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HelpTest Code LAB3788 SHOX Single Gene Analysis
Clinical System Name
SHOX Single Gene Analysis
Synonyms
Short Stature Homeobox gene
SHOX Sequencing
SHOX Deletion
Langer Mesomelic Dysplasia
Leri-Weill Dyschondrosteosis
Description
This test analyzes sequence and deletion/duplication variants in the SHOX gene.
Sample Requirements
Specimen: Whole Blood
Container(s): Lavender/EDTA
Preferred Vol: 3.0 mL
Minimum Vol: 2.0 mL
NOTE: Extracted DNA is NOT an accepted specimen type.
Processing Instructions
Reject due to: Hemolyzed or clotted.
Spin: N
Aliquot: N
Temp: 2 - 8 C
Storage location: Do not spin. Affix large Epic label to tube and store in CPA refrigerator, Send Outs rack.
Off-site collection: Send whole blood refrigerated.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole Blood | Room Temp |
3 d |
| Refrigerated | 7 d | |
| Frozen |
Unacceptable |
Availability
| STAT | TAT |
|---|---|
| N | 2 - 3 w |
Performing Laboratory
ARUP Laboratories
500 Chipeta Way
Salt Lake City, UT 84108-1221
Phone Number: (800) 522-2787
Department
Department: Send Outs/Genetic
Phone Number: (206) 987-2563
Reference Range
Interpretive report is provided.
Methodology
Method: Next Generation Sequencing (NGS) and Multiplex Ligation-dependent Probe Amplification (MLPA)
Analytic Sensitivity/Specificity
NGS
Single nucleotide variants: >99% sensitivity, >99.9% specificity
Deletions 1-10bp: 93.8% sensitivity, >99.9% specificity
Insertions 1-10bp: 94.8% sensitivity, >99.9% specificity
MLPA
>99%
SHOX (NM_006883) exon 6, also known as exon 6b, is not sequenced due to technical limitations of the assay.
The following will not be evaluated:
- Variants outside the coding regions and intron-exon boundaries of targeted gene(s)
- Regulatory region and deep intronic variants
- Breakpoints of large deletions/duplication
The following may not be detected:
- Deletions/duplications/insertions of any size by massively parallel sequencing
- Noncoding transcripts
- Low-level somatic variants
- Certain other variants due to technical limitations in the presence of pseudogenes and repetitive/homologous regions
Clinical Utility
Pathogenic variants in the SHOX gene result in a spectrum of disorders due to haploinsufficiency of the SHOX gene. Clinical features often include short stature, mesomelia (shortening of the lower portion of arm and leg), and abnormal alignment of the radius, ulna, and carpal bones at the wrist (Madelung deformity). Variable expressivity results in some individuals only affected with isolated short stature (ISS), whereas others have short stature and additional findings resulting in syndrome disorders (eg, Leri-Weill dyschondrosteosis [LWD] or Langer mesomelic dysplasia [LMD]).
Clinical Sensitivity:
At least 90% for SHOX deficiency disorders
About 10% of individuals with LWD do not have a demonstrable SHOX pathogenic variant
Send Out Instructions
| Reference Test Name: | SHOX Deficiency Disorders, Sequencing and Deletion/Duplication |
| Reference Lab Test Code: | 3004603 |
| Instructions: | Send out Monday - Friday with the ARUP courier. |