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author:("lihr, Thomas")
1.  Comparative cytogenetics in the genus Hoplias (Characiformes, Erythrinidae) highlights contrasting karyotype evolution among congeneric species 
Background
The Erythrinidae fish family contains three genera, Hoplias, Erythrinus and Hoplerythrinus widely distributed in Neotropical region. Remarkably, species from this family are characterized by an extensive karyotype diversity, with 2n ranging from 39 to 54 chromosomes and the occurrence of single and/or multiple sex chromosome systems in some species. However, inside the Hoplias genus, while H. malabaricus was subject of many studies, the cytogenetics of other congeneric species remains poorly explored. In this study, we have investigated chromosomal characteristics of four Hoplias species, namely H. lacerdae, H. brasiliensis, H. intermedius and H. aimara. We used conventional staining techniques (C-banding, Ag-impregnation and CMA3 -fluorescence) as well as fluorescence in situ hybridization (FISH) with minor and major rDNA and microsatellite DNAs as probes in order to analyze the karyotype evolution within the genus.
Results
All species showed invariably 2n = 50 chromosomes and practically identical karyotypes dominated only by meta- and submetacentric chromosomes, the absence of heteromorphic sex chromosomes, similar pattern of C-positive heterochromatin blocks and homologous Ag-NOR-bearing pairs. The cytogenetic mapping of five repetitive DNA sequences revealed some particular interspecific differences between them. However, the examined chromosomal characteristics indicate that their speciation was not associated with major changes in their karyotypes.
Conclusion
Such conserved karyotypes contrasts with the extensive karyotype diversity that has been observed in other Erythrinidae species, particularly in the congeneric species H. malabaricus. Nevertheless, what forces drive such particularly different modes of karyotype evolution among closely related species? Different life styles, population structure and inner chromosomal characteristics related to similar cases in other vertebrate groups can also account for the contrasting modes of karyotype evolution in Hoplias genus.
doi:10.1186/s13039-015-0161-4
PMCID: PMC4518567
Trahiras; Fish cytogenetics; FISH; Repetitive DNA; Chromosome change and speciation
2.  Prader-Willi syndrome - type 1 deletion, a consequence of an unbalanced translocation of chromosomes 13 and 15, easily to be mixed up with a Robertsonian translocation 
Background
Prader-Willi syndrome, due to microdeletion of proximal 15q, is a well-known cause of syndromic obesity.
Case characteristics
A couple with history of repeated first trimester abortions had a son with balanced Robertsonian translocation of chromosomes 13 and 15 according to cytogenetic banding technique.
Results
Chromosomal analysis for the couple was performed. A balanced translocation involving BP1-BP3 region of proximal 15q was observed in the father.
Discussion
Investigations of the parents is mandatory when a structural rearrangement is detected in a dysmorphic child.
doi:10.1186/s13039-015-0163-2
PMCID: PMC4510909  PMID: 26203302
Structural rearrangement; sSMC; Deletion; Prader-Willi syndrome; Unbalanced translocation; FISH
3.  High rates of submicroscopic aberrations in karyotypically normal acute lymphoblastic leukemia 
Background
Acute lymphoblastic leukemia (ALL) is not a single uniform disease. It consists of several subgroups with different cytogenetic and molecular genetic aberrations, clinical presentations and outcomes. Banding cytogenetics plays a pivotal role in the detection of recurrent chromosomal rearrangements and is the starting point of genetic analysis in ALL, still. Nowadays, molecular (cyto)genetic tools provide substantially to identify previously non-detectable, so-called cryptic chromosomal aberrations in ALL. However, ALL according to banding cytogenetics with normal karyotype - in short cytogenetically normal ALL (CN-ALL) - represent up to ~50 % of all new diagnosed ALL cases. The overall goal of this study was to identify and characterize the rate of cryptic alterations in CN-ALL and to rule out if one single routine approach may be sufficient to detect most of the cryptic alterations present.
Results
Sixty-one ALL patients with CN-ALL were introduced in this study. All of them underwent high resolution fluorescence in situ hybridization (FISH) analysis. Also DNA could be extracted from 34 ALL samples. These DNA-samples were studied using a commercially available MLPA (multiplex ligation-dependent probe amplification) probe set directed against 37 loci in hematological malignancies and/or array-comparative genomic hybridization (aCGH). Chromosomal aberrations were detected in 21 of 61 samples (~34 %) applying FISH approaches: structural abnormalities were present in 15 cases and even numerical ones were identified in 6 cases. Applying molecular approaches copy number alterations (CNAs) were detected in 27/34 samples. Overall, 126 CNAs were identified and only 34 of them were detectable by MLPA (~27 %). Loss of CNs was identified in ~80 % while gain of CNs was present in ~20 % of the 126 CNAs. A maximum of 13 aberrations was detected per case; however, only one aberration per case was found in 8 of all in detail studied 34 cases. Of special interest among the detected CNAs are the following new findings: del(15)(q26.1q26.1) including CHD2 gene was found in 20 % of the studied ALL cases, dup(18)(q21.2q21.2) with the DCC gene was present in 9 % of the cases, and the CDK6 gene in 7q21.2 was deleted in 12 % of the here in detail studied ALL cases.
Conclusions
In conclusion, high resolution molecular cytogenetic tools and molecular approaches like MLPA and aCGH need to be combined in a cost-efficient way, to identify disease and progression causing alterations in ALL, as majority of them are cryptic in banding cytogenetic analyses.
Electronic supplementary material
The online version of this article (doi:10.1186/s13039-015-0153-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s13039-015-0153-4
PMCID: PMC4486437  PMID: 26136832
Multitude multicolor banding (mMCB); Acute lymphoblastic leukemia (ALL); Cryptic rearrangements; Fluorescence in situ hybridization (FISH); Multiplex ligation-dependent probe amplification (MLPA); Array-comparative genomic hybridization (aCGH)
4.  A First Generation Comparative Chromosome Map between Guinea Pig (Cavia porcellus) and Humans 
PLoS ONE  2015;10(5):e0127937.
The domesticated guinea pig, Cavia porcellus (Hystricomorpha, Rodentia), is an important laboratory species and a model for a number of human diseases. Nevertheless, genomic tools for this species are lacking; even its karyotype is poorly characterized. The guinea pig belongs to Hystricomorpha, a widespread and important group of rodents; so far the chromosomes of guinea pigs have not been compared with that of other hystricomorph species or with any other mammals. We generated full sets of chromosome-specific painting probes for the guinea pig by flow sorting and microdissection, and for the first time, mapped the chromosomal homologies between guinea pig and human by reciprocal chromosome painting. Our data demonstrate that the guinea pig karyotype has undergone extensive rearrangements: 78 synteny-conserved human autosomal segments were delimited in the guinea pig genome. The high rate of genome evolution in the guinea pig may explain why the HSA7/16 and HSA16/19 associations presumed ancestral for eutherians and the three syntenic associations (HSA1/10, 3/19, and 9/11) considered ancestral for rodents were not found in C. porcellus. The comparative chromosome map presented here is a starting point for further development of physical and genetic maps of the guinea pig as well as an aid for genome assembly assignment to specific chromosomes. Furthermore, the comparative mapping will allow a transfer of gene map data from other species. The probes developed here provide a genomic toolkit, which will make the guinea pig a key species to unravel the evolutionary biology of the Hystricomorph rodents.
doi:10.1371/journal.pone.0127937
PMCID: PMC4444286  PMID: 26010445
5.  Prenatal screening of cytogenetic anomalies – a Western Indian experience 
Background
Children born with congenital anomalies present a very high rate of perinatal death and neonatal mortality. Cytogenetic analysis is a convincing investigation along with clinical suspicion and biochemical screening tests. The current study was designed to characterize the prevalence and types of chromosomal abnormalities in high risk prenatal samples using different cytogenetic techniques.
Methods
This study was conducted on a total of 1,728 prenatal samples (1,324 amniotic fluids, 366 chorionic villi and 38 cord blood samples) from 1994 to 2014 at Institute of Human Genetics, Ahmedabad, India. Conventional karyotyping was conducted with GTG-banding. Molecular approaches were used (fluorescence in situ hybridization = FISH and/ or array-comparative genomic hybridization = aCGH) when indicated to detect karyotypic abnormalities.
Results
Abnormal karyotypes were detected in 125/1,728 (7.2%) cases. Trisomy 21 was the most common abnormality detected in 46 (2.7%) followed by trisomy 18 in 11 (0.6%) and trisomy 13 in 2 (0.1%) samples. Besides, structural abnormalities such as reciprocal and Robertsonian translocation were detected in 20 [1.2%] cases. Turner syndrome was diagnosed in seven (0.4%) cases; in six (0.34%) cases there was an inversion in the Y-chromosome. Heteromorphic variants were diagnosed in 22 (1.3%) cases. Finally, small supernumerary marker chromosomes (sSMC) were found in six (0.34%) cases.
Conclusion
Conventional GTG-banding along with molecular cytogenetic techniques is useful in detecting genomic alterations and rearrangements. Comprehensive characterization of chromosomal rearrangements like sSMC has the potential to save potentially healthy fetuses from being terminated.
doi:10.1186/s12884-015-0519-y
PMCID: PMC4396805  PMID: 25884925
Karyotyping; GTG-banding; Fluorescence in situ hybridization (FISH); Array-comparative genomic hybridization (aCGH); Cell free DNA in maternal circulation (cfDNA); Chromosomal abnormalities; Prenatal samples
6.  Influence of aflatoxin B1 on copy number variants in human leukocytes in vitro 
Background
Aflatoxin B1 (AFB1) is a mycotoxin produced by Aspergillus spec. The latter are worldwide contaminants of food with mutagenic and carcinogenic activities in animals and humans. AFB1 was shown to have deleterious effects on metabolism of eukaryotes in many model systems, including the ability to inhibit DNA replication. An agent that disturbs DNA replication may also have the potential to induce de novo DNA copy number variations (CNVs).
Results
Blood samples of three clinically healthy carriers were treated in vitro with AFB1 and chromosome preparations were subjected to parental origin determination fluorescence in situ hybridization (pod-FISH). Probes able to visualize CNVs in 8p21.2 and 15q11.2 were applied. In this setting here for the first time an influence of AFB1 on molecular-cytogenetically detectable CNVs could be shown.
Conclusions
The obtained results indicate that: (i) pod-FISH is a single cell directed, sensitive and suitable method for the analysis of mutagen induced CNVs, (ii) AFB1 has the potential to induce in vitro instability of known CNVs in human leukocytes.
doi:10.1186/s13039-015-0131-x
PMCID: PMC4404608  PMID: 25901182
Aflatoxin B1; Mycotoxins; Copy number variation; Parental origin determination fluorescence in situ hybridization (pod-FISH)
7.  Reviewer acknowledgement 2015 
Contributing reviewers
The Editors of Molecular Cytogenetics would like to thank all our reviewers who have contributed to the journal in volume 7 (2014).
doi:10.1186/s13039-015-0122-y
PMCID: PMC4376081  PMID: 25821519
8.  Hyperdiploidy associated with T315I mutation in BCR-ABL kinase domain in an accelerated phase-chronic myeloid leukemia case 
Background
Chronic myeloid leukemia (CML) is genetically characterized by the occurrence of a reciprocal translocation t(9;22)(q34;q11), resulting in a BCR/ABL gene fusion on the derivative chromosome 22, i.e. the Philadelphia (Ph) chromosome. During CML progression 60–80% of the cases acquire additional genetic changes. Even though hyperdiploidy is not a rare finding in advanced phase-CML, hyperdiploidy together with a T315I kinase domain (KD) mutation in the BCR-ABL gene has not yet been reported.
Results
A complete cytogenetic and molecular cytogenetic analysis; molecular biology methods such as quantitative reverse transcription polymerase chain reaction (RQ-PCR) and allele-specific oligonucleotide (ASO)-PCR; and immunophenotypically confirmed CML in acceleration phase (AP). Our case revealed the presence of hyperdiploidy including multiple copies of the Ph chromosome, presence of b3a2 fusion transcript,T315I mutation in BCR-ABL KD in pre imatinib mesylate (IM) treatment. The ratio of BCR-ABL/ABL expression in post nilotinib treatment was 0.07% on international scale.
Conclusions
The patient demonstrated a good response to nilotinib after imatinib failure; while the hyperdiploid clone disappeared the T315I mutation remained during follow-up. The underlying mechanisms and prognostic implications of these cytogenetic abnormalities are discussed.
doi:10.1186/s13039-014-0089-0
PMCID: PMC4305221  PMID: 25621010
Chronic myeloid leukemia; Philadelphia chromosome; Hyperdiploidy; T315I mutation; Prognostic factors
9.  Do novo del(9)(p13) in a childhood T-cell prolymphocytic leukemia as sole abnormality 
T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive subtype of chronic lymphocytic leukemia. Usually it presents in older people with a median age of 61 years. T-PLL is characterized by elevated white blood cell (WBC) count with anemia and thrombocytopenia, hepatosplenomegaly, and lymphadenopathy; less common findings are skin infiltration and pleural effusions. The most frequent chromosomal abnormalities in T-PLL include 14q11.2, chromosome 8, and 11q rearrangements. Also deletions in the short arm of a chromosome 9 are reported in ~30% of T-PLL together with other aberrations. Here we report a childhood T-PLL case with a de novo del(9)(p13) as sole acquired anomaly leading to monosomy of the tumor suppressor gene CDKN2A (cyclin-dependent kinase inhibitor 2A). Also, to the best of our knowledge this is the first case of a childhood T-PLL with this aberration.
doi:10.1186/2162-3619-3-28
PMCID: PMC4423402  PMID: 25954594
Childhood T-cell prolymphocytic leukemia (T-PLL); Chromosomal aberrations; Fluorescence in situ hybridization (FISH); Multicolor banding (MCB)
10.  Comprehensive chronic lymphocytic leukemia diagnostics by combined multiplex ligation dependent probe amplification (MLPA) and interphase fluorescence in situ hybridization (iFISH) 
Background
Banding-karyotyping and metaphase-directed-fluorescence-in-situhybridization (FISH) may be hampered by low mitotic index in leukemia. Interphase FISH (iFISH) is a way out here, however, testing many probes at the same time is protracted and expensive. Here multiplex-ligation-dependent-probe-amplification (MLPA) was used retrospectively in chronic lymphocytic leukemia (CLL) samples initially studied by banding cytogenetics and iFISH. Detection rates of iFISH and MLPA were compared and thus a cost-efficient scheme for routine diagnostics is proposed.
Results
Banding cytogenetics was done successfully in 67/85 samples. DNA was extracted from all 85 CLL samples. A commercially available MLPA probe set directed against 37 loci prone to be affected in hematological malignancies was applied. Besides, routine iFISH was done by commercially available probes for following regions: 11q22.3, 12p11.2-q11.1, 13q14.3, 13q34, 14q32.33 and 17p13.1. MLPA results were substantiated by iFISH using corresponding locus-specific probes.
Aberrations were detected in 67 of 85 samples (~79%) applying banding cytogenetics, iFISH and MLPA. A maximum of 8 aberrations was detected per sample; however, one aberration per sample was found most frequently. Overall 163 aberrations were identified. 15 of those (~9%) were exclusively detected by banding cytogenetics, 95 were found by MLPA (~58%) and 100 (~61%) by routine iFISH. MLPA was not able to distinguish reliably between mono- and biallelic del(13)(q14.3q14.3), which could be easily identified as well as quantified by routine iFISH. Also iFISH was superior to MLPA in samples with low tumor cell load. On the other hand MLPA detected additional aberrations in 22 samples, two of them being without any findings after routine iFISH.
Conclusions
Both MLPA and routine iFISH have comparable detection rates for aberrations being typically present in CLL. As MLPA can detect also rare chromosomal aberrations it should be used as an initial test if routine cytogenetics is not possible or non-informative. Still iFISH should be used additionally to distinguish mono- from biallelic deletions and also to determine rate of mosaicism for 13q14.2 to 13q14.3. In case MLPA is negative the corresponding CLL samples should be tested at least by iFISH using the standard probe set to.
Electronic supplementary material
The online version of this article (doi:10.1186/s13039-014-0079-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s13039-014-0079-2
PMCID: PMC4247644  PMID: 25435911
Chronic lymphocytic leukemia (CLL); Chromosomal aberrations; Multiplex ligation-dependent probe amplification (MLPA); Fluorescence in situ hybridization (FISH)
11.  A Novel Cryptic Three-Way Translocation t(2;9;18)(p23.2;p21.3;q21.33) with Deletion of Tumor Suppressor Genes in 9p21.3 and 13q14 in a T-Cell Acute Lymphoblastic Leukemia 
Acute leukemia often presents with pure chromosomal resolution; thus, aberrations may not be detected by banding cytogenetics. Here, a case of 26-year-old male diagnosed with T-cell acute lymphoblastic leukemia (T-ALL) and a normal karyotype after standard GTG-banding was studied retrospectively in detail by molecular cytogenetic and molecular approaches. Besides fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and high resolution array-comparative genomic hybridization (aCGH) were applied. Thus, cryptic chromosomal aberrations not observed before were detected: three chromosomes were involved in a cytogenetically balanced occurring translocation t(2;9;18)(p23.2;p21.3;q21.33). Besides a translocation t(10;14)(q24;q11) was identified, an aberration known to be common in T-ALL. Due to the three-way translocation deletion of tumor suppressor genes CDKN2A/INK4A/p16, CDKN2B/INK4B/p15, and MTAP/ARF/p14 in 9p21.3 took place. Additionally RB1 in 13q14 was deleted. This patient, considered to have a normal karyotype after low resolution banding cytogenetics, was treated according to general protocol of anticancer therapy (ALL-BFM 95).
doi:10.1155/2014/357123
PMCID: PMC4206928  PMID: 25374696
12.  Supraphysiological androgen levels induce cellular senescence in human prostate cancer cells through the Src-Akt pathway 
Molecular Cancer  2014;13:214.
Background
Prostate cancer (PCa) is the second leading cause of cancer mortality of men in Western countries. The androgen receptor (AR) and AR-agonists (androgens) are required for the development and progression of the normal prostate as well as PCa. However, it is discussed that in addition to their tumor promoting activity, androgens may also exhibit tumor suppressive effects. A biphasic growth response to androgens a growth-promoting and -inhibition has been observed that suggests that administration of supraphysiological androgen levels mediates growth reduction in AR expressing PCa cells.
Methods
Detection of senescence markers, three dimensional interphase fluorescence in situ hybridization (3D-iFISH), qRT-PCR, Western blotting, detection of GFP fusions, prostatectomy, ex vivo culturing.
Results
Here, we describe that supraphysiological levels of androgens induce cell cycle arrest and markers of cellular senescence in human PCa cells, which may in part explain the growth inhibitory role of androgens. The expression of the senescence associated beta galactosidase is observed by treatment with the natural androgen DHT or the less metabolized synthetic androgen R1881. The induction of senescence marker was detected in human PCa cell lines as well as in human primary PCa tissue derived from prostatectomy treated ex vivo. Using interphase FISH (iFISH) suggests that the androgen-induced cellular senescence is associated with localizing the genomic E2F1 locus to senescence associated heterochromatic foci. Analysis of different signaling pathways in LNCaP cells suggest that the p16-Rb-E2F1 pathway is essential for the induction of cellular senescence since treatment with siRNA directed against p16 reduces the level of androgen-induced cellular senescence. Based on the rapid induction of androgen-mediated cellular senescence we identified the Src-PI3K-Akt-signaling pathway and autophagy being in part involved in androgen regulation.
Conclusions
Taken together, our data suggest that AR-agonists at supraphysiological levels mediate induction of cellular senescence in human PCa cells, which may have a protective anti-cancer role. These results provide also new insights for understanding androgen-mediated regulation of PCa growth.
Electronic supplementary material
The online version of this article (doi:10.1186/1476-4598-13-214) contains supplementary material, which is available to authorized users.
doi:10.1186/1476-4598-13-214
PMCID: PMC4171558  PMID: 25216853
Nuclear receptor; Non-genomic signaling; Tumor suppression; Cellular senescence; Autophagy
13.  An adult B-cell precursor acute lymphoblastic leukemia with multiple secondary cytogenetic aberrations 
Background
We report a clinically diagnosed acute lymphoblastic leukemia (ALL) with yet unreported secondary chromosomal aberrations.
Results
A complete cytogenetic and molecular cytogenetic analysis, using GTG banding, fluorescence in situ hybridization (FISH) and array-proven multicolor banding (aMCB), for a female patient with clinically diagnosed ALL and immunophenotypically confirmed pre-B ALL (FAB classifications), revealed the presence of a complex structural rearrangement, der (2) (20qter- > 20q13.33::2q21- > 2p14::2q21 > 2qter) along with t (9;22) (q34;q11), t (12;14) (q12;p12) and a monosomy of chromosome 7.
Conclusions
Molecular cytogenetic studies are suited best for identification and characterization of chromosomal rearrangements in acute leukemia. Single case reports as well as large scale studies are necessary to provide further insights in karyotypic changes taking place in human malignancies.
doi:10.1186/s13039-014-0060-0
PMCID: PMC4172788  PMID: 25254075
Acute lymphoblastic leukemia; Secondary chromosomal abnormalities; Philadelphia chromosome; Fluorescence in situ hybridization; Array-proven multicolor banding; Prognostic factors
14.  Genomic organization of repetitive DNAs and its implications for male karyotype and the neo-Y chromosome differentiation in Erythrinus erythrinus (Characiformes, Erythrinidae) 
Comparative Cytogenetics  2014;8(2):139-151.
Studies have demonstrated the effective participation of repetitive DNA sequences in the origin and differentiation of the sex chromosomes in some biological groups. In this study several microsatellites and retrotranposable sequences were cytogenetically mapped in the Erythrinus erythrinus (Bloch & Schneider, 1801) male genome (karyomorph C), focusing on the distribution of these sequences in the sex chromosomes and in the evolutionary processes related to their differentiation. Males of E. erythrinus – karyomorph C – present 2n = 51 chromosomes (7m + 2sm + 6st + 36a), including the X1X2Y sex chromosomes. The C-positive heterochromatin has a predominant localization on the centromeric region of most chromosome pairs, but also in some telomeric regions. The 5S rDNA sites are located in the centromeric region of 27 chromosomes, including 26 acrocentric ones and the metacentric Y chromosome. The retrotransposons Rex 1 and Rex 6 show a dispersed pattern in the karyotype, contrasting with the Rex 3 distribution which is clearly co-localized with all the 27 5S rDNA sites. The microsatellite sequences show a differential distribution, some of them restricted to telomeric and/or interstitial regions and others with a scattered distribution on the chromosomes. However, no preferential accumulation of these elements were observed in the neo-Y chromosome, in contrast to what usually occurs in simple sex chromosome systems.
doi:10.3897/CompCytogen.v8i2.7597
PMCID: PMC4137284  PMID: 25147625
FISH; microsatellites; retrotransposable sequences; sex chromosomes
15.  De novo 393 kb microdeletion of 7p11.2 characterized by aCGH in a boy with psychomotor retardation and dysmorphic features 
Meta Gene  2014;2:274-282.
We report on a 27 month old boy presenting with psychomotor delay and dysmorphic features, mainly mild facial asymmetry, prominent cup-shaped ears, long eyelashes, open mouth appearance and slight abnormalities of the hands and feet. Array comparative genomic hybridization revealed a 393 kb microdeletion in 7p11.2. We discuss the possible involvement of CHCHD2, GBAS, MRPS17, SEPT14 and PSPH on our patient's phenotype. Additionally, we studied the expression of two other genes deleted in the patient, CCT6A and SUMF2, for which there is scarce data in the literature. Based on current knowledge and the de novo occurrence of this finding in our proband we presume that the aberration is likely to be pathogenic in our case. However, a single gene disorder, elsewhere in the genome or in this very region cannot be ruled out. Further elucidation of the properties of this chromosomal region, as well as of the role of the genes involved will be needed in order to draw safe conclusions regarding the association of the chromosomal deletion with the patient's features.
Highlights
•We report in detail the clinical and cytogenetic findings of a 27-month old male.•We compare our findings with current literature and online databases.•We discuss the possible involvement of certain genes in our patient’s phenotype.
doi:10.1016/j.mgene.2014.03.004
PMCID: PMC4287824  PMID: 25606410
Deletion 7p11.2; Psychomotor delay; Dysmorphic features; CHCHD2; GBAS; MRPS17; SEPT14; PSPH; CCT6A; SUMF2
16.  First Molecular Cytogenetic High Resolution Characterization of the NIH 3T3 Cell Line by Murine Multicolor Banding 
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.
doi:10.1369/0022155413476868
PMCID: PMC3621507  PMID: 23321776
NIH 3T3 cell line; murine multicolor banding (mcb); cytogenetics; genetics; fluorescence in situ hybridization (FISH)
17.  Chromosomal Mapping of Repetitive DNAs in Triportheus trifurcatus (Characidae, Characiformes): Insights into the Differentiation of the Z and W Chromosomes 
PLoS ONE  2014;9(3):e90946.
Repetitive DNA sequences play an important role in the structural and functional organization of chromosomes, especially in sex chromosome differentiation. The genus Triportheus represents an interesting model for such studies because all of its species analyzed so far contain a ZZ/ZW sex chromosome system. A close relationship has been found between the differentiation of the W chromosome and heterochromatinization, with the involvement of different types of repetitive DNA in this process. This study investigated several aspects of this association in the W chromosome of Triportheus trifurcatus (2n = 52 chromosomes), including the cytogenetic mapping of repetitive DNAs such as telomeric sequences (TTAGGG)n, microsatellites and retrotransposons. A remarkable heterochromatic segment on the W chromosome was observed with a preferential accumulation of (CAC)10, (CAG)10, (CGG)10, (GAA)10 and (TA)15. The retrotransposons Rex1 and Rex3 showed a general distribution pattern in the chromosomes, and Rex6 showed a different distribution on the W chromosome. The telomeric repeat (TTAGGG)n was highly evident in both telomeres of all chromosomes without the occurrence of ITS. Thus, the differentiation of the W chromosome of T. trifurcatus is clearly associated with the formation of heterochromatin and different types of repetitive DNA, suggesting that these elements had a prominent role in this evolutionary process.
doi:10.1371/journal.pone.0090946
PMCID: PMC3954618  PMID: 24632562
18.  X chromosome aneuploidy in the Alzheimer’s disease brain 
Background
Although the link between brain aging and Alzheimer’s disease (AD) is a matter of debate, processes hallmarking cellular and tissue senescence have been repeatedly associated with its pathogenesis. Here, we have studied X chromosome aneuploidy (a recognized feature of aged cell populations) in the AD brain.
Results
Extended molecular neurocytogenetic analyses of X chromosome aneuploidy in 10 female AD as well as 10 age and sex matched female control postmortem brain samples was performed by multiprobe/quantitative FISH. Additionally, aneuploidy rate in the brain samples of 5 AD and as 5 age and sex matched control subjects were analyzed by interphase chromosome-specific multicolor banding (ICS-MCB). Totally, 182,500 cells in the AD brain and 182,500 cells in the unaffected brain were analyzed. The mean rate of X chromosome aneuploidy in AD samples was approximately two times higher than in control (control: mean - 1.32%, 95% CI 0.92- 1.71%; AD: mean - 2.79%, 95% CI 1.88-3.69; P = 0.013). One AD sample demonstrated mosaic aneuploidy of chromosome X confined to the hippocampus affecting about 10% of cells. ICS-MCB confirmed the presence of X chromosome aneuploidy in the hippocampal tissues of AD brain (control: mean - 1.74%, 95% CI 1.38- 2.10%; AD: mean - 4.92%, 95% CI 1.14-8.71; P < 0.001).
Conclusions
Addressing X chromosome number variation in the brain, we observed that somatically acquired (post-zygotic) aneuploidy causes large-scale genomic alterations in neural cells of AD patients and, therefore, can be involved in pathogenesis of this common neurodegenerative disorder. In the context of debates about possible interplay between brain aging and AD neurodegeneration, our findings suggest that X chromosome aneuploidy can contribute to both processes. To this end we conclude that mosaic aneuploidy in the brain is a new non-heritable genetic factor predisposing to AD.
doi:10.1186/1755-8166-7-20
PMCID: PMC3995993  PMID: 24602248
Alzheimer’s disease; Aneuploidy; Brain; Chromosome instability; Chromosome X; Molecular cytogenetics; Aging
19.  The strength of combined cytogenetic and mate-pair sequencing techniques illustrated by a germline chromothripsis rearrangement involving FOXP2 
Next-generation mate-pair sequencing (MPS) has revealed that many constitutional complex chromosomal rearrangements (CCRs) are associated with local shattering of chromosomal regions (chromothripsis). Although MPS promises to identify the molecular basis of the abnormal phenotypes associated with many CCRs, none of the reported mate-pair sequenced complex rearrangements have been simultaneously studied with state-of-the art molecular cytogenetic techniques. Here, we studied chromothripsis-associated CCR involving chromosomes 2, 5 and 7, associated with global developmental and psychomotor delay and severe speech disorder. We identified three truncated genes: CDH12, DGKB and FOXP2, confirming the role of FOXP2 in severe speech disorder, and suggestive roles of CDH12 and/or DGKB for the global developmental and psychomotor delay. Our study confirmes the power of MPS for detecting breakpoints and truncated genes at near nucleotide resolution in chromothripsis. However, only by combining MPS data with conventional G-banding and extensive fluorescence in situ hybridizations could we delineate the precise structure of the derivative chromosomes.
doi:10.1038/ejhg.2013.147
PMCID: PMC3925275  PMID: 23860044
mate-pair sequencing; complex chromosomal rearrangements; chromothripsis; FOXP2; CDH12; DGKB
20.  Monitoring of gas station attendants exposure to benzene, toluene, xylene (BTX) using three-color chromosome painting 
Background
Chronic exposure of BTX (benzene, toluene, xylene) may lead to progressive degeneration of bone marrow, aplastic anemia and/or leukemia. In Brazil there is no self-service fuel in gas stations and attendants fill the fuel themselves. Due to this they are chronically exposed to high concentration of BTX. Occupational exposure to benzene has been associated with increased chromosomal aberrations in peripheral blood lymphocytes. Fluorescence in situ hybridization (FISH) using whole chromosome painting (wcp) probes allows the rapid detection of chromosomal aberration. In the present study three-color wcp probes for chromosomes 1, 2 and 4 were used for monitoring 60 gas station attendants.
Results
Blood tests were done and interviews were conducted for each worker. For searching for possible associations between the clinical characteristics and the frequency of chromosomal aberrations the workers were divided into two groups (≤ 10 chromosomal abnormalities per 1,000 metaphases and > 10 chromosomal abnormalities per 1,000 metaphases).The studied workers had a low median age (36 year), albeit long period of BTX exposure (median was 16 years). Low prevalence of smoking and moderate consumption of alcoholic beverages were found in this population. The cytogenetic analysis showed 16.6% (10/60) of workers with a high frequency of chromosomal abnormalities (>10 chromosomal abnormalities per 1,000 metaphases). Translocations were the most frequently observed chromosome aberration. The statistical analysis revealed highly significant differences in skin color (p = 0.002) and a weak significant differences in gender (p = 0.052) distribution between the two groups.
Conclusion
16.6% of the studied population showed elevated frequencies of chromosomal abnormalities, which is highly likely to be correlated with their exposure to BTX during their work. Therefore, further studies are needed for better characterize the work associated damage of the genome in gas station workers. It is necessary to better understand the risks that these workers are exposed, so that we can be effective in preventing diseases and maintaining the health of these workers and possibly the offspring.
doi:10.1186/1755-8166-7-15
PMCID: PMC3974043  PMID: 24576355
Benzene; Toluene; Xylene; Monitoring; Cytogenetic; Painting; Chromosome
21.  Reviewer acknowledgement 2014 
Contributing reviewers
The Editors of Molecular Cytogenetics would like to thank all our reviewers who have contributed to the journal in volume 6 (2013).
doi:10.1186/1755-8166-7-11
PMCID: PMC3924429  PMID: 24529454
22.  Proximal 10q duplication in a child with severe central hypotonia characterized by array-comparative genomic hybridization: A case report and review of the literature 
Proximal 10q duplication is a well-defined but rare genetic syndrome. Duplication of proximal segments of the long arm of chromosome 10 results in a pattern of malformations, which are distinct from those of the more common distal 10q trisomy syndrome. The present study describes the case of a boy with phenotypic abnormalities (severe central hypotonia, mild ataxia, moderate developmental delay and mild dysmorphic features), due to duplication of chromosome region, 10q11.21→q11.22, which was characterized by the array-comparative genomic hybridization (CGH) technique. The phenotypic findings were compared with those in eight additional similar published cases. Major similarities have emerged, suggesting a likely minimal critical region. However, only detailed characterization of additional cases may provide firm conclusions.
doi:10.3892/etm.2014.1520
PMCID: PMC3964923  PMID: 24669257
10q duplication syndrome; array-comparative genomic hybridization; developmental delay; 10q11.21→q11.22
23.  16p11.2–p12.2 duplication syndrome; a genomic condition differentiated from euchromatic variation of 16p11.2 
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.
doi:10.1038/ejhg.2012.144
PMCID: PMC3548261  PMID: 22828807
chromosomes, human, pair 16; chromosome duplication; 16p11.2–p12.2; DNA array; euchromatic variant; copy number variation
24.  Uniparental disomy - clinical consequences due to imprinting and activation of recessive genes 
Molecular Cytogenetics  2014;7(Suppl 1):I21.
doi:10.1186/1755-8166-7-S1-I21
PMCID: PMC4042265  PMID: 24940361
25.  Small supernumerary marker chromosomes – an update 
Molecular Cytogenetics  2014;7(Suppl 1):I11.
doi:10.1186/1755-8166-7-S1-I11
PMCID: PMC4043994  PMID: 24940369

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