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Joubert and Meckel-Gruber Syndromes Sequencing Panel with CNV Detection

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

Sequencing with CNV

Test Code Test Copy GenesCPT Code Copy CPT Codes
10387 AHI1 81407,81479 Add to Order
ARL13B 81479,81479
ARMC9 81479,81479
B9D1 81479,81479
B9D2 81479,81479
C2CD3 81479,81479
CC2D2A 81479,81479
CEP104 81479,81479
CEP120 81479,81479
CEP290 81408,81479
CEP41 81479,81479
CPLANE1 81479,81479
CSPP1 81479,81479
IFT172 81479,81479
INPP5E 81479,81479
KIAA0556 81479,81479
KIAA0586 81479,81479
KIF14 81479,81479
KIF7 81479,81479
MKS1 81479,81479
NPHP1 81406,81405
NPHP3 81479,81479
OFD1 81479,81479
PDE6D 81479,81479
PIBF1 81479,81479
RPGRIP1L 81479,81479
SUFU 81479,81479
TCTN1 81479,81479
TCTN2 81479,81479
TCTN3 81479,81479
TMEM107 81479,81479
TMEM138 81479,81479
TMEM216 81479,81479
TMEM231 81479,81479
TMEM237 81479,81479
TMEM67 81407,81479
TTC21B 81479,81479
TXNDC15 81479,81479
ZNF423 81479,81479
Full Panel Price* $890
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
10387 Genes x (39) $890 81405, 81406, 81407(x2), 81408, 81479(x73) Add to Order

New York State Approved Test

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel 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 via our PGxome Custom Panel tool.

Targeted Testing

For ordering sequencing of 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

Clinical sensitivity for Joubert syndrome and related disorders is 62% - 94% (Parisi et al. 2017. PubMed ID: 20301500) and 50% - 77% for Meckel-Gruber syndrome (Knopp et al. 2015. PubMed ID: 26003401; Hartill et al. 2017. PubMed ID: 29209597).

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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 et al. 2017. PubMed ID: 20301500; Doherty 2009. PubMed ID: 19778711; Parisi et al. 2007. PubMed ID: 17377524; Brancati et al. 2010. PubMed ID: 20615230.

Meckel-Gruber Syndrome (MKS) is also marked by brain malformation, cystic renal disease and polydactyly (Alexiev et al. 2006. PubMed ID: 16879033; Hartill et al. 2017. PubMed ID: 29209597). 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. PubMed ID: 17094077). Nearly all MKS infants are stillborn or die shortly after birth (Hartill et al. 2017. PubMed ID: 29209597; Parisi et al. 2017. PubMed ID: 20301500).

Genetics

JSRD and MKS are genetically heterogeneous; JSRD is known to be caused by pathogenic variants in at least 33 different genes and MKS is caused by pathogenic variants in at least 22 different genes (Hartill et al. 2017. PubMed ID: 29209597; Parisi et al. 2017. PubMed ID: 20301500; Knopp et al. 2015. PubMed ID: 26003401; Shaheen et al. 2016. PubMed ID: 27894351). JSRD and MKS are inherited in an autosomal recessive manner with the exception of OFD1, which displays an X-linked dominant inheritance pattern. Most of the genes reported to cause MKS have also been found to cause JSRD. MKS and JSRD have been proposed to represent a single clinical entity, with a spectrum of overlapping symptoms and causative genes. In support of this, the same pathogenic variants have been found in siblings; one diagnosed with MKS and another with JSRD (Valente et al. 2010. PubMed ID: 20512146). Variants predicted to be more damaging, such as nonsense or frameshift variants, are reported in fetuses with MKS, while milder variants, such as missense variants, are typically found in patients with JSRD (Romani et al. 2014. PubMed ID: 24886560; Slaats et al. 2016. PubMed ID: 26490104; Mougou-Zerelli et al. 2009. PubMed ID: 19777577; Delous et al. 2007. PubMed ID: 17558409).

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. PubMed ID: 19118152). More information about the molecular biology of the gene products along with spectra of pathogenic variants may be found in the individual gene test descriptions.

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.

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.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This panel typically provides ≥98% 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.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

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 23 AR 616490
Joubert Syndrome 25 AR 616781
Joubert Syndrome 26 AR 616784
Joubert Syndrome 3 AR 608629
Joubert Syndrome 30 AR 617622
Joubert Syndrome 31 AR 617761
Joubert Syndrome 32 AR 617757
Joubert Syndrome 33 AR 617767
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 13 AR 617562
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
Orofaciodigital Syndrome XIV AR 615948
Orofaciodigital Syndrome XVI AR 617563

Related Tests

Name
Bardet-Biedl Syndrome Sequencing Panel with CNV Detection
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CONTACTS

Genetic Counselors
Geneticist
Citations
  • Alexiev et al. 2006. PubMed ID: 16879033
  • Brancati et al. 2010. PubMed ID: 20615230
  • Chaumoitre K. et al. 2006. PubMed ID: 17094077
  • Delous et al. 2007. PubMed ID: 17558409
  • Doherty 2009. PubMed ID: 19778711
  • Hartill et al. 2017. PubMed ID: 29209597
  • Hildebrandt et al. 2009. PubMed ID: 19118152
  • Knopp et al. 2015. PubMed ID: 26003401
  • Mougou-Zerelli et al. 2009. PubMed ID: 19777577
  • Parisi et al. 2007. PubMed ID: 17377524
  • Parisi et al. 2017. PubMed ID: 20301500
  • Romani et al. 2014. PubMed ID: 24886560
  • Shaheen et al. 2016. PubMed ID: 27894351
  • Slaats et al. 2016. PubMed ID: 26490104
  • Valente et al. 2010. PubMed ID: 20512146
Order Kits
TEST METHODS

Exome Sequencing with CNV Detection

Test Procedure

For the PGxome we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus ~10 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from patient specimens. Patient DNA corresponding to these regions is captured using Agilent Clinical Research Exome hybridization probes. Captured DNA is sequenced on the NovaSeq 6000 using 2x150 bp paired-end reads (Illumina, San Diego, CA, USA). The following quality control metrics are generally achieved: >97% of target bases are covered at >20x, and mean coverage of target bases >120x. Data analysis and interpretation is performed by the internally developed software Titanium-Exome. In brief, the output data from the NovaSeq 6000 is converted to fastqs by Illumina Bcl2Fastq, and mapped by BWA. Variant calls are made by the GATK Haplotype caller and annotated using in house software and SnpEff. Variants are filtered and annotated using VarSeq (www.goldenhelix.com).

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.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

Analytical Validity

NextGen Sequencing: 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.

Copy Number Variant Analysis: The PGxome test detects most larger deletions and duplications including intragenic CNVs and large cytogenetic events; however aberrations in a small percentage of regions may not be accurately detected due to sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size (e.g., 1-3 exons vs. 4 or more exons), and inadequate coverage. In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of four exon size or larger is >95%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region.

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 sequencing does not reveal any heterozygous differences from the reference sequence, we cannot be certain that we were able to detect both patient alleles.

For technical reasons, the PGxome test is not 100% sensitive. Some exons cannot be efficiently captured, and some genes cannot be accurately sequenced because of the presence of multiple copies in the genome. Therefore, a small fraction of sequence variants will not be detected.

We sequence coding exons for most given transcripts, plus ~10 bp of flanking non-coding DNA for each exon. Unless specifically indicated, test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions, uncharacterized alternative exons, chromosomal rearrangements, repeat expansions, epigenetic effects, and mitochondrial genome variants.

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 amplification.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes if taken 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.

Balanced translocations or inversions are only rarely detected.

Certain types of sex chromosome aneuploidy may not be detected.  

Our ability to detect CNVs due to somatic mosaicism is limited.

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.

A negative finding does not rule out a genetic diagnosis.

Genetic counseling to help to explain test results to the patients and to discuss reproductive options is recommended.

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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