Cryptic unbalanced translocation t(17;18)(p13.2;q22.3) identified by subtelomeric FISH and defined by array-based comparative genomic hybridization in a patient with mental retardation and dysmorphic features

Molecular cytogenetics allows the identification of cryptic chromosome rearrangements, which is clinically useful in mentally retarded and/or dysmorphic individuals with normal results from conventional cytogenetics analysis. We report on a 3-year-old girl with mental retardation, growth deficiency, speech delay, and dysmorphic features including hypertelorism, upslanting palpebral fissures, midfacial hypoplasia, and posteriorly rotated ears. The G-banding analysis showed a 46,XX,t(3;8)(q26.2;p21.1)mat karyotype. However, her clinical features were suggestive of the 18q syndrome. Subtelomeric FISH analysis revealed a der(18) translocated material from chromosome 17. Array-based comparative genomic hybridization (array-CGH) with subtelomeric BAC and PAC clones confirmed the abnormality and refined the breakpoints to 18q22.3-qter and 17p13.2-pter (deletion of 8.5 Mb and duplication of 3.9 Mb, respectively). This case demonstrates the diagnostic utility of combining conventional cytogenetics with molecular chromosome analyses for the identification of subtle chromosome abnormalities.     

t（11;18）（q11;q23）一家系

先证者　男 ,30岁 ,表型正常。婚后 3年 ,其妻怀孕 5次 ,均在孕 2～ 3个月自然流产 ,妇科检查正常。夫妇非近亲结婚。患者外生殖器正常。精液检查精子数量正常。细胞遗传学检查 :外周血细胞染色体观察 ,常规外周血淋巴细胞培养 ,G显带分析30个细胞 ,先证者核型为 46 ,XY,t(11;18) (11pter→ 11q11∷18q2 3→ 18qter;18pter→ 18q2 3∷ 11q11→ 11qter) ,其妻染色体核型正常。先证者性细胞联会复合体 (synaptonemal complex,SC)观察 ,方法参照文献 [1]。睾丸活检微铺展的 SC电镜观察 ,分析 30个精母细胞 (从早粗线期到晚粗线期 )中 SC图…     

t(11;19)(q23;p11) in a child with acute T-cell leukemia

A translocation, t(11;19)(q23;p11), is reported in a child with T-cell leukemia. Our case indicates that the t(11;19) may not be restricted to the monocytic leukemias, as earlier reported, but may occur in other malignancies.     

Formation of der(19)t(1;19)(q23;p13) in acute lymphoblastic leukemia

The t(1;19)(q23;p13), which results in a fusion of TCF3 (previously E2A) at 19p13 with PBX1 at 1q23, is one of the most common translocations in acute lymphoblastic leukemia (ALL). It is seen either as a balanced t(1;19) or as an unbalanced der(19)t(1;19); occasional cases with coexisting t(1;19)- and der(19)-positive clones also have been described. Although it generally has been assumed that the unbalanced form arises from the balanced t(1;19) through loss of the derivative chromosome 1 followed by duplication of the normal homologue, this has never been proved. At least two other mechanisms are possible for the formation of the der(19): an initial trisomy 1 followed by translocation and subsequent loss of the der(1) or a rearrangement during the G2 phase of the cell cycle, with the derivative chromosomes 1 and 19 ending up in separate daughter cells. The different alternatives may be distinguished by investigation of markers proximal to the breakpoint in 1q23 because they would be expected to lead to different allelic patterns. Thus, loss of heterozygosity as a result of the presence of uniparental disomy (UPD)-both copies of a chromosome being derived from only one parent-for chromosome 1 would be present in all der(19)-harboring cases arising via the duplication pathway and in one-third of cases arising via the trisomy pathway, but in none of the der(19) formed via the G2 pathway. In this study, we used quantitative fluorescence PCR with polymorphic microsatellite markers to investigate chromosomes 1 and 19 in two t(1;19)- and four der(19)-positive ALLs. None of the der(19) cases displayed UPD for chromosome 1, excluding that this aberration arises through the duplication pathway. Because previous findings of cases with coexisting t(1;19) and der(19) clones are difficult to explain if the translocation originated in G2, the present results suggest that an unbalanced der(19) may arise from an initial trisomy 1 followed by t(1;19) translocation and loss of the derivative chromosome 1.     

Array-based comparative genomic hybridization characterizes a deletion associated with a t(15;17) in acute promyelocytic leukemia

The majority of de novo leukemias are characterized by well-known recurring translocations or inversions. In approximately 2% to 20% of these cases, deletions accompany these rearrangements. Because such deletions are undetectable by G-banding, aberrant fluorescence in situ hybridization (FISH) signal patterns are often the only indication of their presence. Array-based comparative genomic hybridization (a-CGH) permits examination of the entire genome at a resolution unattainable by G-banding or FISH. We present a case of a deletion of the derivative chromosome 17 of a t(15;17) in acute promyelocytic leukemia, the size and gene content of which were characterized by a-CGH. We hypothesize that this patient's more aggressive disease course is due to loss of one or more of these genes. Such submicroscopic deletions involving the t(15;17) have only rarely been reported, and, to our knowledge, this is the first case in which a-CGH has been applied to its characterization.     

Rubinstein-Taybi syndrome caused by a De Novo reciprocal translocation t(2;16)(q36.3;p13.3)

Rubinstein-Taybi syndrome (RTS) is a multiple congenital anomalies and mental retardation syndrome characterized by facial abnormalities, broad thumbs, and broad big toes. We have shown previously that disruption of the human CREB-binding protein (CBP) gene, either by gross chromosomal rearrangements or by point mutations, leads to RTS. Translocations and inversions involving chromosome band 16p13.3 form the minority of CBP mutations, whereas microdeletions occur more frequently (approximately 10%). Breakpoints of six translocations and inversions in RTS patients described thus far were found clustered in a 13-kb intronic region at the 5' end of the CBP gene and could theoretically only result in proteins containing the extreme N-terminal region of CBP. In contrast, in one patient with a translocation t(2;16)(q36.3;p13.3) we show by using fiber FISH and Southern blot analysis that the chromosome 16 breakpoint lies about 100 kb downstream of this breakpoint cluster. In this patient, Western blot analysis of extracts prepared from lymphoblasts showed both a normal and an abnormal shorter protein lacking the C-terminal domain, indicating expression of both the normal and the mutant allele. The results suggest that the loss of C-terminal domains of CBP is sufficient to cause RTS. Furthermore, these data indicate the potential utility of Western blot analysis as an inexpensive and fast approach for screening RTS mutations.     

t(6;12)(q23;q13) and t(10;16)(q22;p11) in a phyllodes tumor of breast.

Cytogenetic analysis of short-term cultures from a phyllodes tumor showed clonal chromosome changes including t(6;12)(q23;q13) and t(10;16)(q22;p11). This is the first reported karyotype in this tumor type. We discuss the breakpoints of these translocations in relation to the involvement of possible candidate genes.     

T-cell acute lymphoblastic leukemia with t(1;18)(p36;q22)

An 8-year-old white boy with a T-cell acute lymphoblastic leukemia (T-ALL) developed chromosomal abnormalities t(1;18)(p36;q22) and del (6)(q21) at the first bone marrow relapse. Rearrangements of the chromosome region 1p36 have been reported previously in adults with T-ALL.     

Clustering of genomic breakpoints at the MLL locus in therapy‐related acute leukemia with t(4;11)(q21;q23)

Genomic characterization of translocation breakpoints is relevant to identify possible mechanisms underlying their origin. The consistent association of anthracylines (e.g., epirubicin and idarubicin) in inducing therapy‐related acute leukemias (t‐AL) with mixed lineage leukemia (MLL) gene rearrangement suggests that MLL translocations are causative events for t‐AL. Using asymmetric multiplex PCR strategy followed by direct DNA sequencing, we characterized the genomic breakpoints of the MLL and AFF1 genes in two patients who developed t‐AL with t(4;11)(q21;q23). Chemotherapeutic treatment of the primary disease in both patients included topoisomerase II (topo II) targeting agents. In one case, the MLL breakpoint was located in intron 9 at nucleotide position chr11:118354284 while the AFF1 breakpoint was in intron 3 at nucleotide position chr4:87992070. The breakpoint junction sequences revealed an insertion of two nucleotides at the MLL‐AFF1 junction. In the other patient, the MLL breakpoint was located in intron 11 at nucleotide position chr11:118359130‐32 and the AFF1 break was in intron 3 at nucleotide position chr4:87996215‐17. The MLL breakpoint found in the latter patient was identical to that of two previously reported cases, strongly suggesting the presence of a preferential site of DNA cleavage in the presence of topo II inhibitor. In addition, microhomologies at the breakpoint junctions were indicative of DNA repair by the non‐homologous end joining (NHEJ) pathway. This study further supports the evidence that MLL breakpoints in therapy‐related acute leukemia with MLL‐AFF1 are clustered in the telomeric half of the breakpoint cluster region that contains topo II recognition sites. © 2013 Wiley Periodicals, Inc.     

Familial translocation, t(2;5)(p23;q31)

A reciprocal translocation, t(2;5) (p23; q31) was found in healthy individuals through two generations of a family. The balanced aberration resulted in a derivate chromosome 2 in two malformed offspring in the third generation. The family was ascertained through the two unbalanced carriers whose phenotype abnormalities resembled those of two other offspring who died prior to the cytogenetic examination.     

A der(18)t(9;18)(p13;p11) and a der(9;18)(p10;q10) in polycythemia vera associated with a hyperproliferative phenotype in transformation to postpolycythemic myelofibrosis

Chromosomal aberrations in polycythemia vera (PV) are heterogenous and nonrandom. A prognostic predictive value of these aberrations has not been established. The V617F mutation in the JAK2 gene on chromosome 9p24.1 was identified recently in peripheral blood leukocytes in the majority of patients with PV and in approximately half of patients with essential thrombocythemia and idiopathic myelofibrosis. Within the JAK2 V617F-positive PV patients, however, clinical presentation and degree of myeloproliferation varies to a great extent. Here we report four cases of chronic myeloproliferative disorders [two with PV, one with PV in transformation to idiopathic myelofibrosis (IMF) and one IMF patient], with the distinct karyotypic abberations der(18) t(9;18) (p13;p11) and der(9;18)(p10;q10). Two patients had hyperproliferative PV and two had "transitional PV" and IMF, respectively. All four patients harbored the JAK2 V617F mutation. Our data, together with previously published data, clearly indicate an association of these chromosomal abnormalities with a highly proliferative PV phenotype with a propensity to transform into postpolycythemic myelofibrosis. Cytogenetic analysis seems to identify a subgroup of patients with a distinct prognostic profile, and should be performed in conjunction with a JAK2 mutation analysis in patients suspected of a chronic myeloproliferative disease.     

Identification of breakpoint cluster regions at 1p36.3 and 3q21 in hematologic malignancies with t(1;3)(p36;q21)

The reciprocal translocation t(1;3)(p36;q21) is associated with myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML) characterized by trilineage dysplasia, in particular dysmegakaryocytopoiesis, and a poor prognosis. As yet no molecular genetic analyses of the t(1;3) have been reported. In four patients with t(1;3), all of whom had AML-M4, which evolved from MDS, the breakpoints at 3q21 clustered within a 60-kb region centromeric to the breakpoint of the inv(3)(q21q26), whereas the breakpoints at 1p36 clustered within a 90-kb region at 1p36.3. The presence of novel clusters in both the 3q21 and 1p36 breakpoints (BCRs) suggests a common, underlying molecular mechanism for the development of t(1;3)-positive MDS/AML. The Ribophorin I (RPN1) gene close to the BCR at 3q21 was highly expressed without gross structural changes, whereas the GR6 gene located within the BCR at 3q21 was not expressed. No other highly expressed genes were isolated in a 150-kb region at 3q21. Thus, it is likely that a gene at 1p36.3 is activated by the translocation of the 3q21 region or a gene important for transformation lies on 3q21, outside the 150-kb region. Further characterization of the BCRs at 1p36.3 and 3q21 should provide important insights into the molecular genetic mechanisms involved in the genesis of t(1;3)-positive MDS/AML. Genes Chromosomes Cancer 27:229-238, 2000.     

Detection of cryptic chromosome aberrations in a patient with a balanced t(1;9)(p34.2;p24) by array-based comparative genomic hybridization

Mental retardation (MR) is one of the most common phenotypes in congenital disorders, but in many cases the pathogenesis remains unknown. Here, we report on a 5-year-old boy with mild developmental disability, cranial malformation, minor anomalies, and moderate MR. G-banded chromosome analysis revealed that he carried an apparent balanced translocation, t(1;9)(p34.2;p24). However, our array-based comparative genomic hybridization (CGH-array) analysis detected a cryptic genomic duplication and a deletion at the breakpoints. Further fluorescence in situ hybridization (FISH) showed that the duplication was approximately 7.9 Mb in size at 1p34.3-p33, and the deletion was 4 Mb at 9pter-p24. Although some features of the patient were consistent with those of monosomy 9p-syndrome, his features were not typical of cases of the syndrome, suggesting that the small deletion region involved in 9p may limit his phenotype. On the other hand, interstitial duplication at 1p34.3-p33 is very rare and his phenotype did not match with that in previous reports. CGH-array is a potentially useful technique for investigating cryptic copy-number alterations in cases of apparently balanced chromosome rearrangements in patients with unexpected clinical features.     

Fortuitous detection of a submicroscopic deletion at 1q25 in a girl with Cornelia-de Lange syndrome carrying t(5;13)(p13.1;q12.1) by array-based comparative genomic hybridization

We report on a 2-year-old Japanese girl with Cornelia-de Lange syndrome (CdLS) who had mental and growth retardation, together with characteristic facial anomalies and mild extremity malformations. She had a balanced chromosomal translocation, 46,XX,t(5;13)(p13.1;q12.1) de novo. Surprisingly, this was the same translocation that had provided a clue to the identification of a major causative gene for CdLS, NIPBL [Krantz et al., 2004; Tonkin et al., 2004]. Using fluorescence in situ hybridization (FISH), the breakpoint was confirmed to lie within NIPBL at 5p13.1. Furthermore, array-based comparative genomic hybridization (array-CGH) demonstrated a cryptic 1-Mb deletion harboring six known genes at 1q25-q31.1. A FISH analysis of her parents confirmed that the deletion was de novo. Although patients with interstitial deletions at 1q are rare, some of their features were similar to those observed in our patient, indicating that her clinical manifestations are likely to be affected by not only the disruption of NIPBL but also the concomitant microdeletion at 1q25-q31.1. The present case suggests that array-CGH can uncover cryptic genomic aberrations affecting atypical phenotypes even in well-known congenital disorders.     

Molecular characterization of the genomic breakpoints in a case of t(3;21)(q26;q22).

The t(3;21)(q26;q22) is a recurring chromosomal abnormality in blastic crisis of chronic myelogenous leukemia (CML) and in therapy-related myelodysplastic syndrome and acute leukemia. In order to clarify the genetic recombination mechanism underlying the t(3;21), we molecularly cloned the breakpoints and determined their nucleotide sequence in a case of CML in blastic crisis with t(3;21). Near the breakpoint on chromosome 21, three homopyrimidine (CT)-rich sequences were found. We also identified a sequence homologous to the topoisomerase II binding and cleavage consensus sequence surrounding the breakpoint on chromosome 3, and two topoisomerase II binding and cleavage consensus sequences near the breakpoint on chromosome 21. In addition, around the breakpoint on chromosome 21, four chi-like sequences, potential consensus signals for activating recombination, were found. There were no Alu sequences or antigen receptor gene-like heptamer/nonamer signal sequences within the breakpoints on chromosomes 3 and 21. The breakpoints were found adjacent to the topoisomerase II binding and cleavage consensus sequence or the homopyrimidine-rich sequence. Furthermore, the chi-like sequences and the homopyrimidine-rich sequence were detected on chromosome 21 but not on chromosome 3. Genes Chromosomes Cancer 26:92-96, 1999.