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A 1.3Mb chromosome 11-specific yeast artificial chromosome (YAC) that spans a t(1;11) translocation breakpoint associated with major psychosis has been used to enrich cDNAs that are encoded within it and expressed in the human foetal brain. Database analysis of the selected fragments led to the identification of 54 clones matching alpha-tubulin, 4 fragments matching two anonymous human expressed sequence tags (ESTs) and 8 fragments giving no database matches. The clones matching alpha-tubulin led to the identification of a novel alpha-tubulin locus located approximately 250 kb proximal to the translocation breakpoint. Extensive sequence and expression analysis of this locus suggests that this is a processed pseudogene, although a long open reading frame is maintained and the possibility that an abnormally acting protein may be expressed in a highly tissue or developmental specific manner cannot be discounted. The novel cDNA fragments map up to 700 kb proximal to the translocation breakpoint and are associated with potential CpG islands. Reverse transcriptase polymerase chain reaction (RT-PCR) expression analysis and high resolution genomic mapping suggest that they may comprise up to three novel genes. No major disruption of the identified fragments could be detected in the genomic DNA of translocation carriers. The psychosis associated with this translocation may therefore be due to position effects on the transcription of these genes or an involvement of translocated chromosome 1 sequences.

The EWS gene has been identified as being systematically translocated in Ewing's sarcoma. In order to ascertain the basis of a marked interethnic difference in the incidence of Ewing's sarcoma, intron 6 of EWS, which is located near the translocation breakpoint region (EWSR1), was characterized. Sequence analysis of the entire intron 6 region revealed a very high density of Alu elements. Most of these Alu sequences could be classified in previously described subfamilies, facilitating delineation of an evolutionary model that involves successive retroposition events. According to this model, the EWS intron 6 region progressively expanded until about 5 million years ago. More recently (10(5) years ago), in part of the human population, the size of this region decreased by over 50% as the result of a homeologous recombination between two Alu sequences, which removed 2480 bp. This rare allele has only been observed in individuals of African origin, a population that is characterized by the lowest incidence of Ewing's sarcoma.

The metabotropic glutamate receptor subtype 5a (mGluR5a) gene has been localised on the Gene Map of the Human Genome to chromosome 11q, approximately 1 cM from the genetic marker D11S931. D11S931 has been shown to lie close to a translocation breakpoint associated with schizophrenia and other psychiatric disorders in a large Scottish family. Because glutamate receptor genes are excellent candidates for psychiatric disorders, we have investigated the physical distance of this gene from the translocation breakpoint on chromosome 11. We have shown that the mGluR5a gene lies at least 850 kb from the breakpoint and, hence, cannot be directly disrupted in translocation carriers. However, a long range position effect of the translocation on this gene, or co-segregation of the translocation with a mutant allele of mGluR5a cannot be ruled out.

Through linkage analysis and the identification of structural chromosome rearrangements, a number of disease genes have been mapped to the pericentromeric region of the long arm of chromosome 13. Structural rearrangements, or deletions, of the 13q12 region have been implicated in a range of myeloproliferative neoplasms, and other haematopoietic malignancies. In particular, seven cases of a t(8;13) (p11; q12·1) rearrangement have been noted in patients with an atypical myeloproliferative disorder associated with T-cell leukemia and eosinophilia. We have previously identified a CEPH megaYAC, 943E4, which crosses the translocation breakpoint in archival tumour samples from two patients with this t(8;13) translocation. As an initial step in the characterisation of this translocation breakpoint, we have generated a fine structure physical map of this 1·9 Mb YAC. We have used the method of YAC fragmentation to generate a series of deletion constructs of known size, which provide discreet physical landmarks convenient for mapping genetic markers along the 943E4 YAC. Analysis of these deletion constructs defined the order of ESTs and microsatellite markers in 943E4 as: cen-NIB1257-(ATP1AL1/D13S283)- D13S179E-(D13S504E/D13S505E)-D13S824E-D13S182E-D13S221-tel. These markers have also been assigned to physically defined regions relative to the fragmented YAC endpoints and a derived NotI restriction map.

The translocation t(3;8)(p21;q12) is the most common chromosome abnormality observed in pleomorphic adenomas of the salivary glands. In this paper we describe the physical mapping of the breakpoints in an adenoma with a variant t(3;8), viz., an ins(8;3)(q12;p21.3p14.1). Using sequence-tagged sites (STSs) corresponding to landmarks within a previously identified yeast artificial chromosome (YAC) spanning the breakpoint in adenomas with t(3;8), cosmids were isolated from a chromosome 8-specific cosmid library. The 8q12 insertion breakpoint was mapped by FISH to a 300-kb region flanked by MOS and a new STS, CH129. A cosmid within this region was shown to span the breakpoint. To test whether the recently identified FHIT gene, which maps to 3p14.2, was disrupted by the 3p rearrangement, we also isolated an FHIT YAC and mapped this YAC by FISH distal to the most proximal 3p breakpoint. In addition, RT-PCR analysis revealed only a normal-sized FHIT transcript, suggesting that FHIT is not affected by the 3;8-rearrangement.

We report a case control association study using polymorphic markers D1S1621 and D11S931 in unrelated individuals with schizophrenia, unipolar depression and a matched control group. The two polymorphic markers were identified during the positional cloning of the translocation breakpoint t(1:11)(q43:q14.3) that cosegregates with schizophrenia and affective disorders. These markers provided an opportunity to investigate linkage disequilibrium with a postulated schizophrenia susceptibility gene close to the translocation breakpoint in random populations of schizophrenia and unipolar depression individuals compared with a normal control population. No significant differences between allele frequencies for either of the markers in the affected populations were observed in comparison with the control group, which provides evidence against a nearby gene of major effect in the populations studied.

The purpose of this study was to determine the deep sequencing and analytic conditions needed to detect fetal subchromosome abnormalities across the genome from a maternal blood sample. Cell-free (cf) DNA was isolated from the plasma of 11 pregnant women carrying fetuses with subchromosomal duplications and deletions, translocations, mosaicism, and trisomy 20 diagnosed by metaphase karyotype. Massively parallel sequencing (MPS) was performed with 25-mer tags at approximately 10(9) tags per sample and mapped to reference human genome assembly hg19. Tags were counted and normalized to fixed genome bin sizes of 1 Mb or 100 kb to detect statistically distinct copy-number changes compared to the reference. All seven cases of microdeletions, duplications, translocations, and the trisomy 20 were detected blindly by MPS, including a microdeletion as small as 300 kb. In two of these cases in which the metaphase karyotype showed additional material of unknown origin, MPS identified both the translocation breakpoint and the chromosomal origin of the additional material. In the four mosaic cases, the subchromosomal abnormality was not demonstrated by MPS. This work shows that in nonmosaic cases, it is possible to obtain a fetal molecular karyotype by MPS of maternal plasma cfDNA that is equivalent to a chromosome microarray and in some cases is better than a metaphase karyotype. This approach combines the advantage of enhanced fetal genomic resolution with the improved safety of a noninvasive maternal blood test.

We present a case of a 19-year-old phenotypically normal girl with premature ovarian failure. Cytogenetic analysis using G banding and fluorescence in situ hybridization (FISH) from cultured peripheral blood lymphocytes of the patient and the family revealed a de novo X;15 translocation and the imbalance to be 46,X,t(X;15)(Xpter → Xq21::15q11 → 15qter;15pter → 15q11::Xq21 → Xqter). ish (CEPX+, wep15+, ISNRPN+, PML+, D15S10+, wcp15-, SNRRN-, PML-)[20]. The X chromosome inactivation (XCI) assay revealed a completely skewed XCI pattern in which selective pressure favors an active maternal allele. The Affymetrix 2.7 M cytogenetics whole-Genome array confirmed the chromosomal imbalance and identified disruption of the HDX gene at Xq21, the translocation breakpoint. © 2013 Informa Healthcare USA, Inc.

A subgroup of pleomorphic adenomas of the salivary glands is characterized by translocations involving chromosome 8, with consistent breakpoints at 8q12. As part of a positional cloning effort to isolate the gene(s) affected by these translocations we now report the mapping of the 8q12 breakpoint in two primary pleomorphic adenomas with the recurrent t(3;8)(p21;q12). Yeast artificial chromosome (YAC) clones corresponding to eight different loci in 8q11-12 were isolated and mapped by fluorescence in situ hybridization (FISH). The t(3;8) breakpoint was mapped within a 1 Mb region flanked by MOS proximally and by the genetic marker D8S166 distally. One YAC within this region was shown to span the t(3;8) breakpoint in two tumors. This YAC will provide an excellent tool for isolating the gene(s) at the breakpoint(s) in adenomas with t(3;8). Genes Chromosom Cancer 17:166–171 (1996). © 1996 Wiley-Liss, Inc.

Insecticide-resistant and susceptible clones of Myzus persicae were induced to produce sexual morphs and crossed in the laboratory. Progeny clones were analysed for karyotype, esterase (E4, FE4 or S) gene type and activity, and amplified E4 and FE4 genes were located on their chromosomes by fluorescence in situ hybridization (FISH). Amplified FE4 genes of resistant parent clones (800F and French R) were inherited according to expectations. Chromosomal locations of these genes (on autosomes 1 and 3 in 800F, and on 1 and 2 in French R) were confirmed by FISH analysis of progeny that had inherited an autosome 2 marker (a dissociation) from the susceptible parent (DS). Inheritance of amplified E4 genes could not be studied directly as none of the available clones was able to produce mating females. Males from two clones with amplified E4 genes (and with the A1,3 translocation that is common to all E4-producing genotypes) were therefore mated with females from clones with amplified FE4 genes at known chromosomal locations. Progeny were obtained with both E4 and FE4 genes, a combination not yet found in nature. Analysis of F1 and subsequent generations confirmed that the amplified E4 site on autosome 3T is close to the translocation breakpoint, and apparently coallelic with the amplified FE4 site on the normal autosome 3 inherited from 800F. One of the translocated parent clones (4156) had two additional E4 sites, unlinked to the translocation, which were inherited according to expectation. Esterase activities of progeny clones, measured by immunoassay, mostly corresponded to the number of amplified sites inherited, with some discrepancies which could be attributed to copy number differences between sites, inheritance of partially methylated genes from French R, or position effect variegation at the site on 3T. Inheritance of the A1,3 translocation in two crosses differed markedly from expectation.

The human testis determining factor (SRY) has been cloned from the Y chromosome. This gene is a dominant inducer of male differentiation. Mutations in the SRY gene result in an XY individual developing as a sex reversed phenotypic female. Sex reversal in humans can also be caused by mutations located in autosomal or X-linked loci. One such sex-reversing locus (SRAI) is associated with the developmental disorder campomelic dysplasia (CD). Both these syndromes were mapped to human chromosome 17q by the identification of balanced reciprocal translocations in five unrelated patients. The translocation breakpoint of one such XY-female CD patient was mapped and the region surrounding it cloned. The closest distal marker used to map the translocation breakpoint was the SOX9 gene. Because of the close proximity of this gene to the breakpoint, it was subjected to mutation analysis in patients without overt chromosome rearrangements. Analysis of DNA from these patients and their parents identified de novo mutations in the SOX9 gene in patients with both autosomal sex reversal and CD. This showed that mutations in the SOX9 gene are responsible for both syndromes.

The constitutive fragile site at human chromosomal band 3p14.2, FRA3B, has been described as the most active common fragile site in the human genome. FRA3B is cytologically indistinguishable from the chromosome 3 breakpoint observed in the hereditary renal cell carcinoma (hRCC) translocation t(3;8) (p14.2;q24.13). Previous work demonstrated that a 1330-kb YAC clone, YC850A6, spans both the t(3;8) translocation and FRA3B and also encompasses FRA3B-associated breakpoints induced in hamster–human hybrids. This YAC was used to construct a multi-hit cosmid library. Screening of this library resulted in a 350-kb cosmid contig that extends distally from the t(3;8) translocation breakpoint. Seventeen aphidicolin-induced 3p14.2 breakpoints derived from hamster–human hybrids were mapped within this cosmid contig. These breakpoints were found to localize as two distinct clusters, separated by 200 kb, which lie on either side of a region of frequent breakage within FRA3B as defined by FISH analysis using cosmids from the contigs. The most proximal of the breakpoint clusters lies approximately 100 kb distal to the hRCC t(3;8) breakpoint. The distribution of these breakpoints, together with the region of frequent chromosomal breakage mapped by FISH analysis, further confirms the position of FRA3B and helps to define the extent over which its fragility is exerted. These data indicate that FRA3B comprises several hundred kilobases of DNA sequence within 3p14.2. The 350-kb contig and the cosmid library constructed from YAC YC850A6 will be essential for further characterization of the region surrounding FRA3B and in experiments to determine the molecular basis of the fragility of FRA3B.

Split hand/split foot malformation (SHSF) has been described in several patients associated with cytogenetically visible rearrangements involving chromosome 7q. Characterisation of these patients has led to localisation of an autosomal dominant form of SHSF to 7q21-22; the locus has been designated SHFM1. We describe a patient with a complex, apparently balanced cytogenetic rearrangement, including a translocation breakpoint at 7q21.3 near the DSS1 gene. In addition to ectrodactyly of all four limbs, the patient has congenital deafness, submucous cleft palate, microcephaly, and mental retardation. This patient represents an additional case of syndromic ectrodactyly related to the SHFM1 gene region, which may be responsible for both syndromic and non-syndromic ectrodactyly.

Tumors of the Ewing's sarcoma family often present a major diagnostic challenge for the pathologist. In recent years, significant progress has been made in identifying characteristic chromosomal rearrangements associated with certain solid tumors. More than 85% of Ewing's sarcoma and related tumors present a specific t(11;22) (q24;q12) balanced translocation, which generates a fusion transcript of the EWS gene and the FLI-1 gene. The cloning of the t(11;22)(q24;q12) breakpoint has raised the possibility of using a reverse transcription-polymerase chain reaction (RT-PCR) based assay as a diagnostic tool. We report an improvement of the established method, which currently depends on fresh or snap-frozen tissue, so that it is possible to use formalin-fixed, paraffin-embedded tissue as a source of RNA. The described nested RT-PCR assay enables the pathologist to investigate retrospectively archival tumor samples or to confirm the diagnosis in cases where no fresh or frozen material is available.

To contribute to the physical gene map of mouse chromosome 11 (MMU11) and to extend the mapping resources available for this chromosome, we have produced mouse x rat somatic cell hybrids containing only bands B5 to E of MMU11. Characterization of the hybrids by polymerase chain reaction (PCR) amplification and Southern blot analyses of MMU11 markers revealed two hybrids, T16Ad14B and T16Ad19A, that had selectively retained the 3(11) translocation product containing distal MMU11 (bands B5-E). Cytogenetic analysis of the hybrid T16Ad14B by fluorescence in situ hybridization (FISH) and conventional G-banding confirmed the presence of the 3(11) translocation chromosome. Mapping of markers in both the T16Ad14B and T16Ad19A hybrids localized the T16Ad translocation breakpoint between the proximal markers Atplb2 and Acrb and the more distal markers Scya2 and Mpo. Loci for D11Mit5, Rpo2-1, Trp53, Glut4, Acrb, and Atplb2 could all be localized proximal to the T16Ad breakpoint in band B5, between bands B1 and B5 on MMU11.

The t(6;11)(q27;q23) is one of the most common translocations observed in patients with acute myeloid leukemia (AML). The translocation breakpoint involves the MLL gene, which is the human homolog of the Drosophila trithorax gene, at 11q23 and the AF6 gene at 6q27. Reverse transcriptase-polymerase chain reaction (RT-PCR) using an MLL sense primer and an AF6 antisense primer detected the MLL/AF6 fusion cDNA from three leukemia patients with the t(6;11) [two AML and one T-acute lymphoblastic leukemia (ALL)] and one cell line. The fusion point in the AF6 cDNA from these cases is identical, regardless of the leukemia phenotype. The ML-2 cell line, which was established from a patient with AML that developed after complete remission of T-cell lymphoma, has retained an 11q23–24 deletion from the lymphoma stage and has acquired the t(6;11) with development of AML. The ML-2 cells have no normal MLL gene on Southern blot analysis, which indicates that an intact MLL gene is not necessary for survival of leukemic cells. Genes Chromosom Cancer 15:206–216 (1996). © 1996 Wiley-Liss, Inc.

A patient with Prader-Willi syndrome (PWS) was found to carry a de novo balanced reciprocal translocation, t(15;19)(q12;q13.41), which disrupted the small nuclear ribonucleoprotein N (SNRPN) locus. The translocation chromosome 15 was found to be paternal in origin. Uniparental disomy and abnormal DNA methylation were ruled out. The translocation breakpoint was found to have occurred between exon 0 (second exon) and 1 (third exon) of the SNRPN locus outside of the SmN open reading frame (ORF), which is intact. The transcriptional activities of ZNF127, IPW, PAR-1, and PAR-5 were detected with RT-PCR from fibroblasts of the patient, suggesting that these genes may not play a significant role in the PWS phenotype in this patient. Transcription from the first two exons and last seven exons of the SNRPN gene was also detected with RT-PCR; however, the complete mRNA (10 exons) was not detected. Thus, the PWS phenotype in the patient is likely to be the result of disruption of the SNRPN locus.

Objective To determine the role of structural alterations of human chromosome region 3p12-p21 in the possible inactivation of one or more tumour-suppressor genes in the pathogenesis of renal cell carcinoma (RCC), lung cancer and other neoplasms. Materials and methods As microsatellite instability (MI), in particular MI with loss of heterozygosity (LOH), may indicate putative tumour-suppressor gene loci, 20 kidney tumours, including 14 clear cell carcinomas and six non-clear cell neoplasms, were investigated with 10 polymorphic simple sequence-repeat markers spanning 3p12-p21. Six of these markers map to the region of deletion flanked by markers D3S1285 and D3S1295 bracketing the t(3;8) translocation breakpoint in 3p14.2 of hereditary RCC. Results Twelve of 14 clear cell RCCs displayed MI for at least one locus, as opposed to none of the non-clear cell tumours (P=0.001). Locus D3S1274 in 3p13 located in the region deleted in lung cancer line U2020 and loci D3S1313 and D3S1300 in 3p14.3 characterized common regions of instability and LOH. Two patients with RCC who also had lung cancer and colon cancer, respectively, showed LOH at D3S1313 or D3S1300 as the only alterations of their kidney tumours. Conclusions These results suggest that human chromosome region 3p14.3 distal to the hereditary t(3;8) translocation breakpoint and the region deleted in the U2020 lung cancer cell line might be involved in the tumorigenesis or progression of clear cell RCC.

We present three cousins who have normal karyotypes, despite having clinical features of Wolf-Hirschhorn syndrome. Fluorescence in situ hybridisation techniques confirmed that all three relatives were monosomic for the distal short arm of chromosome 4 and that a cryptic translocation involving chromosomes 4 and 11 was segregating within the family. Segregation analysis indicated that the risk of an affected child being born to a parent carrying the translocation was 15%. Molecular analysis showed that loci D4S111 and D4S115 were not deleted in the proband, thus excluding these loci from the "Wolf-Hirschhorn critical region". Surprisingly, DNA studies also suggested that the translocation breakpoint on chromosome 4 was within the region of a preexisting paracentric inversion.

A 200–300 kb region of chromosome 3p14.2, including the fragile site locus FRA3B , is homozygously deleted in multiple tumor-derived cell lines. Exon amplification from cosmids covering this deleted region allowed identification of the human FHIT gene, a member of the histidine triad gene family, which encodes a protein with 69% similarity to an S. pombe enzyme, diadenosine 5′, 5′′′ P 1 , P 4 -tetraphosphate asymmetrical hydrolase. The FHIT locus is composed of ten exons distributed over at least 500 kb, with three 5′ untranslated exons centromeric to the renal carcinoma–associated 3p14.2 breakpoint, the remaining exons telomeric to this translocation breakpoint, and exon 5 within the homozygously deleted fragile region. Aberrant transcripts of the FHIT locus were found in ∼50% of esophageal, stomach, and colon carcinomas.

C-banding polymorphism was analyzed in eight strains of wild Emmer, Triticum dicoccoides Körn, which included six translocation homozygotes reported previously. Polymorphisms were detected in all of the strains examined, and the breakpoints of five spontaneous translocations were successfully identified by C-bands. Of the eight breakpoints that could be precisely identified, one was located in the centromeric region while the remaining seven were located in proximal to distal euchromatic regions. The two breakpoints of one translocation could only be approximately localized to proximal regions due to the scarcity of C-bands. The present results are in contrast with those observed on T. araraticum, another wild tetraploid wheat belonging to the Timopheevi group, in which most of the breakpoints were located in centromeric regions. In T. dicoccoides, the six translocation chromosome types were derived from the standard karyotype primarily by a mechanism other than centric breakage-fusion.

Abnormalities involving chromosome 13 have been reported as the only cytogenetic change in B-cell chronic lymphocytic leukemia (BCLL). Deletions are the most common cytogenetic abnormality and always involve 13q14, but when translocations are seen, the consistent breakpoint is always in 13q14. It is now established that deletions, distal to the RB1 gene in 13q14, are invariably associated with these translocations. We have recently described the smallest such deletion from a series of rearrangements from these tumors isolated in somatic cell hybrids, which spans approximately 1 Mb. In this report, we present the results of a series of a chromosome walking experiments using YACs and have been able to span this small deletion, which must contain the gene that is frequently deleted in BCLL. Four probes from 13q14 (RB1-mgg15-D13S25-D13S31) were used to isolate corresponding YACs for each of the markers. The chromosomal location of these YACs was verified using FISH, which also demonstrated their nonchimeric nature. Vectorette end rescue was then used to demonstrate the overlap of the YACs and to isolate new clones to complete the contig. The extremes of the contig were shown to cross the chromosome 13 translocation breakpoints isolated in somatic cell hybrids that carry the derivatives of chromosome 13 involved in the smallest BCLL deletion. This YAC contig covers the entire deletion and will prove a valuable resource to begin isolating genes from this region, In addition, we have isolated YACs corresponding to the RBI locus, which extends the contig over a 3.8-cM distance on the chromosome. (C) 1995 Academic Press, Inc.

Abnormalities involving chromosome 13 have been reported as the only cytogenetic change in B-cell chronic lymphocytic leukemia (BCLL). Deletions are the most common cytogenetic abnormality and always involve 13q14, but when translocations are seen, the consistent breakpoint is always in 13q14. It is now established that deletions, distal to the RB1 gene in 13q14, are invariably associated with these translocations. We have recently described the smallest such deletion from a series of rearrangements from these tumors isolated in somatic cell hybrids, which spans approximately 1 Mb. In this report, we present the results of a series of a chromosome walking experiments using YACs and have been able to span this small deletion, which must contain the gene that is frequently deleted in BCLL. Four probes from 13q14 (RB1-mgg15-D13S25-D13S31) were used to isolate corresponding YACs for each of the markers. The chromosomal location of these YACs was verified using FISH, which also demonstrated their nonchimeric nature. Vectorette end rescue was then used to demonstrate the overlap of the YACs and to isolate new clones to complete the contig. The extremes of the contig were shown to cross the chromosome 13 translocation breakpoints isolated in somatic cell hybrids that carry the derivatives of chromosome 13 involved in the smallest BCLL deletion. This YAC contig covers the entire deletion and will prove a valuable resource to begin isolating genes from this region. In addition, we have isolated YACs corresponding to the RB1 locus, which extends the contig over a 3.8-cM distance on the chromosome.

In eutherian mammals, the Y-chromosome geneSRYis required for induction of testis development. Although the Y chromosome is sex determining, loci located elsewhere in the genome participate in the complex cascade of genetic interactions required to form a testis. Male to female sex reversal (46,XY females) occurs at a high frequency in individuals afflicted with the skeletal malformation syndrome campomelic dysplasia. Chromosomal translocations in individuals with both syndromes had localized an autosomal sex reversal locus (SRA1) and a campomelic dysplasia locus (CMPD1) to the long arm of human chromosome 17. The molecular cloning of a translocation breakpoint in a sex reversed campomelic dysplasia patient revealed its proximity toSOX9, a gene which is related toSRY. Analysis ofSOX9in patients without chromosomal rearrangements demonstrated single allele mutations in sex reversed campomelic individuals, linking this gene with both bone formation and control of testis development. Identification ofSOX9asSRA1/CMPD1and the role ofSOX9mutations in sex reversal and campomelic dysplasia are discussed.

Uterine leiomyoma is a common tumor of smooth muscle cell origin often characterized by the presence of a balanced t(12;14)(q13-15;q24.1) chromosomal translocation. This breakpoint on chromosome 14 had previously been placed between the markers SPTB and D14S77, a region estimated to span 7 cM. In this study we have used a meiotic breakpoint mapping panel to construct a high resolution genetic map of this interval. Markers that mapped within this interval were used to analyze DNA from a somatic cell hybrid containing the t(12;14) translocated chromosome. The results of this analysis localize the t(12;14) breakpoint on chromosome 14 between D14S298 and D14S540, between which no meiotic recombination was detected. This sets the stage for identifying the gene(s) disrupted by the chromosomal translocation by defining the markers that flank the translocation breakpoint.

Chromosomal band 1p36 probably harbours several neuroblastoma suppressor genes. A neuroblastoma patient has been described with a constitutional balanced translocation, t(1;17)(p36;q12-21). Cytogenetically, no loss of chromosomal material was visible. The 1p36 translocation breakpoint could therefore have inactivated one allele of a tumour suppressor gene, thus predisposing the patient to develop neuroblastoma. We localized this breakpoint by pulsed field gel electrophoresis, analysis of yeast artificial chromosomes, and fluorescence in situ hybridization. Here we report that the breakpoint is within a large cluster of small nuclear RNA U1 (RNU1) and some tRNA genes (TRE, TRN) on chromosomal band 1p36. The size of this cluster is over two megabases and it contains many other locally repeated sequences. Polyadenylated transcripts were identified for some of these sequences. In addition, the cluster is the target for integration of an adenovirus 5/SV40 hybrid virus. The translocation breakpoint maps distal of this viral integration site and proximal of marker PND.

Forty-nine clones derived by microdissection of a schizophrenia-associated t(1;11)(q42.1;q14.3) breakpoint region have been assigned by somatic cell hybrid mapping to seven discrete intervals on the long arm of human chromosome 11. Eleven of the clones were shown to map to a small region immediately distal to the translocation breakpoint on 11q. A 3-Mb contiguous clone map of this region was established by isolation of corresponding YAC recombinants. The contig was oriented and shown to traverse the translocation breakpoint by FISH and microsatellite marker analysis. This contig will facilitate the isolation of candidate sequences whose expression may be affected by the translocation.

Familial adenomatous polyposis (FAP) is an inherited predisposition to colorectal cancer caused by germline mutations in the adenomatous polyposis coli (APC) gene located on chromosome segment 5q21-q22. We detected a germline rearrangement of the APC gene in a Dutch FAP family by screening genomic DNA samples with APC cDNA probes. Subsequent molecular and cytogenetic studies revealed a constitutional reciprocal translocation t(5; 10) (q22; q25) that resulted in the disruption of the APC gene. Southern blot and polymorphic marker analysis indicated that part of the APC gene had been deleted. Analysis of the APC protein product indicated that the translocation breakpoint did not lead t o the formation of a detectable truncated APC protein but apparently resulted in a null allele. Evaluation of the clinical phenotypes in the patients suggested that they exhibited features of an unusual form of FAP characterized by a slightly delayed age of onset of colorectal cancer and a reduced number of colorectal polyps. The latter were mainly sessile and were located predominantly in the proximal colon. To our knowledge, this is the first description of FAP caused by a reciprocal translocation disrupting the APC gene. © 1995 Wiley-Liss, Inc.

Voltage-sensitive sodium channels play a key role in nerve cells where they are responsible for the increase in sodium permeability during the rising phase of action potentials. In Drosophila melanogaster a subset of temperature-sensitive paralytic mutations affect sodium channel function. One such mutation is temperature-induced paralysis locus E (tipE), which has been shown by electrophysiology and ligand binding studies to reduce sodium channel numbers. Three new gamma-ray-induced tipE alleles associated with either visible deletions in 64AB or a translocation breakpoint within 64B2 provide landmarks for positional cloning of tipE. Beginning with the flanking cloned gene Ras2, a 140-kb walk across the translocation breakpoint was completed. Germline transformation using a 42-kb cosmid clone and successively smaller subclones localized the tipE gene within a 7.4-kb genomic DNA segment. Although this chromosome region is rich in transcripts, only three overlapping mRNAs (5.4, 4.4, and 1.7 kb) lie completely within the smallest rescuing construct. The small sizes of the rescuing construct and transcripts suggest that tipE does not encode a standard sodium channel alpha-subunit with four homologous repeats. Sequencing these transcripts will elucidate the role of the tipE gene product in sodium channel functional regulation.

Breakpoints in the reciprocal translocation lines derived from a barley variety 'Chikurin-ibaraki No. 1' (TS lines) were analyzed by means of C- and N-banding techniques, and were precisely localized in 42 out of 48 lines examined. Translocated chromosomes in the remaining 6 lines were identified by chromosome pairing analyses. Thus, it was revealed that all translocations except T3-7 were involved in TS lines. Breakpoints were aII assigned in interband regions, confirming preferential breakage in those regions. The orientation behaviour of quadrivalents at meiotic metaphase I in translocation heterozygotes and its relationships to the partial sterility were investigated using TS lines along with another set of translocation lines derived from 'Bonus' (TS$ lines). An expected fertility of translocation heterozygote was calculated based mainly on the frequency of alternate orientation. A positive correlation was observed between the expected fertility and the observed seed fertility, confirming that the orientation behaviour of quadrivalents could be the main cause of the partial sterility of translocation heterozygote. It was also found that, regardless of translocation, seed fertilities of translocation heterozygotes with the heterogeneous genetic background were significantly higher than those with the homogeneous genetic background. This difference was consistent with the observations on expected fertilities, at least, in the translocation heterozygotes produced with TS$ lines, suggesting that orientation frequencies of quadrivalents could be influenced by the parental genotypes., オオムギ品種「竹林茨城1号」に由来する相互転座系統（TS系統）において、CおよびN分染法を用いた転座切断点の解析を行い，調査した48系統中42系統において切断点の詳細な位置を決定した。残りの6系統については染色体対合の調査に基づき転座染色体を同定した。これらの結果から，TS系統は染色体3と7の転座（T3-7）を除く全種類の相互転座を含むことが明らかとなった。またすべての切断点が染色体のインターバンド部位に存在していたことから，これらの部位で優先的に染色体切断が起こることが確認された。TS系統ならびに品種「Bonus」由来の相互転座系統（TS＄系統）を用いて、相互転座ヘテロにおける減数分裂第一中期の4価染色体行動と部分不稔性との関係を調査した。転座ヘテロ個体の期待稔性を主として交互型4価染色体の分離頻度に基づき算出した。この期待稔性と実際に観察された種子稔性との間に正の相関関係がみられたことから，4価染色体の分離行動が転座ヘテロ個体の部分不稔性を引き起こす主要因であることが確認された。さらに転座ヘテロ個体の種子稔性は、転座の種類に関わらず，ホモの遺伝的背景下よりもヘテロの遺伝的背景下において高くなることが明らかとなった。TS＄系統の相互転座ヘテロでは，期待稔性についてもこのような差異が認められたことから，4価染色体の分離型頻度は転座ヘテロ個体の両親の遺伝子型によって影響されることが示唆された。

Uterine leiomyomata are the most common tumors in women and can cause abnormal uterine bleeding, pelvic pain, and infertility. Approximately 200,000 hysterectomies are performed annually in the U.S. to relieve patients of the medical sequelae of these benign neoplasms. Our efforts have focused on cloning the t(12;14)(q14-q15;q23-q24) breakpoint in uterine leiomyoma to further our understanding of the biology of these tumors. Thirty-nine YACs and six cosmids mapping to 12q14-q15 have been mapped by fluorescence in situ hybridization to tumor metaphase chromosomes containing a t(12;14). One YAC spanned the translocation breakpoint and was mapped to tumor metaphases from a pulmonary chondroid hamartoma containing a t(12;14)(q14-q15;q23-q24) and a lipoma containing a t(12;15)(q15;q24); this YAC also spanned the breakpoint in these two tumors, suggesting that the same gene on chromosome 12 may be involved in the pathobiology of these distinct benign neoplasms.

In a family with a constitutional translocation t(3;6), the oldest member carrying the translocation had developed multiple nonpapillary renal cell carcinomas (RCCs). The translocation breakpoint was positioned between 3p13 and 3p14.1. This is close to the region in which a t(3;8) breakpoint has been reported in a family with hereditary RCC. We defined the location of the t(3;6) and t(3;8) breakpoints by fluorescence in situ hybridization (FISH) analysis with yeast artificial chromosomes (YACs) from the 3p14-13 region. Both interphase nuclei and metaphase cells from translocation-carrying members of both families have been used, allowing the definition of flanking YACs for each breakpoint. We could thereby clearly confirm that the breakpoints are different, the t(3;8) breakpoint being most distal. In addition, we have shown that both translocation breakpoints are located distal to the homozygously deleted region in the U2020 lung cancer cell line. (C) 1995 Wiley-Liss, Inc.

Facioscapulohumeral muscular dystrophy (FSHD) is located on chromosome 4q35, close to the telomere. FSHD patients carry deletions within a cluster of tandemly repeated DNA. Although expression of a functional FSHD gene will be altered in patients, the sequence itself may be unaffected by this deletion. Hence, the FSHD gene could lie outside of the deleted region. This study employs fluorescent in situ hybridization using chromosome 4-specific cosmid and YAC clones to rapidly saturate chromosome 4 with new markers. Some 250 cosmids and 26 YACs were regionally mapped, of which 5 YACs and 55 cosmids mapped to the distal portion of 4q. Only one of these clones (D4S1454) mapped telomerically to a translocation breakpoint specified by D4S187. Using two-color interphase mapping, the following marker order was obtained: Cen-D4S187-D4S1454-HSPCAL2-D4S163-D4S139-+ ++D4F35S1. Absence of additional markers mapping distal to D4F35S1 indicates that the linkage group containing the FSHD gene lies extremely close to the 4q telomere.

We describe the generation of large-fragment microclone libraries from the chromosomal breakpoint of a reciprocal balanced translocation linked to schizophrenia. The abnormality was visible under the phase-contrast microscope, allowing direct dissection from unstained, unhanded met-phases. Two separate microdissection experiments yielded 443 and 672 recombinants, respectively. Following complete EcoRl digestion, inserts with an average size of 0.3 kb (range, 0.2–3 kb) were obtained in the first experiment and 1.5 kb (range, 0.15–6.5 kb) in the second. FISH analysis of pooled clones “painted” back onto the derivative chromosome and assignment of microclones to somatic cell hybrids confirmed the fidelity of the method. Microdissection of chromosome regions identified by karyotype rearrangements in unstained, unhanded metaphases is a potentially powerful tool for positional cloning.

We screened two human yeast artificial chromosome (YAC) libraries by polymerase chain reaction (PCR) with oligonucleotides specific to the BCL1 major translocation breakpoint cluster region at 11q13. Five YACs were isolated. Two of them were chimeric. One of these and remaining three YACs were characterized by hybridization with various known 11q13 probes, Alu-PCR fingerprinting, in situ hybridization, and isolation of YAC ends. A map of this ca 700-kb YAC contig was obtained. This map was consistent with maps established from total human genomic DNA. Every YAC in this region was found unstable and gave rise to reproducibly deleted lineages. Analysis in detail of these deletions over many generations showed that more than a single sequence might be involved. The availability of cloned material will facilitate the search for the still elusive genetic elements responsible for amplifications, deletions and translocations observed at 11q13 in malignancies.

Band 1p36.1-1p36.2 is frequently involved in chromosomal aberrations of neuroblastoma cells, and therefore thought to harbour genetic information which may be involved in tumorigenesis. To map this putative neuroblastoma locus, we screened neuroblastoma cell lines for reciprocal translocations at 1p36.1-2 which may signal the site of an affected gene. We identified a reciprocal 1;15 translocation in cell line NGP by fluorescence in situ hybridisation (FISH). As a strategy to clone the translocation breakpoint, we isolated yeast artificial chromosomes (YACs) specific for loci at 1p36. Screening of cell line NGP by FISH identified a YAC, 1050 kbp in size, which hybridised to both derivative 1;15 and 15;1 chromosomes. We conclude that this YAC, which maps to D1S160, covers the break. This chromosomal position is within the smallest region of overlap (SRO) found in neuroblastoma tumours and within the region of a constitutional interstitial deletion of a neuroblastoma patient. The YAC we describe here should serve as a DNA source for gene cloning approaches towards the isolation of candidates for the putative neuroblastoma suppressor gene.

Deletions of the 22q11.2 have been associated with a wide range of developmental defects (notably DiGeorge syndrome, velocardiofacial syndrome, conotruncal anomaly face syndrome and isolated conotruncal cardiac defects) classified under the acronym CATCH 22. A DiGeorge syndrome patient bearing a balanced translocation whose breakpoint maps within the critical region has been previously described. We report the construction of a cosmid contig spanning the translocation breakpoint and the isolation of a gene mapping 10 kb telomeric to the breakpoint. This gene encodes a novel putative adhesion receptor protein, which could play a role in neural crest cells migration, a process which has been proposed to be altered in DiGeorge syndrome.

Cell line Ad-312/SV40, which was derived from a primary pleomorphic salivary gland adenoma with t(1;12)(p22;q15), was used in fluorescence in situ hybridization (FISH) analysis to characterize its translocation breakpoint region on chromosome 12. Results of previous studies have indicated that the chromosome 12 breakpoint in Ad-312/SV40 is located proximally to locus D12S8 and distally to the CHOP gene. We here describe two partially overlapping yeast artificial chromosome (YAC) clones, Y4854 (500 kbp) and Y9091 (460 kbp), which we isolated in the context of a chromosome walking project with D12S8 and CHOP as starting points. We present a composite long-range restriction map encompassing the inserts of these two YAC clones and show by FISH analysis that both YACs span the chromosome 12 breakpoint as present in Ad-312/SV40 cells. Subsequently, we have isolated cosmid clones corresponding to various sequence-tagged sites (STSs) mapping within the inserts of these YAC clones. These included cRM51, cRM69, cRM85, cRM90, cRM91, cRM110, and cRM111. In FISH studies, cosmid clones cRM85, cRM90, and cRM111 appeared to map distally to the chromosome 12 breakpoint, whereas cosmid clones cRM51, cRM69, cRM91, and cRM110 were found to map proximally to it. These results assign the chromosome 12 breakpoint in Ad-312/SV40 to a DNA region of less than 165 kbp. FISH evaluation of the chromosome 12 breakpoints in five other pleomorphic salivary gland adenoma cell lines indicated that these are located proximally to the one in Ad-312/SV40, at a distance of more than 0.9 Mbp from STS RM91. These results, while pinpointing a potentially critical region on chromosome 12, also provide evidence for the possible involvement of 12q13-q15 sequences located elsewhere.

Aims The localisation of the translocation breakpoint of the Ewing sarcoma family of tumours shows significant variability on relatively large regions of fusion partner genes. As a consequence, many alternative forms of EWSR1-ETS translocation exist which make the RNA-based molecular diagnostics of Ewing sarcoma family of tumours complicated. In addition to the heterogeneity of fusion transcripts, the degradation of RNA also presents a significant difficulty in the molecular analysis of formalin-fixed paraffin-embedded (FFPE) tissues. Our aim was to establish a sensitive method which is able to identify all combinatorially possible EWSR1-FLI1 and EWSR1-ERG translocation transcripts in FFPE tissue samples despite significant RNA-degradation. Methods The combination of fluorescent multiplex PCR with laser-induced capillary electrophoresis was used to detect and identify EWSR1-FLI1 and EWSR1-ERG chimeric transcripts on the basis of amplicon size, and forward primers labelled by distinct fluorophores. Results Using this method, we processed 60 FFPE samples of Ewing sarcoma family of tumours, and identified six types EWSR1-FLI1 and one type EWSR1-ERG chimeric transcripts acceptable for RT-PCR analysis in 27 out of 45 samples. This result shows 60% sensitivity for detecting the most frequent Ewing family of tumour (EFT)-related fusion transcripts. Conclusions The utilisation of fluorescent multiplex PCR and laser-induced fluorescent capillary electrophoresis is effective for the diagnosis of EFT in FFPE tissue, and after the defined modifications it can offer a sensitive method to overcome the diagnostic difficulties connected with heterogeneity of the variant translocations in EFT.

Genetic alterations like point mutations, insertions, deletions, inversions and translocations are frequently found in cancers. Chromosomal translocations are one of the most common genomic aberrations associated with nearly all types of cancers especially leukemia and lymphoma. Recent studies have shown the role of non-B DNA structures in generation of translocations. In the present study, using various bioinformatic tools, we show the propensity of formation of different types of altered DNA structures near translocation breakpoint regions. In particular, we find close association between occurrence of G-quadruplex forming motifs and fragile regions in almost 70% of genes involved in rearrangements in lymphoid cancers. However, such an analysis did not provide any evidence for the occurrence of G-quadruplexes at the close vicinity of translocation breakpoint regions in nonlymphoid cancers. Overall, this study will help in the identification of novel non-B DNA targets that may be responsible for generation of chromosomal translocations in cancer. (C) 2012 Elsevier Inc. All rights reserved.

In B-cell malignancies, the t(11;14)(q13;q32) at the 11q13 BCL1 locus is characterized by a scattering of breakpoint sites along a 100 kb genomic region, between the BCL1 major translocation cluster (MTC) and the PRAD1 (also termed cyclin D1 or CCND1) gene. Recently, the 11q13 breakpoint region was extended on both sides, centromeric to the MTC and telomeric to PRAD1. We report here the molecular cloning of a new t(11;14) breakpoint site, 20 kb centromeric to the MTC, from a patient with prolymphocytic leukemia. We subcloned a non-repetitive DNA fragment near the breakpoint and mapped this new 11q13 probe (pHO11c) relative to already identified breakpoint sites, using long- and short-range physical mapping within the BCL1 locus. Rearrangements in the BCL1 locus are associated with deregulation of the PRAD1 gene, which is often overexpressed, particularly in mantle-cell malignancies. The detectable but weak PRAD1 expression in the case we present suggests that this breakpoint centromeric to the MTC still lies inside the BCL1 locus boundaries. We think that attention should be focused on this region centromeric to the BCL1-MTC, where the investigation of previously unidentified translocations may increase understanding of the PRAD1 gene deregulation in t(11;14) associated pathologies.

An extended YAC contig has been developed for the 3p14 region containing the hereditary renal carcinoma 3;8 translocation breakpoint and the 3p14.2 fragile site FRA3B. This region of chromosome 3 has been implicated by chromosomal translocation, deletion, and loss of heterozygosity in the pathogenesis of several malignant diseases. The contig allows accurate positioning of candidate genes, polymorphic markers, and other 3p rearrangements within this region. The contig, spanning approximately 6 Mb of DNA, contains 51 YACs identified by 27 markers, including a subset of CA repeats located in the 3p14.1-14.2 interval. The order of CA microsatellites, derived from marker content of the YACs, is in agreement with the order previously determined by genetic linkage studies. We find that the protein-tyrosine phosphatase gamma gene, PTPRG, is located minimally 1 Mb proximal to the t(3;8) breakpoint. The more proximal 3p homozygous deletion in the small-cell lung cancer cell line, U2020, is more than 5 Mb from the site of the 3;8 translocation. This integrated physical and genetic map provides a framework for further investigations of malignant diseases associated with proximal 3p loss. In addition, the positioning of separate 3p14.2 aphidicolin-induced breakpoints suggests that FRA3B may represent a region rather than a single site.

Chronic Myeloid Leukaemia (CML) is a hematopoietic disorder characterised by an increased proliferation of predominantly the myeloid lineage in the bone marrow and consequently the accumulation of these cells in the blood. It is caused by a translocation between the q arms of chromosome 9 and 22 resulting in the fusion of the proximal portion of BCR (on chromosome 22) to the distal portion of ABL1 gene (chromosome 9). In most cases of CML, the translocation breakpoint occurs either downstream of BCR exon 13 or 14 and upstream of ABL1 exon 2 (major breakpoint). In a small proportion of CML patients, the breakpoint occurs downstream of BCR exon 1 (minor breakpoint). Patients with either the major or minor breakpoint are monitored in our laboratory using quantitative RT-PCR (Q-RTPCR) from peripheral blood derived RNA in order to assess response to tyrosine kinase inhibitor (TKI) therapy. Here we describe two cases of CML from Saskatchewan with rare, atypical breakpoints. In each case, peripheral blood derived RNA obtained at diagnosis was subjected to Q-RTPCR. Results revealed an estimated molecular burden far inferior to what would be expected of such a specimen. This discordance was investigated using conventional RTPCR using exon specific forward primers targeting BCR exons 1 through 12. For patient #1, the results revealed that the fusion point on BCR occurred downstream of BCR exon 8 and upstream of BCR exon 9 (i.e. in intron 8). Investigational sequencing studies on the PCR products seen in the RTPCR reaction revealed the presence of an atypical breakpoint involving BCR exon 8, SNRPD3 exon 3, and ABL1 exon 3 (b8s3a2 fusion variant). The second case was also subjected to exon-specific forward PCR which revealed the fusion point on BCR occurred downstream of BCR exon 6 and upstream of BCR exon 7. Sequencing analysis revealed that the patient had an in-frame b6a2 fusion variant. In addition, we describe a third Saskatchewan case in which the patient had developed resistance to treatment with imatinib. Sequential kinase domain sequencing studies revealed, in turn, that the patient evolved an imatinib resistant clone harbouring ABL1:p. Met244Val, followed by a clone in which ABL1 exon 04 encompassing codon 244 was deleted, followed by loss of the latter clone and re-emergence of ABL1:p. Met244Val.

Background Females with unbalanced X-autosomal translocations frequently exhibit skewed X-chromosome inactivation, as cells with the least functional imbalance have selective advantage. However, predicting the inactivation status of the translocated autosomal segment and its impact on phenotype is challenging. Active vs inactive state can depend on translocation breakpoint and sequence features of the translocated segment. Objective Report a case with 46,X,der (X)t (X;16)(p11.2;p13.2) karyotype and discuss karyotype/phenotype correlations. Results We report a 18 month old girl with intrauterine growth restriction, failure to thrive, cardiac anomalies and dysmorphic features. Oligonucleotide microarray has revealed a terminal ~9 Mb gain of chromosome 16p and terminal loss of most of Xp. A de novo unbalanced translocation t (X;16)(p11.2;p13.2) was confirmed by karyotype analysis and family studies. Androgen receptor assay further showed complete skewing of X-inactivation, suggesting that derivative X-chromosome was inactive. Phenotype of our patient was not fully consistent with either Xp deletion or 16p13.3 duplication, leaving a question about inactivation status of the translocated 16p material. A case with 46, X,der (X) t (X;16)(q28;p12) karyotype and phenotype consistent with 16p13.3 duplication syndrome was previously reported. Replication studies have shown skewed inactivation of the der (X), not spreading into 16p translocated segment. 1 Conclusions Our patient phenotype suggests that while Androgen Receptor assay provides valuable information in regard of X-inactivation skewing, it has limitations for karyotype/phenotype correlations for patients with unbalanced X-autosomal translocation. Additional analysis of inactivation status of the genes of the translocated segment is underway to understand the phenotype of our patient. Reference Preis W, Barbi G, Liptay S, Kennerknecht I, Schwemmle S, Pohlandt F. X/autosome translocation in three generations ascertained through an infant with trisomy 16p due to failure of spreading of X-inactivation. Am J Med Genet . 1996; 61 (2):117–21

The consistent involvement of the region 12q13-q15 in numerous human tumors speaks in favor of the presence of genes that may contribute to oncogenesis. Mapping genes within this region of chromosome 12 is a necessary step toward the identification of those that play a role in this process. We have undertaken a multiplex analysis using translocation breakpoint mapping to order from the centromere to the telomere a series of 24 loci from the region 12q12-q22. Thirteen adipose tissue tumors with seven different chromosome changes involving the long arm of chromosome 12 (12q) were used. Since most of these loci are genes or anonymous DNA segments largely available to the scientific community, this map should be useful for investigation of genetic disorders associated with chromosome 12q. While these breakpoints were used as natural landmarks to order groups of loci, this work has positioned them more accurately, leading to a better chromosomal definition of the translocations than the one derived from standard cytogenetic studies.

SummaryThe known limits of the distal imprinting region of mouse Chromosome (Chr) 2 are defined by the breakpoints of the translocations T(2;8)2Wa, (T2Wa), and T(2;16)28H, (T28H), in distal H3, and proximal H4 respectively. We have shown that T2Wa and T(2;4)1Go, (T1Go), which has a breakpoint in central H3 map close toa, non-agouti.Ada, adenosine deaminase, lies very near the proximal boundary andRa, ragged, maps very close to the distal boundary, and is less than 0-2 cM from wasted,wst. From the current dataAdacan be taken as the proximal, andRaas the distal gene marker of the imprinting region on the linkage map. From consensus maps twenty three other markers, including fourteen genes, lie betweenAdaandRa, some of which may be useful in investigations of imprinting. Of the markers included in the study reported here, four,Ada,ls, lethal spotting,Raandwstlie or probably lie within the region but none display any evidence of imprinting. We suggest that recombination frequency is elevated in distal Chr 2, because in none of the crosses could the most closely linked marker be ordered in relation to the translocation breakpoint due to the high frequency of double crossovers.

A 3-month-old infant girl had manifestations of the Smith-Lemli-Opitz syndrome (SLOS) including typical positional anomalies of the limbs, apparent Hirschsprung disease, cataracts, ptosis, anteverted nares, cleft of the posterior palate, small tongue, broad maxillary alveolar ridges, and abnormally low serum cholesterol levels. Chromosomal analysis showed a de novo balanced translocation interpreted as 46,XX,t(7;20)(q32.1;q13.2). We hypothesize that the translocation breakpoint in this case interrupts one SLOS allele and that the other allele at the same locus has a more subtle mutation that was inherited from the other parent. This case, as well as cytogenetic observations in other SLOS cases, suggests that SLOS could be due to autosomal recessive mutation at a gene in 7q32.

The ZNF21, ZNF41, and ZNF81 genes encode Krüppel-type zinc-finger proteins (ZFPs) and have previously been mapped to chromosome Xp. Published data describing the clustering of ZFP genes on human autosomes led us to investigate the organization of ZNF21, ZNF41, and ZNF81 on the X chromosome. Rodent-human hybrid analysis sublocalized all three genes to Xp22.11-p11.23. ZNF21, ZNF41, and ZNF81 were then shown to segregate within a series of YACs (95 to 730 kb) containing known markers at Xp11.23, such that these YACs could be assembled into a contig spanning approximately 1.5 Mb of DNA. Southern analysis of intact YACs and YAC DNAs cut with rare-cutter restriction enzymes enabled us to establish the spatial organization of the ZFP gene cluster, the OATL1 pseudogene, the recurrent t(X;18) chromosome translocation breakpoint in synovial sarcoma, and the previously described cluster of ARAF1, SYN1, TIMP, and PFC genes. We have assigned the ETS-related gene ELK1 to a locus tightly linked to the PFC gene; the entire cluster of five genes is contained within a distance of 120 kb. ZNF41 maps to a 440-kb YAC spanning this region, while a more proximal cluster comprising the ZNF21 and ZNF81 genes lies 150 kb distal to the chromosome breakpoint associated with synovial sarcoma.

High frequency loss of alleles and cytogenetic aberrations on the short arm of chromosome 3 have been documented in renal cell carcinoma (RCC). Potentially, three distinct regions on 3p could encode tumor suppressor genes involved in the genesis of this cancer. We report that the introduction of a centric fragment of 3p, encompassing 3p14-q11, into a highly malignant RCC cell line resulted in a dramatic suppression of tumor growth in athymic nude mice. Another defined deletion hybrid contained the region 3p12-q24 of the introduced human chromosome and failed to suppress tumorigenicity. These data functionally define a tumor suppressor locus, nonpapillary renal carcinoma-1 (NRC-1), within 3p14-p12, the most proximal region of high frequency allele loss in sporadic RCC as well as the region containing the translocation breakpoint in familial RCC. Furthermore, we provide functional evidence that NRC-1 controls the growth of RCC cells by inducing rapid cell death in vivo.