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Bardet-Biedl Syndrome Sequencing Panel

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

Sequencing

Test Code TestCPT Code Copy CPT Codes
1053 ARL6 81479 Add to Order
BBIP1 81479
BBS1 81406
BBS10 81404
BBS12 81479
BBS2 81406
BBS4 81479
BBS5 81479
BBS7 81479
BBS9 81479
CEP290 81408
IFT27 81479
LZTFL1 81479
MKKS 81479
MKS1 81479
SDCCAG8 81479
TMEM67 81407
TRIM32 81479
TTC8 81479
WDPCP 81479
Full Panel Price* $1690.00
Test Code Test Total Price CPT Codes Copy CPT Codes
1053 Genes x (20) $1690.00 81404, 81406(x2), 81407, 81408, 81479(x15) Add to Order
Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information. If you would like to order a subset of these genes contact us to discuss pricing.

For Sanger Sequencing click here.
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

Clinical sensitivity for the BBS NGS test is ~80% (Forsythe and Beales 2015).

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Deletion/Duplication Testing via aCGH

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
600 ARL6$690.00 81479 Add to Order
BBS1$690.00 81479
BBS10$690.00 81479
BBS12$690.00 81479
BBS2$690.00 81479
BBS4$690.00 81479
BBS5$690.00 81479
BBS7$690.00 81479
BBS9$690.00 81479
CEP290$690.00 81479
MKKS$690.00 81479
MKS1$690.00 81479
SDCCAG8$690.00 81479
TMEM67$690.00 81479
TRIM32$690.00 81479
TTC8$690.00 81479
Full Panel Price* $1290.00
Test Code Test Total Price CPT Codes Copy CPT Codes
600 Genes x (16) $1290.00 81479(x16) 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

Gross deletions or duplications not detectable by Sanger sequencing have been reported in ARL6, BBS1, BBS2, BBS4, BBS5, BBS7, BBS9, MKS1, SDCCAG8, and TRIM32 (Human Gene Mutation Database). Clinical sensitivity is difficult to predict due to the paucity of documented cases.

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Clinical Features

Bardet-Biedl Syndrome (BBS) is an autosomal recessive disorder marked by primary features of obesity, polydactyly, pigmentary retinopathy, hypogonadism, renal anomalies and mental retardation (Elbedour et al. 1994; Sheffield 2010). Secondary features include diabetes, hypertension and congenital heart defects (Green et al. 1989). Although BBS is a rare condition, diagnosis is complicated by the fact that many of the clinical features (i.e. obesity, diabetes, hypertension and developmental delay) are common. In addition, many of the BBS clinical features overlap with those of other well-described developmental disorders, including Meckel-Gruber Syndrome (MKS), Joubert Syndrome (JBTS), Nephronophthisis (NPH), Senior-Loken Syndrome (SLS) and Leber Congenital Amaurosis (LCA). Thus, molecular testing is often useful for confirmation of a clinical diagnosis and to aid in the treatment and management of BBS.

Genetics

BBS is a genetically heterogeneous disorder known to be caused by pathogenic variants in at least 19 different genes including ARL6/BBS3, BBIP1/BBS18, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, CEP290/BBS14, IFT27/BBS19, LZTFL1/BBS17, MKKS/BBS6, MKS1/BBS13, SDCCAG8/BBS16, TRIM32/BBS11, TTC8/BBS8, and WDPCP/BBS15 (Forsythe and Beales 2015; Leitch et al. 2008; Kim et al. 2010; Otto et al. 2010). TMEM67 is included in this panel as it has been suggested to be a genetic modifier of the BBS phenotype (Leitch 2008). BBS is marked by both intra- and inter-familial phenotypic variability.  It has been suggested that BBS has an oligogenic inheritance pattern. Triallelism hypothesis states that three pathogenic alleles in two loci are necessary for BBS. This hypothesis attempts to explain variable expressivity and the observation that several individuals with BBS have been found to have a third rare, possibly pathogenic variant in a second BBS gene (Katsanis et al. 2001; Katsanis. 2004; Leitch et al. 2008).  However, others have not found evidence for triallelic inheritance patterns in their cohorts (Smaoui, N. et al. 2006; Abu-Safieh et al. 2012).  In the majority of reported cases two pathogenic variants in one gene are sufficient for BBS. However, the severity may be modulated by an additional hypomorphic or loss of function allele(s) at another locus. It is recommended to use an autosomal recessive inheritance model when counseling patients and their families (Forsythe and Beales 2015). 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 symptoms of BBS.

Genes

Official Gene Symbol OMIM ID
ARL6 608845
BBIP1 613605
BBS1 209901
BBS10 610148
BBS12 610683
BBS2 606151
BBS4 600374
BBS5 603650
BBS7 607590
BBS9 607968
CEP290 610142
IFT27 615870
LZTFL1 606568
MKKS 604896
MKS1 609883
SDCCAG8 613524
TMEM67 609884
TRIM32 602290
TTC8 608132
WDPCP 613580
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
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Autosomal Recessive Retinitis Pigmentosa Sequencing Panel
Bardet-Biedl Syndrome via the ARL6/BBS3 Gene
Bardet-Biedl Syndrome via the BBS1 Gene
Bardet-Biedl Syndrome via the BBS10 Gene
Bardet-Biedl Syndrome via the BBS12 Gene
Bardet-Biedl Syndrome via the BBS2 Gene
Bardet-Biedl Syndrome via the BBS4 Gene
Bardet-Biedl Syndrome via the BBS5 Gene
Bardet-Biedl Syndrome via the BBS7 Gene
Bardet-Biedl Syndrome via the BBS9 Gene
Bardet-Biedl Syndrome via the MKKS/BBS6 Gene
Bardet-Biedl Syndrome via the TRIM32/BBS11 Gene
Bardet-Biedl Syndrome via the TTC8/BBS8 Gene
Ciliopathy Sequencing Panel
Comprehensive Neuromuscular Sequencing Panel
Joubert and Meckel-Gruber Syndromes Sequencing Panel
Joubert and Meckel-Gruber Syndromes via the CEP290 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
Limb-Girdle Muscular Dystrophy (LGMD) Sequencing Panel
Meckel-Gruber Syndrome via the MKS1 Gene
Nephronophthisis / Senior-Loken Syndrome and Bardet-Biedl Syndrome via the SDCCAG8 Gene
Nephronophthisis and Senior-Loken Syndrome Sequencing Panel
Retinitis Pigmentosa (includes RPGR ORF15) Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Abu-Safieh L. et al. 2012. European Journal of Human Genetics : Ejhg. 20: 420-7. PubMed ID: 22353939
  • Elbedour K, Zucker N, Zalzstein E, Barki Y, Carmi R. 1994. Cardiac abnormalities in the Bardet-Biedl syndrome: echocardiographic studies of 22 patients. Am. J. Med. Genet. 52: 164–169. PubMed ID: 7802002
  • Forsythe E, Beales PL. 2014. Bardet-Biedl Syndrome. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301537
  • Green JS, Parfrey PS, Harnett JD, Farid NR, Cramer BC, Johnson G, Heath O, McManamon PJ, O’Leary E, Pryse-Phillips W. 1989. The cardinal manifestations of Bardet–Biedl syndrome, a form of Laurence–Moon–Biedl syndrome. New England Journal of Medicine 321: 1002–1009. PubMed ID: 2779627
  • Human Gene Mutation Database (Bio-base).
  • Katsanis N, Ansley SJ, Badano JL, Eichers ER, Lewis RA, Hoskins BE, Scambler PJ, Davidson WS, Beales PL, Lupski JR. 2001. Triallelic inheritance in Bardet-Biedl syndrome, a Mendelian recessive disorder. Science 293: 2256–2259. PubMed ID: 11567139
  • Katsanis N. 2004. The oligogenic properties of Bardet-Biedl syndrome. Human Molecular Genetics 13: 65R–71. PubMed ID: 14976158
  • Kim SK1, Shindo A, Park TJ, Oh EC, Ghosh S, Gray RS, Lewis RA, Johnson CA, Attie-Bittach T, Katsanis N, Wallingford JB. 2010. Planar cell polarity acts through septins to control collective cell movement and ciliogenesis. Science 329:1337-1340. PubMed ID: 20671153
  • Leitch CC, Zaghloul NA, Davis EE, Stoetzel C, Diaz-Font A, Rix S, Al-Fadhel M, Lewis RA, Eyaid W, Banin E, Dollfus H, Beales PL, et al. 2008. Hypomorphic mutations in syndromic encephalocele genes are associated with Bardet-Biedl syndrome. Nature Genetics 40: 443–448. PubMed ID: 18327255
  • Otto EA, Hurd TW, Airik R, Chaki M, Zhou W, Stoetzel C, Patil SB, Levy S, Ghosh AK, Murga-Zamalloa CA, Reeuwijk J van, Letteboer SJF, et al. 2010. Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nature Genetics 42: 840–850. PubMed ID: 20835237
  • Sheffield, V.C. 2010. The blind leading the obese: the molecular pathophysiology of a human obesity syndrome. Trans Am Clin Climatol Assoc 121:172-182. PubMed ID: 20697559
  • Smaoui N. et al. 2006. Investigative Ophthalmology & Visual Science. 47: 3487-95. PubMed ID: 16877420
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TEST METHODS

NextGen Sequencing

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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