The SALSA MLPA probemix P018 SHOX is an in vitro diagnostic (IVD)1
or research use only (RUO) assay for the detection of deletions or duplications in the human short stature homeobox (SHOX) gene and its regulatory regions located on Xp22.33/Yp11.32 as a cause for disorders associated with short stature, including Leri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia (LMD), and Idiopathic short stature (ISS). This assay can be used with human DNA derived from peripheral blood and buccal swab.
In the majority of patients, defects in the SHOX gene region are deletions, but point mutations can occur which will not be detected by MLPA. It is therefore recommended to use this SALSA MLPA probemix in combination with sequence analysis of the SHOX coding region. Copy number changes detected by only a single probe always require validation by another method. This probemix is not intended to be used as a standalone assay for clinical decisions. The results of this test should be interpreted by a clinical molecular geneticist or equivalent.
Please note that this probemix is for In Vitro Diagnostic use (IVD) in the countries specified at the end of this product description. In all other countries, the product is for Research Use Only (RUO).
SHOX is located in the pseudoautosomal region 1 (PAR1) on the short arm of the X and Y chromosomes. Located upstream and downstream of SHOX are highly conserved non-coding elements (CNEs), some of which have been shown to be important SHOX enhancer sequences. Mutations in SHOX or its regulatory regions cause a range of disorders associated with short stature, including LWD, LMD, and ISS, as SHOX is a known transcription factor highly expressed in tissues responsible for bone development (Benito-Sanz et al. 2012b).
LWD is a dominant skeletal disorder characterised by short stature, mesomelic shortening of the limbs, and the characteristic Madelung deformity. LMD is a more severe form of LWD and is a result of mutations in both SHOX alleles (Bertorelli et al. 2007, Campos-Barros et al. 2007, Shears et al. 2002, Zinn et al. 2002). ISS classifies individuals with a height below the third centile when in the absence of an identified cause. Heterozygous mutations of SHOX and/or its regulatory elements are detected in approximately 60% of LWD patients and approximately 5-15% of ISS cases. Homozygous or compound heterozygous mutations of SHOX and/or its downstream enhancers are detected in 75% of LMD patients (Benito-Sanz et al. 2006, Benito-Sanz et al. 2012a, Chen et al. 2009, Huber et al. 2006).
In individuals with a SHOX related disorder, 70-80% of mutations are due to a large deletion, 2-6% is from a partial deletion, and 20-25% are from point mutations (Binder 2011, Caliebe et al. 2012). Duplications have also been reported in LWD and ISS patients (Benito-Sanz et al. 2011b). The MLPA technique can detect most deletions and duplications and therefore complements sequence analysis of SHOX.
More information is available on http://www.ncbi.nlm.nih.gov/books/NBK1215/
This SALSA MLPA probemix P018 SHOX contains 48 MLPA probes with amplification products between 124 and 504 nt: 26 probes located in the SHOX + Xp22 areas (including SHOX and its regulatory regions); 13 probes elsewhere on the X-chromosome and 9 reference probes detecting autosomal chromosomes (table 1 and table 2).
One probe is present for each exon of human SHOX, except for exon 7 which is only present in the alternative SHOXb splice variant. In addition, one probe is included detecting the area just before the SHOX promoter region. Furthermore, several probes are present for the regions that have been identified to be SHOX regulatory regions, located upstream and downstream of SHOX. Finally, several probes for the X-chromosome are included in this probemix that can be used to characterise larger deletions and to distinguish SHOX deletions from a Turner syndrome karyotype.
This probemix contains ten quality control fragments generating amplification products between 64 and 118 nt: four DNA Quantity Fragments (Q-fragments), two DNA Denaturation Fragments (D-fragments), one benchmark fragment, and one chromosome X and two chromosome Y-specific fragments (see table in thr product description). More information on how to interpret observations on these control fragments can be found in the MLPA General Protocol and online at www.mlpa.com.