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Test Code SALL4 S+D/D SALL4 Seq and Del/Dup

Important Note

This test includes sequencing and CNV analysis for the SALL4 genes.

Clinical System Name

SALL4 Seq and Del/Dup

Synonyms

SALL4

Duane-Radial Ray Syndrome

Description

Duane-radial ray syndrome (DRRS, aka Okihiro syndrome, 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 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).

 

 

Sample Requirements

Specimen: Whole Blood

Container(s): Lavender Top/EDTA, Yellow/ACD

Preferred Vol: 5 mL

Minimum Vol: 3 mL (1 mL for small infants)

 

Specimen: DNA

Container(s): Sterile plastic tube

Preferred Vol: 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml

Saliva: Isohelix™ or GeneFiX™ Saliva Collection kit used according to manufacturer instructions.

Specimens & Shipping

Processing Instructions

Reject due to:

Spin: N

Aliquot: N

Temp: 2-8 C

Storage location: Deliver blood to Sendouts refrigerator rack. Store labels in the clear plastic box on front of the CPA fridge.

 

Off-site collection: Send whole blood refrigerated.

Stability

Specimen Type Temperature Time
Whole blood Room temp 2 d
Whole blood Refrigerated 7 d
Whole blood Frozen N
Extracted DNA Room temp 3-4 d
Extracted DNA Refrigerated 1 y
Extracted DNA Frozen Indefinitely

 

Availability

STAT TAT
N 26 d

 

Performing Laboratory

Department:     PreventionGenetics, 3800 S. Business Park Ave., Marshfield, Wisconsin 54449

Phone Number:    (715) 387-0484

 

Department

Department: Send Outs

Phone Number: (206) 987-2563

 

 

Reference Range

Interpretive report is provided.

Methodology

For this Next Generation Sequencing (NGS) test, 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 regions not captured or with insufficient number of sequence reads.

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.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This test provides full coverage of all coding exons of the SALL4 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Special Instructions

PreventionGenetics

Clinical Utility

SALL4 - Related Disorders

Send Out Instructions

Reference Test Name:

Duane-Radial Ray Syndrome and Acro-Renal-Ocular Syndrome via SALL4 Gene Sequencing with CNV Detection

Reference Test Number: 8459
Instructions: Ship whole blood overnight, ambient temperature. PreventionGenetics accepts Saturday delivery

 

Update Date

This page was last updated 12/4/2018.