Ciliopathy Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

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.

Genes in the Ciliopathy Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
AHI1Joubert syndromeAR4770
ALMS1*Alström syndromeAR31281
ANKS6NephronophthisisAR512
ARL6Bardet-Biedl syndrome, Retinitis pigmentosaAR921
ARL13BJoubert syndromeAR97
ARMC4*Ciliary dyskinesiaAR1215
B9D1Meckel syndromeAR88
B9D2Meckel syndromeAR54
BBS1Bardet-Biedl syndromeAR1992
BBS2Bardet-Biedl syndrome, Retinitis pigmentosaAR3084
BBS4Bardet-Biedl syndromeAR1345
BBS5Bardet-Biedl syndromeAR1027
BBS7Bardet-Biedl syndromeAR1236
BBS9Bardet-Biedl syndromeAR2142
BBS10Bardet-Biedl syndromeAR2396
BBS12Bardet-Biedl syndromeAR859
C5ORF42Orofaciodigital syndrome, Joubert syndromeAR63
C21ORF59Ciliary dyskinesiaAR3
CC2D2ACOACH syndrome, Joubert syndrome, Meckel syndromeAR6480
CCDC39Ciliary dyskinesiaAR1338
CCDC40Ciliary dyskinesiaAR1531
CCDC65Ciliary dyskinesiaAR21
CCDC103Ciliary dyskinesiaAR24
CCDC114Ciliary dyskinesiaAR57
CCNOCiliary dyskinesiaAR79
CENPFCiliary dyskinesia -Lethal CiliopathyAR86
CEP41Joubert syndromeAR/Digenic710
CEP83NephronophthisisAR710
CEP164NephronophthisisAR78
CEP290*Bardet-Biedl syndrome, Leber congenital amaurosis, Joubert syndrome, Senior-Loken syndrome, Meckel syndromeAR79252
CFTRCystic fibrosisAR3661767
CSPP1Jeune Asphyxiating Thoracic Dystrophy, Joubert syndromeAR2223
DCDC2DeafnessAR411
DNAAF1Ciliary dyskinesiaAR828
DNAAF2Ciliary dyskinesiaAR43
DNAAF3Primary ciliary dyskinesiaAD/AR33
DNAAF5Ciliary dyskinesiaAR22
DNAH5Ciliary dyskinesiaAR36135
DNAH11*Ciliary dyskinesiaAR2590
DNAI1Ciliary dyskinesiaAR1028
DNAI2Ciliary dyskinesiaAR76
DNAL1Ciliary dyskinesiaAR31
DRC1Primary ciliary dyskinesiaAD/AR32
DYX1C1Ciliary dyskinesiaAR617
GLIS2NephronophthisisAR33
HYDIN*Primary ciliary dyskinesiaAD/AR313
IFT172Retinitis pigmentosa, Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune)AR1821
INPP5EJoubert syndrome, Mental retardation, truncal obesity, retinal dystrophy, and micropenis (MORM syndrome)AR1941
INVSNephronophthisisAR933
IQCB1Senior-Loken syndromeAR1535
KIAA0586Short rib thoracic dysplasia with polydactyly, Joubert syndromeAR1426
KIF7Acrocallosal syndrome, Hydrolethalus syndrome, Al-Gazali-Bakalinova syndrome, Joubert syndromeAR/Digenic1339
LRRC6Ciliary dyskinesiaAR814
MKKSBardet-Biedl syndrome, McKusick-Kaufman syndromeAR1357
MKS1Bardet-Biedl syndrome, Meckel syndromeAR3947
NEK8NephronophthisisAR315
NME8Ciliary dyskinesiaAR16
NPHP1Nephronophthisis, Joubert syndrome, Senior-Loken syndromeAR1264
NPHP3Nephronophthisis, Renal-hepatic-pancreatic dysplasia, Meckel syndromeAR2071
NPHP4Nephronophthisis, Senior-Loken syndromeAR10104
OFD1Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndromeXL129148
RPGRRetinitis pigmentosaXL41184
RPGRIP1LCOACH syndrome, Joubert syndrome, Meckel syndrome, Retinal degeneration in ciliopathy, modifierAD/AR2841
RSPH1Ciliary dyskinesiaAR910
RSPH4ACiliary dyskinesiaAR721
RSPH9Ciliary dyskinesiaAR211
SDCCAG8Bardet-Biedl syndrome, Senior-Loken syndromeAR1218
SPAG1Primary ciliary dyskinesiaAD/AR710
TCTN1Joubert syndromeAR66
TCTN2Joubert syndrome, Meckel syndromeAR1513
TCTN3Orofaciodigital syndrome (Mohr-Majewski syndrome), Joubert syndromeAR810
TMEM67Nephronophthisis, COACH syndrome, Joubert syndrome, Meckel syndromeAR78138
TMEM107Joubert syndromeAD/AR72
TMEM138Joubert syndromeAR66
TMEM216Joubert syndrome, Meckel syndromeAR88
TMEM231Joubert syndrome, Meckel syndromeAR716
TMEM237Joubert syndromeAR610
TRIM32Bardet-Biedl syndrome, Muscular dystrophy, limb-girdleAR715
TTC8Bardet-Biedl syndrome, Retinitis pigmentosaAR516
TTC21BShort-rib thoracic dysplasia, Nephronophthisis, Asphyxiating thoracic dysplasia (ATD; Jeune)AR647
WDR19Retinitis 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/AR1625
ZMYND10Ciliary dyskinesiaAR616
ZNF423Nephronophthisis, Joubert syndromeAD/AR76
  • * 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.

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.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. 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. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. 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. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

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

SEQ81479
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Ciliopathy Panel

ICD-10Disease
Q87.89Bardet-Biedl syndrome
Q04.3Joubert syndrome
Q61Cystic kidneys
Q61.9Meckel syndrome
Q34.8Primary ciliary dyskinesia
Q89.3Situs inversus
Q61.5Nephronophthisis 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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