Dinucleotide repeat polymorphism on chromosome 9q32

Summary A new microsatellite was developed from a cosmid clone (cCI9-246) assigned to human chromosome 9q32.     

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia.Chronic myeloid leukemia (CML) is characterized by the Philadelphia translocation t(9;22)(q34;q11) resulting in the BCR/ABL fusion gene. Submicroscopic deletion of the derivative chromosome 9 occurs in a subset of these patients and is associated with poor prognosis. In the current study, we present two unusual cases of CML selected from a series of 54 consecutive cases. A detailed study using classical cytogenetics and fluorescence in situ hybridization (FISH) analysis was done using dual color extra signal FISH and whole chromosome paint in order to elucidate the mechanism of 9q deletion. One case had two clones on interphase FISH, one with and one without chromosome 9q deletion. The other case had two clones on both cytogenetic and FISH analyses, one with and one without a marker chromosome carrying chromosome 9q sequences. In this latter case, the clone with deletion of the derivative chromosome 9 comprised 21.1% at diagnosis, increasing to 36.8% after 11 months, suggesting a growth advantage. We report here evidence that deletions on 9q in CML may occur through breakage and rearrangement of chromosomes resulting in derivative chromosomes and either a marker chromosome or fragment/episome, followed by loss of chromosome material from the cell.     

Cryptic duplication of 21q in an individual with a clinical diagnosis of Down syndrome

We describe an adult male who was diagnosed with Down syndrome (DS) at 9 months of age, but had repeatedly normal karyotypes until recent mid‐resolution chromosome studies showed a possible duplication of 21q22.13 to 21q22.3. The abnormality was investigated using fluorescent in situ hybridization (FISH) studies. These showed hybridization of a whole chromosome paint probe (wcp21, Oncor Coatasome 21) to the entire length of both chromosome 21 homologues and one very large hybridization signal of a cosmid contig probe localized within bands 21q22.13‐21q22.2(LSI‐21, Vysis) on the ?dup(21q) homologue. CGH analysis identified a ratio of 1.5 for the segment of chromosome 21 involving band 21q22, indicating a gain of part, or all, of the terminal band of chromosome 21. The karyotype was thus defined as 46,XY,?dup(21) (q22.13q22.2).ish dup(21)(LSI‐21++,wcp21+). Common DS characteristics in our case and 12 previously reported cases with duplications involving chromosome 21 included mental retardation, fifth finger clinodactyly, open mouth and oblique eye fissures. Transverse palmar creases and congenital heart defects, seen in DS less than 40% of the time, were infrequent. Presence of these features did not appear to depend on the specific portion of chromosome 21 that was duplicated. A review of 18 additional clinical features showed no consistent phenotype–genotype correlations.     

Molecular cytogenetic characterisation of partial trisomy 9q in a case with pyloric stenosis and a review

Partial trisomy 9q represents a rare and heterogeneous group of chromosomal aberrations characterised by various clinical features including pyloric stenosis. Here, we describe the case of a 1 year old female patient with different dysmorphic features including pyloric stenosis and prenatally detected partial trisomy 9q. This partial trisomy 9q has been analysed in detail to determine the size of the duplication and to characterise the chromosomal breakpoints. According to the data gained by different molecular cytogenetic techniques, such as fluorescence in situ hybridisation (FISH) with whole and partial chromosome painting probes, yeast artificial chromosome (YAC) probes, and comparative genomic hybridisation (CGH), the derivative chromosome 9 can be described as dup(9)(pter→q22.1::q31.1→q22.1::q31.1→ q22.1::q31.1→qter). Four breakpoint spanning YACs have been identified (y806f02, y906g6, y945f5, and y747b3) for the proximal breakpoint. According to this new case and previously published data, the recently postulated putative critical region for pyloric stenosis can be narrowed down to the subbands 9q22.1-q31.1 and is the result of either partial trisomy of gene(s) located in this region or a gene disrupted in 9q31.


Keywords: partial trisomy 9q; pyloric stenosis; FISH; CGH     

Variants of chromosome 9 with additional euchromatic bands: Two case reports

This paper documents a prenatal case of maternally inherited subtle duplication of chromosome 9 bands q21.1 to q21.2 and a second case with two G-bands within the 9qh region. Cytogenetic studies of these cases included G-banding, C-banding, fluorescent in situ hybridization (FISH) using chromosome 9 specific library probe, and the classical satellite probe. In both patients, the additional bands were G-bands and C-band negative. By FISH studies they were negative for the satellite heterochromatin probe and positive for the chromosome 9 painting probe. Therefore, the extra bands were presumably euchromatin and part of chromosome 9. The chromosome 9 variants and their possible mechanisms of origin are discussed. © 1996 Wiley-Liss, Inc.     

INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION DETECTION OF t(2;13)(q35;q14) IN ALVEOLAR RHABDOMYOSARCOMA—A DIAGNOSTIC TOOL IN MINIMALLY INVASIVE BIOPSIES

The identification of t(2;13)(q35;q14) is a useful aid in the accurate diagnosis of rhabdomyosarcoma, distinguishing it from other small round cell tumours and supporting the distinction between alveolar and embryonal forms. Cytogenetic analysis is difficult and with the increased use of minimally invasive biopsy methods and primary chemotherapy, adequate tumour material is not always available. To overcome these difficulties, two-colour interphase fluorescence in situ hybridization (FISH) to detect t(2;13)(q35;q14) was developed and its utility in assessing minimally invasive biopsies was investigated. Two cosmid clones which mapped proximal or distal to the breakpoint region 13q14 and one yeast artificial chromosome clone that mapped distal to the 2q35 breakpoint were identified. In interphase cells containing t(2;13)(q35;q14), the configuration of cosmid and yeast artificial chromosome signals demonstrated the presence of the translocation. Five cases of rhabdomyosarcoma were analysed by interphase FISH. The t(2;13)(q35;q14) was detected in all four alveolar tumours and was confirmed by cytogenetics in two cases, but was absent in one embryonal tumour. This sensitive detection method is applicable to minimal amounts of fresh or frozen tumour.     

Clinical and genomic characterization of siblings with a distal duplication of chromosome 9q (9q34.1-qter)

We report herein on two female siblings exhibiting mild intellectual disability, hypotonia in infancy, postnatal growth retardation, characteristic appearance of the face, fingers, and toes. Their healthy mother had a translocation between 9q34.1 and the 13pter. FISH and array CGH analysis demonstrated that the two children had an additional 8.5 Mb segment of the 9q34.1‐qter at 13pter. The clinical features of the present cases were similar to those of previously reported 9q34 duplication cases; however, the present cases did not exhibit other abnormal behaviors, such as autistic features or attention deficit disorders, those are reportedly associated with 9q34 duplications. A 3.0 Mb region (9q34.1‐q34.3) within 9q34 duplication in our patients are overlapped with duplication region of previously reported cases and is proposed to be critical for the presentation of several phenotypes associated with 9q34 duplications. © 2011 Wiley‐Liss, Inc.     

Combined trisomy 9 and Ullrich-Turner syndrome in a girl with a 46,X,der(9)t(X;9)(q12;q32) karyotype

Total trisomy 9 is a rare disorder with most patients dying before age 4 months. Herein, we report a 9-year-old girl with mental retardation, short stature, a peculiar face and other minor defects, who was diagnosed as having an unbalanced de novo X-autosome translocation with a 46,X,der(9)t(X;9) (q12;q32) karyotype resulting in almost a full trisomy 9(pter→q32) and a partial monosomy X(q12→pter). The clinical findings of our patient, almost exclusively resemble those of trisomy 9p and the Ullrich-Turner syndromes and has few manifestations of 9q trisomy. BrdU replication studies by Giemsa staining showed an earlier replication of 9p in the translocated chromosome, but a marked late-replication pattern for almost the complete 9q arm involved in the translocation. FISH studies confirmed the presence of three 9 centromeres, excluded the presence of the X centromere signal in the rearranged chromosome, and showed that both Xq telomeric sequences were present. BrdU replication studies by FISH showed an usual pattern of striking late-replication around the XIC of the derivative chromosome, but early replication of the chromosome 9p segment and distal Xq. Am. J. Med. Genet. 80:199–203, 1998. © 1998 Wiley-Liss, Inc.     

Subtle overlapping deletions in the terminal region of chromosome 6q24.2-q26: Three cases studied using FISH

Interstitial deletions in the terminal region of chromosome 6 are rare. We describe three new cases with subtle interstitial deletions in the q24-q26 region of the long arm of chromosome 6. The karyotypes were analyzed at a 550 band level. Patient1 is a 9-month-old boy with an interstitial deletion, del(6)(q24.2q25.1), developmental delay, low birth weight, hypotonia, heart murmur, respiratory distress, craniofacial and genital anomalies. This is the first report of a case with deletion del(6)(q24.2q25.1). Patient 2 is a 17-year-old young man with an interstitial deletion del(6)(q25.1q25.3), developmental delay, short stature, mental retardation, autism, head, face, chest, hand and feet anomalies and a history of seizures. For the first time autism was described as a manifestation in 6q deletions. Patient 3 is baby boy with a de novo interstitial deletion, del(6)(q25.1q26), anomalies of the brain, genital organs, limbs and feet. This is the first report of a case with deletion, del(6)(q25.1q26). In all three patients, fluorescence in situ hybridization (FISH) using chromosome 6 painting probe ruled out an insertion. The ESR (6q25.1) and TBP (6q27) probes were used to confirm the breakpoints. Since TBP signal is present in all cases, it confirmed an interstitial deletion proximal to this probe. Patient 1 has a deletion of the ESR locus; Patient 2 and 3 have signals for the ESR locus on both chromosomes 6. Therefore the deletion in Patients 2 and 3 are between ESR and TBP loci distal to that of Patient 1. FISH validated the deletion breakpoints assessed by conventional cytogenetics. Am. J. Med. Genet. 87:17–22, 1999. © 1999 Wiley-Liss, Inc.     

Boy with an interstitial 1q (q31q41) duplication confirmed by fluorescent in situ hybridisation

A 20-year-old man with multiple anomalies caused by a de novo duplication of the long arm of chromosome 1 is presented. The patient suffers from severe mental retardation, epilepsy, bronchial stenosis, and minor anomalies (e.g., hirsutism, midface dysplasia, and beaked nose). A G-banding analysis of the patient's chromosomes showed additional segments in chromosome 1. Fluorescent in situ hybridisation analysis with a chromosome 1 painting probe showed that the extra material originated from chromosome 1. Further analysis with cosmid probes demonstrated that the region involving chromosome bands 1q31 to q41 is present in a tandem duplication. Am. J. Med. Genet. 80:163–168, 1998. © 1998 Wiley-Liss, Inc.     

Ring chromosome 9 [r(9)(p24q34)]: a report of two cases

We report clinical and molecular cytogenetic studies in two patients with ring chromosome 9. Cytogenetics and fluorescent in situ hybridization (FISH) analysis using the p16 gene probe on 9p21, the ABL gene on 9q34, chromosome 9 alpha satellite-centromeric probes, and TelVision 9p and 9q probes which identify subtelomere-specific sequences on chromosome 9p and 9q, revealed 46,XX,r(9)(p24q34).ish r(9)(305J7-T7-,p16+,ABL+, D9S325-) and 46XY,r(9)(p24q34).ish r(9)(305J7-T7-,p16+,ABL+, D9S325-). Based on FISH analysis at least 115 kb was deleted on terminal 9p, and at least 95 kb from terminal 9q. In comparison with other reports of r(9), deletion 9p, and deletion 9q, both patients had clinical characteristics of ring 9 and additional features of deletion 9q or deletion 9p syndrome. The variability between the two cases with r(9) despite similar breakpoints identified by GTG-banding and FISH may be explained by submicroscopic differences between deletion breakpoints, ring instability, interaction of other genes on the phenotype, and variation in fetal environmental conditions.     

Interstitial duplication 8q22-q24: Report of a case proven by FISH with mapped cosmid probes

We report on a 6-month-old malformed female infant with a de novo interstitial duplication of an 8q22-q24 segment. She had an excess dark-band on the 8q distal region by GTG-banded chromosome analysis, which was likely to be 8q23. We performed FISH analysis using cosmid probes mapped to 8q23 and proved that the patient had an 8q duplication including the 8q23 region. © 1996 Wiley-Liss, Inc.     

Two patients with overlapping de novo duplications of the long arm of chromosome 9, including one case with Di George sequence

Duplications of chromosome 9q are rare. We describe the cytogenetic and phenotypic findings in 2 patients, one with a large duplication covering most of 9q (q12–q33.2) and one with a smaller duplication (q21.12–q22.1) who had Di George sequence (DGS). The chromosome 9 origin of the extra material in the second case was confirmed by fluorescence in situ hybridization (FISH) analysis with a whole chromosome 9 paint. Microdeletions of chromosome 22 are common in DGS and have been reported in CHARGE association. This is the first report of an association of a chromosome 9 abnormality with DGS in the absence of a chromosome 22 abnormality and the seventh report of a patient with a duplication of a large portion of 9q (q11–q13 to q32–q33). © 1994 Wiley-Liss, Inc.     

Duplication within chromosome 5q characterized by fluorescence in situ hybridization

We present a 16-month-old boy with developmental delay, minor anomalies, small penis, and lymphedema of the upper limbs. Routine cytogenetic analysis suspected a duplication of 5q. Fluorescent in situ hybridization (FISH) with a cosmid probe (MCC at the 5q22 APC region) showed tandemly duplicated fluorescent signals on one of chromosomes 5, whereas FISH with three YAC probes (TYAC12 at 5q35, HTY3182 at 5q34, and TYAC139 at 5q31) did not give duplicated signals. These findings indicate a duplication of 5q22 band in one chromosome 5. The boy we describe here is the first case of a pure partial duplication of 5q to be proven by FISH techniques. A review of previously reported cases of putative partial 5q duplication showed no consistent phenotype.     

Paracentric inversion involving the long arm of chromosome 9 resulting in deletion of abl gene

We report on a new chromosomal finding in a newborn male with hypertelorism, apparently low-set malformed ears with patent canal, micrognathia with narrow high-arched palate, bilateral webbing of neck with low posterior hairline, widely spaced nipples, and complex heart anomalies. Initially, what appeared to be a simple paracentric inversion of the long arm of chromosome 9, that is, 46,XY, inv(9)(q31q34) by routine GTG-banding technique was later determined to be a paracentric inversion with deletion of the band 9q34.1 by FISH technique using an abl unique sequence DNA probe. Thus the cytogenetic diagnosis was modified to 46,XY,der(9) inv(9)(q31q34.1)del(q34.1). Nevertheless, the presence of telomeric repeat sequences in the inverted chromosome 9 suggests that either healing has occurred by adding [TTAGGG]_n sequences to the nontelomeric end (q31) by the enzyme telomerase or telomeric sequences were not affected during this inversion process. This abnormality is a rare occurrence and has never been reported before either because of a high rate of lethality or it has been undetected by routine cytogenetic techniques. The other abnormal cases with apparent paracentric inversions could also have a complex nature with congenital anomalies associated with loss of “few” DNA sequences as exemplified here. Am. J. Med. Genet. 68:409–411, 1997. © 1997 Wiley-Liss, Inc.     

Three patients with terminal deletions within the subtelomeric region of chromosome 9q

We report on three male infants with de novo terminal deletions of chromosome 9q34.3. The clinical features are compared to the nine cases described in the literature. Case 1 and 3 were ascertained following the use of subtelomeric FISH to screen for a chromosomal anomaly, case 2 was confirmed by FISH probe following detection of a 9q deletion on standard karyotyping. Deletions in this region result in severe developmental delay, a distinct facial phenotype, cardiac anomalies, obesity, and respiratory failure, which may result in premature death. The delineation of the 9q deletion phenotype will aid diagnosis and genetic counseling as subtelomere FISH screening becomes more widely available.     

Typical and partial cat eye syndrome: identification of the marker chromosome by FISH

Three children are reported with typical cat eye syndrome (CES) and three more children with partial CES because of absence of coloboma, in which the supernumerary marker chromosome was studied by FISH. Using a genomic library, and also a centromeric and particularly a cosmid probe of 22q11, partial tetrasomy was shown in all cases.     

Partial duplication of 3q (q25.1→q26.1) without the Brachmann-de Lange phenotype

Partial duplications of chromosome 3 have previously been reported to have phenotypic characteristics similar to Brachmann-de Lange syndrome (BDLS). We present the case of a 13-Year-old girl with an apparent duplication in the 3q25.1→q26.1 region but none of the manifestations commonly seen in BDLS. The chromosome 3 duplication was confirmed with a FISH painting probe of the involved region. These results suggest that the region critical for Brachmann-de Lange syndrome is not within the duplicated region of 3q25.1→q26.1. © 1993 Wiley-Liss, Inc.     

Cosmids and transcribed sequences from chromosome 11q23

Summary To obtain cosmid markers and transcribed sequences from a specific chromosome region, a series of radiation-reduced hybrids (RHs) containing various regions of human chromosome 11 was prepared from microcell hybrid A9 (neo11) cells containing a normal human chromosome 11 tagged with pSV2neo at 11p11.2. Among 15 radiation hybrid clones isolated, RH(11)-9 which contains a q23 fragment in addition to theneo integration site, was used for the construction of a cosmid library. Cosmid clones having human DNA sequences were screened, and localized by Southern hybridization with the radiation hybrid panel. Fifty-nine cosmids were assigned to 11q23 and 6 cosmids to 11p11.2. Exon amplification proceeded with 23 of the 59 cosmids and 16 putative exons were cloned. Three of them were identical to those constituting a known gene which locates on q23 (ATDC), and the others were unknown. Thus, the RHs containing various subchromosomal fragments of chromosome 11 were useful for constructing region-specific DNA markers. The RH-(11)-9 cells and putative exons also facilitate the positional cloning of genes in the 11q23 region.