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Duane-Radial Ray Syndrome and Acro-Renal-Ocular Syndrome via the SALL4 Gene

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

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
832 SALL4$730.00 81479 Add to Order
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 18 days.

Clinical Sensitivity
Sequencing of SALL4 is predicted to detect disease mutations in up to 80% of individuals with a clinical diagnosis of DRRS and AROS (Al-Baradie et al. Am J Hum Genet 71:1195–1199, 2002; Kohlhase et al. Hum Mol Genet 11:2979–2987, 2002; Kohlhase et al. J Med Genet 40:473–478, 2003; Borozdin et al. J Med Genet 41:e102, 2004; Kohlhase et al. Hum Mutat 26:176–83, 2005). Large deletions involving single or multiple exons have been reported to account for 10-15% cases (Borozdin et al. J Med Genet 41:e113, 2004; Borozdin et al. Hum Mutat 28:830, 2007); such deletions would not generally be detected by sequence analysis.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 SALL4$690.00 81479 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 Features

Duane-radial ray syndrome (DRRS, aka Okihiro syndrome; OMIM#607323) is characterized by uni- or bilateral Duane anomaly and radial ray malformation that can include thenar hypoplasia and/or hypoplasia or aplasia of the thumbs; hypoplasia or aplasia of the radii; shortening and radial deviation of the forearms; triphalangeal thumbs; and duplication preaxial polydactyly. Acro-renal-ocular syndrome (AROS; OMIM#102490) is characterized by radial ray malformations, renal abnormalities, ocular coloboma, and Duane anomaly. DRRS and AROS are allelic disorders, both caused by mutations in the SALL4 gene. Rarely, SALL4 mutations may also cause clinically typical Holt-Oram syndrome (i.e. radial ray malformations and cardiac malformations without additional features). Additional clinical features in patients with a SALL4 mutation include sensorineural and/or conductive deafness (Kohlhase GeneReviews 2008).

Genetics

Duane-radial ray syndrome (DRRS) and Acro-renal-ocular syndrome (AROS) are inherited in an autosomal dominant manner with ~95% penetrance. SALL4 is the only gene known to be associated with these two disorders; about half of cases are caused by de novo mutations. SALL4 encodes sal-like protein 4, a C2H2 zinc finger transcription factor of the SAL type (Kohlhase et al. Hum Mol Genet 11:2979–2987, 2002). Sal-like protein 4 appears to be an essential developmental regulator. SALL4 cooperates with SALL1 in anorectal, heart, brain, and kidney development (Sakaki-Yumoto et al. Development 133:3005–3013, 2006). It is regulated by TBX5 in patterning and morphogenesis of the first digit of the upper limbs (Koshiba-Takeuchi et al. Nat Genet 38:175–183, 2006). The majority of mutations in SALL4 are nonsense and frameshift mutations leading to haploinsufficiency of sal-like protein 4.

Testing Strategy

This test involves bidirectional sequencing using genomic DNA of all coding exons of the SALL4 gene plus ~20 bp of flanking non-coding DNA on each side. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.

Indications for Test

Candidates for this test are patients with clinical and radiographic features consistent with DRRS or AROS, cases with typical Holt-Oran syndrome but tested negative for TBX5 gene, those with some features of Townes-Brocks syndrome but tested negative for SALL1 gene, and family members of patients who have known SALL4 mutations.

Gene

Official Gene Symbol OMIM ID
SALL4 607343
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
Duane-Radial Ray Syndrome 607323
Ivic Syndrome 147750

Related Tests

Name
Comprehensive Cardiology Sequencing Panel
Congenital Fibrosis of Extraocular Muscles (Ocular Motility Disorder) or Strabismus Syndromes Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Al-Baradie, R., et.al. (2002). "Duane radial ray syndrome (Okihiro syndrome) maps to 20q13 and results from mutations in SALL4, a new member of the SAL family." Am J Hum Genet 71(5): 1195-9. PubMed ID: 12395297
  • Borozdin, W., et.al. (2004). "Novel mutations in the gene SALL4 provide further evidence for acro-renal-ocular and Okihiro syndromes being allelic entities, and extend the phenotypic spectrum." J Med Genet 41(8): e102. PubMed ID: 15286162
  • Borozdin, W., et.al. (2004). "SALL4 deletions are a common cause of Okihiro and acro-renal-ocular syndromes and confirm haploinsufficiency as the pathogenic mechanism." J Med Genet 41(9): e113. PubMed ID: 15342710
  • Borozdin, W., et.al. (2007). "Multigene deletions on chromosome 20q13.13-q13.2 including SALL4 result in an expanded phenotype of Okihiro syndrome plus developmental delay." Hum Mutat 28(8): 830. PubMed ID: 17623483
  • Jürgen Kohlhase (2008). "SALL4-Related Disorders."
  • Kohlhase, J., et.al. (2002). "Okihiro syndrome is caused by SALL4 mutations." Hum Mol Genet 11(23): 2979-87. PubMed ID: 12393809
  • Kohlhase, J., et.al. (2003). "Mutations at the SALL4 locus on chromosome 20 result in a range of clinically overlapping phenotypes, including Okihiro syndrome, Holt-Oram syndrome, acro-renal-ocular syndrome, and patients previously reported to represent thalidomide embryopathy." J Med Genet 40(7): 473-8. PubMed ID: 12843316
  • Kohlhase, J., et.al. (2005). "SALL4 mutations in Okihiro syndrome (Duane-radial ray syndrome), acro-renal-ocular syndrome, and related disorders." Hum Mutat 26(3): 176-83. PubMed ID: 16086360
  • Koshiba-Takeuchi, K., et.al. (2006). "Cooperative and antagonistic interactions between Sall4 and Tbx5 pattern the mouse limb and heart." Nat Genet 38(2): 175-83. PubMed ID: 16380715
  • Sakaki-Yumoto, M., et.al. (2006). "The murine homolog of SALL4, a causative gene in Okihiro syndrome, is essential for embryonic stem cell proliferation, and cooperates with Sall1 in anorectal, heart, brain and kidney development." Development 133(15): 3005-13. PubMed ID: 16790473
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TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all 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 for example 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 and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

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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