• Test Code:
    1277
  • Department:
    Molecular Genetics
  • Test Synonyms:
    NephronophthisisOrofaciodigital syndrome type 1Senior-Loken syndromeJoubert SyndromeMeckel-Gruber syndromeBardet-Biedl syndromeHeterotaxiasPrimary Ciliary DysfunctionACVR2BAHI1AIPL1ARL13BARL6ATXN10B9D1B9D2BBS1BBS10BBS12BBS2BBS4BBS5BBS7BBS9C2orf71C5orf42 CC2D2ACCDC28BCCDC39CCDC40CDH23CEP290CEP41CFTRCITED2CLRN1CRB1CRELD1CRXDFNB31DNAAF1DNAAF2DNAAF3DNAH11DNAH5DNAI1DNAI2DNAL1DYNC2H1EVCEVC2FOXH1GATA4GDF1GLIS2GPR98GUCY2DHYLS1IFT43IFT80 IMPDH1INPP5EINVSIQCB1KCNJ13KIF7LCA5LEFTY2LRATMKKSMKS1MYO7ANEK1NEK8NKX2-5NME8NODALNPHP1NPHP3NPHP4OFD1PCDH15PKD2PKHD1RD3RDH12RPE65RPGRRPGRIP1RPGRIP1LRSPH4ARSPH9 SCNN1ASCNN1BSCNN1GSDCCAG8SHROOM3SMAD2SPATA7TCTN1TCTN2TMEM138TMEM216TMEM237TMEM67TOPORSTRIM32TSC1TSC2TTC21BTTC8TULP1UMODUSH1CUSH1GUSH2AVHLWDPCPWDR19WDR35XPNPEP3ZIC3
  • CPT Code(s):
    81408
Background:

Ciliopathies are a heterogeneous group of genetic disorders affecting multiple systems. Clinical phenotypes may include retinitis pigementosa, polydactylism, global developmental delays, cognitive impairments, brain malformations, impaired kidney function, abnormal left/right axis of the body and seizures. This class of disorders includes nephronophthisis, orofaciodigital syndrome type 1, Senior-Loken syndrome, Joubert syndrome, Meckel-Gruber syndrome, Bardet-Biedl syndrome, heterotaxias, and primary ciliary dysfunction. These conditions can be inherited in an autosomal dominant, recessive or X-linked pattern. This panel tests the coding regions for 114 genes associated with ciliopathies.

Reasons for Referral:

  • Patient display phenotypes associated with ciliopathy disorders
  • Carrier testing
  • Positive family history

Methodology:

Genomic DNA is analyzed using next-generation sequencing (NGS) on the Illumina NextSeq 2000 platform, with target enrichment performed using hybridization-based probes to capture exonic (coding) regions of the gene(s). Single nucleotide variants (SNVs) and small insertions or deletions (INDELs) are identified using the Illumina DRAGEN Enrichment Workflow, executed onboard the NextSeq2000. This pipeline combines software and hardware acceleration to generate high-confidence germline haplotype calls. Clinical and analytical validation of DRAGEN was performed in our laboratory. Based on validation study results, for SNVs, this assay achieves >96% analytical sensitivity and >99% positive predictive value (PPV). For INDELs <50 bp, the analytical sensitivity is >87% and the PPV is >97%. INDELs >50 bp may be detected but the sensitivity for these is reduced.

Exon-level copy number variants (CNVs) are detected using the Germline Copy Number Variation Best Practices pipeline from GATK. A Bayesian model, clinically validated in our laboratory, enables detection of deletions and duplications involving three or more contiguous exons in genes with adequate probe coverage and without complicating factors (e.g. pseudogene homology, short tandem repeats, segmental duplications). Please note that exon-centric microarray remains the gold standard for exonic copy number variant calling. If exon-centric microarray is of interest, please contact the laboratory for additional information.

This test is not designed to detect polynucleotide repeats, low-level mosaicism, structural rearrangements or balanced alterations (e.g. inversions, gene conversion events, translocations, etc.) or variants in difficult regions. Additionally, variants located in regions of insufficient coverage, including introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and of high GC content may not be detected. This test does not provide complete coverage of all exons and noncoding regions may have limited information and ability to interpret. Variants in introns that are greater than 10 bp from the intron-exon junction may be analyzed. Please contact the laboratory if interrogation of intronic sequence greater than 10 bp from the intron-exon boundary is desired.

The 114 Ciliopathies-associated genes are listed below:

ACVR2B, AHI1, AIPL1, ARL13B, ARL6, ATXN10, B9D1, B9D2, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, C2orf71, C5orf42, CC2D2A, CCDC28B, CCDC39, CCDC40, CDH23, CEP290, CEP41, CFTR, CITED2, CLRN1, CRB1, CRELD1, CRX, DFNB31, DNAAF1, DNAAF2, DNAAF3, DNAH11, DNAH5, DNAI1, DNAI2, DNAL1, DYNC2H1, EVC, EVC2, FOXH1, GATA4, GDF1, GLIS2, GPR98, GUCY2D, HYLS1, IFT43, IFT80, IMPDH1, INPP5E, INVS, IQCB1, KCNJ13, KIF7, LCA5, LEFTY2, LRAT, MKKS, MKS1, MYO7A, NEK1, NEK8, NKX2-5, NME8, NODAL, NPHP1, NPHP3, NPHP4, OFD1, PCDH15, PKD2, PKHD1, RD3, RDH12, RPE65, RPGR, RPGRIP1, RPGRIP1L, RSPH4A, RSPH9, SCNN1A, SCNN1B, SCNN1G, SDCCAG8, SHROOM3, SMAD2, SPATA7, TCTN1, TCTN2, TMEM138, TMEM216, TMEM237, TMEM67, TOPORS, TRIM32, TSC1, TSC2, TTC21B, TTC8, TULP1, UMOD, USH1C, USH1G, USH2A, VHL, WDPCP, WDR19, WDR35, XPNPEP3, ZIC3

For a comprehensive list of regions with limited coverage on this panel, please refer to the following table.

Specimen Requirements:

Blood:  EDTA or ACD (Solution A or B):

  • Adult: 5 mL
  • Child: 5 mL
  • Infant: 2-3 mL

Saliva: 2 ORAgene™ Saliva Collection Kits (OGR-500) used according to manufacturer instructions.  Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.

Assisted Saliva: 4 ORAgene™ Assisted Saliva Collection Kits (OGR-575) used according to manufacturer instructions.  Please contact KDL Client Services for an Assisted Saliva Collection Kit for patients that cannot provide a blood sample.

Buccal Cells: 4 CytoSoft™ Cytology Brush (Medical Packaging CYB-1) used according to manufacturer instructions.  Please contact KDL Client Services for a Buccal Collection Kit for patients that cannot provide a blood sample.

Skin Fibroblast: Punch Biopsy (Cell cultures will be prepared at KDL and used for testing), or 2 T-25 confluent flasks.

DNA: 1-2µg at a minimum of 50-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS).

Notice Regarding Molecular Genetic Testing on Prenatal Specimens:

Maternal cell rule-out testing will be performed on all prenatal specimens received. Please provide maternal blood (or saliva) in addition to the fetal specimen. Additional charges apply for the maternal cell rule-out test.

For routine testing of blood and saliva (or DNA extracted from these specimens), KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion.  For extraordinary circumstances, where testing must be performed within the above windows, please contact the laboratory.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information, including ethnicity, clinical history, and family history.

    Test Performed (Days):

    Weekly

    Turn Around Time:

    8 weeks

    Shipment Sensitivity Requirements:

    • Package and ship specimen to remain cold, but not frozen. 
    • Ship via overnight express, using the FedEx priority overnight label provided. 
    • Contact Client Services for shipping kits and instructions at (855) 535-1522.

    References:

    1. The Ciliopathies: An Emerging Class of Human Genetic Disorders: Annu Rev Genomics Hum Genet. 2006;7:125-48.

    Additional Info: