Single nucleotide polymorphism (SNP) based chromosome microarrays provide both a high-density whole genome analysis of copy number and genotype. In the past 21 months we have analyzed over 13,000 samples primarily referred for developmental delay using the Affymetrix SNP/CN 6.0 version array platform. In addition to copy number, we have focused on the relative distribution of allele homozygosity (HZ) throughout the genome to confirm a strong association of uniparental disomy (UPD) with regions of isoallelism found in most confirmed cases of UPD. We sought to determine whether a long contiguous stretch of HZ (LCSH) greater than a threshold value found only in a single chromosome would correlate with UPD of that chromosome. Nine confirmed UPD cases were retrospectively analyzed with the array in the study, each showing the anticipated LCSH with the smallest 13.5 Mb in length. This length is well above the average longest run of HZ in a set of control patients and was then set as the prospective threshold for reporting possible UPD correlation. Ninety-two cases qualified at that threshold, 46 of those had molecular UPD testing and 29 were positive. Including retrospective cases, 16 showed complete HZ across the chromosome, consistent with total isoUPD. The average size LCSH in the 19 cases that were not completely HZ was 46.3 Mb with a range of 13.5-127.8 Mb. Three patients showed only segmental UPD. Both the size and location of the LCSH are relevant to correlation with UPD. Further studies will continue to delineate an optimal threshold for LCSH/UPD correlation.

We present a large review of 446 cases of paracentric inversions (PAI), including 120 new cases, to assess their incidence, distribution, inheritance, modes of ascertainment, interchromosomal effects, viable recombinant offspring, and clinical relevance. All 23 autosomes and sex chromosomes had inversions. However, none were identified in chromosome arms 18p, 19q, 20q, and Yp. PAI were most commonly reported in chromosomes 1, 3, 5, 6, 7, 11, and 14 and less frequently in chromosomes 4, 16, 17, 18, 19, 20, 21, 22, and Y. Inversions were most common in chromosome arms 6p, 7q, 11q, and 14q and observed least in chromosome arms 2p, 2q, 3q, 4q, and 6q. Frequently encountered breakpoints included 3(p13p25), 6(p12p23), 6(p12p25), 7(q11q22), and 11(q21q23). Ascertainment was primarily incidental (54.5%), mental retardation and/or congenital anomalies (22.2%), spontaneous abortions (11.4%), associations with syndromes (3.0%), and infertility (2.0%) accounted for the remainder. Ascertainment was neither related to the length of the inverted segment nor to specific inversions except for PAI of Xq which often presented with manifestations of Ullrich-Turner syndrome. Sixty-six percent of PAI were inherited while 8.5% were de novo. Recombination was observed in 17 cases, 15 of which resulted in a monocentric chromosomal deletion or duplication. No common factors were identified that suggested a tendency towards recombination. The incidence of viable recombinants was estimated to be 3.8%. This review documents that PAI are perhaps more commonly identified than suggested in previous reviews. Despite the possible bias of ascertainment in some cases, there may be associated risks with PAI that require further examination. Our data suggest that PAI carriers do not appear to be free of risks of abnormalities or abnormal progeny and caution is recommended when counseling.

The recombination rate in meiosis between the mouse X and Y chromosomes was analyzed. Mice heterozygous at two pseudoautosomal alleles, the steroid sulfatase gene and the Mov-15 provirus marker, were crossed. The provirus in the Mov-15 transgenic mouse strain had been previously shown to be carried in the pseudoautosomal region of the sex chromosomes. Recombination frequencies were shown to be 7-fold higher in this region in male meiosis than in female meiosis. Three-point crosses indicated the occurrence in male meiosis of double recombination events in the pseudoautosomal region, with little or no crossover interference, which is in marked contrast to observations made on the similar region of the human sex chromosomes. This result is contrary to a previous model, which predicted a single crossover event in male meiotic pairing of mammalian sex chromosomes.

The XIST gene, expressed only from the inactive X chromosome, is a critical component of X inactivation. Although apparently unnecessary for maintenance of inactivation, XIST expression is thought to be sufficient for inactivation of genes in cis even when XIST is located abnormally on another chromosome. This repression appears to involve the association of XIST RNA with the chromosome from which it is expressed. Reactivated genes on the inactive X chromosome, however, maintain expression in several somatic cell hybrid lines with stable expression of XIST. We describe here another example of an XIST-expressing humanhamster hybrid that lacks X-linked gene repression in which the human XIST gene present on an active X chromosome was reactivated by treatment with 5-aza-2-deoxycytidine. These data raise the possibility that human XIST RNA does not function properly in human-rodent somatic cell hybrids. As part of our approach to address this question, we reactivated the XIST gene in normal male fibroblasts and then compared their patterns of XIST RNA localization by subcellular fractionation and in situ hybridization with those of hybrid cells. Although XIST RNA is nuclear in all cell types, we found that the in situ signals are much more diffuse in hybrids than in human cells. These data suggest that hybrids lack components needed for XIST localization and, presumably, XIST-mediated gene repression.Stable expression of XIST is required on the inactive X chromosome for the establishment of mammalian X chromosome inactivation (reviewed in ref. 1). The role of XIST in the maintenance of repression has been questioned, however. Previous studies of inactive X chromosomes with XIST deletions indicate that XIST RNA is not necessary to maintain X inactivation (2, 3), presumably because other repressive systems, such as promoter methylation, histone deacetylation, and͞or late replication, are maintaining inactivation. Our studies of human-hamster hybrids containing an inactive X chromosome with azacytidine-reactivated genes indicate that XIST expression is not sufficient to prevent reactivation or to reinitiate silencing of these genes (4). A similar conclusion was reached by other workers studying reactivation of X-linked genes in another cell hybrid system (5).To examine this phenomenon further, we reactivated the silent XIST gene on the human active X chromosome in a human-hamster hybrid and in normal human male fibroblasts. The rationale for reactivation was based on the apparent regulation of XIST expression by 5Ј-CG-3Ј dinucleotide methylation. This region is hypermethylated on the silent, active X allele and is hypomethylated on the expressed, inactive X allele in both human (6, 7) and murine (8-11) somatic tissues. A further indication that 5Ј hypermethylation is important in Xist regulation is that the active X allele is expressed in somatic cells of male mice deficient in DNA methyltransferase (12, 13).Repression by 5Ј-CG-3Ј dinucleotide methylation commonly is found for X-inactivated genes, and reactivat...

In the human there is an X-linked gene affecting steroid sulphatase (STS) activity which, when deficient, is associated with X-linked congenital ichthyosis. The gene (STS) is located on the distal tip of the short arm and is only partially inactivated when it is on the inactive X-chromosome. In the mouse, the genetics of STS are not clear; the results of one study using XX:X0 oocyte comparisons indicated X-linkage, but three other studies using STS variants have produced segregation data compatible with autosomal linkage of murine STS. Here we present the results of STS assays of crosses of deficient C3H/An male mice to normal X0 animals which demonstrate X-linkage of STS in the mouse and indirectly indicate the existence of a functional STS allele on the Y-chromosome which undergoes obligatory recombination during meiosis with the X-linked allele.

Eight X autosome translocations were studied with replication banding to localize spreading of late replication into the autosomal segments. Partial spreading into the autosomal segment was seen in four translocations and no spreading of late replication was seen in four translocations. In those translocations with partial spreading of late replication into the autosomal segment, late replication did not always spread continuously from the X chromosome breakpoint throughout the autosome. Instead, it appeared to skip some bands and affect others. The data on the pattern of replication, taken to indicate also a spread of inactivation into these autosomal segments, correlated well with the clinical data in most cases and suggest that spreading of late replication is often incomplete and may be discontinuous.

Three genes on the human inactive X chromosome retained in the Chinese hamster X human hybrid cell line X8/6T2 have been reactivated using the demethylating agent, 5-azacytidine (5-aza-CR). Pulse-labeling and histochemical methods permitted detection and measurement of reactivation rates of the hypoxanthine phosphoribosyltransferase (Hpt) and glucose-6-phosphate dehydrogenase (G6pd) genes within 48 h of treatment. About 50% of the cells became active for these genes, which represents a reactivation rate some 30-fold greater than previously reported in similar systems. The phosphoglycerate kinase (Pgk) gene was not reactivated as frequently as the Hpt or G6pd genes. Segregation analysis of progeny of treated cells showed that enzyme-positive and enzyme-negative cells were produced in proportions supporting the notion that 5-aza-CR causes demethylation by replicative loss and that demethylation leads to reactivation.

Individuals with isolated terminal deletions of 8p have been well described in the literature, however, molecular characterization, particularly by microarray, of the deletion in most instances is lacking. The phenotype of such individuals falls primarily into two categories: those with cardiac defects, and those without. The architecture of 8p has been demonstrated to contain two inversely oriented segmental duplications at 8p23.1, flanking the gene, GATA4. Haploinsufficiency of this gene has been implicated in cardiac defects seen in numerous individuals with terminal 8p deletion. Current microarray technologies allow for the precise elucidation of the size and gene content of the deleted region. We present three individuals with isolated terminal deletion of 8p distal to the segmental duplication telomeric to GATA4. These individuals present with a relatively mild and nonspecific phenotype including mildly dysmorphic features, developmental delay, speech delay, and early behavior issues.