Polycystic kidneys and del (4)(q21.1q21.3): further delineation of a distinct phenotype.

A three year-old boy was evaluated because of growth and developmental delay, hypotonia and dysmorphic features. G-banding analysis revealed a small interstitial deletion of the long arm of chromosome four described as 46,XY,del (4)(q21.1q21.3). This patient's findings on physical exam included relative macrocephaly, frontal bossing, short fingers with clinodactyly and were consistent with the phenotypes of previously reported deletions involving the 4q21--> 4q22 band region (Am. J. Med. Genet. 68 (1997) 400-405). To date there are 10 reported live-born cases with such deletions and similar features. The case reported here delimits a minimal critical region for this phenotype to chromosomal region 4q21. Our patient was also found to have cysts in both his kidneys. The gene for type II polycystic kidney disease (PKD2) has been mapped to chromosomal region 4q21--> 4q23. FISH analysis, with a probe including the PKD2 gene, demonstrated hemizygosity at this locus. Thus the absence of one of the PKD2 alleles in the case reported here is associated with early bilateral cyst development. Kidney ultrasound/autopsy studies were reported in seven of the patients with the characteristic phenotype, and were positive for cysts in four cases including the one presented here (Clin. Genet. 31 (1987) 199-205; Am. J. Med. Genet. 68 (1997) 400-405; Am. J. Med. Genet. 40 (1991) 77-790. Our report supports the presence of a distinct phenotype associated with a deleted chromosomal region within 4q21. Hemizygosity for the PKD2 gene is likely in such deletions and may lead to renal cyst formation.

Loss of heterozygosity of the TP53 tumor suppressor gene and detection of point mutations by the non-isotopic RNAse cleavage assay in prostate cancer.

Mutation within the TP53 tumor suppressor gene is a frequent occurrence in human cancers, resulting in a poor prognosis, response to therapy, and overall survival time. Mutations have been primarily detected in advanced prostate cancer; however, the involvement of the gene through loss of heterozygosity (LOH) in primary prostate cancers has not been investigated due to lack of identifiable polymorphisms within this gene. Using the nonisotopic RNAse cleavage assay (NIRCA), we screened for point mutations and identified an ApaI restriction site polymorphism located in intron 7 within the TP53 gene. This polymorphism allowed us to detect LOH in informative samples in a population of patients that underwent prostate biopsies and a population that underwent radical prostatectomies. Within the combined study population, 31 of 80 patients (38.75%) were informative for the polymorphism. Loss of heterozygosity was detected in 10 of the 31 samples (32.3%). Point mutations were identified in two samples. The identification of LOH in these patients suggests that the TP53 tumor suppressor gene may play a more active role in prostate cancer than was previously believed.

A Philadelphia negative chronic myelogenous leukemia with the chimeric BCR/ABL gene on chromosome 9 and a b3-a2 splice junction.

Approximately 5% of patients with chronic myelogenous leukemia (CML) do not reveal the Philadelphia (Ph) chromosome cytogenetically and are termed Ph-negative CML cases. We report one such case, which appeared normal by routine banding techniques. The BCR/ABL rearrangement was detected by reverse transcriptase-polymerase chain reaction and Southern blotting analysis, which suggested a b3-a2 splice junction. Dual color fluorescence in situ hybridization (FISH) with BCR and ABL DNA probes showed that the chimeric fusion gene was localized on chromosome 9q34, rather than at the typical location on chromosome 22q11. The BCR/ABL rearrangement was detected in 75% of the patient's bone-marrow population, whereas the remaining 25% of the cells appeared normal. The use of dual color FISH in the diagnosis of CML is extremely valuable not only in identifying cases of Ph-negative CML, but also in quantifying the proportion of transformed cell populations. This information ultimately results in an enhancement of our ability to monitor therapy, follow disease progression, and determine transplant eligibility.

Rapid denaturation improves chromosome morphology and permits multiple hybridizations during fluorescence in situ hybridization.

Denaturation of chromosomal DNA for fluorescence in situ hybridization (FISH) is an essential step in a procedure associated with a number of variables. In our experience, shorter denaturation time in 70% formamide/2 x SSC at 72 C provides sufficient denaturation, where the hydrogen bonds are broken between the purines and pyrimidines of the double helix. This shortened exposure improves retention of morphology of human chromosomes from lymphocytes, aminocytes, fibroblasts and bone marrow, and allows the same metaphases to be denatured repeatedly and rehybridized with different probes. This approach is useful in investigations where sample volume is limited.

Characterization of an isodicentric Y-chromosome for the long arm in a newborn with mixed gonadal dysgenesis.

A newborn infant was referred for evaluation because of ambiguous genitalia. Examination of the genitalia revealed a hypospadiac phallus measuring 1.5 cm in length with chordee. Subtle phenotypic features consistent with Turner syndrome were present including hypertelorism, anti-mongoloid slant to the eyes, mild widening of the neck, but no definitive webbing, shield like chest and positive cubitus valgus. A pelvic and renal sonogram confirmed the presence of a uterus and normal-appearing kidneys. There was incomplete fusion of the scrotum. No gonads were palpable within the scrotal sac. The patient was assigned a female gender on the basis of the presence of a uterus, the phenotypic appearance of the genitalia and the malignant potential of the gonads. The cytogenetic findings with QFQ-banding revealed an abnormal karyotype, i.e., mos 46,X,idic(Y) (p11.2)[77]/45,X[29]/46,X,idic(Y) (p11?) [2]/ 47,XY,idic(Y)(p11.2)[2]/47,X,idic(Y)(p11.2), + idic(Y)(p11.2)[1]/46,XY[1]. The presence of an abnormal isodicentric Y-chromosome was evaluated by FISH-technique to ensure a finer characterization than routine methods. The genotype-phenotype correlation could not be established since mosaicisms of highly variable nature can exhibit an unpredictable outcome.

Characterization of a complex translocation [t(4;9;22)(p16;q34;q11)] in chronic myelogenous leukemia by fluorescence in situ hybridization technique.

A patient was referred with a high leukocyte count and diagnosed with chronic myelogenous leukemia (CML). Although practically asymptomatic since the time of diagnosis, he had a variable and inconsistent response to treatment. All of his bone marrow cells had a complex, three-way translocation, involving chromosomes 4, 9 and 22. Translocation of chromosome 4 to chromosome 9 was undetectable by routine cytogenetic techniques; however, by the fluorescence in situ hybridization technique, a three-way translocation was identified, 46,XY,t(4;9;22)(p16;q34;q11). Although, other chromosomes are frequently involved in complex or variant translocations with chromosome 9 and 22, participation of chromosome 4 is a very rare event. So far, two previous cases have been described in the literature with translocations involving chromosome 4p16. We present a third case of CML having similar break points whose clinical presentation is unusual.

T-cell receptor J beta 1/J beta 2 locus rearrangements in an HTLV-1-positive T-cell lymphoma with complex chromosomal aberrations.

We report a case of human T-cell lymphotropic virus type 1 (HTLV-1)-infected adult T-cell lymphoma that has multiple chromosomal abnormalities, including the presence of an additional 7q22-36, which contains the locus of the T-cell receptor (TCR) beta chain gene. Specific TCR J beta 1/J beta 2 gene rearrangements were detected in both marrow and peripheral blood DNA, with evidence of further evolution of the transformed clonal population within the peripheral lymphocytes. To our knowledge, this is the first case in which gene rearrangements have been associated with additional TCR loci. Consequently, it is advised that every effort should be made to correlate chromosomal abnormalities with gene rearrangement by molecular methods.

Clinical manifestations of trisomy 4p syndrome.

UNLABELLED: Trisomy 4p syndrome is a distinct clinical entity which was noted almost a quarter century ago by Wilson et al. [71] and later was delineated by Gonzalez and colleagues [29]. The variation in the length of duplicated segment usually associated with monosomy of other genetic material which has resulted in confusion and as a result a so-called 4p syndrome could not be recognized without cytogenetic analysis. We wish to draw the attention of clinicians to this subject by presenting the description of over 75 cases including one from our clinic and stress the point that molecular approaches are imperative to characterize this anomaly. After extensive review, it appears that patients retaining at least the distal two-thirds to the entire short arm share an overlapping phenotypic expression that constitutes pure trisomy 4p syndrome which includes prominent glabella, bulbous nose with flat or depressed nasal bridge, retrognathia, pointed chin, short neck with low hairline, enlarged ears with abnormal helix and antihelix, rocker-bottom feet with prominent heel. Arachnodactyly and camptodactyly. Molecular characterization of 4p is imperative. We have also included an extensive bibliography for clinicians who may find it useful as a single reference source for evaluating their future cases. CONCLUSION: The 4p-syndrome is a distinct entity but without cytogenetic evaluation, the syndrome can not be recognized.

Characterization of chromosome 11 with a complex inversion and deletion in an AML [M2] using fluorescence in situ hybridization.

We report on a new case of AML [M2] where chromosome 11 was rearranged in a highly complex manner involving band 11q23. Routine G banding failed to identify the nature of this aberration which later was accomplished using whole chromosome 11-specific painting probe by the FISH technique. Chromosome 11 band q23 is frequently involved in reciprocal translocations with various chromosomes, but to have sole morbidity of such a complex nature is an atypical finding in AML [M2]. The band q23 of chromosome 11 involves the mixed lineage leukemia gene and rearrangement of this chromosomal region has been found in a variety of neoplasias. Henceforth, its precise identification has become imperative for classification of hematological malignancies and in turn to devise therapeutic strategies.

Mechanisms of the origin of a G-positive band within the secondary constriction region of human chromosome 9.

We report on a so-called rare variant where a G-positive band was sandwiched within the secondary constriction (qh) region of chromosome 9 and is apparently different from previous cases when characterized by the fluorescence in situ hybridization technique. The major differences included duplication of beta-satellite and satellite III DNA sequences and bands 9q13-->q21.1, without duplication or inversion of the alphoid sequences. Based on the reported cases, at least four types of variations can be accounted for. A variety of mechanisms have been proposed to describe the origin of a G-positive band within the 9qh region, which appears to be similar when studied by routine cytogenetic techniques but differs by molecular methods. It is hypothesized that the clinical consequences depend upon the size of the G-positive band(s) duplicated, and a genetic inactivation mechanism might have some sort of influence during the so-called heterochromatinization process. It appears that heterochromatin, once thought to be composed of junk DNA, may have some role after all in suppression of gene(s) and/or spreading of inactivation, if genes are embedded within the heterochromatic region. Apparently, the mixture of different types of DNA creating patches of genetic debris have become a fundamental hidden treasure, where genetically active chromatin could be inactivated without dire consequences. The variable nature of heterochromatin has resulted in cytogenetic heteromorphisms of a number of human chromosomes. Their characterization by molecular techniques is becoming imperative, because fetal wastage have occurred in many situations where variant chromosomes were wrongly identified as chromosomal abnormalities.

Identification of a non-fluorescent isodicentric Y chromosome by molecular cytogenetic techniques.

A 12 1/2-month-old girl was referred because of short stature, short neck, large internipple distance and simian crease on her right hand. By routine cytogenetic techniques the presence of an unidentifiable marker chromosome and loss of one X chromosome was noted (i.e. 45, X/46, X, mar/47, X, mar, +mar). By fluorescence in situ hybridization (FISH) technique, the marker chromosome was identified as an isodicentric non-fluorescent Y chromosome ((45, X/46, X, idic (Ynf)/47, X, idic (Ynf), +idic (Ynf)). Although the clinical significance of this finding cannot be assessed at present, possible development of gonadoblastoma in such cases is a major concern and warrants follow-up evaluations.

Two Prader-Willi/Angelman syndrome loci present in an isodicentric marker chromosome.

We found an abnormal 47,XX,+mar karyotype in a patient with developmental delay, hypotonia, microcephaly, failure to thrive, and cognitive delay. When metaphases were hybridized with Prader-Willi and Angelman loci-specific probes by the FISH technique, two sites were noted at opposite positions on the marker chromosome. The alphoid satellite DNA probe documented the isodicentric nature while retention of the p arms on both sides of the marker chromosome was demonstrated by beta satellite probe. The patient does not exhibit manifestations of either syndrome despite the presence of these loci in tetrasomic dose. The present investigation suggests that other marker chromosomes be reevaluated, as their clinical manifestations are quite variable.

T-cell receptor J beta I/J beta II locus rearrangements concurring with a complex chromosomal aberration in an HTLV-1 positive T-cell lymphoma.

Human T-lymphotropic virus type I (HTLV-1) integration has been associated with the development of adult T-cell leukemia/lymphoma (ATL). Recently, a correlation between T-cell receptor (TCR) gene rearrangements and chromosomal aberrations has been implicated in this leukemia. We present a case of HTLV-1 infected adult T-cell lymphoma that initially presented with a normal karyotype and germline J beta I/J beta II loci. As the disease evolved to the aggressive stage, a complex chromosomal rearrangement with a duplication of chromosome 6p23-->pter translocated to a derivative chromosome 16, was identified by molecular cytogenetic techniques. The nature of this complex abnormality would have been difficult to determine if only conventional banding techniques were performed. Rearrangement involving one J beta allele was also detected at that time. After initiation of chemotherapy, no germline J beta loci were detected, suggesting a possible second rearrangement involving this locus that was homologous. Although no known immune response genes are located at the breakpoints involved in this abnormality, the chromosomal aberration concurred with the initial J beta rearrangement.

New translocations [t(6;15)(p25;q22) and t(6;19)(q16;q13.3)] with t(9;22)(q34;q11) in a Ph-positive chronic myelogenous leukemia.

A case with typical features of chronic myelogenous leukemia (CML) with two complex aberrations in addition to the standard t(9;22) is reported. Cytogenetic evaluation of the patient's bone marrow cells (BMC) showed 46,XX,t(6;19)(q16;p13.3),t(9;22)(q34;q11) in 60% of the mitotic cells and 46,XX,idem, t(6;15)(p25;q22) in the remaining 40% dividing cells. The patient's peripheral blood smear exhibited the usual differential observed in chronic-phase CML and was clinically indistinguishable from patients with the t(9;22) as the only translocation. We performed Southern blotting on BglII-digested DNA with the Trans-Probe (OSI) and in addition to the 4.8-, 2.3-, and 1.1-kilobase (kb) germline fragments, we detected an additional fragment at 7 kb. This probe spans the entire 5.8-kb M-breakpoint cluster region (BCR), and a single breakpoint in this region will appear as either one or two additional fragments. Because only one additional fragment was observed, both cell lines apparently share the same breakpoint in the ABL/BCR gene. Apparently the second aberrant cell line with the additional t(6;15) represents clonal evolution of the original abnormal clone.

Direct visualization of the transposed ABL gene in a duplicated masked Ph chromosome.

In a small percentage of cases of chronic myelogenous leukemia (CML), where the Ph chromosome is masked because of highly complex translocations and sub-microscopic rearrangements, precise identification of chromosomal aberrations by routine banding techniques has been difficult. We report on a new case of CML in which a single copy of a masked Ph chromosome was duplicated during blast crisis, i.e., the karyotype was 47,XY,dir ins(22;9)(q11;q34.1q34.2),t(1;22) (q21;q11), + der (22)t(1;22)(q21;q11). The chromosome in situ suppression hybridization (CISS) technique with whole chromosome 1 and 22 specific painting probes demonstrated that 22q11-qter had been translocated to 1q21, whereas 22q11 was the recipient of 1q21-qter. Furthermore, a cosmid probe identified the location of the ABL gene on only one chromosome 9 (band q34). The other ABL gene could be detected on both derivative chromosomes 22 at band q11 which was flanked by the translocated part of the long arm of chromosome 1, thus providing direct visualization of the ABL insertion in a double masked Ph chromosome. A breakpoint within the 5.8 kb major breakpoint cluster [M-BCR] region was shown by Southern blotting.

Molecular topography of the secondary constriction region (qh) of human chromosome 9 with an unusual euchromatic band.

Heterochromatin confined to pericentromeric (c) and secondary constriction (qh) regions plays a major role in morphological variation of chromosome 9, because of its size and affinity for pericentric inversion. Consequently, pairing at pachytene may lead to some disturbances between homologous chromosomes having such extreme variations and may result in abnormalities involving bands adjacent to the qh region. We encountered such a case, where a G-positive band has originated de novo, suggesting a maternal origin from the chromosome 9 that has had a complete pericentric inversion. In previously reported cases, the presence of an extra G-positive band within the 9qh region has been familial, and in the majority of those cases it was not associated with any clinical consequences. Therefore, this anomaly has been referred to as a "rare" variant. The qh region consists of a mixture of various tandemly repeated DNA sequences, and routine banding techniques have failed to characterize the origin of this extra genetic material. By the chromosome in situ suppression hybridization technique using whole chromosome paint, the probe annealed with the extra G-band, suggesting a euchromatic origin from chromosome 9, presumably band p12. By the fluorescence in situ hybridization technique using alpha- and beta-satellite probes, the dicentric nature was further revealed, supporting the concept of unequal crossing-over during maternal meiosis I, which could account for a duplication of the h region. The G-positive band most likely became genetically inert when it was sandwiched between two blocks of heterochromatin, resulting in a phenotypically normal child. Therefore, an earlier hypothesis, suggesting its origin from heterochromatin through so-called euchromatinization, is refuted here.(ABSTRACT TRUNCATED AT 250 WORDS)