Molecular Genetic Testing
(from the National Institutes of Health Gene Reviews article on Pitt Hopkins Syndrome: http://www.ncbi.nlm.nih.gov/books/NBK100240/ )
- Sequence analysis. Sequencing of all 18 TCF4 coding exons (exons 2 to 19), splice junctions, and immediate intronic flanking regions detects approximately 70% of mutations [Whalen et al 2012].
- Deletion/duplication analysis. Approximately 30% of TCF4 mutations are whole- or partial-gene deletions, varying in size from a single exon to ~12 Mb [Whalen et al 2012]. Of these, at least ten reports describe single-exon or partial-gene deletions, detectable only by deletion/duplication analysis (Table 1) [Brockschmidt et al 2007, Rosenfeld et al 2009, Lehalle et al 2011, Whalen et al 2012].
- Chromosome microarray analysis (CMA) (also known as array comparative genomic hybridization [aCGH]) detects a deletion in about one third of individuals with PTHS. Note: High-resolution chromosome analysis is required to determine if a translocation is present in these individuals.
- Cytogenetic testing. Cytogenetically visible deletions or chromosomal rearrangements disrupting TCF4 have been detected in at least seven individuals with PTHS [Gustavsson et al 1999, Giurgea et al 2008, Kalscheur et al 2008, Kato et al 2010, Marangi et al 2011]. In addition, the size of a number of the deletions detected by CMA would make them cytogenetically visible [Whalen et al 2012].
To confirm/establish the diagnosis of Pitt-Hopkins syndrome in a proband
1. Perform TCF4 sequence analysis. Note: Whalen et al  propose a tiered sequencing strategy, beginning with exon 18, which harbors 25% of mutations; however, such testing may not be widely available.
2. If a mutation is not found by sequence analysis, perform exon-level deletion/duplication analysis.
3. If a mutation or deletion is not found by deletion/duplication analysis and a strong clinical suspicion of PTHS remains, perform a karyotype to look for an apparently balanced translocation involving the 18q21.2 region (which would not be detected by either sequence analysis or CMA).