Molecular Genetics Ciliopathies Panel

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

Next generation sequencing will analyze the exons or coding regions of 114 Ciliopathies-associated genes using Illumina NextSeq 500 technology.  Samples are prepared using hybridization probes to enrich exonic regions. This assay does not assess regions of insufficient coverage, introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and regions of high GC or polynucleotide repeats, but may contain variants that impact gene function. 

Exon-level deletion/duplication analysis is performed by running the NGS data through the Genome Analysis Toolkit (GATK) Germline Copy Number Variation best practices pipeline from GATK, version 4.1.4.1. A Bayesian model was validated clinically in our lab. The model can detect copy changes at a resolution of three (3) or more probe targets (exons) for deletions and duplications in genes that do not have pseudogenes, and is not designed to detect low-level mosaicism or balanced alterations.

The 114 Ciliopathies-associated genes are listed below:

Gene Name	Gene Coverage
ACVR2B, AHI1, AIPL1, ARL13B, ARL6, ATXN10, B9D1, B9D2, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, C2orf71, CC2D2A, CCDC28B, CCDC39, CCDC40, CDH23, CEP290, CEP41, CFTR, CLRN1, CRB1, CRELD1, CRX, DFNB31, DNAAF1, DNAAF3, DNAH11, DNAH5, DNAI1, DNAI2, DNAL1, DYNC2H1, EVC2, GLIS2, GPR98, HYLS1, IFT43, IFT80, IMPDH1, INVS, IQCB1, LCA5, LEFTY2, LRAT, MKKS, MKS1, MYO7A, NEK1, NEK8, NME8, NODAL, NPHP1, NPHP3, NPHP4, OFD1, PCDH15, 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	95%-100%
CITED2, DNAAF2, EVC, INPP5E, KCNJ13, KIF7	90%-95%
C5orf42, FOXH1, GUCY2D, NKX2-5, PKD2	75%-90%
GDF1, GATA4	50%-75%

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.

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 CVS or Amniotic Fluid Specimens:

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

For routine testing of blood, saliva and buccal swabs, 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 outside of the above windows, please contact our lab.

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

Weekly

8 weeks

• 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.

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