Ciliopathy Panel

  • bpg-method PLUS
  • bpg-method SEQ
  • bpg-method DEL/DUP

Test code: KI0701

The Blueprint Genetics Ciliopathy Panel is an 83 gene test for genetic diagnostics of patients with clinical suspicion of Bardet-Biedl syndrome, cystic kidneys, Joubert syndrome, Meckel syndrome, nephronophthisis with retinal dystrophy, primary ciliary dyskinesia or situs inversus.

The panel covers genes associated with autosomal recessive, autosomal dominant and X-linked forms of ciliopathies. This comprehensive Panel includes Primary Ciliary Dyskinesia, Nephronophtisis, Senior-Loken Syndrome, Bardet-Biedl Syndrome, Joubert Syndrome and Meckel Syndrome Panels.

About Ciliopathy

Ciliopathies comprise a group of disorders associated with genetic mutations encoding defective proteins, which result in either abnormal formation or function of cilia. Ciliary gene mutations are now known to cause single organ disease, as well as complex syndromes. Ciliopathies have a broad range of phenotypes encompassing a number of different autosomal recessive, dominant and X-linked syndromes. As cilia are a component of almost all cells, ciliary dysfunction can manifest as a collection of features that include primarily retinal degeneration, renal disease and cerebral anomalies. Additional manifestations include congenital fibrocystic diseases of the liver and pancreas, diabetes, obesity and skeletal dysplasias. Phenotypically heterogeneous, ciliopathic features can manifest from variation at a single locus while mutations affecting a number of different loci can, at the same time, result in similar phenotypes. Ciliopathies can be classified according to whether there is aberrant function in an intact cilium or complete absence/loss of the mature cilium. The latter is the case with severe multi-organ phenotypes. Classical ciliopathies include polycystic kidney disease (PKD), retinal degeneration, laterality defects, chronic respiratory problems, situs inversus, hydrocephalus and infertility.

Availability

Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more: http://blueprintgenetics.com/faqs/#prenatal

Genes in the Ciliopathy Panel and their clinical significance
Gene Associated phenotypes Inheritance ClinVar HGMD
AHI1 Joubert syndrome AR 53 84
ALMS1* Alström syndrome AR 50 291
ANKS6 Nephronophthisis AR 5 12
ARL6 Bardet-Biedl syndrome, Retinitis pigmentosa AR 13 21
ARL13B Joubert syndrome AR 9 9
ARMC4* Ciliary dyskinesia AR 13 15
B9D1 Meckel syndrome AR 8 9
B9D2 Meckel syndrome AR 5 4
BBS1 Bardet-Biedl syndrome AR 48 100
BBS2 Bardet-Biedl syndrome, Retinitis pigmentosa AR 32 90
BBS4 Bardet-Biedl syndrome AR 20 51
BBS5 Bardet-Biedl syndrome AR 14 30
BBS7 Bardet-Biedl syndrome AR 14 39
BBS9 Bardet-Biedl syndrome AR 22 49
BBS10 Bardet-Biedl syndrome AR 54 98
BBS12 Bardet-Biedl syndrome AR 11 57
C5ORF42 Orofaciodigital syndrome, Joubert syndrome AR 68 98
C21ORF59 Ciliary dyskinesia AR 3 4
CC2D2A COACH syndrome, Joubert syndrome, Meckel syndrome AR 71 86
CCDC39 Ciliary dyskinesia AR 16 38
CCDC40 Ciliary dyskinesia AR 19 32
CCDC65 Ciliary dyskinesia AR 1
CCDC103 Ciliary dyskinesia AR 3 4
CCDC114 Ciliary dyskinesia AR 6 7
CCNO Ciliary dyskinesia AR 9 9
CENPF Ciliary dyskinesia -Lethal Ciliopathy AR 11 7
CEP41 Joubert syndrome AR/Digenic 7 10
CEP83 Nephronophthisis AR 9 10
CEP164 Nephronophthisis AR 8 8
CEP290* Bardet-Biedl syndrome, Leber congenital amaurosis, Joubert syndrome, Senior-Loken syndrome, Meckel syndrome AR 96 266
CFTR Cystic fibrosis AR 410 1765
CSPP1 Jeune asphyxiating thoracic dystrophy, Joubert syndrome AR 25 25
DCDC2 Deafness AR 9 9
DNAAF1 Ciliary dyskinesia AR 9 30
DNAAF2 Ciliary dyskinesia AR 6 3
DNAAF3 Primary ciliary dyskinesia AD/AR 6 3
DNAAF5 Ciliary dyskinesia AR 2 2
DNAH5 Ciliary dyskinesia AR 60 141
DNAH11* Ciliary dyskinesia AR 30 90
DNAI1 Ciliary dyskinesia AR 12 28
DNAI2 Ciliary dyskinesia AR 11 6
DNAL1 Ciliary dyskinesia AR 3 1
DRC1 Primary ciliary dyskinesia AD/AR 3 2
DYX1C1 Ciliary dyskinesia AR 9 11
GLIS2 Nephronophthisis AR 3 3
HYDIN* Primary ciliary dyskinesia AD/AR 5 15
IFT172 Retinitis pigmentosa, Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune) AR 20 23
INPP5E Joubert syndrome, Mental retardation, truncal obesity, retinal dystrophy, and micropenis (MORM syndrome) AR 23 44
INVS Nephronophthisis AR 12 33
IQCB1 Senior-Loken syndrome AR 19 37
KIAA0586 Short rib thoracic dysplasia with polydactyly, Joubert syndrome AR 20 29
KIF7 Acrocallosal syndrome, Hydrolethalus syndrome, Al-Gazali-Bakalinova syndrome, Joubert syndrome AR/Digenic 15 40
LRRC6 Ciliary dyskinesia AR 7 16
MKKS Bardet-Biedl syndrome, McKusick-Kaufman syndrome AR 15 59
MKS1 Bardet-Biedl syndrome, Meckel syndrome AR 42 51
NEK8 Nephronophthisis AR 4 16
NME8 Ciliary dyskinesia AR 1 5
NPHP1 Nephronophthisis, Joubert syndrome, Senior-Loken syndrome AR 14 73
NPHP3 Nephronophthisis, Renal-hepatic-pancreatic dysplasia, Meckel syndrome AR 24 72
NPHP4 Nephronophthisis, Senior-Loken syndrome AR 12 108
OFD1 Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome XL 133 156
RPGR Retinitis pigmentosa XL 62 202
RPGRIP1L COACH syndrome, Joubert syndrome, Meckel syndrome, Retinal degeneration in ciliopathy, modifier AD/AR 35 45
RSPH1 Ciliary dyskinesia AR 11 10
RSPH4A Ciliary dyskinesia AR 8 21
RSPH9 Ciliary dyskinesia AR 4 11
SDCCAG8 Bardet-Biedl syndrome, Senior-Loken syndrome AR 12 18
SPAG1 Primary ciliary dyskinesia AD/AR 13 10
TCTN1 Joubert syndrome AR 6 6
TCTN2 Joubert syndrome, Meckel syndrome AR 17 13
TCTN3 Orofaciodigital syndrome (Mohr-Majewski syndrome), Joubert syndrome AR 9 10
TMEM67 Nephronophthisis, COACH syndrome, Joubert syndrome, Meckel syndrome AR 82 153
TMEM107 Joubert syndrome AD/AR 10 3
TMEM138 Joubert syndrome AR 6 8
TMEM216 Joubert syndrome, Meckel syndrome AR 14 8
TMEM231 Joubert syndrome, Meckel syndrome AR 9 19
TMEM237 Joubert syndrome AR 6 10
TRIM32 Bardet-Biedl syndrome, Muscular dystrophy, limb-girdle AR 11 16
TTC8 Bardet-Biedl syndrome, Retinitis pigmentosa AR 5 16
TTC21B Short-rib thoracic dysplasia, Nephronophthisis, Asphyxiating thoracic dysplasia (ATD; Jeune) AR 8 53
WDR19 Retinitis pigmentosa, Nephronophthisis, Short -rib thoracic dysplasia with or without polydactyly, Senior-Loken syndrome, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Asphyxiating thoracic dysplasia (ATD; Jeune) AD/AR 20 28
ZMYND10 Ciliary dyskinesia AR 6 16
ZNF423 Nephronophthisis, Joubert syndrome AD/AR 10 7

*Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Gene Genomic location HG19 HGVS RefSeq RS-number
BBS4 Chr15:73001820 c.77-216delA NM_033028.4 rs113994189
CEP290 Chr12:88494960 c.2991+1655A>G NM_025114.3 rs281865192
CFTR Chr7:117229530 c.1680-877G>T NM_000492.3 rs397508261
CFTR Chr7:117251609 c.3140-26A>G NM_000492.3 rs76151804
CFTR Chr7:117280015 c.3718-2477C>T NM_000492.3 rs75039782
OFD1 ChrX:13773245 c.1130-22_1130-19delAATT NM_003611.2 rs312262865
OFD1 ChrX:13768358 c.935+706A>G NM_003611.2 rs730880283

The strengths of this test include:

  • Blueprint Genetics is one of the few laboratories worldwide with CAP and ISO-15189 accreditation for NGS panels and CLIA certification
  • Superior sequencing quality
  • Careful selection of genes based on current literature, our experience and the most current mutation databases
  • Transparent and easy access to quality and performance data at the patient level that are accessible via our Nucleus portal
  • Transparent and reproducible analytical validation for each panel (see Test performance section; for complete details, see our Analytic Validation)
  • Sequencing and high resolution del/dup analysis available in one test
  • Inclusion of non-coding disease causing variants where clinically indicated (please see individual Panel descriptions)
  • Interpretation of variants following ACMG variant classification guidelines
  • Comprehensive clinical statement co-written by a PhD geneticist and a clinician specialist

 

This test does not detect the following:

  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Variants in regulatory or non-coding regions of the gene unless otherwise indicated (please see Non-coding disease causing variants covered by the panel). This mean for instance intronic variants locating deeper than 15 nucleotides from the exon-intron boundary.

 

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments
  • Disorders caused by long repetitive sequences (e.g. trinucleotide repeat expansions)

 

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

Blueprint Genetics offers a comprehensive Ciliopathy Panel that covers classical genes associated with Bardet-Biedl syndrome, cystic kidneys, Joubert syndrome, Meckel syndrome, nephronophthisis with retinal dystrophy, primary ciliary dyskinesia and situs inversus. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ 81479
DEL/DUP 81479


ICD codes

Commonly used ICD-10 codes when ordering the Ciliopathy Panel

ICD-10 Disease
Q87.89 Bardet-Biedl syndrome
Q04.3 Joubert syndrome
Q61.9 Meckel syndrome
Q61.9 Cystic kidney disease
Q34.8 Primary ciliary dyskinesia
Q89.3 Situs inversus
Q61.5 Nephronophthisis with retinal dystrophy

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

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