Evaluation of candidate tumour suppressor genes on chromosome 18 in colorectal cancers.

Chromosome deletions are the most common genetic events observed in cancer. These deletions are generally thought to reflect the existence of a tumour suppressor gene within the lost region. However, when the lost region does not precisely coincide with a hereditary cancer locus, identification of the putative tumour suppressor gene (target of the deletion) can be problematic. For example, previous studies have demonstrated that chromosome 18q is lost in over 60% of colorectal as well as in other cancers, but the lost region could not be precisely determined. Here we present a rigorous strategy for mapping and evaluating allelic deletions in sporadic tumours, and apply it to the evaluation of chromosome 18 in colorectal cancers. Using this approach, we define a minimally lost region (MLR) on chromosome 18q21, which contains at least two candidate tumour suppressor genes, DPC4 and DCC. The analysis further suggested genetic heterogeneity, with DPC4 the deletion target in up to a third of the cases and DCC or a neighbouring gene the target in the remaining tumours.

Human exonuclease I interacts with the mismatch repair protein hMSH2.

DNA mismatch repair (MMR) plays a vital role in the faithful replication of DNA, and its inactivation leads to a mutator phenotype that has been associated with the common cancer susceptibility syndrome Hereditary Non-Polyposis Colorectal Cancer (HNPCC). Here, we report on a novel human exonuclease (hExoI) that is related to the yeast exonuclease 1. The hExoI cDNA comprises 2541 bp, which code for a Mr 94,000 protein that appears to be highly expressed in testis tissue and at very low levels in other tissues. The hExoI gene has 14 exons and is located on chromosome 1q43, as determined by fluorescence in situ hybridization and radiation hybrid mapping. hExoI was found to interact strongly with the human MMR protein hMSH2, suggesting its involvement in the MMR process and/or DNA recombination.

Refined chromosomal localization of the mismatch repair and hereditary nonpolyposis colorectal cancer genes hMSH2 and hMSH6.

The genomic loci for the mismatch repair genes hMSH2 and hMSH6 were mapped by fluorescence in situ hybridization, analysis of radiation hybrid panel markers, and linkage analysis of syntenic chromosome regions between human and mouse. Both genes were localized to chromosome 2p21, adjacent to the luteinizing hormone/choriogonadotropin receptor gene (LHCGR; 2p21), telomeric to the D2S123 polymorphic marker, and centromeric to the calmodulin-2 gene (CALM-2; 2p22-21) and son-of-sevenless gene (SOS; 2p22-21). The genomic locations of hMSH2 and hMSH6 appears to be within 1 Mb of each other because they could not be separated by interphase fluorescence in situ hybridization. These results clarify the position of the chromosome 2 hereditary nonpolyposis colorectal cancer locus, which was originally reported to be associated with an adjacent region (chromosome 2p14-16).

Clinical and molecular characterisation of 80 patients with 5p deletion: genotype-phenotype correlation.

The majority of deletions of the short arm of chromosome 5 are associated with cri du chat syndrome (CdCS) and patients show phenotypic and cytogenetic variability. To perform a genotype-phenotype correlation, 80 patients from the Italian CdCS Register were analysed. Molecular cytogenetic analysis showed that 62 patients (77.50%) had a 5p terminal deletion characterised by breakpoint intervals ranging from p13 (D5S763) to p15.2 (D5S18). Seven patients (8.75%) had a 5p interstitial deletion, four (5%) a de novo translocation, and three (3.75%) a familial translocation. Of the remaining four patients, three (3.75%) had de novo 5p anomalies involving two rearranged cell lines and one (1.25%) had a 5p deletion originating from a paternal inversion. The origin of the deleted chromosome 5 was paternal in 55 out of 61 patients (90.2%). Genotype-phenotype correlation in 62 patients with terminal deletions highlighted a progressive severity of clinical manifestation and psychomotor retardation related to the size of the deletion. The analysis of seven patients with interstitial deletions and one with a small terminal deletion confirmed the existence of two critical regions, one for dysmorphism and mental retardation in p15.2 and the other for the cat cry in p15.3. Results from one patient permitted the cat cry region to be distally narrowed from D5S13 to D5S731. Furthermore, this study lends support to the hypothesis of a separate region in p15.3 for the speech delay.

Genetic syndromes and uniparental disomy: a study of 16 cases of Brachmann-de Lange syndrome.

Uniparental disomy is responsible for a proportion of cases in Prader-Willi, Angelman, and Wiedemann-Beckwith syndromes. In these syndromes, the chromosomes involved are thought to contain one or more imprinted genes. When two copies of the imprinted (inactivated) gene are inherited from a single parent through uniparental disomy or the active gene is deleted, the phenotype of the syndrome results. Our goal is to identify additional syndromes caused by uniparental disomy. Our approach is to select syndromes that appear to have more than one mode of inheritance and are occasionally associated with a cytogenetic abnormality. Given this criterion, we have chosen Brachmann-de Lange Syndrome (BDLS) to investigate since the phenotype is similar to that found in patients with dup(3q). We have studied 16 probands with BDLS and their parents using a multiplex of four PCR-based polymorphic loci on chromosome 3. None of the probands studied had uniparental disomy for chromosome 3 and all demonstrated normal biparental inheritance for at least one locus. Given these results, uniparental disomy of chromosome 3 does not appear to be a major contributor to the syndrome. Additionally, both maternally and paternally derived chromosome abnormalities have resulted in the dup(3q) phenotype and dominant inheritance of BDLS from both mildly affected mothers and fathers have been reported which suggests that imprinting is not involved in these syndromes.

Confirmation of a cryptic unbalanced translocation using whole chromosome fluorescence in situ hybridization.

We report on a 7-year-old boy with minor anomalies, growth retardation, and developmental delay with an initial 46,XY,der(18)t(18;?)(q23;?) chromosome constitution. To determine the origin of the additional chromosome segment, several candidate regions were identified including 4q and 18q. Clinical comparison showed more similarities to individuals with partial dup(4q) than to those with a dup(18q). Whole chromosome fluorescence in situ hybridization (FISH) was used to demonstrate the correct origin of the translocated region, clarifying the karyotype as 46,XY,der(18)t(4;18)(q28.2;q22.2), thus generating information of clinical importance. This illustrates the use of whole chromosome FISH to identify chromosome regions that cannot be determined conclusively using standard cytogenetic banding techniques.

Analysis of clinical variation seen in patients with 18q terminal deletions.

Twenty-six patients with deletions of 18q were analyzed at the clinical and molecular levels in an attempt to delineate regions of chromosome 18 important to the 18q- syndrome phenotype. Molecular cytogenetic analysis was carried out using fluorescence in situ hybridization (FISH), and deletions ranging from 18q21.1-qter to 18q22.3-qter were detected. The parental origin of the deletions was determined by the analysis of inheritance of microsatellite markers. No correlation between size, parental origin, or severity of the resulting phenotype was found. The results suggest that a critical region for 18q- syndrome lies in the most distal portion of 18q and that it confers susceptibility for the various clinical manifestations of the 18q- syndrome when present in one copy.

Characterization of a complex chromosomal rearrangement in a patient with a typical catlike cry and no other clinical findings of cri-du-chat syndrome.

We report on the clinical, cytogenetic, and molecular cytogenetic findings in a 4-year-old girl who was evaluated for developmental delay and a catlike cry from birth. No other findings of cri-du-chat syndrome were present. Karyotype analysis demonstrated a de novo deletion and inverted duplication of the 5p region. The abnormality was confirmed and further defined by detailed FISH analysis using cosmid and lambda phage clones previously mapped to distinct regions of 5p. The analyses documented deletion of 5p15.3-->pter and an inverted duplication of 5p14-->5p15.3. The deleted segment on 5p contains the region implicated in the isolated catlike cry feature of the cri-du-chat syndrome, confirming that the genes involved in the catlike cry map to the distal end of 5p. Except for the catlike cry and possibly the developmental delay that may be due to the deletion of 5p, the duplication of 5p14-->5p15.3 in this patient did not present with additional anomalies. This study further demonstrates the usefulness of the molecular cytogenetic approach for characterizing complex chromosome rearrangements. Such analyses of patients with an isolated catlike cry can avoid an incorrect diagnosis of the cri-du-chat syndrome, which is associated with a more severe prognosis.

Molecular cytogenetic determination of a deletion/duplication of 1q that results in a trisomy 18 syndrome-like phenotype.

We report on an infant who presented at birth with some characteristics of trisomy 18 syndrome, including low birth weight, facial abnormalities, overlapping fingers, and congenital heart defects. On chromosome analysis, no additional chromosome 18 was observed and both chromosome 18 homologues appeared normal. However, a small piece of chromosomal material of unknown origin was detected at the tip of the long arm of chromosome 1. Fluorescence in situ hybridization (FISH) using whole chromosome 18 painting probes disclosed no additional hybridization at the telomere of 1q, suggesting that the material was derived from another chromosome. Further chromosome painting experiments suggested that the telomeric addition was of chromosome 1 origin. To identify subchromosomal regions involved in the rearrangement, additional FISH analyses were performed using single copy and repetitive DNA probes mapping to different portions of chromosome 1. The analyses showed that probes mapping to 1q34-43 were duplicated in the derivative chromosome 1. In addition, a DNA probe mapping to 1q44 was found to be deleted from the derivative chromosome 1. Our composite analysis suggests that a deletion and a duplication of chromosome 1q can result in some of the clinical findings usually associated with trisomy 18 syndrome. These results demonstrate the usefulness of FISH analysis when karyotype analysis is not consistent with the clinical description.

Clinical phenotype and molecular analysis of a three-generation family with an interstitial deletion of the short arm of chromosome 5.

We report on a 3-generation family with an interstitial deletion of the short arm of chromosome 5. Varied manifestations were found among the affected individuals including microcephaly, hypertonia, and micrognathia; mental retardation was common to all affected individuals. High resolution chromosome analysis was interpreted as del(5) (pter- > p14.3::p13.3- > qter). Molecular comparison of the deletion in this family with individuals with other 5p deletions suggests that the clinical findings are due specifically to the chromosomal material deleted from 5p13.

Variability in a family with an insertion involving 5p.

Cri-du-chat syndrome is due to a partial deletion of the short arm of chromosome 5 and comprises a catlike cry, minor facial anomalies, growth delays, and psychomotor retardation. We identified a family with an insertion involving chromosome areas 5p and 16q. Four relatives are balanced carriers and have a normal phenotype, 5 have inherited the insertion in an unbalanced form with 2 resulting in partial trisomy of 5p and 3 in partial monosomy of 5p. The 3 individuals show a variable phenotype with respect to mental delay and some of the findings of cri-du-chat syndrome. The extent of the 5p deletion in this family was determined using previously mapped markers. The deletion in this family was informative for further refining the phenotypic map for the cri-du-chat syndrome. This family demonstrates the importance of performing phenotype-genotype correlation studies based on the presence rather than the absence of abnormalities.

No relationship between the size of the deletion and the level of developmental delay in cri-du-chat syndrome.

Molecular cytogenetic and developmental assessment was performed on 50 individuals with cri-du-chat syndrome. Fluorescent in situ hybridization analysis was used to confirm a terminal deletion karyotype and map more precisely the location of the deletion breakpoint. We identified terminal deletion breakpoints mapping from 5p15.2 to 5p13. Developmental assessment was performed using the Vineland Adaptive Behavior Scales test. Composite Vineland Scores ranged from 20-75. In general, the communication score was higher than the composite score. Comparison of the size of the deletion with the composite Vineland score, as well as the Vineland Communication score, demonstrated that there was no correlation between the size of the deletion and the level of developmental delay. These results demonstrate that patients with cri-du-chat syndrome show high variability in the level of developmental achievement.

Growth charts for cri-du-chat syndrome: an international collaborative study.

Low birth weight and slow growth are frequently observed in the patients with cri-du-chat syndrome. To provide a growth reference standard for children with cri-du-chat syndrome, syndrome-specific growth charts have been developed from a combination of cross-sectional and longitudinal measurements on 374 patients from North America, Italy, Australia, and the British Isles. The data were obtained from pediatric records, parent reporting, and personal examinations at national 5p- parent support group meetings in the U.S., Italy, U.K., and Australia. The growth curves include height and weight measurements for patients ages 0 to 18 years and head circumference measurements for patients ages 0 to 15 years. Birth weight was above the 5th percentile of general population in 50% of cases: mean weight 2.8 kg +/- 1.85 SD for males and 2.6 kg +/- 1.51 SD for females. Growth curve medians were usually at or below the 5th centile of reference populations throughout life. The median head circumference falls below the 2nd centile, and this change increases with age. The charts show that compared with the standard population, most children with cri-du-chat syndrome are small at birth and as they grow most, but not all, have significant microcephaly and compromised weight for age, and to a lesser extent, compromised height for age. Am. J. Med. Genet. 94:153-162, 2000.

Duplication 3q syndrome: molecular delineation of the critical region.

The phenotype of dup(3q) syndrome partially overlaps with Brachmann-de Lange phenotype. Convulsions and eye, palate renal, and cardiac anomalies are more frequent in dup(3q) syndrome, while limb deficiencies, hirsutism, and synophrys are more characteristic of Brachmann-de Lange syndrome. Whether the two syndromes have a biological relationship has yet to be demonstrated. Using two patient translocation cell lines, each involving distal 3q, we have narrowed the critical region of the dup(3q) syndrome to the interval 3q26.31-q27.3 and initiated its molecular characterization. We have mapped in this region 6 cosmid clones spanning approximately 3-5 Mb. The critical region appears to overlap with the region where a balanced translocation was found in a Brachmann-de Lange patient. This work provides the mapping framework for finer molecular analysis of dup(3q) syndrome.

De novo direct tandem duplication of the short arm of chromosome 7(p21.1-p14.2).

We report on a 6-year-old boy with moderate developmental retardation and unusual dermatoglyphics. Cytogenetic analysis demonstrated a duplication of chromosome sub-region 7p21.2-p14.2. Confirmation of the specific duplicated region was determined by quantitative Southern blotting by using a DNA fragment previously localized to the portion of chromosome 7 thought to be duplicated. This patient did not have the internal malformations seen with other dup(7p) patients.

Parental origin of chromosome 5 deletions in the cri-du-chat syndrome.

The parental origin of de novo deletions leading to the cri-du-chat syndrome has been investigated. Since the cri-du-chat syndrome is correlated with deletions involving the short arm of chromosome 5 (5p), DNA fragments known to detect restriction fragment length polymorphisms (RFLPs) along 5p were used to establish whether the paternal or the maternal chromosome had suffered the deletion. In cases where only one parent was available, somatic cell hybrids were used in conjunction with RFLP analysis to determine the origin of the deleted chromosome. The deleted chromosome 5 was of paternal origin in 20/25 cases.

Isolation of chromosome 18-specific brain transcripts as positional candidates for bipolar disorder.

Several studies have proposed the existence of susceptibility loci for bipolar disorder on chromosome 18. To identify possible candidate genes for this disease, we isolated brain-expressed transcripts by direct cDNA selection on chromosome 18-specific biotinylated cosmid clones. Longer cognate cDNA clones of the selected cDNAs were isolated from a normalized infant brain cDNA library. Physical mapping by PCR on a panel of somatic cell hybrids was conducted by the use of primers derived from partial sequences on either the 5' or 3' ends of the clones. In our initial analysis, 48 cDNA clones were found to be chromosome 18-specific, mapping to different subchromosomal regions. Sequence redundancy among these clones yielded 30 unique transcripts, five of which were represented in previously known genes. Further sequencing of the remaining 25 unique cDNA clones confirmed the absence of significant homology to known genes, indicating that these transcripts represented novel genes. Mapping with the use of a radiation hybrid panel positioned the brain cDNAs to within = 100 to 1100 kb from reference sequence tag sites (STSs) and assembled them into six high resolution linkage groups. The majority of the transcripts were found to cluster to discrete locations on 18p and 18q, previously hypothesized as susceptibility regions for bipolar disorder, identifying them as positional candidate genes.

Neuropsychiatry of 18q- syndrome.

Our understanding of neuropsychiatric abnormalities in patients with deletions of the long arm of chromosome 18 (18q- syndrome) is based mainly on sporadic case reports. We characterized the neuropsychiatric phenotype in 27 patients across a wide age range (2-47 years) with breakpoints ranging from 18q22.3-18q21.2. Adaptive behavior scores (Vineland Composite) were significantly higher in females than in males (62 +/- 5 vs. 43 +/- 3). Intelligence ranged from borderline to severely deficient (IQ, 73- < 40), with academic achievement similarly impaired. Performance in specific neuropsychological functions, including attention, novel problem solving, memory, language, visuomotor integration, and fine motor dexterity, was consistently in the moderately-to-severely impaired range. Behavioral problems were common in both sexes, including aggressivity, hyperactivity, and temper tantrums. Contrary to the few previous reports, we found no evidence of psychosis in any patients. In a subset of patients selected on the basis of no prior knowledge of behavioral problems, 1 of 16 patients (6%) had autism, as defined by the Autistic Diagnostic Interview--Revised (ADI-R) [Lord et al., 1994: J Autism Dev Disord 24:659-685]. Thus, the prevalence of autism in 18q- syndrome is probably no greater than that in other developmental disabilities with a similar level of cognitive impairment. In contrast to what has been believed since 18q- was first described 30 years ago, we found no relationship between chromosome deletion size and any measure of cognition or behavior; nor were there any correlations between any of these measures with the presence or absence of abnormalities on MRI or somatosensory-evoked potentials.

Affective disorder associated with a balanced translocation involving chromosome 14 and 18.

We report a case of a women with psychiatric illness that includes bipolar disorder who has a karyotype of 46,XX,t(14;18)(q11.2;q22.1). The region on chromosome 18 that is involved in the translocation has been implicated in other families through linkage and association studies as possibly containing a gene for bipolar illness.

White matter changes associated with deletions of the long arm of chromosome 18 (18q- syndrome): a dysmyelinating disorder?

PURPOSE: To evaluate the MR findings in the central nervous systems of patients with deletions of the long arm of chromosome 18 (18q- syndrome). METHODS: Sixteen patients with 18q- syndrome ranging in age from 3 to 46 years (mean, 17 years) were studied with high-field-strength MR imaging. Images were analyzed for abnormal T2 hyperintensity in the white matter, abnormal T2 hypointensity in the deep gray matter, and atrophy. RESULTS: Ten of 16 patients had abnormal white matter. Diffuse, bilaterally symmetric deep white matter T2 hyperintensity, most pronounced in the periventricular regions, was most common, noted in eight cases. Focal deep white matter lesions and/or abnormalities involving the subcortical white matter were also noted in four cases. The cerebellum, brain stem, and corpus callosum were spared. Ventriculomegally associated with volume loss, and abnormal T2 hypointensity in the basal ganglia and/or thalami were each present in 11 patients. CONCLUSIONS: The 18q- syndrome is associated with white matter disease and abnormal T2 hypointensity in the deep gray matter. The basis for the white matter abnormalities is unknown, but may be related to one of the two genes for myelin basic protein included in the deleted segment of chromosome 18.