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Introduction: Chromosomal abnormalities are mostly found in 0.5–0.8% of live-born infants with developmental and morphological defects. Paracentric inversions are structural intrachromosomal rearrangements resulting in a risk of chromosomally unbalanced gametes in carriers. Case Presentation: Herein, we report a patient with dicentric rearrangement of chromosome 18 due to maternal paracentric inversion of chromosome 18. The patient was a girl, aged 3 years and 11 months. She was referred due to multiple congenital abnormalities, severe intellectual disability, and motor retardation. She had microcephaly, prominent metopic suture, synophrys, epicanthic folds, telecanthus, wide-set alae nasi, wide columella, bilateral cleft lip and palate, pectus carinatum, umbilical hernia, pes planus, and anteriorly displaced anus. She had bilateral external auditory canal stenosis and mild right-sided and moderate left-sided sensorineural hearing loss. Echocardiography showed secundum-type atrial septal defect and mild tricuspid failure. Brain magnetic resonance imaging showed only thinning of posterior areas of the corpus callosum. Chromosome analysis showed 46,XX,dic rec(18) by GTG and C banding. Dicentric chromosome was confirmed by fluorescence in situ hybridization analysis. Paternal karyotype was normal 46,XY but maternal chromosome analysis showed a paracentric inversion in chromosome 18 with 46,XX,inv(18)(q11.2?q21.3?) karyotype. Array CGH was performed on a peripheral blood sample from the patient and showed duplication at 18p11.32p11.21 and 18q11.1q11.2, and deletion at 18q21.33q23. The patient’s final karyotype is arr 18p11.32p11.21(64,847_15,102,598)×3,18q11.1q11.2(18,542,074_22,666,470)×3,18q21.33q23(59,784,364_78,010,032)×1. Discussion: To the best of our knowledge, this is the first report of a patient with dicentric chromosome 18 due to a parental paracentric inversion of chromosome 18. We present the genotype-phenotype correlation with literature review.

BackgroundSilver-Russell Syndrome (SRS) is a rare growth-related genetic disorder mainly characterized by prenatal and postnatal growth failure. Although molecular causes are not clear in all cases, the most common mechanisms involved in SRS are loss of methylation on chromosome 11p15 (approximate to 50%) and maternal uniparental disomy for chromosome 7 (upd(7)mat) (approximate to 10%).Case presentationWe present a girl with clinical suspicion of SRS (intrauterine and postnatal growth retardation, prominent forehead, triangular face, mild psychomotor delay, transient neonatal hypoglycemia, mild hypotonia and single umbilical artery). Methylation and copy number variations at chromosomes 11 and 7 were studied by methylation-specific multiplex ligation-dependent probe amplification and as no alterations were found, molecular karyotyping was performed. A deletion at 5p15.33p15.2 was identified (arr[GRCh37] 5p15.33p15.2(25942-11644643)x1), similar to those found in patients with Cri-du-chat Syndrome (CdCS). CdCS is a genetic disease resulting from a deletion of variable size occurring on the short arm of chromosome 5 (5p-), whose main feature is a high-pitched mewing cry in infancy, accompanied by multiple congenital anomalies, intellectual disability, microcephaly and facial dysmorphism.ConclusionsThe absence of some CdCS features in the current patient could be due to the fact that in her case the critical regions responsible do not lie within the identified deletion. In fact, a literature review revealed a high degree of concordance between the clinical manifestations of the two syndromes. The costs of the publication and molecular analyses of this research were funded by grants from Instituto de Salud Carlos III (Institute of Health Carlos III) of the Spanish Ministry of Economy and Competitiveness, co-financed by the European Regional Development Fund (PI16/00073), the Department of Health of the Basque Government (GV2016111105; GV2017111040), and the University of the Basque Country UPV/EHU (PIF17/29).

We report on a male patient with intra-uterine growth retardation, microcephaly, coloboma, laryngomalacia and developmental delay. Array CGH analysis revealed a 649 kb duplication on chromosome 1p34.1. Only five patients with overlapping duplications have been reported thus far. Ten known genes are located in the duplicated region, including the POMGNT1 gene encoding for O-mannose beta-1,2-N-acetylglucosaminyltransferase. This gene, mutated in muscle-eye-brain disease, might be causative for the observed phenotype in our patient. (C) 2009 Elsevier Masson SAS. All rights reserved.

We report on a male patient with intra-uterine growth retardation, microcephaly, coloboma, laryngomalacia and developmental delay. Array CGH analysis revealed a 649 kb duplication on chromosome 1p34.1. Only five patients with overlapping duplications have been reported thus far. Ten known genes are located in the duplicated region, including the POMGNT1 gene encoding for O-mannose beta-1,2-N-acetylglucosaminyltransferase. This gene, mutated in muscle-eye-brain disease, might be causative for the observed phenotype in our patient. (C) 2009 Elsevier Masson SAS. All rights reserved.

Ongoing genomics projects of tomato (Solanum lycopersicum ) and potato (Solanum tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, BACs can be positioned on pachytene comple-ments by fluorescent in situ hybridization (FISH) on homoeologous chromosomes of related species. Here we present the first results of such a cross-species multi-colour cytogenetic mapping of tomato BACs on potato chromosome 6 and vice versa. The experiments were performed under low hybridization stringency, while blocking with Cot-100 was essential in suppressing excessive hybridization of repeat signals in both within-species FISH and cross-species FISH of tomato BACs. In the short arm we detected a large paracentric inversion that covers the whole euchromatin part with breakpoints close to the telomeric heterochromatin and at the border of the short arm pericentromere. The long arm BACs revealed no deviation in the co-linearity between tomato and potato. Further comparison between tomato cultivars Cherry VFNT and Heinz 1706 revealed co-linearity of the tested tomato BACs, whereas one of the six potato clones (RH98-856-18) showed minor putative rearrangements within the inversion. Our results present cross-species multi-colour BAC-FISH as a unique tool for comparative genetic studies across Solanum species

Tomato powdery mildew caused by Oidium neolycopersici has become a globally important disease of tomato (Lycopersicon esculentum). To study the defense responses of tomato triggered by tomato powdery mildew, we first mapped a set of resistance genes to O. neolycopersici from related Lycopersicon species. An integrated genetic map was generated showing that all the dominant resistance genes (Ol-1, Ol-3, Ol-4, Ol-5, and Ol-6) are located on tomato chromosome 6 and are organized in three genetic loci. Then, near-isogenic lines (NIL) were produced that contain the different dominant Ol genes in a L. esculentum genetic background. These NIL were used in disease tests with local isolates of O. neolycopersici in different geographic locations, demonstrating that the resistance conferred by different Ol genes was isolate-dependent and, hence, may be race-specific. In addition, the resistance mechanism was analyzed histologically. The mechanism of resistance conferred by the dominant Ol genes was associated with hypersensitive respo-nse, which varies in details depending on the Ol-gene in the NIL, while the mechanism of resistance governed by the recessive gene ol-2 on tomato chromosome 4 was associated with papillae formation.

SUMMARY Race-specific resistance in plants against microbial pathogens is governed by several distinct classes of resistance (R) genes. This review focuses on the class that consists of the plasma membrane-bound leucine-rich repeat proteins known as receptor-like proteins (RLPs). The first isolated resistance genes of the RLP class are the tomato Cf genes, which confer resistance to the fungal pathogen Cladosporium fulvum. To date, several other RLP genes are known to be implicated in resistance in other plant-pathogen interactions. These include HcrVf2 from apple, Ve1 and Ve2 from tomato, and RPP27 from Arabidopsis, which are involved in resistance to Venturia, Verticillium and Peronospora, respectively. Furthermore, the tomato RLP gene LeEix initiates defence responses upon elicitation with a fungal ethylene-inducing xylanase (EIX) of non-pathogenic Trichoderma. The tomato Cf genes, which are the most intensively studied RLP resistance genes, are usually found in clusters of several homologues. Whereas some of these homologues are functional Cf resistance genes, others have no known function in resistance. Different evolutionary processes contribute to variation in functional Cf genes, and functional as well as non-functional homologues may provide a source for the generation of novel Cf resistance genes. To date, little is known of the proteins that interact with Cf proteins to initiate defence responses. In contrast to the LeEix protein and the corresponding EIX elicitor, for which a direct interaction was found, no direct interaction between Cf proteins and the corresponding C. fulvum elicitors has been demonstrated. Analogous to the CLAVATA signalling complex, which comprises an RLP, a receptor-like kinase (RLK) and a small proteineous ligand, Cf proteins may form a complex with RLKs and thus initiate signalling upon recognition of the corresponding elicitors. The presence of RLP resistance genes in diverse plant species suggests that these genes play an important role in the extracellular recognition of plant pathogens.

The acrofacial dysostoses (AFD) are a heterogeneous group of disorders characterised by defects in craniofacial and limb development. The hallmarks include downward slanting palpebral fissures, malar hypoplasia, and receding chin (retrognathia) combined with variable limb malformations. The predominantly preaxial form is called Nager AFD and the predominantly postaxial form is called Genee-Wiedeman or Miller syndrome.1 A translocation t(X;9) suggests the localisation of a gene for Nager AFD on chromosome 9q32.2 More distally, on 9q34, one of the two major genes for tuberous sclerosis ( TSC1 ) is located. Tuberous sclerosis (TSC) is an autosomal dominant trait with variable expression most frequently characterised by neurological impairment (seizures and learning difficulties), by dermatological manifestations (facial angiofibromas, periungual fibromas, shagreen patches, and hypopigmented macules), and by renal manifestations including angiomyolipomas and cystic disease.3 The second gene for TSC, TSC2 , maps to chromosome 16p13.3 tail to tail with the major gene for autosomal dominant polycystic kidney disease (ADPKD), the PKD1 gene. These genes are separated by 63 bp.4 The main symptom of ADPKD is the occurrence of a large number of fluid filled cysts in the kidneys. Cysts can in general be detected by ultrasonography or CT scanning around the second or third decade of life and end stage renal failure occurs at a mean age of 53 years in PKD1 patients.5 ADPKD is a systemic disorder with possible extrarenal manifestations such as cysts in other organs (particularly the liver), hypertension, cardiac valve abnormalities, and cerebral aneurysms. Features of TSC and ADPKD have been observed in patients with a TSC2-PKD1 contiguous gene syndrome. In these patients, a large portion of the adjacent TSC2 and PKD1 genes has been deleted on one chromosome. In a study by Sampson et al ,6 17 of 22 patients with such a deletion were …

Fishing for a diagnosis; A family with primary infertility and two members with mental retardation and subtle facial dysmorphism is described. In the two retarded persons chromosomal rearrangements (partial monosomy of chromosome 5 and partial trisomy of chromosome 7) were detected. One member of the family had died with major congenital malformations. Her fibroblasts had been stored and her chromosomes showed the inverse pattern (partial trisomy of chromosome 5 and partial monosomy of chromosome 7). It appeared that in familial mental retardation with or without congenital malformations FISH-techniques should be used to detect submicroscopic chromosomal aberrations, which are not detectable by routine chromosome studies.

The expression frequency of common fragile sites induced by aphidicolin (Apc), bromodeoxyuridine (BrdU), and caffeine was evaluated on prometaphase chromosomes obtained from the peripheral blood lymphocytes of 32 patients with colon cancer, 30 of their clinically healthy family members and 30 age-matched normal controls. The proportion of-damaged cells (P < 0.001), the mean number of chromosomal aberrations and the expression frequencies of fragile sites were significantly higher in the patient and relative groups compared to the control group. Our findings show an increased genetic instability in patients with colon cancer and their first-degree relatives. In addition, common fragile sites can be used as a suitable marker for determining genetic predisposition to cancer.

Cytogenetically, testicular germ cell tumors of adolescents and adults (TGCTs) are characterized by gain of 12p-sequences, most often through isochromosome formation (i(12p)), Fluorescence in situ hybridization (FISH) has shown that i(12p))-negative TGCTs also cryptically contain extra 12p-sequences. The consistency of 12p-over-representation in all histological subtypes of TGCTs, including their preinvasive stage, suggests that gain of one or more genes on 12p is crucial in the development of this cancer. So far, studies aimed at the identification of the relevant gene(s) were based on the 'candidate-gene approach'. No convincing evidence in favor of or against a particular gene has been reported. We combined conventional karyotyping, comparative genomic hybridization, and FISH to identify TGCTs with amplifications of restricted regions of 12p, Out of 49 primary TGCTs (23 without i(12p), 13 with and 13 unknown), eight tumors (six without i(12p) and two unknown) showed amplifications corresponding to 12p11.1-p12.1. Using bicolour-FISH, physical mapping, and semi-quantitative polymerase chain reactions, the size of the shortest region of overlap of amplification (SROA) was estimated to be between 1750-3000 kb, In addition, we mapped a number of genes in and around this region. While fourteen known genes could be excluded as candidates based on their location outside this region, we demonstrate that KRAS2, JAW1 and SOX5 genes are localized within the SROA, While KRAS2 and JAW1 map to the proximal border of the SROA, SOX5 maps centrally in the SROA, KRAS2 and JAW1 are expressed in all TGCTs, whereas one 12p amplicon-positive TGCT lacks expression of SOX5, The critical region of 12p over-represented in TGCTs is less than 8% of the total length of the short arm of chromosome 12, It will be helpful in the identification of the gene(s) involved in TGCT-development.

Cytogenetically, testicular germ cell tumors of adolescents and adults (TGCTs) are characterized by gain of 12p-sequences, most often through isochromosome formation (i(12p)), Fluorescence in situ hybridization (FISH) has shown that i(12p))-negative TGCTs also cryptically contain extra 12p-sequences. The consistency of 12p-over-representation in all histological subtypes of TGCTs, including their preinvasive stage, suggests that gain of one or more genes on 12p is crucial in the development of this cancer. So far, studies aimed at the identification of the relevant gene(s) were based on the 'candidate-gene approach'. No convincing evidence in favor of or against a particular gene has been reported. We combined conventional karyotyping, comparative genomic hybridization, and FISH to identify TGCTs with amplifications of restricted regions of 12p, Out of 49 primary TGCTs (23 without i(12p), 13 with and 13 unknown), eight tumors (six without i(12p) and two unknown) showed amplifications corresponding to 12p11.1-p12.1. Using bicolour-FISH, physical mapping, and semi-quantitative polymerase chain reactions, the size of the shortest region of overlap of amplification (SROA) was estimated to be between 1750-3000 kb, In addition, we mapped a number of genes in and around this region. While fourteen known genes could be excluded as candidates based on their location outside this region, we demonstrate that KRAS2, JAW1 and SOX5 genes are localized within the SROA, While KRAS2 and JAW1 map to the proximal border of the SROA, SOX5 maps centrally in the SROA, KRAS2 and JAW1 are expressed in all TGCTs, whereas one 12p amplicon-positive TGCT lacks expression of SOX5, The critical region of 12p over-represented in TGCTs is less than 8% of the total length of the short arm of chromosome 12, It will be helpful in the identification of the gene(s) involved in TGCT-development.

beta-catenin is a multifunctional protein: it plays a central role in the cell-cell adhesive junctions, and participates in transduction of the morphogenic Wingless/Wnt-signal. Upon detailed analysis of the human beta-catenin gene, an intragenic polymorphic microsatellite marker could be identified. This marker shows 62% heterozygosity and was used in a study of eleven different tumor types. A high level of beta-catenin allelic imbalance was observed for small cell lung carcinoma, squamous cell lung carcinoma and cervix carcinoma. Other microsatellite markers on 3p24-21 could demonstrate frequent but not invariable codeletion of flanking chromosomal loci. This intragenic polymorphic marker will allow selection of tumor types and tumor samples possibly bearing recessive mutations in the remaining allele of the beta-catenin gene.

Multiple renal cell rumours from three unrelated patients have been analysed for loss of heterozygosity of 3p, mutation of VHL, and chromosome 7 and 17 imbalances, Loss of 3p alleles is characteristic for clear cell type tumours and the combination of +7, +17 for chromophilic cell type rumours. Thus, we could classify adenomas and carcinomas of the three patients according to the genomic patterns of the tumours. Adenomas appeared to be mostly of the chromophilic cell type. In some adenomas, however, allelic losses of chromosome 3 were detected, pointing to a clear cell phenotype. irrespective of showing loss or retention of the 3p25 region, none of the adenomas had a VHL mutation. Therefore, inactivation of VHL does not seem to be an early event in the development of renal cell rumours. Results of an analysis of regions of loss and retention of alleles of 3p markers in multiple rumours of the individual patients suggest that losses at either 3p25 or 3p12-p14 are associated with adenomas. Additional loss at 3p21 is most likely required to lead to development of a more malignant clear cell carcinoma. (C) 1997 Wiley-Liss, Inc.

In renal cell carcinoma (RCC), mostly occurring as sporadic cases, the short arm of chromosome 3 is a frequent target of deletion events. Taking into account cytological classifications of RCC, the deletions appear to be characteristic of clear cell or nonpapillary RCC only. This subtype constitutes most sporadic RCC and RCC as part of the Von Hippel-Lindau disease caused by germline mutations of VHL at 3p25. In a proportion of sporadic rumours, somatic mutations of VHL occur, again only in clear cell or nonpapillary RCC. However, in a sizable proportion of sporadic clear cell RCC, VHL mutations are absent. Therefore, a role for VHL in RCC development in general seems unlikely. Familial papillary RCC is not linked to chromosome 3. A rat model of hereditary RCC, the EKER rat, is associated with a germline mutation of the rat homologue of the tuberous sclerosis gene on human chromosome 16. Analysis of allelic losses of chromosome 3 in 143 highly informative sporadic rumours published in the literature points to a small segment of 3p21.3 as a candidate tumour-suppressor region. A 2-Mb fragment containing this segment suppresses tumourigenicity when present in mouse fibrosarcoma cells. A similar effect could be attributed to the region 3p12-p14 on the basis of results from its introduction into an RCC cell line. The responsible gene should not be sought at 3p14 translocation breakpoints segregating with RCC in a few rare families because there is evidence that RCC in these cases is due to events involving VHL or another gene distal to the breakpoint. FHIT is also an unlikely candidate according to observations comparing RCC and a variety of normal tissues. Results of an analysis of sporadic patients with multiple renal rumours indicate an association of allelic losses of the VHL and 3p12-p14 regions with adenomas and suggest that losses of the 3p21 region are necessary for malignant development to clear cell or nonpapillary RCC. (C) 1997 Wiley-Liss, Inc.

Interstitial deletions of chromosome 3p14p12 are a rare chromosome rearrangement. Twenty-six patients have been reported in the literature to date, however, a specific clinical phenotype has not yet been delineated. We describe three patients (two new) with overlapping chromosome 3p14p12 deletions and review the clinical and molecular data of 11 well-characterized, published cases. These patients had a number of features in common, such as short stature, failure to thrive, facial dysmorphism, congenital heart defects, urogenital abnormalities, neurological problems, hearing loss, and global developmental delay, suggesting that the interstitial chromosome 3p14p12 deletion gives rise to a multiple congenital anomaly syndrome. Some of the patients show clinical overlap with other complex syndromes such as CHARGE syndrome. Genotype-phenotype analysis revealed candidate genes for parts of the clinical features suggesting that the 3p14 deletion is a contiguous gene syndrome. (c) 2015 Wiley Periodicals, Inc.

High frequencies of allelic loss on the short arm of chromosome 3 in small cell lung cancer (SCLC) and a number of other tumors suggest the existence of a tumor suppressor gene(s) within the deleted regions. Two small cell lung cancer lines, NCI H740 and GLC20, have been described which have homozygous deletions in the region 3p21.3. The deleted region overlaps with a 2 Mb fragment of human DNA present in the interspecies hybrid HA(3)BB9F, that suppresses tumor formation by mouse A9 fibrosarcoma cells. Human sequences from this cell hybrid were isolated using inter Alu PCR. From this starting point, a P1 contig was developed for the region of 450 Kb that is common to the homozygous deletions seen in the SCLC lines NCI H740 and GLC20 and is also present in HA(3)BB9F, the suppressed A9 hybrid. Individual P1 clones were assayed for their ability to suppress the tumorigenicity of the mouse fibrosarcoma cell line A9 as assayed by injection of transfected A9 cells into athymic nude mice. The introduction of one of the P1 clones into A9 cells resulted in suppression of tumor growth whereas two other P1 clones from the contig failed to suppress tumor formation in athymic nude mice. These data functionally delimit a tumor suppressor locus to a region of 80 kb within a P1 clone at 3p21.3.

Chromosomal deletions and translocations of human chromosome region 3p14 are observed in various human malignancies and suggest the existence of a tumor suppressor gene locus within this region. Tumors most frequently affected by these aberrations are small-cell lung cancer and renal-cell carcinoma. In continuation of our previously published YAC contig of chromosome region 3p14.2-p14.3, we report here on the construction of a YAC contig of at least 11 Mb that consisted of 171 YACs and covers the entire subregion 3p14.1. This contig includes the t(3;8) breakpoint of a hereditary renal-cell carcinoma localized in 3p14.2 and extends into human chromosome region 3p12-p13. It defines the order of 34 DNA probes in relation to reference markers D3S6 and D3S30 as well as the human protein tyrosine phosphatase-gamma gene. For 31 DNA probes we identified nonchimeric YACs by fluorescence in situ hybridization. The minimal tilling pathway consists of 16 yeast artificial chromosomes. As a prerequisite for identification of a putative tumor suppressor gene within this region, this contig renders human chromosome region 3p14.1 accessible to gene isolation.

Small cell lung cancer (SCLC) has been correlated with a deletion in the short arm of chromosome 3, with the region 3p21 being lost from one homolog in almost all cases. Two SCLC cell lines have homozygous deletions in 3p21, and these deletions overlap with a fragment of chromosome 3 that has tumor suppression activity in vivo. We have isolated some cDNA clones from this region that are homologous to the genes constituting the semaphorin family. They represent a novel human semaphorin, termed sema III/F (HGMW-approved symbol SEMA3F), which is expressed as a 3.8-kb transcript in a variety of cell lines and tissues; it is detected as early as Embryonic Day 10 in mouse development. There is high expression in mammary gland, kidney, fetal brain, and lung and lower expression in heart and liver. Although there is reduced expression of this gene in several SCLC lines, no mutations were found. This semaphorin homolog has characteristics of a secreted member of the semaphorin III family, with 52% identity with mouse semaphorin E and 49% identity with chicken collapsin/semaphorin D. (C) 1996 Academic Press, Inc.

Small cell lung cancer (SCLC) has been correlated with a deletion in the short arm of chromosome 3, with the region 3p21 being lost from one homolog in almost all cases. Two SCLC cell lines have homozygous deletions in 3p21, and these deletions overlap with a fragment of chromosome 3 that has tumor suppression activity in vivo. We have isolated some cDNA clones from this region that are homologous to the genes constituting the semaphorin family. They represent a novel human semaphorin, termed sema III/F (HGMW-approved symbol SEMA3F), which is expressed as a 3.8-kb transcript in a variety of cell lines and tissues; it is detected as early as Embryonic Day 10 in mouse development. There is high expression in mammary gland, kidney, fetal brain, and lung and lower expression in heart and liver. Although there is reduced expression of this gene in several SCLC lines, no mutations were found. This semaphorin homolog has characteristics of a secreted member of the semaphorin III family, with 52% identity with mouse semaphorin E and 49% identity with chicken collapsin/semaphorin D. (C) 1996 Academic Press, Inc.

Starting from five markers, with a well-defined order from distal to proximal 3p21, nine other markers could be inserted in this 3p21 map. Five were precisely mapped genetically. The other markers were ordered by FISH and/or deletion hybrid mapping. The overall 3p21 order from distal to proximal is as follows: D3S1298-D3S1260-(D3S966, D3S1448 (= D3S1449))-D3S1029-D3S32-D3S643-D3F15S2 -D3S2968-D3S1235-D3S1289-D3S1447-D3S1295.

A variety of cytogenetic aberrations have been reported in sporadic and familial renal cell carcinoma. Rearrangements of the short arm of chromosome 3 (3p), trisomy 17, and nuclear hyperdiploidy have been reported to be common clonal chromosome changes. We analyzed a total of ten tumor-derived cell lines from patients who underwent nephrectomy for renal cell carcinoma employing conventional cytogenetics. All patients received an immunomodulatory therapy based on recombinant interleukin-2 (rIL-2). Tumor stage and grade, histo- and cytopathology, and patients' response to immunotherapy were assessed and correlated statistically to rearrangement of 3p, trisomy 17, and nuclear hyperdiploidy. Trisomy 17 as clonal aberration could be revealed only in papillary renal cell carcinoma, whereas tumors with compact or tubulopapillary growth pattern lacked this abnormality (p 49 chromosomes) karyotypes. The correlation between hyperdiploidy and tumor progression was found to be statistically significant (p

In a loss of heterozygosity analysis of 3p, we examined 44 sporadic cases of renal cell carcinoma (RCC) and matched normal tissue with 18 markers distributed over the whole p-arm. The majority of these markers clustered in three regions that have been suggested to be involved in the development of RCC, namely the p25 region, where the von Hippel Lindau (VHL) gene is located; the p21 region, which has been identified as a common region of overlap (SRO) of heterozygous deletions; and the p14 region, which is the location of the constitutional t(3;8) breakpoint occurring in an RCC family. Thirty-one our of these 44 tumors were analyzed with 9 additional markers from the 3p12-14 region to further delimit the SRO in this region. Our analysis shows that when deletions were detected the 3p21 region was always included. The 3p21markers D3F15S2 and UBEIL were always contained within these 3p21 deletions. The t(3;8) breakpoint region showed the lowest percentage of loss of heterozygosity. Moreover, in three cases the t(3;8) breakpoint region retained heterozygosity, whereas a region more proximal to the breakpoint showed allelic losses. This supports exclusion of the t(3;8) region from a role in the development of sporadic RCC. In a number of tumors, two or three 3p regions with allelic losses were present separated by a region of retention of heterozygosity. In these tumors, deletions at 3p21 occurred in combination with deletions of either the VHL region, or the region proximal to the t(3;8), or both, suggestive of multiple gene involvement in the development of sporadic RCC with a primary role of the 3p21 region. (C) 1996 Wiley-Liss, Inc.

A variety of cytogenetic aberrations have been reported in sporadic and familial renal cell carcinoma. Rearrangements of the short arm of chromosome 3 (3p), trisomy 17, and nuclear hyperdiploidy have been reported to be common clonal chromosome changes. We analyzed a total of ten tumor-derived cell lines from patients who underwent nephrectomy for renal cell carcinoma employing conventional cytogenetics. All patients received an immunomodulatory therapy based on recombinant interleukin-2 (rIL-2). Tumor stage and grade, histo- and cytopathology, and patients' response to immunotherapy were assessed and correlated statistically to rearrangement of 3p, trisomy 17, and nuclear hyperdiploidy. Trisomy 17 as clonal aberration could be revealed only in papillary renal cell carcinoma, whereas tumors with compact or tubulopapillary growth pattern lacked this abnormality (p 49 chromosomes) karyotypes. The correlation between hyperdiploidy and tumor progression was found to be statistically significant (p

Human chromosomal region 3p12-p23 is proposed to harbor at least three tumor suppressor genes involved in the development of lung cancer, renal cell carcinoma, and other neoplasias. In order to identify one of these genes we defined sequence tagged sites (STSs) specific for 3p13-p24.2 by analyzing a chromosome 3p14 microdissection library. STSs were used for isolating yeast artificial chromosome (YAC) clones from the Centre d'Etude du Polymorphisme Humain (CEPH) YAC libraries. Thirty-eight YACs were assembled into a contig approximately 2.5 Mb in size spanning the t(3;8) and t(3;6) translocation breakpoints associated with hereditary renal cell carcinoma and hematologic malignancies, respectively Chromosomal localization and chimeric status of 126 YACs was analyzed by fluorescence in situ hybridization (FISH). The order of 17 YACs determined by double-color FISH wets in agreement with the STS-based arrangement of the YAC-contig.

Loss of heterozygosity (LOH) studies have suggested that somatic mutations of a tumour suppressor gene or genes on chromosome 3p are a critical event in the pathogenesis of non-familial renal cell carcinoma (RCC). Germline mutations of the von Hippel - Lindau (VHL) disease gene predispose to early onset and multifocal clear cell renal cell carcinoma, and the mechanism of tumorigenesis in VHL disease is consistent with a one-hit mutation model. To investigate the role of somatic VHL gene mutations in non-famitial RCC, we analysed 99 primary RCC for VHL gene mutations by SSCP and heteroduplex analysis. Somatic VHL gene mutations were identified in 30 of 65 (46%) sporadic RCC with chromosome 3p allele loss and one of 34 (3%) tumours with no LOH for chromosome 3p. The VHL gene mutations were heterogeneous (17 frameshift deletions, eight missense mutations, four frameshift insertions, one nonsense and one splice site mutation), but no mutations were detected in the first 120 codons of cloned coding sequence. Most RCCs with somatic VHL mutations (23 of 27 (85%) informative cases) had chromosome 3p25 allele loss in the region of the VHL gene so that both alleles of the VHL gene had been inactivated as expected from a two-hit model of tumorigenesis. Detailed histopathology was available for 59 of the tumours investigated: 18 of 43 (42%) RCC with a clear cell appearance had a somatic VHL gene mutation but none of 16 non-clear cell RCC (eight chromophilic, three chromophobe and five oncocytoma) (chi 2 = 7.77, P

All types of lung carcinoma are characterized by a high frequency of loss of sequences from the short arm of chromosome 3, the smallest region of overlap containing D3F15S2 in band p21. Here we characterize a 440-kilobase segment from this region, which we found homozygously deleted in one of our small cell lung cancer-derived cell lines. The homozygous deletion maps between UBE1L and ZnF16, just centromeric to D3F15S2. Yeast artificial chromosomes with inserts originating from the deleted region are very unstable and readily lose parts of their insert.

Background In order to help establish heterotic groups of Chinese northern wheat cultivars (lines), Diversity arrays technology (DArT) markers were used to investigate the genetic diversity and population structure of Chinese common wheat (Triticum aestivum L.). Results In total, 1637 of 7000 DArT markers were polymorphic and scored with high confidence among a collection of 111 lines composed mostly of cultivars and breeding lines from northern China. The polymorphism information content (PIC) of DArT markers ranged from 0.03 to 0.50, with an average of 0.40, with P > 80 (reliable markers). With principal-coordinates analysis (PCoA) of DArT data either from the whole genome or from the B-genome alone, all lines fell into one of two major groups reflecting 1RS/1BL type (1RS/1BL and non-1RS/1BL). Evidence of geographic clustering of genotypes was also observed using DArT markers from the A genome. Cluster analysis based on the unweighted pair-group method with algorithmic mean suggested the existence of two subgroups within the non-1RS/1BL group and four subgroups within the 1RS/1BL group. Furthermore, analysis of molecular variance (AMOVA) revealed highly significant (P < 0.001) genetic variance within and among subgroups and among groups. Conclusion These results provide valuable information for selecting crossing parents and establishing heterotic groups in the Chinese wheat-breeding program.

A characteristic balanced reciprocal chromosomal translocation [t(2;13)(q35;q14)] has been identified in more than 50% of alveolar rhabdomyosarcomas. As the first step in characterization of the genes involved in this translocation, we constructed somatic cell hybrids that retained either the derivative chromosome 2 or the derivative chromosome 13 without a normal chromosome 13 homologue. Ten linked DNA probes known to be located within bands 13q13-q14 were mapped relative to the breakpoint on chromosome 13, allowing localization of the breakpoint region between two loci separated by 5.5 cM. A long-range restriction map extending approximately 2,300 kb around these loci failed to provide evidence of rearrangement. Additionally, we confirmed that the FMS-like tyrosine kinase gene (FLT), previously localized to 13q12 by in situ hybridization, is located proximal to the breakpoint, and we demonstrated that FLT is not a target for disruption by this tumor-specific translocation.

A combination of cytogenetic and molecular studies has implicated the p21 region of human chromosome 3 as the probable site of a gene the loss of which contributes to the development of small cell lung cancer. We report here the isolation of a gene from this region which is expressed in normal lung tissue and in cell lines derived from a number of different types of tumor, but the expression of which in small cell lung cancer cell lines is undetectable by RNA blot analysis. Although the more sensitive polymerase chain reaction did detect transcripts, a novel quantitative polymerase chain reaction assay showed that their concentration in small cell lung cancer cell lines is less than 3% of that in normal lung.

Ongoing genomics projects of tomato (Solanum lycopersicum ) and potato (Solanum tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, BACs can be positioned on pachytene comple-ments by fluorescent in situ hybridization (FISH) on homoeologous chromosomes of related species. Here we present the first results of such a cross-species multi-colour cytogenetic mapping of tomato BACs on potato chromosome 6 and vice versa. The experiments were performed under low hybridization stringency, while blocking with Cot-100 was essential in suppressing excessive hybridization of repeat signals in both within-species FISH and cross-species FISH of tomato BACs. In the short arm we detected a large paracentric inversion that covers the whole euchromatin part with breakpoints close to the telomeric heterochromatin and at the border of the short arm pericentromere. The long arm BACs revealed no deviation in the co-linearity between tomato and potato. Further comparison between tomato cultivars Cherry VFNT and Heinz 1706 revealed co-linearity of the tested tomato BACs, whereas one of the six potato clones (RH98-856-18) showed minor putative rearrangements within the inversion. Our results present cross-species multi-colour BAC-FISH as a unique tool for comparative genetic studies across Solanum species

Imbalances of 3p telomeric sequences cause 3p- and trisomy 3p syndrome, respectively, showing distinct, but also shared clinical features. No causative genes have been identified in trisomy 3p patients, but for the 3p- syndrome, there is growing evidence that monosomy for one or more of four genes at 3pter, CHL1, CNTN4, CRBN and MEGAP/srGAP3, may play a causative role. We describe here an analysis of a complex chromosome 3p aberration in a severely mentally retarded patient that revealed two adjacent segments with different copy number gains and a distal deletion. The deletion in this patient included the loci for CHL1, CNTN4, and CRBN, and narrowed the critical segment associated with the 3p- syndrome to 1.5 Mb, including the loci for CNTN4 and CRBN. We speculate that the deletion contributes more to this patient's phenotype than the gains that were observed. We suggest that 3p- syndrome associated features are primarily caused by loss of CNTN4 and CRBN, with loss of CHL1 probably having an additional detrimental effect on the cognitive functioning of the present patient. (c) 2006 Wiley-Liss, Inc.

Homozygous deletions or loss of heterozygosity (LOH) at human chromosome band 3p12 are consistent features of lung and other malignancies, suggesting the presence of a tumor suppressor gene(s) (TSG) at this location. Only one gene has been cloned thus far from the overlapping region deleted in lung and breast cancer cell lines U2020, NCI H2198, and HCC38. It is DUTTI (Deleted in U Twenty Twenty), also known as ROBO1, FLJ21882, and SAX3, according to HUGO. DUTTI, the human ortholog of the fly gene ROBO, has homology with NCAM proteins. Extensive analyses of DUTTI in lung cancer have not revealed any mutations, suggesting that another gene(s) at this location could be of importance in lung cancer initiation and progression. Here, we report the discovery of a new, small, homozygous deletion in the small cell lung cancer (SCLC) cell line GLC20, nested in the overlapping, critical region. The deletion was delineated using several polymorphic markers and three overlapping PI phage clones. Fiber-FISH experiments revealed the deletion was approximately 130 kb. Comparative genomic sequence analysis uncovered short sequence elements highly conserved among mammalian genomes and the chicken genome. The discovery of two EST clusters within the deleted region led to the isolation of two noncoding RNA (ncRNA) genes. These were subsequently found differentially expressed in various tumors when compared to their normal tissues. The ncRNA and other highly conserved sequence elements in the deleted region may represent miRNA targets of importance in cancer initiation or progression. Published 2006 Wiley-Liss, Inc.(dagger).

This study reports the clinical features of 63 patients with agenesis of the corpus callosum who received in-depth genetic, clinical, and laboratory testing with the aim to contribute to a better description of the large spectrum of associated malformations and to assist clinicians in the diagnosis. Thirty patients manifested complete agenesis and 33 patients displayed partial agenesis. Other associated nervous system malformations were detected in 14 patients with partial agenesis of the corpus callosum (mostly correlated to posterior fossa malformations) and in 10 patients with complete agenesis (more frequently associated with malformations of cortical development). Involvement of organs and apparatus other than the nervous system was present in 41 patients (ascribed to known syndromes in 21 cases). Cytogenetically detectable chromosomal abnormalities (7 patients) and subtelomeric rearrangements (3 patients) were found. Neuromotor skills were impaired in almost all cases (58/63). Mental retardation of different severity was present in 52 cases, whereas 2 patients were borderline and 9 patients had normal intelligence quotient. This study demonstrates that there is no unique prognosis for agenesis of the corpus callosum as this condition is associated with a broad range of clinical manifestations, oscillating between the limits of the norm and severe psychomotor delay.

Resistance against the tomato fungal pathogen Cladosporium fulvum is often conferred by Hcr9 genes (Homologues of the C. fulvum resistance gene Cf-9) that are located in the Milky Way cluster on the short arm of chromosome 1. These Hcr9 genes mediate recognition of fungal avirulence gene products. In contrast, the resistance gene Cf-Ecp2 mediates recognition of the virulence factor Ecp2 and is located in the Orion (OR) cluster on the short arm of chromosome 1. Here, we report the map- and homology-based cloning of the OR Hcr9 cluster. A method was optimised to generate clone-specific fingerprint data that were subsequently used in the efficient calculation of genomic DNA contigs. Three Hcr9s were identified as candidate Cf-Ecp2 genes. By PCR-based cloning using specific OR sequences, orthologous Hcr9 genes were identified from different Lycopersicon species and haplotypes. The OR Hcr9s are very homologous. However, based on the relative low sequence homology to other Hcr9s, the OR Hcr9s are classified as a new subgroup.

Introduction: It has been estimated that cytogenetically visible rearrangements are present in ~1% of newborns. These chromosomal changes can cause a wide range of deleterious developmental effects, including mental retardation (MR). It is assumed that many other cases exist where the cause is a submicroscopic deletion or duplication. To facilitate the detection of such cases, different techniques have been developed, which have differing efficiency as to the number of loci and patients that can be tested. Methods: We implemented multiplex amplifiable probe hybridisation (MAPH) to test areas known to be rearranged in MR patients (for example, subtelomeric/pericentromeric regions and those affected in microdeletion syndromes) and to look for new regions that might be related to MR. Results: In this study, over 30 000 screens for duplications and deletions were carried out; 162 different loci tested in each of 188 developmentally delayed patients. The analysis resulted in the detection of 19 rearrangements, of which ~65% would not have been detected by conventional cytogenetic analysis. A significant fraction (46%) of the rearrangements found were interstitial, despite the fact that only a limited number of these loci have so far been tested. Discussion: Our results strengthen the arguments for whole genome screening within this population, as it can be assumed that many more interstitial rearrangements would be detected. The strengths of MAPH for this analysis are the simplicity, the high throughput potential, and the high resolution of analysis. This combination should help in the future identification of the specific genes that are responsible for MR.

SUMMARY Cladosporium fulvum is a fungal pathogen of tomato that grows exclusively in the intercellular spaces of leaves. Ecp2 is one of the elicitor proteins that is secreted by C. fulvum and is specifically recognized by tomato plants containing the resistance gene Cf-Ecp2. Recognition is followed by a hypersensitive response (HR) resulting in resistance. HR-associated recognition of Ecp2 has been observed in Nicotiana paniculata, N. sylvestris, N. tabacum and N. undulata that are non-host plants of C. fulvum. Absence of Ecp2-recognition did not lead to growth of C. fulvum on Nicotiana plants. We show that HR-associated recognition of Ecp2 is mediated by a single dominant gene in N. paniculata. However, based on PCR and hybridization analysis this gene is not homologous to known Cf-genes.

Fragile sites are non-staining gaps and breaks in specific points of chromosomes that are inducible by various culture conditions. Previous studies have shown that various clastogenic agents increase expression of fragile sites. In this study, the expression of common fragile sites induced by aphidicolin was evaluated on prometaphase chromosomes obtained from peripheral blood lymphocytes. Chromosomal aberrations and fragile site expression of 60 individuals, including 20 patients with non-small cell lung cancer (NSCLC), 20 of their clinically healthy family members, and 20 age-matched normal healthy controls without history of any cancer type were studied. Both the proportion of damaged cells (P < 0.001) and the mean number of gaps and breaks per cell (P < 0.001) were significantly higher in both the patients and relatives' groups when compared with the control group. However, they were insignificant when the patients were compared to their relatives (P > 0.05). We determined four aphidicolin type common fragile sites in our study. These sites in patients with NSCLC and relatives were the following: 1p21, 2q33, 3p14, and 16q23. In these fragile sites, 2q33, 3p14, and 16q23 sites were statistically significant when compared with control group (P < 0.001, P < 0.0005, and P < 0.05, respectively). Consequently, we believe that fragile site studies may be helpful to detection of cancer risk.

Fishing for a diagnosis; A family with primary infertility and two members with mental retardation and subtle facial dysmorphism is described. In the two retarded persons chromosomal rearrangements (partial monosomy of chromosome 5 and partial trisomy of chromosome 7) were detected. One member of the family had died with major congenital malformations. Her fibroblasts had been stored and her chromosomes showed the inverse pattern (partial trisomy of chromosome 5 and partial monosomy of chromosome 7). It appeared that in familial mental retardation with or without congenital malformations FISH-techniques should be used to detect submicroscopic chromosomal aberrations, which are not detectable by routine chromosome studies.

Fragile sites are non-staining gaps and breaks in specific points of chromosomes. These sites also include acentric fragments, triradial figures and several rearrangements. Although this issue has been controversial recently, they may be related to structural chromosomal rearrangement in some neoplasms. In this study, the expression of fragile sites induced by aphidicolin (Apc), 5-bromodeoxyuridine (BrJU) and caffeine was investigated on prometaphase chromosomes obtained from the peripheral blood lymphocytes of 36 patients with rectum cancer, 30 first-degree relatives and 30 normal healthy controls. The results of the structural chromosome aberrations determined in patients and their first-degree relatives were significantly higher than those in control subjects (P < 0.001). We determined aphidicolin type common fragile sites (1p36, 1p31, 1p21, 1q21, 1q25, 1q44, 2p24, 2q21, 2q33, 2q37, 3p14, 5q21, 5q33, 13q13, 14q24, 16q23 and 18q21). When the rates of sites such as 1p21, 1q25, 2q33, 3p14, 5q21 and 14q24 in patients and in their first-degree relatives were compared with the control group, the difference was statistically significant. Our results indicated an increased genetic instability in patients with rectum cancer and their first degree relatives. Therefore, the increase of fragile site expression may be an important marker showing genetic predisposition to rectum cancer.

Made available in DSpace on 2019-09-12T16:57:23Z (GMT). No. of bitstreams: 0 Previous issue date: 1999 National Institute of Dental and Craniofacial Research (NIDCR) Gingival fibromatosis (GF) occurs in several genetic forms as a simple Mendelian trait, in malformation syndromes, and in some chromosomal disorders. Specific genes responsible for GF have not been identified. An autosomal dominant form of hereditary gingival fibromatosis (HGF, MIM 135300) was recently mapped to chromosome 2p21 in a large Brazilian family and there was an earlier report of GF in a boy with a cytogenetic duplication involving 2p13-->p21. We thus hypothesised that a common gene locus may be responsible for GF in both the Brazilian family and the boy with the chromosome 2p duplication. We performed additional genetic linkage studies on the Brazilian family and molecular cytogenetic studies on the patient with the cytogenetic duplication to correlate more precisely the genetic interval of the HGF phenotype with the duplicated 2p interval. Additional linkage analysis of new family members resulted in refinement of the candidate region for HGF to an 8 Mb region. Molecular cytogenetic analysis of the 2p13-->p21 duplication associated with GF showed that the duplicated region was proximal to the candidate interval for HGF. Thus, our results support the presence of two different gene loci on chromosome 2p that are involved in GF. Wake Forest Univ, Bowman Gray Sch Med, Dept Pediat, Med Genet Sect, Winston Salem, NC 27157 USA; Universidade de Taubaté (Unitau), Dept Periodont, Sao Paulo, Brazil; Katholieke Univ Leuven Hosp, Ctr Human Genet, B-3000 Louvain, Belgium

beta-catenin is a multifunctional protein: it plays a central role in the cell-cell adhesive junctions, and participates in transduction of the morphogenic Wingless/Wnt-signal. Upon detailed analysis of the human beta-catenin gene, an intragenic polymorphic microsatellite marker could be identified. This marker shows 62% heterozygosity and was used in a study of eleven different tumor types. A high level of beta-catenin allelic imbalance was observed for small cell lung carcinoma, squamous cell lung carcinoma and cervix carcinoma. Other microsatellite markers on 3p24-21 could demonstrate frequent but not invariable codeletion of flanking chromosomal loci. This intragenic polymorphic marker will allow selection of tumor types and tumor samples possibly bearing recessive mutations in the remaining allele of the beta-catenin gene.

Starting from five markers, with a well-defined order from distal to proximal 3p21 nine other markers could be inserted in this 3p21 map. Five were precisely mapped genetically. The other markers were ordered by FISH and/or deletion hybrid mapping. The overall 3p21 order from distal to proximal is as follows: D3S1298-D3S1260-(D3S966, D3S1448 (= D3S1449))-D3S1029-D3S32-D3S643-D3F15S2-D3S2968-D3S1235-D3S1289-D3S1447-D3S1295.

Human chromosomal region 3p12-p23 is proposed to harbor at least three tumor suppressor genes involved in the development of lung cancer, renal cell carcinoma, and other neoplasias. In order to identify one of these genes we defined sequence tagged sites (STSs) specific for 3p13-p24.2 by analyzing a chromosome 3p14 microdissection library. STSs were used for isolating yeast artificial chromosome (YAC) clones from the Centre d'Etude du Polymorphisme Humain (CEPH) YAC libraries. Thirty-eight YACs were assembled into a contig approximately 2.5 Mb in size spanning the t(3;8) and t(3;6) translocation breakpoints associated with hereditary renal cell carcinoma and hematologic malignancies, respectively Chromosomal localization and chimeric status of 126 YACs was analyzed by fluorescence in situ hybridization (FISH). The order of 17 YACs determined by double-color FISH wets in agreement with the STS-based arrangement of the YAC-contig.

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