FISH with locus-specific probes on stretched chromosomes: a useful tool for genome organization studies.
Explore the source record for details and available documents.
Chromosomes↗
Biomedical subjects
L Larizza
Publications and source records attributed to L Larizza.
Cryptic subtelomeric translocation t(2;16)(q37;q24) segregating in a family with unexplained stillbirths and a dysmorphic, slightly retarded child.
We here describe a submicroscopic translocation affecting the subtelomeric regions of chromosomes 2q and 16q, and segregating in a family with stillbirths, early pregnancy losses, and two dysmorphic and slightly retarded babies. FISH analysis showed a 46,XY,der(2)t(2;16)(q37.3;q24.3) in the propositus, and a balanced t(2;16) in his mother, her conceptus and maternal grandfather. FISH with YACs and BACs made it possible to map the 2q37 breakpoint precisely between the regions covered by y952E1 and y746H1, and the 16q breakpoint between the regions encompassed by bA 309g16 and bA 533d19. The contribution of 2q37.3 monosomy and 16q24.3 trisomy to the proband's phenotype is compared with that in reported patients with similar imbalances of either chromosome.
Chromosomes, Human, Pair 16↗
Patient with large 17p11.2 deletion presenting with Smith-Magenis syndrome and Joubert syndrome phenotype.
We report on a 22-year-old woman carrying a del(17)(p11.2p12) and presenting with the clinical manifestations of both Smith-Magenis syndrome (SMS) and Joubert syndrome (JS). Her facial anomalies, brachydactyly, severe mental retardation, and self-injuring behavior could be attributed to SMS, whereas the cerebellar vermis hypoplasia, hypotonia, ataxic gait, developmental delay, and abnormal respiratory pattern were suggestive of JS. By fluorescent in situ hybridization analyses with Yeast Artificial Chromosomes (YAC) mapping to the 17p11.2 region, as well as locus-specific probes generated through a novel procedure, we could establish that the deletion encompasses a 4-Mb interval with centromeric and telomeric breakpoints at loci D17S793 and D17S953, the latter close to the locus Charcot Marie Tooth 1A (CMT1A)-REP. The deletion differs from that commonly found in SMS in its telomeric boundary, which is more distal than usually observed. The presence of JS phenotype in our patient and the detection of an unusual SMS deletion might suggest the presence of a JS gene in close proximity to the SMS locus.
Abnormalities, Multiple↗
Mapping to distal Xq28 of nonspecific X-linked mental retardation MRX72: linkage analysis and clinical findings in a three-generation Sardinian family.
Families with mentally retarded males found to be negative for FRAXA and FRAXE mutations are useful in understanding the genetic basis of X-linked mental retardation. According to the most recent data (updated to 1999), 69 MRX loci have been mapped and 6 genes cloned. Here we report on a linkage study performed on 20 subjects from a 4-generation Sardinian family segregating a non-specific X-linked recessive mental retardation (XLMR)(MRX72) associated with global delay of all psychomotor development. Five of 8 affected males have been tested for mental age, verbal and performance skills and behavioral anomalies; mental impairment ranged from mild to severe. Only minor anomalies were present in the affected subjects. Two-point linkage analysis based on 28 informative microsatellites spanning the whole X chromosome demonstrated linkage between the disorder and markers DXS1073 and F8c in Xq28 (maximum Lod score of 2. 71 at straight theta = 0.00). Multipoint linkage analysis confirmed the linkage with a Z(max) of 3.0 at straight theta = 0.00 at DXS1073 and F8c. Recombination in an affected male at DXS1073 and F8c allowed us to delimit centromerically and telomerically the region containing the putative candidate gene. The region, where MRX72 maps, overlaps that of another MRX families previously mapped to Xq28, two of which harbored mutations in GDI. Involvement of this gene was excluded in our family, suggesting another MRX might reside in Xq28.
Adolescent↗
RNA hyperediting and alternative splicing of hematopoietic cell phosphatase (PTPN6) gene in acute myeloid leukemia.
The SH2 domain-containing tyrosine phosphatase PTPN6 (SHP-1, PTP1C, HCP) is a 68 kDa cytoplasmic protein primarily expressed in hematopoietic cell development, proliferation and receptor-mediated mitogenic signaling pathways. By means of direct dephosphorylation, it down-regulates a broad spectrum of growth-promoting receptors, including the Kit tyrosine kinase, activated to elicit a prominent cascade of intracellular events by stem cell factor binding. The pivotal contribution of PTPN6 in modulating myeloid cell signaling has been revealed by the finding that shp-1 mutation is responsible for the overexpansion and inappropriate activation of myelomonocytic populations in motheaten (me/me) and motheaten viable (me(v)/me(v)) mice. Association of PTPN6 with c-Kit and negative modulation of the myeloid leukocyte signal transduction pathways prompted us to examine the expression of the protein tyrosine phosphatase PTPN6 gene in CD34(+)/CD117(+) blasts from acute myeloid leukemia patients. We identified and cloned cDNAs representing novel PTPN6 mRNA species, derived from aberrant splicing within the N-SH2 domain leading to retention of intron 3. Sequence analysis of cDNA clones revealed multiple A-->G editing conversions. The editing of PTPN6 mRNA mainly occurred as an A-->G conversion of A(7866), which represents the putative branch site in IVS3 of PTPN6 mRNA. Evidence that editing of A(7866) abrogates splicing has been obtained in vitro by using an edited clone and its backward clone generated by site-directed mutagenesis. The level of the aberrant intron-retaining splice variant, evaluated by semi-quantitative RT-PCR, was lower in CD117(+)-AML bone marrow mononuclear cells at remission than at diagnosis, suggesting the involvement of post-transcriptional PTPN6 processing in leukemogenesis.
Acute Disease↗
A tumor suppressor locus in familial and sporadic chordoma maps to 1p36.
Previous cytogenetic/FISH data have demonstrated 1p36 deletions in a relapsing familial clivus chordoma developed by a patient who has 2 daughters, respectively affected with childhood astrocytoma and clivus chordoma. Using an approach that combined the LOH (loss of heterozygosity) study of the father chordoma and the daughter astrocytoma and a segregation analysis from parents to sibs using 17 CA-repeats spanning 1p36.32-1p36.11, we mapped the cancer susceptibility locus in this family to the 1p36 region. The LOH and haplotype information was elaborated using a pairwise linkage analysis that gave a maximum lod score of 1.2. Additional LOH data relating to 6 sporadic chordomas allowed us to define an SRO (the smallest region of overlapping loss) of about 25 cM from D1S2845 (1p36.31) to D1S2728 (1p36.13). Our overall findings converge on mapping to 1p36 a tumor-suppressor gene involved in familial and sporadic chordoma.
Adult↗
Non-random trisomies of chromosomes 5, 8 and 12 in the prolactinoma sub-type of pituitary adenomas: conventional cytogenetics and interphase FISH study.
Specimens from 53 pituitary adenomas (PAs), including 17 NFPA, 16 PRL-, 9 ACTH-, 9 GH- and 2 TSH-secreting tumors, underwent cytogenetic analysis by the direct and short-term culture methods. Only 8 tumors (15%) appeared to have an abnormal karyotype. To increase the resolution of cytogenetic analysis, direct preparations from 31 PAs were investigated by interphase FISH with probes specific for chromosomes 5, 8, 12 and X, for which gain in pituitary tumors has been reported. Of these 31 PAs, 17 (54.8%) had an abnormal dosage of one or more of the 4 chromosomes tested. Separate or combined trisomies of chromosomes 5, 8 and 12 were found in 10/10 prolactinomas and in 4/9 NFPA, whereas the combined loss of chromosomes 5 and 8 was observed in 1/6 ACTH- and 1/6 GH-secreting PAs. Present and earlier data on 23 PAs showed that tumors with the highest frequency of abnormal karyotypes revealed by cytogenetics and/or interphase FISH were PRL (78%), followed by NFPA (26%) and GH (18%). Recurrent structural rearrangements affecting chromosomes 1, 3 and 12 were also identified in prolactinomas, which therefore appear to be the only pituitary adenoma sub-type with a defined trend of tumor-specific chromosomal changes. Cytogenetic and FISH analyses of different pituitary tumor sub-types indicate that they may harbour genetically distinct lesions.
Adult↗
C-kit mutations in core binding factor leukemias.
Explore the source record for details and available documents.
Adolescent↗
Novel mutations of ubiquitin protein ligase 3A gene in Italian patients with Angelman syndrome.
Angelman syndrome is a neurobehavioral disorder caused by defects of imprinted gene(s) on chromosome 15q11-13. AS-specific DNA methylation is found in patients carrying 3-4 Mb deletions ( approximately 70%), paternal uniparental disomy (3-5%) or imprinting center mutations (2-9%), while normal methylation pattern with biparental inheritance characterizes the remaining approximately 20-25% AS patients (Stalker et al.,1998; Tsai et al.,1998). Mutations in the Ubiquitin protein ligase 3A gene (UBE3A) have been found in the latter group, but only preliminary figures are available on their frequencies. We selected a sample of 25 AS patients with a clinical diagnosis of AS and a normal methylation pattern in order to search for mutations of the UBE3A gene. Automated sequencing of exons 8, 9, 10, 11 and 12 performed on our 25 patients allowed us to identify three novel mutations: an 897insA in two unrelated familial cases, a 2544insA and an E167X in two sporadic cases. Mutation R482X previously reported in a sporadic patient was identified in a third familial case. Hum Mutat 15:387, 2000.
Adolescent↗
Trisomy 4 leading to duplication of a mutated KIT allele in acute myeloid leukemia with mast cell involvement.
A G-->T transversion at nucleotide 2467 of the c-KIT gene leading to Asp816-->Tyr (D816Y) substitution in the phosphotransferase domain has been previously identified in a patient with rapidly progressing AML-M2 and mast cell involvement; the patient's blasts had a 47,XY, +4,t(8;21)(q22;q22) karyotype. Herein we confirm the simultaneous presence of both major chromosomal changes by multicolor fluorescence in situ hybridization (FISH) on interphase CD34+ mononuclear cells. By setting up culture leukemic blasts, spontaneous differentiation of adherent cells with mast-cell like features was proved by histochemical and immunoenzymatic analyses. Fluorescence in situ hybridization evidence of trisomy 4 confirmed the origin of differentiated cells from the leukemic blasts. Semiquantitative polymerase chain reaction (PCR) and phosphoimage densitometry of wild-type and mutated KIT alleles on bone marrow blasts made it possible to demonstrate that chromosome 4 trisomy led to a double dosage of the mutated KIT allele. This finding, and that of trisomy 7 and MET mutation in hereditary renal carcinoma represent the only cases of human tumors in which an increased number of chromosomes carrying an oncogene activated by point mutation have been detected.
Acute Disease↗
19p deletion in recurring leiomyosarcoma lesions from the same patient.
Ten leiomyosarcomas (LMS) affecting the same patient over a period of 3 years were cytogenetically studied to detect nonrandom chromosomal changes with a pathogenetic significance. All tumors, likely metastases of a previous LMS presentation, were classified as small, including eight that developed before chemotherapy; the diagnoses were based on standard immunohistochemistry methods for smooth muscle tumors. Scoring of 613 metaphases revealed monosomy of chromosome 22 in six LMS, monosomy of chromosome 19 in three, and deletion of chromosome 19p in all ten. Interphase fluorescence in situ hybridization (FISH) of the 22-alphoid-specific probe allowed loss of the target chromosome to be detected in four tumors at higher frequencies than those detected by cytogenetics. Double-color FISH of the 19p- and 19q-specific YAC performed on one tumor made it possible to distinguish the monosomic and 19p deleted cells, the relative frequencies of which were found to be 10% and 20%, respectively. The deletion breakpoint could be mapped at 19p13 between YAC 957d12 and YAC 947g4. The recurrence of the 19p deletion in a subset of tumor cells from all of the analyzed LMS suggests that this structural aberration is a significant change in the development of leiomyosarcomas.
Adult↗
NF1 microdeletion syndrome: refined FISH characterization of sporadic and familial deletions with locus-specific probes.
Two familial and seven sporadic patients with neurofibromatosis 1-who showed dysmorphism, learning disabilities/mental retardation, and additional signs and carried deletions of the NF1 gene-were investigated by use of a two-step FISH approach to characterize the deletions. With FISH of YAC clones belonging to a 7-Mb 17q11.2 contig, we estimated the extension of all of the deletions and identified the genomic regions harboring the breakpoints. Mosaicism accounted for the mild phenotype in two patients. In subsequent FISH experiments, performed with locus-specific probes generated from the same YACs by means of a novel procedure, we identified the smallest region of overlapping (SRO), mapped the deletion breakpoints, and identified the genes that map to each deletion interval. From centromere to telomere, the approximately 0.8-Mb SRO includes sequence-tagged site 64381, the SUPT6H gene (encoding a transcription factor involved in chromatin structure), and NF1. Extending telomerically from the SRO, two additional genes-BLMH, encoding a hydrolase involved in bleomycin resistance, and ACCN1, encoding an amiloride-sensitive cation channel expressed in the CNS-were located in the deleted intervals of seven and three patients, respectively. An apparently common centromeric deletion breakpoint was shared by all of the patients, whereas a different telomeric breakpoint defined a deletion interval of 0.8-3 Mb. There was no apparent correlation between the extent of the deletion and the phenotype. This characterization of gross NF1 deletions provides the premise for addressing correctly any genotype-phenotype correlation in the subset of patients with NF1 deletions.
Chromosome Deletion↗
Maternal chromosome 7 hetero/isodisomy in Silver-Russell syndrome and PEG1 biallelic expression.
Silver-Russell syndrome (SRS) is characterized by a severe intrauterine and postnatal growth retardation, relative macrocephaly associated with 'mild' facial anomalies. The diagnostic importance of skeletal asymmetry remains controversial. The aetiology of the syndrome is heterogeneous. Maternal uniparental disomy of chromosome 7 (mUPD7) has been reported in approximately 7% of patients, but two carriers of chromosomal abnormalities involving the band 17q25 have also been described. We investigated a clinically selected sample of 20 SRS patients for the presence of mUPD7 using polymorphic microsatellite markers spanning the whole chromosome. Maternal UPD7 was found in only one patient corresponding to an incidence of 5%. The allelic distribution in this patient was consistent with heterodisomy. Segregation analysis of chromosome 14 and 16 showed a biparental contribution in all the 20 patients. Blood RNA from the mUPD7 patient and a normal donor were evaluated for the expression of Paternally Expressed Gene (PEG1), an imprinted gene on chromosome 7q32. Biallelic expression of the gene in adult blood tissues was found in both samples. Our results confirm the causal role of mUPD7 in a minority of SRS patients.
Abnormalities, Multiple↗
Delineation and physical separation of novel translocation breakpoints on chromosome 1p in two genetically closely associated childhood tumors.
Sporadic childhood tumors associated with Beckwith-Wiedemann syndrome (BWS) all show abnormalities of the same region on chromosome 11. In addition to chromosome 11, other chromosome regions are affected in some of these tumor types. In this study we analyzed the region on chromosome 1p involved in the etiology of BWS-associated tumors, Wilms tumor, rhabdomyosarcoma, and hepatoblastoma. For this purpose we determined the location of two novel translocation breakpoints in this chromosome region in cells from a Wilms tumor and cells from a rhabdomyosarcoma. We constructed a map of the region and found that both breakpoints are separated by at least 875 kb. We identified a PAC clone which crosses the rhabdomyosarcoma breakpoint and found several exons within this clone. We established that this breakpoint is located proximal to the PAX7 gene and, therefore, identified a new region involved in the etiology of rhabdomyosarcomas.
Beckwith-Wiedemann Syndrome↗
Reproductive follow-up of carriers of familial reciprocal balanced translocations involving chromosome 9 and comparison with predicted outcome.
Reproductive follow-up of carriers of familial reciprocal balanced translocations involving chromosome 9 and comparison with predicted outcome: Chromosome 9 is commonly implicated in reciprocal translocations (rcp). Twenty-seven families segregating rcp involving chromosome 9 were selected with the aim of comparing the theoretical risk of Mental Retardation with Congenital Anomalies (MCA/MR) calculated according to Human Cytogenetics Forum with the observed reproductive follow-up. The 27 families include 157 subjects. The reproductive follow-up showed that the majority of mothers underwent full-term pregnancies (88/130), and that there were 37 spontaneous and five voluntary abortions. Eighty-one subjects were karyotyped: 18 had a normal karyotype, 50 carried an rcp, ten had an unbalanced rcp-related karyotype and three an abnormal rcp-unrelated karyotype. Of the 88 live-born individuals, seven had an abnormal rcp-related karyotype with partial chromosome 9 trisomy (four cases) or partial 9p monosomy (three cases), and 48 were rcp carriers, two of whom also presented additional anomalies. The evaluation of reproductive outcomes in the 27 families studied revealed good concordance between the Human Cytogenetics Forum predictions and the observed follow-up in relation to the most probable mode of unbalance at birth, and the higher risk of MCA/MR in rcp carriers with unbalanced live-borns in comparison with those generating healthy progeny
Chromosomes, Human, Pair 9↗
FISH characterization of two supernumerary r(1) associated with distinct clinical phenotypes.
Only a few reports on supernumerary r(1) chromosomes associated with a clinical phenotype have been published. We describe two unrelated patients with congenital malformations and developmental delay who were found to have a de novo supernumerary r(1) in 50% (Case 1) and 80% (Case 2) of the examined cells. Conventional cytogenetic techniques (QFQ, CBG, and DA-DAPI), complemented by fluorescence in situ hybridization studies using alpha satellite probes, showed that both small marker chromosomes (SMCs) primarily consisted of the centromere and heterochromatin of chromosome 1, a conclusion that was also supported by chromosome 1 painting. In an attempt to establish phenotype-genotype correlations, a further investigation was performed using YACs mapped to the chromosome 1 pericentromeric region. A fluorescent signal was evident after hybridization with Y934G9 (1q21) in Case 1 and Y959C4 (1p11.1-12) in Case 2. Partial trisomy of unique sequences flanking pericentromeric sequences is shown to underlie the clinical phenotype in both patients. This evidence should be taken into account when SMCs are ascertained, particularly in prenatal diagnosis.
Abnormalities, Multiple↗
New case of the Richieri-Costa/Guion-Almeida syndrome.
We describe a boy with multiple congenital anomalies/mental retardation (MCA/MR) syndrome. He has growth retardation, microbrachycephaly, coloboma of the iris, and typical facial anomalies including cleft lip/palate. This phenotype overlaps with that described by Richieri-Costa and Guion-Almeida in three Brazilian brothers. The new patient provides further evidence of the existence of this rare clinical entity.
Abnormalities, Multiple↗
First cytogenetic study of a recurrent familial chordoma of the clivus.
Two recurrences of a familial clivus chordoma, arisen from a patient who developed the primary tumor at age of 8 years, were investigated by cytogenetic and the fluorescence in situ hybridization (FISH) approach. Of the patient's 3 daughters, 2 developed, respectively, a clivus chordoma and an astrocytoma in infancy, a familial aggregation highly suggestive of a genetic background. After a 31-year hiatus, 2 tumor recurrences, developed over 17 months, were removed surgically. Both were hypo- or nearly diploid, and had a pronounced karyotypic heterogeneity with clonal and non-clonal rearrangements affecting several chromosomes. The same rearrangement, a dic(1;9)(p36.1;p21), was shared in both tumor specimens and, in 90% of the cells, chromosome 1p appeared to be involved in unbalanced translocations with different chromosomes, leading to variable losses of 1p. Previous cytogenetic data concerning chordoma are limited to 10 sporadic tumors with an abnormal karyotype; although no tumor-specific rearrangements have been identified, chromosome 1p appears to be involved frequently.
Adolescent↗