The Editors of Molecular Cytogenetics would like to thank all our reviewers who have contributed to the journal in volume 6 (2013).
Chromosome 16 contains multiple copy number variations (CNVs) that predispose to genomic disorders. Here, we differentiate pathogenic duplications of 16p11.2–p12.2 from microscopically similar euchromatic variants of 16p11.2. Patient 1 was a girl of 18 with autism, moderate intellectual disability, behavioural difficulties, dysmorphic features and a 7.71-Mb (megabase pair) duplication (16:21 521 005–29 233 146). Patient 2 had a 7.81-Mb duplication (16:21 382 561–29 191 527), speech delay and obsessional behaviour as a boy and, as an adult, short stature, macrocephaly and mild dysmorphism. The duplications contain 65 coding genes of which Polo-like kinase 1 (PLK1) has the highest likelihood of being haploinsufficient and, by implication, a triplosensitive gene. An additional 1.11-Mb CNV of 10q11.21 in Patient 1 was a possible modifier containing the G-protein-regulated inducer of neurite growth 2 (GPRIN2) gene. In contrast, the euchromatic variants in Patients 3 and 4 were amplifications from a 945-kb region containing non-functional immunoglobulin heavy chain (IGHV), hect domain pseudogene (HERC2P4) and TP53-inducible target gene 3 (TP53TG3) loci in proximal 16p11.2 (16:31 953 353–32 898 635). Paralogous pyrosequencing gave a total copy number of 3–8 in controls and 8 to >10 in Patients 3 and 4. The 16p11.2–p12.2 duplication syndrome is a recurrent genomic disorder with a variable phenotype including developmental delay, dysmorphic features, mild to severe intellectual disability, autism, obsessive or stereotyped behaviour, short stature and anomalies of the hands and fingers. It is important to differentiate pathogenic 16p11.2–p12.2 duplications from harmless, microscopically similar euchromatic variants of proximal 16p11.2, especially at prenatal diagnosis.
chromosomes, human, pair 16; chromosome duplication; 16p11.2–p12.2; DNA array; euchromatic variant; copy number variation
The t(3;12)(q26;p13) translocation is a recurrent chromosomal aberration observed in myeloid malignancies. The translocation results in the generation of the ETV6/myelodysplastic syndrome 1 (MDS1)/ectopic viral integration site 1 (EVI1) fusion gene. However, the present case report is the first to present this rearrangement in acute myelogeneous leukemia (AML)-M4. Notably, this case is the first report of AML-M4 with an initial trisomy 8 and secondary acquired t(3;12)(q26;p13). Cells harboring the t(3;12) translocation were found to exhibit a higher proliferative capacity than cells with pure trisomy 8, which is consistent with the role of the ETV6/MDS1/EVI1 fusion transcript in the development and progression of malignancy.
t(3;12)(q26;p13); ETV6/MDS1/EVI1; acute myeloid leukemia M4; trisomy 8
The chromosomal homologies of human (Homo sapiens = HSA) and silvered leaf monkey (Trachypithecus cristatus = TCR) have been previously studied by classical chromosome staining and by fluorescence in situ hybridization (FISH) applying chromosome-specific DNA probes of all human chromosomes in the 1980s and 1990s, respectively.
However, as the resolution of these techniques is limited we used multicolor banding (MCB) at an ~250-band level, and other selected human DNA probes to establish a detailed chromosomal map of TCR. Therefore it was possible to precisely determine evolutionary conserved breakpoints, orientation of segments and distribution of specific regions in TCR compared to HSA. Overall, 69 evolutionary conserved breakpoints including chromosomal segments, which failed to be resolved in previous reports, were exactly identified and characterized.
This work also represents the first molecular cytogenetic one characterizing a multiple sex chromosome system with a male karyotype 44,XY1Y2. The obtained results are compared to other available data for old world monkeys and drawbacks in hominoid evolution are discussed.
Evolutionary conserved breakpoints; Multicolor banding; Old world monkeys; XY1Y2 sex system
Recurrent pregnancy loss is a common occurrence and a matter of concern for couples planning the pregnancy. Chromosomal abnormalities, mainly balanced rearrangements, are common in couples with repeated miscarriages.
The purpose of this study is to evaluate the contribution of chromosomal anomalies causing repeated spontaneous miscarriages and provide detailed characterization of a few structurally altered chromosomes.
MATERIALS AND METHODS:
A retrospective cytogenetic study was carried out on 4859 individuals having a history of recurrent miscarriages. The cases were analyzed using G-banding and fluorescence in situ hybridization wherever necessary.
Chromosomal rearrangements were found in 170 individuals (3.5%). Translocations were seen in 72 (42.35%) cases. Of these, reciprocal translocations constituted 42 (24.70%) cases while Robertsonian translocations were detected in 30 (17.64%) cases. 7 (4.11%) cases were mosaic, 8 (4.70%) had small supernumerary marker chromosomes and 1 (0.6%) had an interstitial microdeletion. Nearly, 78 (1.61%) cases with heteromorphic variants were seen of which inversion of Y chromosome (57.70%) and chromosome 9 pericentromeric variants (32.05%) were predominantly involved.
Chromosomal analysis is an important etiological investigation in couples with repeated miscarriages. Characterization of variants/marker chromosome enable calculation of a more precise recurrent risk in a subsequent pregnancy thereby facilitating genetic counseling and deciding further reproductive options.
Break points; chromosomal abnormalities; recurrent loss of pregnancy; small supernumerary marker chromosome; translocations
Plasma cell leukemia (PCL) is a rare lymphoproliferative disorder, accounting for 1-2% of all plasma cell neoplasms, characterized by the presence of >2 × 109/l of plasma cells circulating in the peripheral blood, and exists in two forms: primary PCL (pPCL, 60% of the cases), and secondary PCL (sPCL), the latter being a leukemic transformation in patients with a previously diagnosed multiple myeloma. PCL is an aggressive disease with poor prognosis and a short median survival of 7 months.
Here, we report a pPCL case with hepatosplenomegaly, anemia, thrombocytopenia, fever, fatigue, weight loss, and plasma cell count up to 60% in peripheral blood and 80% in bone marrow. Immunophenotype was compatible with PCL. A del(9)(p22.3) was characterized using banding cytogenetics and array-proven multicolor banding (aMCB), the latter being of enormous significance to characterize breakpoint regions in detail.
To the best of our knowledge, this is the first report of pPCL associated with a partially monosomy 9pter to 9p22.3 as a sole chromosomal abnormality.
Primary plasma cell leukemia; Multiple myeloma; Del(9)(p22.3); Array-proven multicolor banding; Prognostic factors
The Philadelphia (Ph) chromosome is present in more than 90% of patients suffering from chronic myeloid leukemia (CML). It is the product of a reciprocal translocation between the long arms of chromosomes 9 and 22, resulting in the transfer of the 3′ portion of the proto-oncogene ABL from 9q34 to the 5′ portion of the breakpoint cluster region (BCR) on 22q11. Currently, most CML cases are treated with Imatinib and variant rearrangements are thought to have no specific prognostic significance, although the events of therapy resistance have not yet been studied. In this study we report a novel case of CML exhibiting an uncommon t(2;7)(p13.1;p21.3) besides t(9;22)(q34;q11). This unusual translocation has been characterized by fluorescence in situ hybridization (FISH) and array-proven multicolor banding (aMCB), the latter being extremely significant in characterizing breakpoint regions in detail. The underlying mechanisms and prognostic implications of this cytogenetic abnormality are discussed in this study.
chronic myeloid leukemia; ETV1; ATR1; fluorescence in situ hybridization; high resolution array-proven multicolor banding; imatinib mesylate
Alterations in the human chromosomal complement are expressed phenotypically ranging from (i) normal, via (ii) frequent fetal loss in otherwise normal person, to (iii) sub-clinical to severe mental retardation and dysmorphism in live births. A subtle and microscopically undetectable chromosomal alteration is uniparental disomy (UPD), which is known to be associated with distinct birth defects as per the chromosome involved and parental origin. UPD can be evident due to imprinted genes and/or activation of recessive mutations.
The present study comprises of data mining of published UPD cases with a focus on associated phenotypes. The goal was to identify non-random and recurrent associations between UPD and various genetic conditions, which can possibly indicate the presence of new imprinted genes.
SETTINGS AND DESIGN:
Data mining was carried out using the homepage “http://www.fish.uniklinikum-jena.de/UPD.html.”, an online catalog of published cases with UPD.
MATERIALS AND METHODS:
The UPD cases having normal karyotype and with or without clinical findings were selected to analyze the associated phenotypes for each chromosome, maternal or paternal involved in UPD.
Our results revealed many genetic conditions (other than the known UPD syndromes) to be associated with UPD. Even in cases of bad obstetric history as well as normal individuals chance detection of UPD has been reported.
The role of UPD in human genetic disorders needs to be studied by involving larger cohorts of individuals with birth defects as well as normal population. The genetic conditions were scrutinized in terms of inheritance patterns; majority of these were autosomal recessive indicating the role of UPD as an underlying mechanism.
Autosomal recessive; birth defects; data mining; phenotypic expression; uniparental disomy
The editors of Molecular Cytogenetics would like to thank all our reviewers who have contributed to the journal in volume 5 (2012).
Since being established in 1963, the murine fibroblast cell line NIH 3T3 has been
used in thousands of studies. NIH 3T3 immortalized spontaneously and became
tetraploid shortly after its establishment. Here we report the first molecular
cytogenetic characterization of NIH 3T3 using fluorescence in situ hybridization
based multicolor banding (mcb). Overall, a complex rearranged karyotype
presenting 16 breakpoints was characterized. Also it was possible to deduce the
resulting gains and losses of copy numbers in NIH 3T3. Overall, only 1.8% of the
NIH 3T3 genome is disome, 26.2% tri-, 60% tetra-, 10.8% quinta-, and 1.2%
hexasome. Strikingly, the cell line gained only 4 derivative chromosomes since
its first cytogenetic description in 1989. An attempt to align the observed
imbalances of the studied cell line with their homologous regions in humans gave
the following surprising result: NIH 3T3 shows imbalances as typically seen in
human solid cancers of ectodermal origin.
NIH 3T3 cell line; murine multicolor banding (mcb); cytogenetics; genetics; fluorescence in situ hybridization (FISH)
Heterochromatic variants of pericentromere of chromosome 9 are reported and discussed since decades concerning their detailed structure and clinical meaning. However, detailed studies are scarce. Thus, here we provide the largest ever done molecular cytogenetic research based on >300 chromosome 9 heteromorphism carriers.
In this study, 334 carriers of heterochromatic variants of chromosome 9 were included, being 192 patients from Western Europe and the remainder from Easter-European origin. A 3-color-fluorescence in situ hybridization (FISH) probe-set directed against for 9p12 to 9q13~21.1 (9het-mix) and 8 different locus-specific probes were applied for their characterization. The 9het-mix enables the characterization of 21 of the yet known 24 chromosome 9 heteromorphic patterns. In this study, 17 different variants were detected including five yet unreported; the most frequent were pericentric inversions (49.4%) followed by 9qh-variants (23.9%), variants of 9ph (11.4%), cenh (8.2%), and dicentric- (3.8%) and duplication-variants (3.3%). For reasons of simplicity, a new short nomenclature for the yet reported 24 heteromorphic patterns of chromosome 9 is suggested. Six breakpoints involved in four of the 24 variants could be narrowed down using locus-specific probes.
Based on this largest study ever done in carriers of chromosome 9 heteromorphisms, three of the 24 detailed variants were more frequently observed in Western than in Eastern Europe. Besides, there is no clear evidence that infertility is linked to any of the 24 chromosome 9 heteromorphic variants.
Chromosome 9; Heteromorphism; Breakpoints; Western Europe; Eastern Europe
Chronic myelogenous leukemia (CML) is characterized by the Philadelphia (Ph) chromosome created by the reciprocal translocation t(9:22)(q34;q11), resulting in the chimeric gene breakpoint cluster region (BCR)-Abelson (ABL). Variant Ph chromosome translocations involving chromosomes other than 9 and 22 occur in 5–10% of CML cases. In the present study, a novel case of a Ph chromosome-positive CML in the chronic phase (CP) is reported, with a three-way Ph translocation involving three chromosomal regions, 9q34, 10p11.2 and 22q11.2, in addition to the loss of the Y chromosome, where the latter was a secondary abnormality. Since the majority of CML cases are currently treated with imatinib, variant rearrangements generally have no specific prognostic significance, although the mechanisms involved in resistance to therapy have yet to be investigated. The underlying mechanisms and prognostic implications of these cytogenetic abnormalities are discussed in the present study.
chronic myeloid leukemia; three-way Philadelphia translocation; fluorescence in situ hybridization; multicolor banding; imatinib mesylate
The so-called Philadelphia (Ph) chromosome is present in more than 90% of chronic myeloid leukemia (CML) cases. Amplification or duplication of the BCR-ABL gene has been found to be one of the key factors leading to drug resistance to imatinib mesylate (IM). In the present study, we identified the presence of isodicentric Ph chromosomes [idic(Ph)] in an IM-resistant patient. Fluorescence in situ hybridization (FISH) analysis on metaphase chromosomes confirmed the heterogeneity and amplification of the fused BCR-ABL gene. FISH analysis superimposed on G-banding confirmed the presence of idic(Ph) chromosomes. Reverse transcription-polymerase chain reaction (RT-PCR) products revealed the presence of the BCR-ABL fusion transcript b3a2. The idic(Ph) chromosomes in CML were shown to be fused at the satellite regions of the short arms. The patient did not respond to IM chemotherapy and did not achieve remission. In this study, the impact of the idic(Ph) chromosomes on genomic instability, heterogeneity and amplification of the BCR-ABL gene in IM-resistant patients is discussed.
chronic myeloid leukemia; isodicentric Philadelphia chromosomes; fluorescence in situ hybridization; imatinib mesylate
Here, we present a case with an unusual chromosomal rearrangement in a child with a predominant phenotype of high-pitched crying showing deletion encompassing CTNND2 due to an unbalanced translocation of chromosomes 4 and 5. This rearrangement led to a duplication of ~35 Mb in 4qter which replaced 18 Mb genetic materials in 5pter. Even though, in this patient, there was no clinically obvious modification to the classical phenotypes of CdCS, and the influence of the 4q-duplication cannot be completely excluded in this case. However, the region 4q34.1–34.3 was previously reported as a region not leading to phenotypic changes if present in three copies, an observation which could possibly be supported by this case. Conclusion. This study showed that in a patient with an unbalanced translocation resulting in 5p deletion, the presence of partial trisomy of chromosome 4q could be clinically insignificant.
Chronic myelogenous leukemia (CML) is characterized by the Philadelphia (Ph) chromosome, created by a reciprocal translocation t(9:22)(q34;q11) which forms the chimeric gene, BCR-ABL. Variant Ph chromosome translocations involving chromosomes other than 9 and 22 have been identified in 5–10% of CML cases. Four-way Ph chromosome translocations are an extremely rare event in myeloid malignancies and the phenotypic consequences of such rearrangements have not been investigated. Deletions in chromosome 9 are known to be associated with a poor prognosis. In the present study, a novel case of Ph chromosome-positive CML in blast crisis is reported. A four-way Ph translocation was identified, involving five chromosomal regions, 9p21, 9q34, 12p13.3, 20q11.2 and 22q11.2, as well as an unbalanced translocation, der(7)t(7;8)(p11.2;q11.2). Since the majority of CML cases are currently treated with imatinib, variant rearrangements in general have no specific prognostic significance, although the mechanisms involved in resistance to therapy have yet to be investigated. In the present case, multiple partial deletions, including ABL and ASS genes on chromosome 9, the region 7p11.2 to 7pter, 8q11.2 to 8pter and two regions on chromosome 12, were identified. An additional Ph chromosome was also detected. Immunophenotyping indicated that the patient had biphenotypic leukemia. The patient did not respond positively to imatinib chemotherapy and died for unknown reasons, one month after diagnosis. The underlying mechanisms and prognostic implications of these cytogenetic abnormalities are discussed.
chronic myeloid leukemia; four-way Philadelphia translocation; fluorescence in situ hybridization; array-proven multicolor banding; imatinib mesylate
The so-called Philadelphia (Ph) chromosome is found in over 90% of cases of chronic myeloid leukemia (CML). Of these cases, 2–10% demonstrate complex translocations involving a third chromosome in addition to chromosomes 9 and 22. Since the majority of CML cases are currently treated with imatinib, variant rearrangements tend to have no specific prognostic significance, although the mechanisms involved in resistance to therapy have yet to be investigated. This study evaluated a CML case with complex chromosomal aberrations not previously observed. A four-chromosome translocation involving chromosomal regions including 11p11.2 and 20q11.21 in addition to 9q34 and 22q11 was characterized in detail using array-proven multicolor banding (aMCB), a technique which has proven to be of significance in characterizing breakpoint regions in detail. Underlying mechanisms and prognostic factors are discussed.
chronic myeloid leukemia; KAI1; KIF3B; variant Philadelphia chromosome; fluorescence in situ hybridization; high-resolution array-proven multicolor banding; imatinib mesylate
Recently, array-comparative genomic hybridization (aCGH) platforms have significantly improved the resolution of chromosomal analysis allowing the identification of genomic copy number gains and losses smaller than 5 Mb. Here we report on a young man with unexplained severe mental retardation, autism spectrum disorder, congenital malformations comprising hypospadia and omphalocele, and episodes of high blood pressure. An ~ 6 Mb interstitial deletion that includes the causative genes is identified by oligonucleotide-based aCGH.
Our index case exhibited a de novo chromosomal abnormality at 2q22 [del(2)(q22.1q22.3)dn] which was not visible at the 550 haploid band level. The deleted region includes eight genes: HNMT, SPOPL, NXPH2, LOC64702, LRP1B, KYNU, ARHGAP15 and GTDC1.
aCGH revealed an ~ 6 Mb deletion in 2q22.1 to 2q22.3 in an as-yet unique clinical case associated with intellectual disability, congenital malformations and autism spectrum disorder. Interestingly, the deletion is co-localized with a fragile site (FRA2K), which could be involved in the formation of this chromosomal aberration. Further studies are needed to determine if deletions of 2q22.1 to 2q22.3 define a new microdeletion syndrome.
Array-comparative genomic hybridization (aCGH); Fluorescence in situ hybridization (FISH); 2q22 deletion syndrome; Birth defects; Hypospadia; omphalocele; Severe mental retardation; Essential hypertension; High blood pressure
Acute lymphoblastic leukemia (ALL), CD10+ B-cell precursor, represents the most frequent type of childhood ALL from 3 to 6 years of age. The t(12;21)(p13;q22) occurs in 25% of cases of B-cell precursor ALL, it is rare in children less than 24 months and have been related to good prognosis. Some relapse cases and unfavorable prognosis in ALL CD10+ are associated with t(12;21) bearing additional aberrations as extra copies of chromosome 21 and ETV6 gene loss. This report describes the case of a 15 month-year old girl, who displayed a karyotype with addition on chromosome 12p plus trisomy 10 and tetrasomy of chromosome 21. Molecular cytogenetic studies revealed two extra copies of the der(21) t(12;21), trisomy 10 and deletion of the second ETV6 gene due to the dic(12;18). These findings show the great importance of molecular cytogenetic studies to clarify complex karyotypes, to define prognostic, to carry out risk group stratification and to support correctly disease treatment in childhood acute lymphoblastic leukemia.
Small supernumerary marker chromosomes (sSMC) are detected in 0.043% of general population and can be characterized for their chromosomal origin, genetic content and shape by molecular cytogenetic approaches. Even though recently progress was achieved towards genotype-phenotype-correlations of sSMC, nothing is known on the influence that an additional derivative extra chromosome has on the nuclear architecture.
Here we present the first three-dimensional interphase fluorescence in situ hybridization (FISH) studies for the nuclear architecture of sSMC. It could be shown that sSMC derived from chromosomes 15, 16 or 18 preferentially colocalized with one of their corresponding sister chromosomes. This was true in B- and T-lymphocytes as well as in skin fibroblasts. Additionally, a case with a complex sSMC with a karyotype 47,XY,+der(18)t(8;18)(8p23.2 ~ 23.1;18q11.1) was studied. Here the sSMC co-localized with one homologous chromosome 8 instead of 18.
Overall, there is a kind of "attraction" between an sSMC and one of its homologous sister chromosomes. This seems to be transmitted by the euchromatic part of the sSMC rather than its heterochromatic one.
The so-called Philadelphia (Ph) chromosome is present in more than 90% of chronic myeloid leukemia (CML) patients. Approximately, 5–10% of these patients show complex translocations involving a third chromosome in addition to chromosomes 9 and 22. Since at present the majority of CML cases are treated with imatinib, variant rearrangements do not exhibit specific prognostic significance. However, events of therapy resistance remain to be studied. In this study, we report a unique case of CML exhibiting an uncommon t(21;22)(p12;q11). This translocation has been characterized by fluorescence in situ hybridization (FISH) and array-proven multicolor banding (aMCB). Using specific probes for the BCR and ABL genes, results of FISH showed a three-way variant Philadelphia translocation (9;22;21)(q34;q11;p12) with a BCR/ABL fusion residing on the der(22) and the 3′BCR region translocated on the short arm of the derivative chromosome 21. In addition, the aMCB technique is significant in the detection of the breakpoints of genetic changes. The underlying mechanisms and prognostic significance of these changes are discussed.
chronic myeloid leukemia; variant Philadelphia chromosome; fluorescence in situ hybridization; high-resolution array-proven multicolor banding; imatinib mesylate
Genomic instability, a hallmark of cancer, occurs preferentially at specific genomic regions known as common fragile sites (CFSs). CFSs are evolutionarily conserved and late replicating regions with AT-rich sequences, and CFS instability is correlated with cancer. In the last decade, much progress has been made toward understanding the mechanisms of chromosomal instability at CFSs. However, despite tremendous efforts, identifying a cancer-associated CFS gene (CACG) remains a challenge and little is known about the function of CACGs at most CFS loci. Recent studies of FATS (for Fragile-site Associated Tumor Suppressor), a new CACG at FRA10F, reveal an active role of this CACG in regulating DNA damage checkpoints and suppressing tumorigenesis. The identification of FATS may inspire more discoveries of other uncharacterized CACGs. Further elucidation of the biological functions and clinical significance of CACGs may be exploited for cancer biomarkers and therapeutic benefits.
replication; instability; CFS; cancer; FATS; checkpoint