Reciprocal translocation between the proximal regions of the long arms of chromosomes 13 and 15 resulting in unbalanced offspring: characterization by fluorescence in situ hybridization and DNA analysis

Summary We describe two female siblings with similar clinical features consisting of hydrocephalus, scaphocephaly, hypotonia, mongoloid eye slant, blepharophimosis, micrognathia, supernumerary mouth frenula and mental retardation. Routine cytogenetic studies in the elder patient did not reveal any abnormality, and initially it was assumed that the syndrome had an autosomal recessive inheritance. However, a slightly larger chromosome 13 was seen in routine G-banded metaphases of the mother and the youngest of the two siblings. A shorter chromosome 15 was detected in the mother only. High resolution banding showed that the abnormal chromosome 13 contained an extra G-positive band at 13q12. The short chromosome 15 in the mother appeared to have a deletion of band q12. Fluorescence in situ hybridization using DNA markers specific to chromosomes 13 and 15 unequivocally showed that the mother was a carrier of a balanced reciprocal translocation t(13;15)(q12;q13), whereas the youngest sibling's karyotype was 46,XX,-13,+der(15)t(13;15)(q12;q13)mat, resulting in partial monosomy 13pterq12 and partial trisomy 15pterq13. The proband is thus trisomie for the critical region responsible for Prader-Willi syndrome and Angelman syndrome; this was confirmed by DNA analysis demonstrating one paternal and two maternal alleles from multiallelic marker loci mapping to 15q11-q13. This report illustrates the sensitivity and specificity offered by fluorescence in situ hybridization and its usefulness in the diagnosis and delineation of subtle chromosomal rearrangements.     

The structural gene for human coagulation factor X is located on chromosome 13q34

The gene coding for coagulation factor X was studied in a family segregating chromosomal abnormalities involving chromosomes 13 and 6. An individual monosomic for 13q34 was deficient in levels of clotting factors VII and X, while her brother, who is trisomic for 13q34, had elevated levels. DNA dosage studies with a cloned human factor X gene demonstrated that the low levels of factor X expression in the individual with the chromosome 13q34 deletion were due to the absence of one copy of the factor X structural gene. This confirms the assignment of the human gene coding for factor X to 13q34.     

Partial trisomy 13 due to maternal translocation t(2;13)]

The authors report an observation of partial trisomy 13p13 leads to qter and suggest a clinical map of chromosome 13. Increase of fetal hemoglobin seems to be controlled by region 1 of 13q. Bands q13 q14 and q21 seem to be responsible for inner organ malformations. Lastly, the distal segment q22 leads to qter is responsible for trigonocephaly and limb abnormalities.     

Exclusion of human chromosome 13q34 as the site of the cystic fibrosis mutation.

We have studied a family in which both cystic fibrosis (CF) and an unbalanced translocation between chromosomes 6 and 13 are found. As CF occurs in the child who is effectively monosomic for the translocated part of the long arm of chromosome 13, it was suggested that the locus of the gene mutation causing CF is on chromosome 13q34. The gene for human coagulation factor X is located at 13q34, and we have found a restriction fragment length polymorphism (RFLP) that is revealed by a cloned cDNA coding for this protein. Linkage analysis in eight CF families shows no evidence of cosegregation between CF and the gene for factor X, strongly suggesting that the locus for the defect causing cystic fibrosis is not at 13q34.     

Two cases of terminal deletion of chromosome 13: clinical features, conventional and molecular cytogenetic analysis

We report the cases of two unrelated patients with psychomotor retardation and craniofacial abnormalities, in whom cytogenetic studies have revealed a terminal deletion of chromosome 13 confirmed by fluorescence in situ hybridization (FISH). This del(13)(q33.2) is the smallest terminal deletion of the 13q reported so far. Interestingly enough, the serum level of coagulation factors VII and X, whose genes are located in 13q34, were reduced in both patients. These cases illustrate the difficulties in identifying precisely chromosome deletions and demonstrate that FISH techniques allow to obtain a more precise correlation between clinical phenotype and cytogenetic abnormalities.     

Deletion of 13q in two patients with retinoblastoma,one probably due to 13q- mosaicism in the mother

Summary We examined the peripheral blood chromosomes of eight patients with retinoblastoma. In two of them an interstitial deletion of 13q was found. The breakpoints were determined as follows: case 1, 13q1221; case 2, 13q1231. In both cases, band 13q14 was deleted. In case 2 the lymphocytes of the mother showed the identical interstitial 13q deletion in 3 of 100 mitoses, thus raising the possibility of maternal origin of the 13q deletion in a child. In one patient, retinoblastoma was unilateral; in the other, bilateral. Both patients were mentally retarded.     

Partial 4q duplication due to Inherited der(13),t(4;13)(q26;q34)mat in a girl with a deficiency of Factor X

A girl with mental retardation had a partial trisomy 4q. The chromosome aberration originated from a maternal balanced translocation t(4;13)(q26;q34). The value for Factor X was half the normal value, raising the question of the location of a gene related to the production of Factor X on chromosome 4.     

Characterization of microsatellites from flow-sorted porcine Chromosome 13

Porcine flow-sorted Chromosome (Chr) 13 was PCR amplified with primers based on porcine short interspersed element (SINE) sequences. The product was cloned, gridded in microtiter plates, and screened with a [GT]₁₀ oligonucleotide which gave 45 positive clones. Sequencing of these clones showed that 36 were unique, and 26 [GT]_n microsatellites were characterized. Six other simple repeat sequences, the majority of which were associated with the 3 end of the SINE sequence, were also detected. Twenty-one primers sets were selected, and 13 of these detected useful polymorphisms in the grandparents (n=26) of the European porcine mapping collaboration (PiGMaP) reference families. These 13 markers were mapped in the PiGMaP reference families, and a two-point linkage analysis was performed. The Lod scores indicated that three of the markers were not linked and the remaining 11 formed two linkage groups of two and nine markers respectively. The larger linkage group was also linked to the transferrin locus, permitting assignment of nine markers to porcine Chr 13.The nucleotide sequence data reported in this paper will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession numbers: X79915, 13N14F; X79916, 13N17R; X79917, 13N18R; X79918, 13N32R; X79919, 13R33R; X79920, 13R33U; X79921, 13R43U; X79922, 13R44R; X79923, 13N03R; X79924, 13N04R; X79925, 13N05R; X79926, 13N06R; X79927, 13N12U     

Congenital heart defect and mental retardation in a patient with a 13q33.1-34 deletion

13q deletion syndrome is a rare genetic disorder caused by deletions of the long arm of chromosome 13. Patients with 13q deletion display a variety of phenotypic features. We describe a one-year-old female patient with congenital heart defects (CHD), facial anomalies, development and mental retardation. We identified a 12.75Mb deletion in chromosome region 13q33.1-34 with high resolution SNP Array (Human660W-Quad, Illumina, USA). This chromosome region contains about 55 genes, including EFNB2, ERCC5, VGCNL1, F7, and F10. Comparing our findings with previously reported 13q deletion patients with congenital heart defects, we propose that the 13q33.1-34 deletion region might contain key gene(s) associated with cardiac development. Our study also identified a subclinical deficiency of Factors VII and X in our patient with Group 3 of 13q deletion syndrome.     

Translocation (X;13)(p11.21;q12.3) in a girl with incontinentia pigmenti and bilateral retinoblastoma

A de novo t(X;13)(p11.21;q12.3) translocation is described in an 19-month-old girl with incontinentia pigmenti (IP) and bilateral retinoblastoma. Based on previously reported two girls and this patient, each with a structural X chromosome abnormality and IP, it was assumed that the locus for IP is at Xp11.21. Q-banding analysis revealed that the translocated chromosomes were of paternal origin. The derivative X chromosome was late-replicating in 9% of cultured peripheral blood lymphocytes and in 1% of skin fibroblasts. The erythrocyte esterase D activity in the patient was normal. Several possibilities were considered for possible causative relationship between the X/13 translocation and the development of retinoblastoma. One possibility involved functional monosomy of 13q14 in a minority of retinoblasts due to the spreading of inactivation of the translocated X chromosome segment.     

An 800-kb region of deletion at 13q14 in human prostate and other carcinomas

Deletions of regions at 13q14 have been detected by various genetic approaches in human cancers including prostate cancer. Several studies have defined one region of loss of heterozygosity (LOH) at 13q14 that seems to reside in a DNA segment of 7.1 cM between genetic markers D13S263 and D13S153. To define the smallest region of overlap (SRO) for deletion at 13q14, we first applied tissue microdissection and multiplex PCR to detect homozygous deletion and/or hemizygous deletion at 13q14 in 134 prostate cancer specimens from 114 patients. We detected deletions at markers D13S1227, D13S1272, and A005O48 in 13 (10%) of these tumor specimens. Of the 13 tumors with deletions, 12 were either poorly differentiated primary tumors or metastases of prostate cancer. To fine-map the deletion region, we then constructed a high-resolution YAC/BAC/STS/EST physical map based on experimental and database analyses. Several markers encompassing the deletion region were analyzed for homozygous deletion and/or hemizygous deletion in 61 cell lines/xenografts derived from human cancers of the prostate, breast, ovary, endometrium, cervix, and bladder, and a region of deletion was defined by duplex PCR assay between markers A005X38 and WI-7773. We also analyzed LOH at 13q14 in the 61 cell lines/xenografts using the homozygosity mapping of deletion approach and 26 microsatellite markers. We found 24 (39%) of the cell lines/xenografts to show LOH at 13q14 and defined a region of LOH by markers M1 and M5. Combination of homozygous or hemizygous deletion and LOH results defined the SRO for deletion to be an 800-kb DNA interval between A005X38 and M5. There are six known genes located in or close to the SRO for deletion. This region of deletion is at least 2 Mb centromeric to the RB1 tumor-suppressor gene and the leukemia-associated genes 1 and 2, each of which is located at 13q14. These data suggest that the 800-kb DNA segment with deletion contains a gene whose deletion may be important for the development of prostate and other cancers. This study also provides a framework for the fine-mapping, cloning, and identification of a novel tumor-suppressor gene at 13q14.     

Regional localization of alpha-galactosidase (GLA) to Xpter----q22, hexosaminidase B (HEXB) to 5q13----qter, and arylsulfatase B (ARSB) to 5pter----q13

Two series of somatic cell hybrids were made by fusion of human cells with karyotypes 46,X,t(X;2;15)(q22;p12;p12) and 46,XX,t(5;7)(q13;p15) and rodent cells. Chromosome and isozyme analysis of human chromosomes and gene products in the hybrids localized GLA to Xpter----q22, HEXB to 5q13----qter, in both cases narrowing the regional assignments, and ARSB to 5pter----q13.     

The phenotype in partial 13q trisomies,apropos of a familial (13;15)(q22;q26) translocation

Summary A 12 month-old male patient with a karyotype 46, XY,-15,+der(15),t(13;15)(q22;q26)pat is presented. His stillborn sib showed malformations compatible with the 13q deletion syndrome, probably due to a 46,XY, der(13) karyotype. Phenotypic analysis of 41 cases from the literature with partial distal 13q (D13q) trisomies indicate that the segment 13q22 qter in trisomy with or without another concomitant aneusomy is sufficient to produce the majority of the trisomy 13 syndrome features, some of which (cleft palate, increased HbF and projections in PMN) are present in different non-overlapping partial 13q trisomies. About 82% of the D13q trisomies are inherited, more frequently from the mother.     

Deficiency of coagulation factors VII and X associated with deletion of a chromosome 13 (q34). Evidence from two cases with 46,XY,t(13;Y)(q11;q34)

Summary Deficiency of coagulation factors VII and X was found in two patients (Erlangen and Nancy) who shared the same chromosomal aberration 46,XY,t(13;Y)(q11;q34) with probable loss of a terminal segment of 13q. Loci involved in synthesis or constitution of these factors may be located at 13 (q34).The paper is dedicated to Prof. Dr. G. Koch on the occasion of his 70th birthday     

High proportion of 22q13 deletions and SHANK3 mutations in Chinese patients with intellectual disability

Intellectual disability (ID) is a heterogeneous disorder caused by chromosomal abnormalities, monogenic factors and environmental factors. 22q13 deletion syndrome is a genetic disorder characterized by severe ID. Although the frequency of 22q13 deletions in ID is unclear, it is believed to be largely underestimated. To address this issue, we used Affymetrix Human SNP 6.0 array to detect the 22q13 deletions in 234 Chinese unexplained ID patients and 103 controls. After the Quality Control (QC) test of raw data, 22q13 deletions were found in four out of 230 cases (1.7%), while absent in parents of the cases and 101 controls. A review of genome-wide microarray studies in ID was performed and the frequency of 22q13 deletions from the literatures was 0.24%, much lower than our report. The overlapping region shared by all 4 cases encompasses the gene SHANK3. A heterozygous de novo nonsense mutation Y1015X of SHANK3 was identified in one ID patient. Cortical neurons were prepared from embryonic mice and were transfected with a control plasmid, shank3 wild-type (WT) or mutant plasmids. Overexpression of the Y1015 mutant in neurons significantly affected neurite outgrowth compared with shank3 WT. These findings suggest that 22q13 deletions may be a more frequent cause for Chinese ID patients than previously thought, and the SHANK3 gene is involved in the neurite development.     

Regional assignment of arylsulfatase A,mitochondrial aconitase and NADH-cytochrome b5 reductase by somatic cell hybridization

Summary By using somatic cell hybrids between HPRT deficient hamster cells and fibroblasts derived from a patient with a X/22 translocation t(X;22)(q13;q112), we have assigned the genes for human ARSA, DIA 1, and ACO 2 to region q112qter of human chromosome 22 and the gene for human PGK close to the breakpoint in band Xq13.     

Chromosome 13 restriction fragment length polymorphisms

Summary The gene locus for hereditary retinoblastoma is on human chromosome 13, band q14. With this gene localization in mind, we cloned DNA fragments from this chromosome. Three of the fragments identify restriction fragment length polymorphisms. These three fragments are from the region 13q12–13q22, the chromosome region which contains the retinoblastoma locus. We expect that these restriction fragment length polymorphisms will be linked to the retinoblastoma locus, and that they will serve in certain retinoblastoma families as predictors of retinoblastoma gene carriers.They will also be useful in studies of other gene loci thought to be on chromosome 13.This research was supported by grants from the National Institutes of Health HD04807, CA29883, and EY04543, by a grant from Fight for Sight, Inc., New York City, and by the Anna Fuller Fund     

The gene for clotting factor 10 is mapped to 13q32----qter

The structural gene for the human clotting factor 10 (F10) has been mapped to chromosome 13 with a cDNA probe hybridized to DNAs from a panel of human X hamster hybrids. In situ hybridization was used to assign F10 to region 13q32----qter of chromosomes from normal human lymphocytes.     

Location of the X inactivation center in primates and other mammals

Summary In humans, the X chromosome inactivation center and an X inactivation-associated metaphase fold are at the same location (bands Xq1321) or are very closely associated. In other mammals, the location of the X inactivation center is unknown, but it has been suggested that the relationship between the inactivation center and the inactivation-associated fold may make it a useful marker for both identifying the inactivated X and locating the inactivation center in other mammalian species. If a similar metaphase fold is present in other mammals, the inactivation center would be located at the same site or very nearby. All of nine primate species did express an inactivation-associated fold. In most, the fold was located at the band homologous to human Xq13q21. In one of two chimpanzees, band Xq23q24 was implicated. In five other mammals an inactivation-associated fold was observed, but in two species, no fold was observed.     

Structural genes of coagulation factors VII and X located on 13q34

From 7 cases of abnormalities involving chromosome 13, the structural gene(s) coding for coagulation factors VII and X were located in the region 13q34-13qter. Gene-dosage effects for these coagulation factors seem to act in both directions, causing a decrease when there is monosomy of segment 13q34, but also, as has not been demonstrated before, an increase when there is trisomy of this same segment.