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Test Code SALL1 S+D/D SALL1 Seq and Del/Dup

Important Note

This test includes sequencing and CNV analysis of the SALL1 gene.

Clinical System Name

SALL1 Seq and Del/Dup

Synonyms

Townes-Brocks Syndrome

Description

Townes-Brocks syndrome (TBS) is a genetic condition that affects several parts of the body. The most common features of this condition are an obstruction of the anal opening (imperforate anus), abnormally shaped ears, and hand malformations that most often affect the thumb. Most people with this condition have at least two of these three major features.  Other clinical features include kidney abnormalities, mild to profound hearing loss, heart defects, and genital malformations. These features vary among affected individuals, even within the same family. Intellectual disability or learning problems have also been reported in about 10 percent of people with Townes-Brocks syndrome.  SALL1 is the only gene in which mutations are known to cause TBS.

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: Affix large Cerner labels to tubes and place in refrigerator send-outs rack.

 

Off-site collection: Send whole blood refrigerated.

Stability

Specimen Type Temperature Time
Whole blood Room temp 3 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

PreventionGenetics 3800 South Business Park Avenue Marshfield, WI 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 SALL1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Special Instructions

PreventionGenetics

Send Out Instructions

Reference Test Name:

Townes-Brocks Syndrome via SALL1 Gene Sequencing with CNV Detection

 
Reference Test Number: 8227  
Instructions: Ship whole blood overnight, ambient temperature. PreventionGenetics accepts Saturday delivery  

 

Update Date

This page was last updated 12/4/2018.