Duplication/deletion mosaicism of the 7q(21.1 --> 31.3) region

Mosaicism for structural aberrations is a rare event and the coexistence of a cell line with a duplication and another with a deletion of the same chromosome segment is even more infrequent. We report a boy with a 46,XY,del(7q)/46,XY,dup(7q) mosaicism. High-resolution cytogenetic analysis and fluorescent in situ hybridization (FISH) performed at birth showed a trisomy for region 7q21.1 to 7q31.3 in 90% of metaphases analyzed and monosomy for the same region in 10% of metaphases. At the age of 12 months, karyotype on peripheral blood and exfoliated urinary epithelial cells was 46,XY,dup(7)(q21.1q31.3) in all cells analyzed. The patient presented malformations and psychomotor retardation. His phenotype is compared with other previously case reports describing patients with an interstitial duplication of 7(q21 or q22 --> q31.3). Due to the absence of a normal cell line, we propose a post-zygotic origin of the abnormality during the first mitotic division and a progressive loss of the deleted cells during pre- and post-natal development by selective pressure. The patient described here emphasizes the possible existence of an undetectable cell line in patients previously diagnosed of pure partial 7q trisomy or monosomy to explain the great clinical variability between reported patients. We also describe the culture of urinary epithelial cells in order to perform cytogenetic analysis as a useful non-invasive method.     

恶性髓系血液病-7/7q-异常的分子细胞遗传学分析

目的 分析染色体-7／7q-在骨髓增生异常综合征(myelodysplastic syndrome，MDS)和急性髓细胞白血病(acute myeloblastic leukemia，AMI，)中的发生频率；探讨荧光原位杂交技术(fluorescence in situ hybridization，FISH)在检测和鉴定-7／7q-异常中的价值。方法 回顾性分析所有接受细胞遗传学分析(conventional cytogenetic analysis，CCA)的MDS／AML患者的核型特征，其中70份进行FISH分析。应用双色荧光直接标记的7号着丝粒探针(CEP7，光谱绿)和7q31基因序列探针(D7S486，光谱桔红)，15份正常样本作为对照。结果 -7／7q-在AML和MDS中出现频率分别为4．5l％(31／687例)和5．7l％(28／490例)，分别占异常核型病例的5．68％和l0．29％。7q-常见的缺失区域为7q21—22(10例)和7q31—35(10例)。FISH证实伴有克隆性-7／7q-异常，但在随机性-7／7q-异常或正常核型中未检出-7／7q-异常。在核型分析出现7q-异常的病例中，FISH检出7／11例可同时伴有-7克隆的出现，而且7q-异常的细胞数显著高于-7异常细胞数(42．5％vs8．4％，P=0．025)。1例核型为del(7)(q22)患者FISH证实为染色体易位；1例7q 患者FISH显示dup(7q)；1例复杂异常核型，FISH确定其累及7q。结论 FISH是鉴定或确定7q结构异常的强有力工具，能精确地评价-7／7q-。7q-异常通常与-7异常在同一个样本中共存，且7q-细胞数显著增高，推测-7克隆衍生于7q-的丢失。     

Familial insertion (3;5)(q25.3;q22.1q31.3) with deletion or duplication of chromosome region 5q22.1-5q31.3 in ten unbalanced carriers

We report on the clinical and cytogenetic data of a large family with an unbalanced insertion translocation (3;5)(q25.3;q22.1q31.3). Analysis of GTG-banded chromosomes demonstrated that unbalanced inheritance of a parental insertion translocation caused either a partial deletion or duplication 5q in this family. The derivative chromosomes were characterized further using microdissection and FISH with band-specific probes. The clinical picture of the proband with a partial deletion of chromosome 5 was characterized by moderate psychomotor retardation, mild facial dysmorphism, cleft palate, and single transverse crease. The family members with a partial duplication of chromosome 5 were borderline intelligent, had mild facial dysmorphism, a cardiac anomaly, and a high-pitched voice. The unbalanced carriers were compared with patients reported in the literature with a duplication or deletion of chromosome region 5q22.1 --> 5q31.3.     

Complex chromosomal rearrangements leading to MECOM overexpression are recurrent in myeloid malignancies with various 3q abnormalities

Chromosomal rearrangements involving 3q26 are recurrent findings in myeloid malignancies leading to MECOM overexpression, which has been associated with a very poor prognosis. Other 3q abnormalities have been reported and cryptic MECOM rearrangements have been identified in some cases. By fluorescence in situ hybridization (FISH) analysis, we investigated 97 acute myeloid leukemia/myelodysplastic syndrome patients with various 3q abnormalities to determine the role and the frequency of the involvement of MECOM. We identified MECOM rearrangements in 51 patients, most of them showed 3q26 involvement by chromosome banding analysis (CBA): inv(3)/t(3;3) (n = 26) and other balanced 3q26 translocations (t(3q26)) (n = 15); the remaining cases (n = 10) showed various 3q abnormalities: five with balanced translocations involving 3q21 or 3q25; two with homogenously staining region (hsr) on 3q; and three with other various 3q abnormalities. Complex rearrangements with multiple breakpoints on 3q, masking 3q26 involvement, were identified in cases with 3q21/3q25 translocations. Furthermore, multiple breaks were observed in two cases with t(3q26), suggesting that complex rearrangement may also occur in apparently simple t(3q26). Intrachromosomal gene amplification was another mechanism leading to MECOM overexpression in two cases with hsr on 3q. In the last three cases, FISH analysis revealed 3q26 involvement that was missed by CBA because of metaphases' suboptimal quality. All cases with MECOM rearrangements showed overexpression by real‐time quantitative PCR. Finally, MECOM rearrangements can occur in patients with 3q abnormalities even in the absence of specific 3q26 involvement, underlining that their frequency is underestimated. As MECOM rearrangement has been associated with very poor prognosis, its screening should be performed in patients with any 3q abnormalities. © 2016 Wiley Periodicals, Inc.     

Candidate region for Coffin-Siris syndrome at 7q32-->34

Reports of possible genetic associations or linkages for attention deficit hyperactivity disorder are appearing at an increasing rate. As with many other neuropsychiatric disorders, claims of positive findings are frequently followed by negative reports. In this review, the evidence underpinning genetic hypotheses for the origins of ADHD is reviewed with particular emphasis on what is the heritable phenotype. It is concluded that advances in identifying mutations or allelic variations in genes predisposing to ADHD are likely, but the general replication of such findings must await a better characterization of the heritable phenotypic elements of ADHD and a better understanding of its genetic heterogeneity.     

Partial duplication of 13q31.3-q34 and deletion of 13q34 associated with diaphragmatic hernia as a sole malformation in a fetus

Partial duplications and deletions of chromosome 13 are rare and the phenotypic expressions of both aneuploidies are highly variable. Here we report on a fetus diagnosed prenatally with partial trisomy of 13q and a diaphragmatic hernia as a sole malformation. The parents had decided to terminate the pregnancy after the finding of diaphragmatic hernia by ultrasound scan, which was also confirmed by autopsy of the fetus. Subsequently chromosome analysis, fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (array CGH) was carried out on fetal tissue. The chromosome analysis revealed additional material on chromosome 13, which was shown to be from the same chromosome, by FISH analysis. Array CGH demonstrated a partial duplication and a small deletion at the distal long arm of chromosome 13. The parents had normal karyotypes. This is the first case of a de novo pure partial duplication of 13q31.3-q34 and distal deletion of 13q34 with a phenotype apparently only involving a diaphragmatic hernia and three lung lobes on both sides. Microarray analysis was useful in refining the chromosomal imbalance and suggesting a candidate region for diaphragmatic hernia. ? 2012 Wiley Periodicals, Inc.     

Chromosome abnormalities involving band 13q14 in hematologic malignancies

Fifteen patients with hematologic disorders showed abnormalities involving chromosome band 13q14. Nine patients had an interstitial deletion of this band, similar to that reported in some retinoblastoma tumors and as a constitutional abnormality in a small proportion of cases of familial retinoblastoma. In five patients, band 13q14 was involved in translocations and in one case there was a deletion of one chromosome #13 and a translocation involving the homologous #13. The diagnosis in the majority of our patients (11 of 15) was chronic lymphocytic leukemia. In these patients the abnormalities were detected in cultures stimulated with 4-phorbol 12-myristate 13-acetate (PMA). It is possible that the utilization of this agent is a fundamental requirement for the reliable demonstration of abnormalities involving 13q14 in patients with B-cell malignancies. The incidence of abnormalities involving 13q14 and their significance in the development of neoplasias, other than retino-blastoma, is discussed.     

Characterization of chromosome arm 20q abnormalities in myeloid malignancies using genome‐wide single nucleotide polymorphism array analysis

Deletion of the long arm of chromosome 20 is a common abnormality associated with myeloid malignancies. We characterized abnormalities of chromosome 20 as defined by metaphase cytogenetics (MC) in patients with myeloid neoplasms to define commonly deleted regions (CDR) and commonly retained regions (CRR) using genome‐wide, high resolution single nucleotide polymorphism array (SNP‐A) analysis. We reviewed the MC results of a cohort of 1,162 patients with myeloid malignancies, including myelodysplastic syndromes (MDS), MDS/myeloproliferative neoplasia (MDS/MPN), and acute myeloid leukemia (AML). We further analyzed a subcohort of 532 patients by SNP‐A using the Affymetrix Genome‐Wide Human SNP Array 6.0 and GeneChip Human Mapping 250K Nsp arrays. By MC, 5% (54/1,162) harbored a deletion of 20q; in 30% (16/54), del(20q) was the sole cytogenetic abnormality. By SNP‐A analysis, we identified del(20q) in 23 patients, 3 not detected by MC. In four cases, monosomy 20 with a marker chromosome by MC was proven to be an interstitial deletion of 20q by SNP‐A. We defined 2 CDR and 2 CRR on chromosome arm 20q: CDR1 spanned 2.5 Mb between bands 20q11.23 and 20q12, while CDR2 encompassed 1.8 Mb within 20q13.12. CRR1 spanned 1.9 Mb within 20q11.21 and CRR2 encompassed 2.5 Mb within 20q13.33. In contrast to other chromosomes frequently affected by deletions, no somatic copy neutral loss of heterozygosity (CN‐LOH) was detected. Our data suggest that SNP‐A is useful for the detection of cryptic aberrations of chromosome 20q and allows for a more precise characterization of complex karyotypes. Furthermore, SNP‐A allowed definition of a CDR on 20q. © 2010 Wiley‐Liss, Inc.     

伴复杂核型异常的髓系恶性血液病中17号染色体异常分析

目的 研究伴复杂核型异常(complex chromosomal abnormalities,CCAs)的髓系恶性血液病中17号染色体的异常特征.方法 经R显带常规细胞遗传学分析显示CCAs的73例髓系恶性血液病,包括21例急性髓系白血病(acute myeloid leukemia,AML)、36例慢性髓系白血病(chronic myeloid leukemia,CML)、16例骨髓增生异常综合征(myelodysplastic syndrome,MDS),并进一步多重荧光原位杂交分析.结果 73例伴CCAs的髓系恶性血液病中,17号染色体异常最常见,占46.5%(34/73),其中AML12例,CML13例,MDS9例,9例CML慢性期患者均未见17号染色体异常.结构异常较多见,总发生率为43.8%(32/73);AML、CML、MDS3组发生率分别为52.4%(11/21)、33.3%(12/36)、56.3%(9/16);所有病例中发生数目异常共15.1%(11/73),三组发生率分别为25.0%(3/12)、38.5%(5/13)、33.3%(3/9),11例数目异常均为-17.有9例同时出现数目异常和结构异常.伴有17号染色体的结构异常中,以非平衡易位多见,3组分别为16、15、8个;平衡易位2个,分别为发生于AML中的t(15;17)及发生于CML中的t(15;17;22).17号染色体结构易位的对手染色体多变,包括了除5号、6号和22号外的所有染色体.结构易位频率最高的对手染色体是15号,占8.2%(6/73);其次为2号,占5.4%(4/73).6例存在17号与15号易位的病例中5例为急性早幼粒白血病,1例为CML急变期.结论 伴CCAs的髓系恶性血液病中17号染色体异常发生率高,以结构异常为主.所有的数目异常均为-17;结构异常以非平衡易位多见.     

Frequent allelic loss of 21q11.1 approximately q21.1 region in advanced stage oral squamous cell carcinoma

A fine mapping of loss of heterozygosity (LOH) was performed in oral squamous cell carcinoma (OSCC), using 12 markers on 21q11.1 approximately q21.1. We studied 43 resected primary invasive tumors and their paired normal tissues, concurrent dysplasia or carcinoma in situ in separate areas from 8 of the specimens, and 6 local recurrent carcinomas. LOH status was compared between lesions of different phases of progression within the same patient. A high frequency of LOH was observed for D21S1410, D21S120, and D21S1433 (60% each) in the primary lesions, constituting two interstitial deleted regions encompassing eight known genes. Cases showing LOH of D21S120 were significantly associated with advanced clinical stages (III and IV; P=0.02). Consistent allelic loss was observed in 64.2% of the informative cases between the precursor lesions and their corresponding invasive tumors, and in 59.5% of those between the primary lesions and their recurrent counterparts. Fewer than half of the different lesions within a given patient showed discordant allelic loss for tested markers. Our results suggest that 21q11.1 approximately q21.1 harbors tumor suppressor genes in OSCC. Genetic divergence may develop during tumor clone evolution.     

A t(1;9)(q23.3 approximately q25;q34) affecting the ABL1 gene in a biphenotypic leukemia

Recurring chromosome translocations, which are found in leukemia, can result in the inappropriate expression of oncogenes or in the formation of chimeric genes that code for structurally and functionally abnormal proteins. The chromosomal t(1;9)(q23.3 approximately q25;q34) was found in a patient with biphenotypic leukemia. Fluorescence in situ hybridization (FISH) analysis revealed that the break on chromosome 9 occurred in the ABL1 gene. The breakpoint on chromosome 1 occurred distal to the PBX1 gene at 1q23.3, as shown by FISH using BAC RP11-503N16 and RP11-403P14, which flank the PBX1 locus; hence, the ABL1 gene can be fused with another gene distal to PBX1 gene.     

The human Penumbra gene is mapped to a region on chromosome 7 frequently deleted in myeloid malignancies

We previously cloned the murine Penumbra gene based on its differential expression in proerythroblasts/erythroblasts. Subsequently, we identified human Penumbra cDNA from a human bone marrow cDNA library and the human Penumbra gene from a BAC library. Penumbra is a new member of the tetraspanin protein family and exhibits growth-suppressive activity in vitro. In this study, we designed a human Penumbra probe contig and used fluorescent in situ hybridization (FISH) to analyze seven cases of myeloid malignancies with 7q deletions. Five patients with cytogenetic deletions involving 7q31.2 approximately q32 also showed deletions of Penumbra by FISH; these were not present in two patients with cytogenetic deletions not involving 7q31.2 approximately q32. Our findings provide the first FISH evidence supporting the mapping of human Penumbra to 7q31.2 approximately q32 and demonstrate the potential of the Penumbra probe in the detection of 7q31 approximately q32-related deletions in myeloid malignancies.     

An interstitial duplication of chromosome 13q31.3q32.1 further delineates the critical region for postaxial polydactyly type A2

Postaxial polydactyly type A2 (PAP-A2; OMIM 602085) is a common feature seen in patients with a partial duplication of the long arm of chromosome 13. Dose dependency has been shown for digital malformations in this region, deletions resulting in oligodactyly and duplications in polydactyly. We aimed to narrow down the critical region for PAP-A2 in order to identify candidate genes.We performed chromosomal analysis, FISH and array-CGH in a patient with an interstitial duplication of chromosome 13q31.3q32.1 and a mild phenotype including postaxial polydactyly. The duplicated region spanned 5.59 Mb (89.67–95.25 Mb) and contained eleven known genes, including GPC5 and GPC6.GPC5 and GPC6 show homology with GPC3 and GPC4, genes involved in Simpson-Golabi-Behmel syndrome, an overgrowth syndrome in which also polydactyly can occur. Mouse studies have shown expression of both GPC5 and GPC6 in developing limbs. Therefore, we propose that GPC5 and GPC6 are the most likely candidate genes for PAP-A2.     

Clinical significance of allelic loss of chromosome region 5q22.3 approximately q23.2 in nonpapillary renal cell carcinoma

To analyze the clinical significance of copy number gain and loss at chromosome region 5q21 approximately q23, 105 nonpapillary renal cell carcinomas (RCC) were examined by interphase cytogenetic analysis using the dual-color fluorescence in situ hybridization (FISH) technique. DNA probes for D5S23 (5p15.2), cCI5-243 (5q21.2 approximately q21.3), and cCI5-215 (5q22.3 approximately q23.2) were used, and the signals for cCI5-243 and cCI5-215 were compared with those for D5S23 as the numerical control. Aneusomy (three or more copies) of chromosome 5 was found in 22 tumors (21.0%). Aneusomy was significantly correlated with loss at 5q21 approximately q23, while disomy with gain at 5q21 approximately q23 (P<0.05). Aneusomy was also significantly related to poor disease-specific survival (P<0.01). Gain and loss at cCI5-243 were seen in 34 (32.4%) and 59 (56.2%) tumors, respectively, while gain and loss at cCI5-215 occurred in 55 (52.4%) and 45 (42.9%) cases, respectively. The frequency of gain at cCI5-215 was significantly correlated with a smaller tumor diameter (7 cm or less, P<0.05), while loss with a larger one (>7 cm, P<0.05). Both loss at cCI5-215 and aneusomy of chromosome 5 were significantly related to poor disease-specific survival (P<0.05). In conclusion, alterations of chromosome 5 (including allelic loss of 5q22.3 approximately q23.2) could be a useful genetic marker for predicting the patient prognosis of RCC.     

Secondary nonrandom chromosomal abnormalities of band 13q34 in Burkitt lymphoma-leukemia

Clonal abnormalities of the long arm of chromosome 13 were detected in 9 of 54 patients with Burkitt lymphoma-leukemia. All abnormalities involved band 13q34, in three patients as t(1;13). The 13q34 abnormalities are thus the second most frequent secondary chromosomal abnormalities, after those of chromosome I, in these lymphoid proliferations.     

RAS, FLT3, and TP53 mutations in therapy-related myeloid malignancies with abnormalities of chromosomes 5 and 7

Oncogenic mutations in the KRAS2, NRAS, or FLT3 gene are detected in more than 50% of patients with de novo acute myeloid leukemia (AML). RAS mutations are also prevalent in de novo myelodysplastic syndrome (MDS), especially chronic myelomonocytic leukemia and juvenile myelomonocytic leukemia. However, few studies have examined these genetic lesions in therapy-related myeloid malignancies. Monosomy 7/del(7q) and monosomy 5/del(5q) represent the most common cytogenetic abnormalities in therapy-related MDS and AML (t-MDS/t-AML) and are strongly associated with prior exposure to alkylating agents. Mutational analysis of bone marrow specimens from a well-characterized cohort of 26 t-MDS/t-AML patients with abnormalities of chromosomes 5 and/or 7 revealed 3 with RAS mutations. Further analyses of 23 of these cases uncovered one FLT3 internal tandem duplication and five TP53 mutations. The four patients with RAS or FLT3 mutations had monosomy 7, including one with abnormalities of chromosomes 5 and 7. One specimen demonstrated mutations in both KRAS2 and TP53. RAS and FLT3 mutations, which are thought to stimulate the proliferation of leukemia cells, appear to be less common in t-MDS/t-AML than in de novo AML, whereas TP53 mutations are more frequent.     

A group of previously not recognized cytogenetic abnormalities in myeloid hematological malignancies.

We have identified a group of previously not reported chromosome abnormalities related to myeloid hematological malignancies. Cases 1 and 2 were observed to have an additional i(4)(p10) as the sole anomaly with similar clinical features of myeloid disorders; that is, acute nonlymphocytic leukemia (ANLL-M2) and myelodysplastic syndrome (MDS)-refractory anemia with an excess of blasts in transformation, respectively. Fluorescence in situ hybridization studies with the use of a 4p-specific microdissection probe further confirmed the presence of an i(4)(p10) in these patients. Case 3 was diagnosed with ANLL-M1 and had an additional i(8)(p10) as the only change, also confirmed by a whole-chromosome painting procedure. In cases 4-6, deletions of 18q at breakpoints q12, q23, and q21 were identified as the sole anomaly in a myeloproliferative disorder (MPD), MPD, and MDS, respectively. X-autosome translocations other than t(X;10)(p11;p11) and t(X;11)(q13;q23) have not been reported as recurrent or primary changes in hematological disorders. In the present study, a t(X;9)(q26;q22) and t(X;5)(q13;q33) as the sole anomaly were found in cases 7 and 8, respectively. Both cases had the same diagnosis of MDS. Considering that trisomies 4 (+4) and 8 (+8) are common anomalies in MDS and ANLL, our findings strongly indicate that amplification of genes on 4p and 8p, but not on 4q and 8q, may play a crucial role in the pathogenesis of MDS and ANLL. In addition, genes on 18q12-23 and on Xq13-26 may be involved in the pathogenesis of myeloid disorders.