A, Summary of the chromosomal aberrations in patients with and without DVD. Patient numbers correspond to descriptions in table 1. The location of FOXP2 is denoted by the dotted line. Two known clusters of imprinted genes on 7q are shown above the chromosome. SGCE, PEG10, MEST, COPG2IT1, and MESTIT1 are paternally expressed, and PPPIR9A and CPA4 are maternally expressed. A new paternally imprinted gene, KLF14, is also now known to reside at 7q32 (L. Parker-Katiraee, personal communication). B, FOXP2 locus at 7q31.2. A consensus transcript encompassing all known exons of the gene is presented. Coding exons are shown in black. The translocation breakpoint (transl. bkpt.) for patient 6 and the proximal deletion breakpoint (prox. del. bkpt.) for patient 4 map between exons s1 and s2. The KE mutation and the CS translocation breakpoint,2 as well as a nonsense mutation in exon 7 that segregates with the DVD phenotype,7 are also shown. Known functional motifs are indicated below the exons coding for each. Mapping reagents, including BAC clones, long-PCR FISH probes, and microsatellite markers, are shown. Markers HSC274–HSC279 are in GenBank, under accession numbers BV123532, BV123533, BV123528, BV123529, BV123530, and BV123531, respectively. Additional probes and mapping reagents can be found at the Chromosome 7 Annotation Project Web site and will be distributed on request.

Results of qPCR used to estimate FOXP2 expression in cell lines from patients with deletions, a translocation, matUPD7, and patUPD7 and from controls. GAPDH was used as reference. Analysis was performed with a subset of samples for which RNA was available. Taqman qPCR of FOXP2 exons 13–14 was run on (A) six patients with deletions (patients 1–4 and the two nonverbal patients, 18 and 21), one patient with a translocation (patient 6), six patients with matUPD7 (patients 7–12), two patients with patUPD7 (patients 16 and 17), seven control samples, and (B) patient 8 with matUPD7 and his parents. There was a significant difference between the groups (ANOVA P=.0003). There was a statistically significant difference between the patients with matUPD7 and controls and between patients with deletions and controls (ANOVA and Dunnett's post hoc test). The expression for patient 8 was also significantly lower than in his parents (two-tailed t test P=.03). Statistical analysis was not performed for the patients with the translocation and patUPD7 because of small sample size. All samples were run in triplicate, and the experiment was repeated twice, with consistent results. Bars indicate SEM. For qPCR, 2 μg of total RNA was reversely transcribed in a 100-μl reaction with random hexamers, with the use of Taqman Reverse Transcription Reagents kit, and real-time PCR was performed using an ABI7700 sequence-detection system. PCR was performed in 25-μl reactions with 45 cycles of amplification. Each plate contained a water control, a calibrator sample (control 1 cDNA), and serially diluted concentrations of control 3 cDNA (range 62.5–0.5 ng), from which a standard curve was generated for transcript quantification.