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Nephronophthisis and Senior-Loken Syndrome Sequencing Panel

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

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
1058 ANKS6 81479 Add to Order
CEP164 81479
CEP290 81408
CEP83 81479
DCDC2 81479
GLIS2 81479
INVS 81479
IQCB1 81479
NEK8 81479
NPHP1 81406
NPHP3 81479
NPHP4 81479
RPGRIP1L 81479
SDCCAG8 81479
TMEM67 81407
TTC21B 81479
WDR19 81479
ZNF423 81479
Full Panel Price* $1840.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1058 Genes x (18) $1840.00 81406, 81407, 81408, 81479(x15) Add to Order
Pricing Comment

If you would like to order a subset of these genes contact us to discuss pricing.

Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Sensitivity for Nephronophthisis testing is approximately 30% overall (Hildebrandt et al. 2009). This NGS test can detect the ~279kb deletion in the NPHP1 gene if it is present in the homozygous state.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 CEP290$690.00 81479 Add to Order
GLIS2$690.00 81479
INVS$690.00 81479
IQCB1$690.00 81479
NEK8$690.00 81479
NPHP1$690.00 81405
NPHP3$690.00 81479
NPHP4$690.00 81479
RPGRIP1L$690.00 81479
SDCCAG8$690.00 81479
TMEM67$690.00 81479
Full Panel Price* $1290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (11) $1290.00 81405, 81479(x10) Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Approximately 20% of individuals with nephronophthisis have a homozygous deletion encompassing the NPHP1 gene (Hoefele et al 2005; Hildebrandt et al 2009). Gross deletions or duplications that may not be detectable by NGS have been reported in CEP290, NPHP1, TMEM67 and SDCCAG8 (Human Gene Mutation Database).

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Clinical Features

Nephronophthisis (NPH) is the most common genetic cause of progressive renal failure in children and young adults. NPH is characterized by polyuria, growth retardation and progressive deterioration of renal function with normal or slightly reduced kidney size (Hildebrandt et al. 1997; Hildebrandt et al. 2009). Nephronophthisis, when associated with Leber Congenital Amaurosis, is known as Senior-Loken syndrome (SLS) (Otto et al. 2005; Hildebrandt et al. 2009). NPH clinical features overlap with a group of diseases known as ciliopathies, which includes Meckel-Gruber Syndrome, Joubert Syndrome, Bardet-Biedl Syndrome and Leber congenital amaurosis.

Genetics

Nephronophthisis and Senior-Loken syndrome are genetically heterogeneous disorders. NPH and SLS are inherited in an autosomal recessive manner. NPH and SLS are caused by pathogenic variants in genes encoding proteins involved in cilia/centrosome structure, maintenance or function (Hildebrandt et al. 2009). See individual gene test descriptions for more information on molecular biology of gene products.

Testing Strategy

For this NextGen panel, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Indications for Test

This test is for patients with Nephronophthisis or Senior-Loken Syndrome.

Genes

Official Gene Symbol OMIM ID
ANKS6 615370
CEP164 614848
CEP290 610142
CEP83 615847
DCDC2 605755
GLIS2 608539
INVS 243305
IQCB1 609237
NEK8 609799
NPHP1 607100
NPHP3 608002
NPHP4 607215
RPGRIP1L 610937
SDCCAG8 613524
TMEM67 609884
TTC21B 612014
WDR19 608151
ZNF423 604557
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Panel
Autosomal Recessive Retinitis Pigmentosa Sequencing Panel
Bardet-Biedl Syndrome Sequencing Panel
Ciliopathy Sequencing Panel
Comprehensive Inherited Retinal Dystrophies (includes RPGR ORF15) Sequencing Panel
Heterotaxy, Situs Inversus and Kartagener's Syndrome Sequencing Panel
Joubert and Meckel-Gruber Syndromes Sequencing Panel
Joubert and Meckel-Gruber Syndromes via the CEP290 Gene
Joubert and Meckel-Gruber Syndromes via the RPGRIP1L Gene
Joubert Syndrome, Meckel-Gruber Syndrome, and Nephronophthisis via the TMEM67 Gene
Leber Congenital Amaurosis 10 (LCA10) via the CEP290 Gene
Leber Congenital Amaurosis Sequencing Panel
Nephronophthisis / Senior-Loken Syndrome and Bardet-Biedl Syndrome via the SDCCAG8 Gene
Nephronophthisis and Joubert Syndrome via the NPHP1 Gene
Nephronophthisis and Senior-Loken Syndrome via the CEP164 Gene
Nephronophthisis and Senior-Loken Syndrome via the IQCB1/NPHP5 Gene
Nephronophthisis and Senior-Loken syndrome via the NPHP3 Gene
Nephronophthisis and Situs Inversus via the ANKS6 Gene
Nephronophthisis via the GLIS2 / NPHP7 Gene
Nephronophthisis via the INVS / NPHP2 Gene
Nephronophthisis via the NEK8/NPHP9 Gene
Nephronophthisis via the NPHP4 Gene
Nephrotic Syndrome (NS)/Focal Segmental Glomerulosclerosis (FSGS) Sequencing Panel
Primary Ciliary Dyskinesia (PCD)/Immotile Cilia Syndrome and Cystic Fibrosis Sequencing Panel
Primary Ciliary Dyskinesia (PCD)/Immotile Cilia Syndrome Sequencing Panel
Retinitis Pigmentosa (includes RPGR ORF15) Sequencing Panel
Short Rib Skeletal Dysplasia Sequencing Panel
Skeletal Disorders and Joint Problems Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Hildebrandt F. et al. 1997. Nature Genetics. 17: 149-53. PubMed ID: 9326933
  • Hildebrandt F. et al. 2009. Journal of the American Society of Nephrology : Jasn. 20: 23-35. PubMed ID: 19118152
  • Hoefele Julia et al. 2005. Human Mutation. 25: 411-411 PubMed ID: 15776426
  • Human Gene Mutation Database (Bio-base).
  • Otto E.A. et al. 2005. Nature Genetics. 37: 282-8. PubMed ID: 15723066
Order Kits
TEST METHODS

NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

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.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

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.   

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 Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

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 PCR.

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

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

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.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

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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