CMA = chromosomal microarray analysis; del/dup = deletion/duplication; IC = imprinting center; MS-MLPA = methylation-specific multiplex ligation-dependent probe amplification; UPD = uniparental disomy

See Molecular Genetics for more details.

About 10% of individuals with the presumptive clinical diagnosis of AS have normal results for all testing methods described in this table [Williams et al 2010].

Individuals with AS caused by a 5- to 7-Mb deletion of 15q11.2-q13, uniparental disomy (UPD), or an imprinting defect have only an unmethylated (i.e., "paternal") contribution (i.e., an abnormal parent-specific DNA methylation imprint).

DNA methylation analysis will not distinguish the genetic mechanism.

More than 90% of imprinting defects are thought to be epigenetic pathogenic variants occurring during maternal oogenesis or in early embryogenesis [Buiting et al 2016, Beygo et al 2019]. Characterization of the imprinting defect as either an imprinting center deletion or epigenetic defect is available primarily through research laboratories.

Beygo et al [2019]

FISH analysis with the D15S10 and/or the SNRPN probe can identify the common 15q11.2-q13 deletion, but typically this deletion is not detected by routine cytogenetic analysis.

CMA has a slightly higher sensitivity for 15q11.2-q13 deletions than FISH and will provide detailed information regarding size of the deletion. CMA also can identify deletions and duplications in other regions of the genome.

SNP-based chromosomal microarray can identify UPD, but not UPD due to heterodisomy.

UPD is detected using polymorphic DNA markers, which requires a DNA sample from the affected individual and both parents.

Gene-targeted deletion/duplication analysis detects deletions or duplications in intragenic or other targeted regions. Methods used may include a range of techniques such as quantitative PCR, long-range PCR, MLPA, and a gene-targeted microarray designed to detect single-exon deletions or duplications.

Although 3% of all individuals with AS have imprinting center defects, <10% will have detectable small deletions in the imprinting center.

Sequence analysis detects variants that are benign, likely benign, of uncertain significance (VUS), 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. Since UBE3A is imprinted, demonstration of paternal inheritance of a VUS will downgrade classification to benign. For issues to consider in interpretation of sequence analysis results, click here.

CMA usually detects large 15q11.2-q13 deletions, but in rare instances has detected UBE3A multiexon or whole-gene deletions.