Table 1. [Molecular Genetic Testing Used in Saethre-Chotzen Syndrome]. - GeneReviews® - NCBI Bookshelf

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Table 1.

Molecular Genetic Testing Used in Saethre-Chotzen Syndrome

Gene ¹	Method	Proportion of Probands with a Pathogenic Variant ² Detectable by Method
TWIST1	Sequence analysis ³	72% ⁴
	Gene-targeted deletion/duplication analysis ^5, 6	23% ⁴
	CMA ^6, ⁷	23% ^4, 8
	Karyotype	5% ⁹

1.: See Table A. Genes and Databases for chromosome locus and protein.
2.: See Molecular Genetics for information on allelic variants detected in this gene.
3.: Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Variants may include small intragenic deletions/insertions and missense, nonsense, and splice site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.
4.: Gripp et al [2000], Cai et al [2003a], de Heer et al [2005], Kress et al [2006], Foo et al [2009], Roscioli et al [2013], Paumard-Hernández et al [2015], The Human Gene Mutation Database
5.: Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include a range of techniques such as quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications. Gene-targeted deletion/duplication testing will detect deletions ranging from a single exon to the whole gene; however, breakpoints of large deletions and/or deletion of adjacent genes (e.g., those described by Cai et al [2003a] or Tahiri et al [2015]) may not be detected by these methods.
6.: Note that most reported deletions and duplications are large enough to likely be detected by CMA; however, gene-targeted deletion/duplication analysis does have a higher resolution.
7.: Chromosomal microarray analysis (CMA) uses oligonucleotide or SNP arrays to detect genome-wide large deletions/duplications (including TWIST1) that cannot be detected by sequence analysis. The ability to determine the size of the deletion/duplication depends on the type of microarray used and the density of probes in the 7p21 region. CMA designs in current clinical use target the 7p21 region.
8.: CMA should be considered in individuals with features of SCS and developmental delay.
9.: Cai et al [2003a], Shetty et al [2007], Touliatou et al [2007], The Human Gene Mutation Database

From: Saethre-Chotzen Syndrome

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