A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes.

Significant efforts have been recently made to obtain the three-dimensional (3D) structure of the genome with the goal of understanding how structures may affect gene regulation and expression. Chromosome conformational capture techniques such as Hi-C, have been key in uncovering the quantitative information needed to determine chromatin organization. Complementing these experimental tools, co-polymers theoretical methods are necessary to determine the ensemble of three-dimensional structures associated to the experimental data provided by Hi-C maps. Going beyond just structural information, these theoretical advances also start to provide an understanding of the underlying mechanisms governing genome assembly and function. Recent theoretical work, however, has been focused on single chromosome structures, missing the fact that, in the full nucleus, interactions between chromosomes play a central role in their organization. To overcome this limitation, MiChroM (Minimal Chromatin Model) has been modified to become capable of performing these multi-chromosome simulations. It has been upgraded into a fast and scalable software version, which is able to perform chromosome simulations using GPUs via OpenMM Python API, called Open-MiChroM. To validate the efficiency of this new version, analyses for GM12878 individual autosomes were performed and compared to earlier studies. This validation was followed by multi-chain simulations including the four largest human chromosomes (C1-C4). These simulations demonstrated the full power of this new approach. Comparison to Hi-C data shows that these multiple chromosome interactions are essential for a more accurate agreement with experimental results. Without any changes to the original MiChroM potential, it is now possible to predict experimentally observed inter-chromosome contacts. This scalability of Open-MiChroM allow for more audacious investigations, looking at interactions of multiple chains as well as moving towards higher resolution chromosomes models.

Two Separate Cases: Complex Chromosomal Abnormality Involving Three Chromosomes and Small Supernumerary Marker Chromosome in Patients with Impaired Reproductive Function.

For medical genetic counseling, estimating the chance of a child being born with chromosome abnormality is crucially important. Cytogenetic diagnostics of parents with a balanced karyotype are a special case. Such chromosome rearrangements cannot be detected with comprehensive chromosome screening. In the current paper, we consider chromosome diagnostics in two cases of chromosome rearrangement in patients with balanced karyotype and provide the results of a detailed analysis of complex chromosomal rearrangement (CCR) involving three chromosomes and a small supernumerary marker chromosome (sSMC) in a patient with impaired reproductive function. The application of fluorescent in situ hybridization, microdissection, and multicolor banding allows for describing analyzed karyotypes in detail. In the case of a CCR, such as the one described here, the probability of gamete formation with a karyotype, showing a balance of chromosome regions, is extremely low. Recommendation for the family in genetic counseling should take into account the obtained result. In the case of an sSMC, it is critically important to identify the original chromosome from which the sSMC has been derived, even if the euchromatin material is absent. Finally, we present our view on the optimal strategy of identifying and describing sSMCs, namely the production of a microdissectional DNA probe from the sSMC combined with a consequent reverse painting.

[Molecular characterisation and phenotypic description of two patients with reciprocal chromosomal aberrations in the region of the 3q29 microdeletion/microduplication syndromes]. / Caracterizacion molecular y descripcion fenotipica de dos casos con aberraciones cromosomicas reciprocas en la region de los sindromes de microdelecion/microduplicacion 3q29.

INTRODUCTION: The 3q29 microdeletion and microduplication syndromes are characterised by a marked phenotypic heterogeneity, and delayed development and a mild-moderate degree of intellectual disability are the most frequent clinical manifestations. CASE REPORTS: Two patients with reciprocal chromosomal aberrations in the 3q29 region. The patient with 3q29 microdeletion presented learning disabilities, borderline microcephaly, mild facial dysmorphism, attentional deficit and impulsiveness, and anxious and obsessive traits. The patient with reciprocal 3q29 microduplication presented learning disabilities, mild facial dysmorphism and a disruptive behavioural profile that was not previously associated with this duplication. CONCLUSIONS: The phenotypes of these patients are compared and the literature about paediatric patients with 3q29 microdeletions and microduplications is reviewed.

TITLE: Caracterizacion molecular y descripcion fenotipica de dos casos con aberraciones cromosomicas reciprocas en la region de los sindromes de microdelecion/microduplicacion 3q29.Introduccion. Los sindromes de microdelecion y microduplicacion 3q29 se caracterizan por una marcada heterogeneidad fenotipica, y el retraso del desarrollo y la discapacidad intelectual de grado leve-moderado son las manifestaciones clinicas mas frecuentes. Casos clinicos. Dos pacientes con aberraciones cromosomicas reciprocas en la region 3q29. La paciente con la microdelecion 3q29 presenta dificultades de aprendizaje, microcefalia limite, dismorfismo facial leve, deficit atencional e impulsividad, y rasgos ansiosos y obsesivos. El paciente con la microduplicacion 3q29 reciproca presenta dificultades de aprendizaje, dismorfismo facial leve y un perfil conductual disruptivo no asociado previamente con esta duplicacion. Conclusion. Se comparan los fenotipos de estos pacientes y se revisa la bibliografia de pacientes pediatricos con microdeleciones y microduplicaciones 3q29.

Distinctive genotypes in infants with T-cell acute lymphoblastic leukaemia.

Infant T-cell acute lymphoblastic leukaemia (iT-ALL) is a very rare and poorly defined entity with a poor prognosis. We assembled a unique series of 13 infants with T-ALL, which allowed us to identify genotypic abnormalities and to investigate prenatal origins. Matched samples (diagnosis/remission) were analysed by single nucleotide polymorphism-array to identify genomic losses and gains. In three cases, we identified a recurrent somatic deletion on chromosome 3. These losses result in the complete deletion of MLF1 and have not previously been described in T-ALL. We observed two cases with an 11p13 deletion (LMO2-related), one of which also harboured a deletion of RB1. Another case presented a large 11q14·1-11q23·2 deletion that included ATM and only five patients (38%) showed deletions of CDKN2A/B. Four cases showed NOTCH1 mutations; in one case FBXW7 was the sole mutation and three cases showed alterations in PTEN. KMT2A rearrangements (KMT2A-r) were detected in three out of 13 cases. For three patients, mutations and copy number alterations (including deletion of PTEN) could be backtracked to birth using neonatal blood spot DNA, demonstrating an in utero origin. Overall, our data indicates that iT-ALL has a diverse but distinctive profile of genotypic abnormalities when compared to T-ALL in older children and adults.

[Familial presentation of microdeletion and inverted microduplication with array-CGH]. / Microdelecion y microduplicacion inversa de presentacion familiar con array-CGH.

INTRODUCTION. Over the years the field of genetics has advanced significantly. Following the polymerase chain reaction and mass sequencing techniques, the array-CGH technique (comparative genomic hybridization) has helped to improve genetic procedures. A resolution of up to 200 kb is currently being accomplished in the human genome. CASE REPORTS. We report the case of two sisters with delays in developmental milestones and a characteristic phenotype with normal results from initial studies of the karyotype and subtelomeric regions. Array-CGH was later used to detect a deletion and duplication that were different in each of the sisters, this being the result of a balanced paternal translocation. In the two cases, despite being the result of the same translocation, the genetic and phenotype expression were different. CONCLUSIONS. The precision achieved by means of array-CGH is making it possible to establish a correlation between minimum gains or losses of the genome and the clinical features. Chromosome 3 codes for genes that play a fundamental role in neurological development (contactins, neurotransmitter modulator proteins, etc.) and chromosome 10 codes for proteins involved in apoptosis and proteins regulating transcription. In the literature there have been reports of chromosome 3 deletion syndrome and monosomy 10. Likewise, there are also descriptions of rearrangements between these chromosomes in individuals from the same family. Nevertheless, we describe two cases of a family with a micro-deletion and an inverted microduplication, detected by means of array-CGH, that have not been reported to date. This technique can provide a diagnostic and prognostic approximation as regards development and offer genetic counselling.

TITLE: Microdelecion y microduplicacion inversa de presentacion familiar con array-CGH.Introduccion. A lo largo de los años se han logrado avances en torno a la genetica; tras la reaccion en cadena de la polimerasa y las tecnicas de secuenciacion masiva, la tecnica array-CGH (comparative genomic hybridization) ha contribuido a mejorar los procedimientos geneticos. Actualmente esta consiguiendo una resolucion de hasta 200 kb en el genoma humano. Casos clinicos. Se presentan dos hermanas con retraso en los hitos del desarrollo y fenotipo caracteristico con estudio inicial de cariotipo y de regiones subtelomericas normales. Posteriormente, mediante array-CGH se detecto en cada una una delecion y una duplicacion diferentes, fruto de una translocacion equilibrada paterna. En ambas, siendo fruto de una misma translocacion, muestra diferente expresion genetica y fenotipica. Conclusiones. La precision conseguida mediante el array-CGH esta permitiendo correlacionar minimas ganancias o perdidas del genoma con la clinica. En el cromosoma 3 se encuentran codificados genes fundamentales en el desarrollo neurologico (contactinas, proteinas moduladoras de neurotransmisores…), y en el cromosoma 10, proteinas implicadas en la apoptosis y proteinas reguladoras de la transcripcion. En la bibliografia se han descrito el sindrome de delecion del cromosoma 3 y la monosomia 10. Igualmente, hay descritos reordenamientos entre estos cromosomas en individuos de una misma familia. Sin embargo, aportamos dos casos de una familia con una microdelecion y una microduplicacion inversa, detectados mediante array-CGH, no descritos hasta el momento. Dicha tecnica puede ofrecer una aproximacion diagnostica y pronostica en cuanto a la evolucion y ofertar consejo genetico.

Fluorescent in situ hybridization as a predictor of relapse in urothelial carcinoma.

OBJECTIVE: To assess the value of the study of chromosomal alterations by fluorescent in situ hybridization in a series of patients diagnosed of urothelial carcinoma and a minimum follow up of twenty four months, as well as evaluate its putative predictive potential. MATERIAL AND METHODS: The overall series includes 338 samples from 98 patients with 84 episodes of urothelial carcinoma. A subgroup of 24 patients who had at least one recurrence during the follow up was used to evaluate the predictive potential of the test. Three categories were considered (positive coherent episode, negative coherent episode, and incoherent episode) depending on the relationship between the fluorescent in situ hybridization result in the concomitant study of the new episode and those of the preceding samples. RESULTS: Fluorescent in situ hybridization showed higher sensitivity regardless of grade, negative predictive value and accuracy, while specificity and positive predictive value were superior with conventional cytology. In the recurrence, series 19/29 episodes were coherent, 11/19 were positive coherent with urothelial carcinoma all high grade and 8/19 negative coherent, most low grade. CONCLUSIONS: Fluorescent in situ hybridization test shows good sensitivity during a follow up of twenty four months and is able to predict recurrence, especially in cases of high grade. Our data demonstrate the existence of urothelial carcinomas without detectable chromosomal abnormalities by currently available methodology. The results support a multidisciplinary follow up combining fluorescent in situ hybridization, cytology and cystoscopy.

Acquired EVI1 rearrangement involved in the transformation from 5q- syndrome to pre-B lymphocytic leukemia in a Chinese patient.

The anomalous EVI1 rearrangements/t(3;3)(q21;q26) is more frequently found in myelocytic malignancies. 5q- syndrome is a newly defined subtype of myelodysplastic syndrome (MDS) first proposed by the World Health Organization in 2001. Cases of acute lymphocytic leukemia (ALL) with 5q- anomaly or t(3;3)/EVI1 rearrangement have rarely been reported. We report a rare 5q- syndrome case which ultimately transformed to acute lymphocytic leukemia accompanied by a secondary cytogenetic anomaly of t(3;3)(q21;q26) and EVI1 rearrangement around 3 years after the diagnosis of 5q- syndrome. This rare case suggests that the 5q- clone of MDS may originate from a multipotent cell with a capacity to differentiate toward both myeloid and lymphoid lineages. It also indicates that although the t(3;3)/EVI1 rearrangement is mostly related to myelocytic neoplasms, the t(3;3)/EVI1-rearrangement may also play an important role in the development of ALL. The results of the necessary tests must be analyzed sufficiently prior to making a final diagnosis.

Numerical chromosomal changes and risk of development of myelodysplastic syndrome--acute myeloid leukemia in patients with Fanconi anemia.

Fanconi Anemia (FA) is an inherited bone marrow failure syndrome characterized by congenital abnormalities, progressive marrow failure and predisposition to myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and solid tumors. The most common acquired chromosomal aberrations in FA patients are trisomy of 1q and monosomy of chromosome 7; the latter is known to be associated with poor prognosis. A few reports also suggest that gains of 3q are associated with progression to MDS-AML and overall poor prognosis. It is not uncommon for patients with Fanconi anemia to have easily detectable (oligoclonal) chromosomal alterations in their still normal (nonmalignant) marrow, which makes it even more challenging to determine the import of such alterations. We conducted a retrospective longitudinal analysis of fluorescent in situ hybridization (FISH) analysis for gains in 1q and 3q and for monosomy 7 and 7q deletions on 212 bone marrow samples from 77 children with FA treated at our institution between 1987 and 2007. Given the baseline increased chromosomal instability and defective DNA repair in patients with FA, which leads to unbalanced chromosomal aberrations such as deletions, insertions, and translocations, for the purpose of this analysis an abnormal clone was defined as ≥10% abnormal cells. Chromosome 3 and 7 aberrations were associated with increased risk of developing MDS-AML (P = 0.019 and P < 0.001 respectively), although the significance of chromosome 3 aberrations disappeared when different observation times were accounted for. Gain of 1q alone did not predict development of MDS-AML. In conclusion, children with FA should be followed closely with FISH analyses, because some of the clonal chromosomal abnormalities may be early indicators of progression toward MDS-AML and thus also of the need for hematopoietic stem cell transplantation.

Development of a dual-color, double fusion FISH assay to detect RPN1/EVI1 gene fusion associated with inv(3), t(3;3), and ins(3;3) in patients with myelodysplasia and acute myeloid leukemia.

Approximately 2-3% of adult patients with acute myeloid leukemia harbor a rearrangement of RPN1 (at 3q21) and EVI1 (at 3q26.2) as inv(3)(q21q26.2), t(3;3)(q21;q26.2), or ins(3;3)(q26.2;q21q26.2). The most recent World Health Organization (WHO) classification has designated AML with inv(3) or t(3;3) and associated RPN1/EVI1 fusion, as a distinct AML subgroup associated with an unfavorable prognosis. We have created a dual color, double fusion fluorescence in situ hybridization (D-FISH) assay to detect fusion of the RPN1 and EVI1 genes. A blinded investigation was performed using 30 normal bone marrow samples and 51 bone marrow samples from 17 patients with inv(3)(q21q26.2), 11 patients with t(3;3)(q21;q26.2), and one patient with ins(3;3)(q26.2;q21q26.2) previously defined by chromosome analysis. The unblinded results indicated abnormal RPN1/EVI1 fusion results in 30 (97%) of 31 samples from the inv(3)(q21q26.2) group including seven bone marrow samples for which chromosome analysis was unsuccessful or failed to detect an inv(3)(q21q26.2). Abnormal FISH results were detected in 14 (88%) of 16 samples with t(3;3)(q21;q26.2) and in the sole sample with an ins(3;3)(q26.2;q21q26.2). All 30 negative controls were normal and were used to establish a normal cutoff of 0.6% for the typical abnormal D-FISH signal pattern. Overall, this D-FISH assay was more accurate than chromosome analysis and based on the normal cutoff of 0.6%, this assay can be used for minimal residual disease detection and disease monitoring in patients with RPN1/EVI1 fusion.

Jumping translocation in acute monocytic leukemia (M5b) with alternative breakpoint sites in the long arm of donor chromosome 3.

An 86-year-old man presented with acute hepatic failure, worsening thrombocytopenia, and anemia having been diagnosed and managed expectantly with cytogenetically normal RAEB-1. After 20 months a diagnosis of disease transformation to acute monocytic leukemia (M5b) was made. Conventional G-banded analysis of unstimulated bone marrow cultures demonstrated a jumping translocation (JT) involving proximal and distal breakpoints on donor chromosome 3 at bands 3q1?2 and 3q21, respectively. Recipient chromosomes included the long-arm telomeric regions of chromosomes 5, 10, 14, 16, and 19. A low-level trisomy 8 clone was also found in association with both proximal and distal JT clones. Conventional G-banded analysis of unstimulated peripheral blood cultures detected the proximal 3q1?2 JT clone involving recipient chromosome 10 several weeks after transformation to acute monocytic leukemia. Interestingly, JTs involving recipient chromosomes 5, 14, 16, and 19 were not detected in this peripheral blood sample. Palliative care was administered until his demise 2.2 months after disease transformation. There have been fewer than 70 cases of acquired JTs reported in the literature, including one myeloproliferative neoplasm and five acute myeloid leukemias involving a single breakpoint site on donor chromosome 3. Our case is unique as it is the first acquired case to demonstrate a JT involving alternative pericentromeric breakpoint sites on a single donor chromosome consisting of a proximal breakpoint at 3q1?2 and a more distal breakpoint at 3q21.

Primary central nervous system mucosa-associated lymphoid tissue lymphoma: case report and literature review.

Primary presentation of intradural non-Hodgkin lymphoma is rare. Recently, B-cell lymphomas of mucosa-associated lymphoid tissue (MALT) have been recognized as an important pathologic subtype. When MALT lymphomas present in the central nervous system (CNS), they are distinguishable from primary high-grade CNS lymphomas. We present the clinicopathologic features of 5 patients with primary CNS MALT lymphoma treated at our institution from 1999 to 2006. Four out of 5 patients were women, and all patients presented with headaches, focal motor deficits, or cranial nerve palsy. Radiologic studies demonstrated ill-defined dural masses in 3 and well-defined masses in 2 patients. Pathology revealed small to medium-sized cells with a moderate amount of cytoplasm and irregular nuclear borders, expressing pan B-cell markers (CD19, CD20, and CD79a) but lacking CD10, CD23, and cyclin D1, confirming low-grade MALT lymphoma. Plasma cells were encountered in all the biopsies with variable reactive T-cell infiltration. wedge chain restriction was seen in 3 patients. Therapy consisted of either surgical resection, whole-brain radiation, or systemic or intrathecal chemotherapy. There was no evidence of recurrence or systemic relapse in 4 patients at 4 years of follow-up. One patient died in 2 months, unrelated to CNS lymphoma. This case series illustrates the rare occurrence of low-grade dural B-cell lymphoma and the need to consider this entity in the differential diagnosis of CNS lesions.

Acquired acute myelogenous leukemia after therapy for acute promyelocytic leukemia with t(15;17): a case report and review of the literature.

Therapy-related myelodysplastic syndrome (t-MDS) and therapy-related acute myelogenous leukemia (t-AML) in patients with acute promyelocytic leukemia (APL) are rare events. The cumulative exposure to chemotherapy with alkylating agents and topoisomerase II inhibitors is associated with t-AML that may develop any time after the completion of the treatment. We report the case of an acquired AML who previously received therapy for APL, after two years of being diagnosed. The diagnosis was established by morphologic findings, membrane markers, cytogenetic studies, and fluorescence in situ hybridization (FISH). To our knowledge this is the first documented case in Puerto Rico of a patient with APL that developed a t-AML without the characteristic chromosomal and morphologic findings of APL.

t(3;9;22) 3-way chromosome translocation in chronic myeloid leukemia is associated with poor prognosis.

Chronic myelogenous leukemia (CML) is genetically characterized by the reciprocal translocation of chromosome 9 and 22. Around 5-8% of CML develop complex variant Ph translocations involving one or more chromosomal regions besides 9 and 22. Chromosome 3 is not frequently involved in complex translocations in CML. We report in this study a case of CML displaying a t(3;9;22) 3-way translocation. A review of the literature appears to indicate that CML patients with this translocation tend to have an aggressive course and poor outcome. Additional 3-way chromosome translocations associated with CML are also reviewed.

Unbalanced jumping translocation involving 3q in myeloproliferative disease.

An 87-year-old woman was diagnosed with unclassified myeloproliferative disease having an acquired jumping translocation with the long arm of chromosome 3 translocating to the short arm telomeric region of chromosome 8 (major clone) and the long arm telomeric region of chromosome 10 (minor clone). Each abnormal clone was also associated with an extra copy of chromosome 8. Although there was no evidence of transformation to an acute leukemia, the patient deteriorated until her demise 7 months after disease presentation. There have been fewer than 70 cases of acquired jumping translocations reported in the literature. To our knowledge, this is the first acquired jumping translocation case to be reported in a patient with myeloproliferative disease.

Investigation of bone marrow involvement in malignant lymphoma using fluorescence in situ hybridization: possible utility in the detection of micrometastasis.

We evaluated the usefulness of interphase fluorescence in situ hybridization (FISH) for the detection of bone marrow involvement of lymphoma, comparing the results with those of microscopic examination. Bone marrow aspirates obtained for staging work-up from 150 patients with non-Hodgkin lymphoma were used in this study. Interphase FISH study using four probes and conventional G-banding were performed on bone marrow aspirates. The four probes included locus specific identifier (LSI) immunoglobulin heavy chain (IGH) dual-color break-apart rearrangement probe, an LSI p16 SpectrumOrange/CEP 9 SpectrumGreen probe, an LSI BCL6 dual-color break-apart rearrangement probe. Among 150 cases, 29 cases (19.3%) showed infiltration of neoplastic lymphoid cells by microscopic examination. Chromosomal aberrations were detected by FISH in eight patients and by conventional cytogenetic study in three patients. FISH study showed 14q32 rearrangement in four patients (4/126, 3.2%), 9q21 rearrangement in no patients (0/144, 0%), 3q27 rearrangement in four patients (4/131. 3.1%), and a gain of 1q21q32 in two patients (2/115, 1.7%). Among eight patients with abnormal FISH patterns, six had normal karyotypes or no analyzable metaphase according to the conventional cytogenetic study. Seven patients with FISH abnormality showed bone marrow involvement of lymphoma by microscopic examination. One patient, who was defined as having no evidence of bone marrow involvement by microscopic examination, showed a 3q27 aberration in the FISH study. Although the number of patients with BM involvement that was detected by FISH was low, abnormal FISH patterns were detected in six patients who did not have abnormal karyotypes. Therefore, FISH analysis would be beneficial in cytogenetic diagnosis and follow-up study of minimal residual diseases, once the cytogenetic changes are detected at initial diagnosis.

[New chromosomal syndromes]. / Syndromes chromosomiques émergents.

Mental retardation occurs in 2-3% of the general population either in isolation or in combination with facial dysmorphism and/or malformations. Chromosomal abnormalities are a most common etiology. Karyotype displays chromosome aberrations in about 10% of patients but it has a limited resolution (5 Mb). Recently, the development of new molecular cytogenetic tools, especially array CGH, allowed to detect smaller abnormalities and increased the diagnosis capability of 15-20%. Among these newly detected rearrangements, some of them are recurrent and define new recognized syndromes. We will first briefly explain the non-allelic homologous recombination (NAHR) mechanism that underlines the origin of recurrent microdeletions and microduplications. Then we will describe eight new syndromes, four microdeletions (del 17q21.31, del 3q29, del 15q24, del 2q32.3q33) and four microduplications (dup 22q11.2, dup 7q11.23, dup 17p11.2, duplication of MECP2). A better knowledge of these new recurrent chromosomal syndromes will allow to improve care for patients, to develop targeted chromosomal diagnosis and to identify genes involved in neurocognitive functions.