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Although microdeletions of the long arm of chromosome 17 are being reported with increasing frequency, deletions of chromosome band 17q24.2 are rare. Here we report four patients with a microdeletion encompassing chromosome band 17q24.2 with a smallest region of overlap of 713 kb containing five Refseq genes and one miRNA. The patients share the phenotypic characteristics, such as intellectual disability (4/4), speech delay (4/4), truncal obesity (4/4), seizures (2/4), hearing loss (3/4) and a particular facial gestalt. Hallucinations and mood swings were also noted in two patients. The PRKCA gene is a very interesting candidate gene for many of the observed phenotypic features, as this gene plays an important role in many cellular processes. Deletion of this gene might explain the observed truncal obesity and could also account for the hallucinations and mood swings seen in two patients, whereas deletion of a CACNG gene cluster might be responsible for the seizures observed in two patients. In one of the patients, the PRKAR1A gene responsible for Carney Complex and the KCNJ2 gene causal for Andersen syndrome are deleted. This is the first report of a patient with a whole gene deletion of the KCNJ2 gene.

Segmental duplications, which comprise approximately 5%-10% of the human genome, are known to mediate medically relevant deletions, duplications, and inversions through nonallelic homologous recombination (NAHR) and have been suggested to be hot spots in chromosome evolution and human genomic instability. We report seven individuals with microdeletions at 17q23.1q23.2, identified by microarray-based comparative genomic hybridization (aCGH). Six of the seven deletions are approximately 2.2 Mb in size and flanked by large segmental duplications of >98% sequence identity and in the same orientation. One of the deletions is approximately 2.8 Mb in size and is flanked on the distal side by a segmental duplication, whereas the proximal breakpoint falls between segmental duplications. These characteristics suggest that NAHR mediated six out of seven of these rearrangements. These individuals have common features, including mild to moderate developmental delay (particularly speech delay), microcephaly, postnatal growth retardation, heart defects, and hand, foot, and limb abnormalities. Although all individuals had at least mild dysmorphic facial features, there was no characteristic constellation of features that would elicit clinical suspicion of a specific disorder. The identification of common clinical features suggests that microdeletions at 17q23.1q23.2 constitute a novel syndrome. Furthermore, the inclusion in the minimal deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome., (Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

The 22q13.3 deletion syndrome results from loss of terminal segments of varying sizes at 22qter. Few genotype-phenotype correlations have been found but all patients have mental retardation and severe delay, or absence of, expressive speech. We carried out clinical and molecular characterization of 13 patients. Developmental delay and speech abnormalities were common to all and comparable in frequency and severity to previously reported cases. Array-based comparative genomic hybridization showed the deletions to vary from 95 kb to 8.5 Mb. We also carried out high-resolution 244K array comparative genomic hybridization in 10 of 13 patients, that defined the proximal and distal breakpoints of each deletion and helped determine the size, extent, and gene content within the deletion. Two patients had a smaller 95 kb terminal deletion with breakpoints within the SHANK3 gene while three other patients had a similar 5.5 Mb deletion implying the recurrent nature of these deletions. The two largest deletions were found in patients with ring chromosome 22. No correlation could be made with deletion size and phenotype although complete/partial SHANK3 was deleted in all patients. There are very few reports on array comparative genomic hybridization analysis on patients with the 22q13.3 deletion syndrome, and we aim to accurately characterize these patients both clinically and at the molecular level, to pave the way for further genotype-phenotype correlations. (c) 2010 Wiley-Liss, Inc.

We report on a patient with DiGeorge syndrome (DGS) phenotype or anomaly and an unbalanced translocation [45,XY,-10,-22,+der(10),t(10;22)(p13;q11)] resulting in monosomy of 10p13-pter and 22q11-pter. Because both regions involved in this rearrangement have been implicated in DGS, we performed a molecular cytogenetic analysis of both loci in this patient. Results indicate that the chromosome 22 DGS locus is intact but that the terminal deletion of the short arm of chromosome 10 is adjacent to or partially overlapping with the recently defined consensus deleted region observed in DGS patients with 10p deletions. We conclude that the DGS anomaly in our patient is likely to be due to haploinsufficiency of genes located on chromosome 10p. Most, if not all, of the region included in the previously described 10p smallest region of deletion overlap is not deleted in our patient. Therefore, this deletion breakpoint either narrows the previously proposed 10p region or defines a second region within 10p critical for the DGS anomaly.

At least three different sizes of GH-1 gene deletions (approximately 6.7, 7.0 and 7.6 kilobases) have been detected by Southern blot analysis of DNA from individuals with familial isolated GH deficiency type IA (IGHD1A). It is likely that these deletions result from unequal crossing over events between homologous regions that flank the GH-1 gene. Heterogeneity in clinical phenotypes is suggested by reports of good responses to exogenous GH treatment in most IGHD1A subjects with 7.6 kilobase deletions as opposed to poor responses in many subjects with smaller deletions. To determine if characteristic differences in gene deletions could be detected that correlate with response to treatment we analyzed the DNA sequences that normally flank the GH-1 gene. Digestion patterns of the PCR amplification products of these sequences from DNA of IGHD type IA patients with the restriction endonucleases BglI, HaeII, or SmaI showed characteristic differences for each of the three deletion sizes studied. The location and size of all deletions agreed with previous size estimates based on Southern blot analysis. Interestingly, clinical differences observed in the development of high titers of anti-GH antibodies and poor growth responses after GH treatment are unexplained, since discordant outcomes were observed in patients who had deletions of the same size and approximate location.

We examined the association between clinical status and exposure to tobacco smoke in 44 patients homozygous for the F508 cystic fibrosis mutation. Heavy exposure to tobacco smoke was significantly associated with lower Shwachman scores, poorer results of pulmonary function tests, and a fivefold increase in the number of pulmonary-related hospitalizations during the previous year.

Familial growth hormone deficiency type 1A is an autosomal recessive disease caused by deletion of both growth hormone-1 (GH1) alleles. Ten patients from heterogeneous geographic origins showed differences in restriction fragment length polymorphism haplotypes in nondeleted regions that flanked GH1, suggesting that these deletions arose from independent unequal recombination events. Deoxyribonucleic acid (DNA) samples from nine of ten patients showed that crossovers occurred within 99% homologous, 594-base pair (bp) segments that flanked GH1. A DNA sample from one patient indicated that the crossover occurred within 454-bp segments that flanked GH1 and contained 274-bp repeats that are 98% homologous. Although Alu repeats, which are frequent sites of recombination, are adjacent to GH1, they were not involved in any of the recombination events studied. These results suggest that length and degree of DNA sequence homology are important in defining recombination sites that resulted in GH1 deletions.

Familial isolated GH deficiency type 1A (IGHD1A) results from deletion of both GH alleles. To facilitate detection of cases of IGHD1A, we have developed a rapid method that uses polymerase chain reaction amplification of small amounts of genomic DNA, digestion with a single restriction endonuclease, and visualization of DNA fragments after gel electrophoresis. Employing this method we have identified two subjects with IGHD1A among a cohort of seven Chinese subjects with severe growth retardation due to GHD.

An 11 year old Austrian boy with isolated growth hormone deficiency type I A is described. On institution of GH therapy at the age of 2 2/12 years there was only a short growth response and anti-GH-antibodies with high binding capacity were detected, and growth was inhibited. Examination of the nuclear DNA by restriction endonuclease analysis demonstrated a defect of the GH-N gene in the patient. The results suggest the deletion in this Austrian family is different from that seen in other patients. The parents were heterozygous for the deletion and had a subnormal GH response to stimulation with arginine, but their somatomedin-C concentrations and their heights were normal. The patients' sister was of normal height, hormone analyses were normal, and the GH-N gene was not affected.

Multiple endocrine neoplasia type II (MEN-II or Sipple's syndrome) is an autosomal dominant disorder characterized by medullary thyroid cancers, pheochromocytomas, and parathyroid adenomas. A blind analysis of high resolution G-banded chromosomes was performed on blood specimens from eight MEN-II individuals from three unrelated families and six control subjects. Seven of eight MEN-II patients and one of six control subjects were determined to have a deletion at 20p12.2. These findings support the hypothesis that MEN-II patients have a 20p12.2 deletion (chi 2 = 6.99; p less than 0.01). Genomic DNA from seven of the eight MEN-II patients was studied using the DNA probe, D20S5, localized by in situ hybridization to 20p12. The probe binding site is not deleted in some MEN-II patients, as demonstrated by the presence of two alleles detected as restriction fragment length polymorphisms. Thus, D20S5 does not hybridize to DNA sequences that are deleted based on cytogenetic analysis in MEN-II patients.

Crossover sites resulting from unequal recombination within the human growth hormone (GH) gene cluster that cause GH1 gene deletions and isolated GH deficiency type 1A were localized in nine patients. In eight unrelated subjects homozygous for 6.7-kilobase (kb) deletions, the breakpoints are within two blocks of highly homologous DNA sequences that lie 5' and 3' to the GH1 gene. In seven of these eight cases, the breakpoints map within a 1250-base-pair (bp) region composed of 300-bp Alu sequences of 86% homology and flanking non-Alu sequences that are 600 and 300 bp in length and are of 96% and 88% homology, respectively. In the eighth patient, the breakpoints are 5' to these Alu repeats and are most likely within a 700-bp region of 96% homologous DNA sequences. In the ninth patient homozygous for a 7.6-kb deletion, the breakpoints are contained within a 29-bp perfect repeat lying 5' to GH1 and the human chorionic somatomammotropin pseudogene (CSHP1). Together, these results indicate that the presence of highly homologous DNA sequences flanking GH1 predispose to recurrent unequal recombinational events presumably through chromosomal misalignment.

Congenital adrenal hyperplasia (CAH) is a common genetic disorder due to defective 21-hydroxylation of steroid hormones. The human P450XXIA2 gene encodes cytochrome P450c21 [steroid 21-monooxygenase (steroid 21-hydroxylase), EC 1.14.99.10], which mediates 21-hydroxylation. The P450XXIA2 gene may be distinguished from the duplicated P450XXIA1 pseudogene by cleavage with the restriction endonuclease Taq I, with the XXIA2 gene characterized by a 3.7-kilobase (kb) fragment and the XXIA1 pseudogene characterized by a 3.2-kb fragment. Restriction endonuclease mapping by several laboratories has suggested that deletion of the P450XXIA2 gene occurs in about 25% of patients with CAH, as their genomic DNA lacks detectable 3.7-kb Taq I fragments. We have cloned human P450c21 cDNA and used it to study genomic DNA prepared from 51 persons in 10 families, each of which includes 2 or more persons with CAH. After Taq I digestion, apparent deletions are seen in 7 of the 20 alleles of the probands; using EcoRI, apparent deletions are seen in 9 of the 20 alleles. However, the apparently deleted alleles seen with Taq I do not coincide with those seen with EcoRI. Furthermore, studies with Bgl II, EcoRI, Kpn I, and Xba I yield normal patterns with at least two enzymes in all cases. Since all probands yielded normal patterns with at least two of the five enzymes used, we conclude that the P450XXIA2 gene "deletions" widely reported in CAH patients probably represent gene conversions, unequal crossovers, or polymorphisms rather than simple gene deletions.