPGRIP1L 81479
TCTN1 81479
TCTN2 81479
TCTN3 81479
TMEM138 81479
TMEM216 81479
TMEM231 81479
TMEM237 81479
TMEM67 81407
TTC21B 81479
ZNF423 81479
Full Panel Price* $1890.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1057 Genes x (28) $1890.00 81406, 81407(x2), 81408, 81479(x24) Add to Order

New York State Approved Test

Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information. If you would like to order a subset of these genes contact us to discuss pricing.

For Sanger Sequencing click here.
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 28 days.

Clinical Sensitivity

Clinical sensitivity for this NextGen test for JSRD and MKS is ~ 50% (Parisi and Glass 2013).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 AHI1$690.00 81479 Add to Order
ARL13B$690.00 81479
B9D1$690.00 81479
C5orf42$690.00 81479
CC2D2A$690.00 81479
CEP290$690.00 81479
CEP41$690.00 81479
INPP5E$690.00 81479
KIF7$690.00 81479
MKS1$690.00 81479
NPHP1$690.00 81405
NPHP3$690.00 81479
OFD1$690.00 81479
RPGRIP1L$690.00 81479
TCTN1$690.00 81479
TCTN2$690.00 81479
TMEM138$690.00 81479
TMEM216$690.00 81479
TMEM237$690.00 81479
TMEM67$690.00 81479
Full Panel Price* $1290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (20) $1290.00 81405, 81479(x19) 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

Gross deletions or duplications not detectable by Sanger sequencing have been reported in AHI1, CC2D2A, CEP290, MKS1, NPHP1, OFD1, and TMEM67 (Human Gene Mutation Database). Clinical sensitivity is difficult to predict due to the paucity of documented cases.

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Clinical Features

Joubert Syndrome and related disorders (JSRD) are marked by hypotonia, abnormal ocular movements, neonatal respiratory difficulties, intellectual disability, hypoplasia of the cerebellar vermis, and malformation of the brainstem. The brain malformations lead to the "molar tooth sign" on cranial MRI, which is pathognomonic for JSRD. Other variable JSRD features include cystic kidneys, nephronophthisis, retinal dystrophy, ocular coloboma, occipital encephalocele, polydactyly, ataxia, and hepatic fibrosis. For more information, see (Parisi and Glass 2013; Doherty 2009; Parisi et al. 2007).

Meckel-Gruber Syndrome (MKS) is a lethal autosomal recessive condition, also marked by brain malformation, cystic renal disease and polydactyly (Alexiev et al. 2006). In MKS, the pathognomonic feature is occipital encephalocele, which is generally identified during routine sonography between 12 and 20 weeks of gestation. MKS is a common cause of prenatal echogenic kidneys (Chaumoitre et al. 2006). Nearly all MKS infants are stillborn or die shortly after birth.

Genetics

Both JSRD and MKS are genetically heterogeneous; JSRD is known to be caused by pathogenic variants in at least 20 different genes and MKS is caused by pathogenic variants in at least 12 different genes (Parisi and Glass 2013). Most of the genes reported to cause MKS have also been found to cause JSRD, with the exception of B9D2, KIF14, NPHP3, and TTC21B. In addition, all genes reported to cause MKS and JSRD play some role in the structure, function and maintenance of the primary cilia and/or basal body organelle (Hildebrandt et al. 2009). Thus, MKS and JSRD have been proposed to represent a single clinical entity, with a spectrum of overlapping symptoms and causative genes. JSRD and MKS are inherited in an autosomal recessive manner with the exception of OFD1, which is inherited in an X-linked dominant manner. More information about the molecular biology of the gene products may be found in the individual gene test descriptions.

Testing Strategy

For this NextGen panel, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for each of the genes listed below. 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 any regions not captured or with insufficient number of sequence reads. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Indications for Test

This test is for individuals with symptoms suggestive of MKS or JSRD and their families.

Diseases

Name Inheritance OMIM ID
Acrocallosal Syndrome, Schinzel Type AR 200990
Joubert Syndrome AR 614615
Joubert Syndrome 1 AR 213300
Joubert Syndrome 10 XL 300804
Joubert Syndrome 13 AR 614173
Joubert syndrome 14 AR 614424
Joubert syndrome 15 AR 614464
Joubert syndrome 16 AR 614465
Joubert syndrome 18 AR 614815
Joubert syndrome 19 AR 614844
Joubert Syndrome 2 AR 608091
Joubert syndrome 20 AR 614970
Joubert Syndrome 21 AR 615636
Joubert Syndrome 22 AR 615665
Joubert Syndrome 3 AR 608629
Joubert Syndrome 4 AR 609583
Joubert Syndrome 5 AR 610188
Joubert Syndrome 6 AR 610688
Joubert Syndrome 7 AR 611560
Joubert Syndrome 8 AR 612291
Joubert Syndrome 9 AR 612285
Meckel Syndrome 1 AR 249000
Meckel Syndrome 10 AR 614175
Meckel syndrome 11 AR 615397
Meckel Syndrome 12 AR 616258
Meckel Syndrome 2 AR 603194
Meckel Syndrome 3 AR 607361
Meckel Syndrome 4 AR 611134
Meckel Syndrome 5 AR 611561
Meckel Syndrome 6 AR 612284
Meckel Syndrome 7 AR 267010
Meckel Syndrome 8 AR 613885
Meckel Syndrome 9 AR 614209

Related Tests

Name
OFD1-Related Disorders via the OFD1 Gene
Acrocallosal, Fetal Hydrolethalus, and Joubert Syndromes via the KIF7 Gene
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Panel
Autosomal Recessive Retinitis Pigmentosa Sequencing Panel
Bardet-Biedl Syndrome Sequencing Panel
Ciliopathy Sequencing Panel
Joubert and Meckel-Gruber Syndromes via the CC2D2A Gene
Joubert and Meckel-Gruber Syndromes via the CEP290 Gene
Joubert and Meckel-Gruber Syndromes via the RPGRIP1L Gene
Joubert Syndrome via the INPP5E Gene
Joubert Syndrome via the AHI1 Gene
Joubert Syndrome via the ARL13B Gene
Joubert Syndrome via the C5orf42 Gene
Joubert Syndrome via the TMEM138 Gene
Joubert Syndrome via the TMEM216 Gene
Joubert Syndrome via the TMEM237 Gene
Joubert Syndrome, Meckel-Gruber Syndrome, and Nephronophthisis via the TMEM67 Gene
Leber Congenital Amaurosis 10 (LCA10) via the CEP290 Gene
Leber Congenital Amaurosis Sequencing Panel
Meckel-Gruber Syndrome / Joubert Syndrome via the TCTN2 Gene
Meckel-Gruber syndrome via the B9D1 Gene
Meckel-Gruber Syndrome via the MKS1 Gene
Nephronophthisis and Joubert Syndrome via the NPHP1 Gene
Nephronophthisis and Senior-Loken Syndrome Sequencing Panel
Nephronophthisis and Senior-Loken syndrome via the NPHP3 Gene
Nephrotic Syndrome (NS)/Focal Segmental Glomerulosclerosis (FSGS) Sequencing Panel
Retinitis Pigmentosa (includes RPGR ORF15) Sequencing Panel
Short Rib Skeletal Dysplasia Sequencing Panel
X-Linked Intellectual Disability Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Alexiev B.A. et al. 2006. Archives of Pathology & Laboratory Medicine. 130: 1236-8. PubMed ID: 16879033
  • Chaumoitre K. et al. 2006. Ultrasound in Obstetrics & Gynecology. 28: 911-7. PubMed ID: 17094077
  • Doherty D. 2009. Seminars in Pediatric Neurology. 16: 143-54. PubMed ID: 19778711
  • Hildebrandt F. et al. 2009. Journal of the American Society of Nephrology. 20: 23-35. PubMed ID: 19118152
  • Human Gene Mutation Database (Bio-base).
  • Parisi M, Glass I. 2013. Joubert Syndrome and Related Disorders. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301500
  • Parisi M.A. et al. 2007. European Journal of Human Genetics. 15: 511-21. PubMed ID: 17377524
Order Kits
TEST METHODS

NextGen Sequencing using PG-Designed 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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