JAK2-mutated acute myeloid leukemia: comparison of next-generation sequencing (NGS) and single nucleotide polymorphism array (SNPa) findings between two cases

JAK2 mutations are rare in de novo acute myeloid leukemia (AML), and JAK2-mutated acute myeloid leukemia (AML) patients usually have a previous history of myeloproliferative neoplasms (MPNs). Current advances in laboratory techniques, such as single nucleotide polymorphism array (SNPa) and next-generation sequencing (NGS), have facilitated new insight into the molecular basis of hematologic diseases. Herein, we present two cases of JAK2-mutated AML in which both SNPa and NGS methods added valuable information. Both cases had leukemogenic collaboration, namely, copy-neutral loss of heterozygosity (CN-LOH), detected on chromosome 9. One of the cases exhibited both JAK2 and IDH2 mutations, most likely having originated as an MPN with leukemic transformation, while the other case was classified as a de novo AML with JAK2, CEBPA, and FLT3 mutations.

[Research progress in lampbrush chromosomes and some suggestions for their use in genetics teaching].

Lampbrush chromosomes (LBCs) are transient giant transcripts that exist at the diplotene stage of the first meiotic division in female gametocytes of almost all animals except mammals. LBCs are named for their lampbrush-like structure, however, they received the lowest research attention in studies of three classical cytogenetic chromosomes. They have been excellent models for studying the structure, organization, transcription, and transcriptional processing of chromosomes during meiosis. Here we briefly summarized these studies and LBCs forming mechanism and also discussed their possible functions, such as providing enough transcriptional products for embryonic development by oocytes LBCs or polyploidy demonstrated by previous reports. Finally, we discussed the possibility of introducing this typical case into our genetics teaching to inspire students' interest in genetics.

Evidence of incipient speciation in astyanax scabripinnis species complex (teleostei: characidae)

Two populations of the Astyanax scabripinnis complex, isolated by a waterfall with over 100 meters depth and inhabiting different altitudes of the same river (1850 m a.s.l. and 662 m a.s.l.) were compared in reproductive data, geometric morphometry, tooth morphology, anal-fin rays counts, and karyotype, in order to test the hypothesis of speciation between the two populations. The results in the geometric morphometry analysis showed differences between the populations. Discriminant function analysis (DFA) and canonical variance analysis revealed sexual dimorphism. Secondary sexual characters, such as hooks in the anal fin rays of the males are absent in the lower altitude population. Both populations had the same macro karyotype structure, except for the absence of B chromosomes in the lower altitude population. The fluorescence in situ hybridization showed differences for both markers (18S rDNA and 5S rDNA), and reproductive data suggests pre-zygotic reproductive isolation among the two populations. The data showed the absence of gene flow, indicating that an incipient speciation process has occurred, which leads the two populations to follow independent evolutionary pathways.

Duas populações do complexo Astyanax scabripinnis isoladas por uma queda d´água de mais de 100 metros de altura e localizadas em diferentes altitudes do mesmo rio (662 m e 1850 m a.s.l.) foram comparadas através de dados de reprodução, cariótipo, morfometria geométrica, morfologia dentária, e número de raios da nadadeira anal, de modo a testar a hipótese de especiação entre as duas populações. Os resultados de morfometria geométrica mostraram diferenças entre as populações. A análise da função discriminante (DFA) e a análise de variância canônica (CVA) demonstraram a presença de dimorfismo sexual. Caracteres sexuais secundários, como ganchos em raios da nadadeira anal dos machos, estão ausentes na população de menor altitude. Ambas as populações têm a mesma macro estrutura cariotípica, exceto pela ausência de cromossomos B na população de menor altitude. A hibridação in situ mostrou diferenças para ambos os marcadores (rDNA 18S e rDNA 5S), e os dados de reprodução sugerem isolamento reprodutivo pré-zigótico entre as duas populações. Os dados mostram ausência de fluxo gênico, indicando que ocorreu um processo de especiação incipiente, o que leva as duas populações seguirem vias evolutivas independentes.

DNA barcode of parodontidae species from the La Plata river basin - applying new data to clarify taxonomic problems

In the past years, DNA barcoding has emerged as a quick, accurate and efficient tool to identify species. Considering the difficulty in identifying some Parodontidae species from the La Plata basin and the absence of molecular data for the group, we aimed to test the effectiveness of DNA barcoding and discuss the importance of using different approaches to solve taxonomic problems. Eight species were analyzed with partial sequences of Cytochrome c oxidase I. The mean intraspecific K2P genetic distance was 0.04% compared to 4.2% for mean interspecific K2P genetic distance. The analyses of distance showed two pairs of species with K2P genetic divergence lower than 2%, but enough to separate these species. Apareiodon sp. and A. ibitiensis, considered as the same species by some authors, showed 4.2% genetic divergence, reinforcing their are different species. Samples of A. affinis from the Uruguay and Paraguay rivers presented 0.3% genetic divergence, indicating a close relationship between them. However, these samples diverged 6.1% from the samples of the upper Paraná River, indicating that the latter represents a potentially new species. The results showed the effectiveness of the DNA barcoding method in identifying the analyzed species, which, together with the morphological and cytogenetic available data, help species identification.

Nos últimos anos o DNA barcoding surgiu como uma ferramenta rápida, precisa e eficiente para identificar espécies. Considerando a dificuldade na identificação de algumas espécies de Parodontidae da bacia do rio da Prata e da ausência de dados moleculares para o grupo, testamos a eficácia do código de barras de DNA e discutimos a importância do uso de diferentes abordagens para resolver problemas taxonômicos. Oito espécies foram analisadas com sequencias parciais do gene citocromo c oxidase I. A distância genética média K2P intraespecífica foi de 0,04% comparado com 4,2% para distância genética média K2P interespecífica. As análises de distância mostraram dois pares de espécies com divergência genética K2P inferior a 2%, mas o suficiente para separar estas espécies. Apareiodon sp. e A. ibitiensis, consideradas a mesma espécie por alguns autores, mostraram 4,2% de divergência genética, confirmando serem espécies diferentes. Amostras de A. affinis dos rios Uruguai e Paraguai apresentaram 0,3% de divergência genética, indicando um maior grau de relação entre elas, no entanto, esses exemplares divergiram em 6,1% em relação aos exemplares do alto rio Paraná, o que indica que estes últimos representam uma espécie potencialmente nova. Os resultados mostraram a eficácia do método de DNA barcoding na identificação das espécies analisadas, os quais, em conjunto com os dados morfológicos e citogenéticos disponíveis auxiliam na identificação inequívoca das espécies.

Caracterização citogenética para identificação dos níveis de ploidia em cinco espécies do gênero Mentha L / Citogenetic characterization to determination of ploidy level on five Mentha L. species

Neste trabalho foi feita a caracterização citogenética da: microsporogênese, tétrades, estimativa da viabilidade do pólen pelo método de coloração e contagem do número máximo de nucléolos por célula interfásica, para identificação dos níveis de ploidia, em cinco espécies do gênero Mentha L. Foram coletadas inflorescências em 30 plantas de cada espécie, em duas florações sucessivas, nos anos 2006 e 2007. As inflorescências foram tratadas em etanol-ácido acético (3:1), em temperatura ambiente durante seis horas, transferidas para álcool 70% (v/v) e conservadas em geladeira até análise. Nas análises da microsporogênese, tétrades e pólen o corante usado foi carmin propiônico 2% e na identificação dos nucléolos nitrato de prata (AgNO3). Os resultados demonstraram que as cinco espécies são poliplóides. M. crispa heptaplóide (2n=7x=84) com 11 nucléolos, M. spicata tetraplóide (2n=4x=48) com 8 nucléolos, M.x gentilis pentaplóide (2n=5x=60) com 12 nucleólos, M. piperita e M.x piperita ambas hexaplóides (2n=6x=72) com 8 e 9 nucléolos respectivamente. M. spicata e M. crispa mantiveram as mais altas porcentagens de células normais na microsporogênese, na formação de tétrades e na estimativa da viabilidade do pólen por coloração, sugerindo maior estabilidade meiótica quando comparados aos demais poliplóides estudados.

The cytogenetic characterization of five species of Mentha L. genus, including the data: regularity of microsporogenesis and tetrads, and polen viability, using the coloration method and the counting of the maximum number of nucleolus by interphasic cell were carried out in this study to identify the ploid levels. These analyses were performed from inflorescences collected in 30 plants of each species, during two successive florations in 2006 and 2007. Inflorescences were treated in 3:1 ethanol:acetic acid mixture at room temperature during six hours, then transferred to 70%(v/v) ethanol solution and refrigerated until the analysis. For microsporogenis, tetrad and pollen analysis, we used carmine propionic 2% (m/v) and for nucleolus identification, we used AgNO3 solution. It was possible to observe that all five species were polyploids. M. crispa heptaploid (2n=7x=84) with 11 nucleolus, M. spicata tetraploid (2n=4x=48) with 8 nucleolus, M. x gentilis pentaploid (2n=5x=60) with 12 nucleolus, M. piperita and M. x piperita both hexaploid (2n=6x=72) with 8 and 9 nucleolus respectively. M. spicata and M. crispa kept the highest percentual values of normal cells in microsporogenesis as well as in tetrads formation and pollen viability, suggesting a higher meiotic stability when compared to the other polyploids studied.

Multicolour interphase cytogenetics: 24 chromosome probes, 6 colours, 4 layers.

From the late 1980s onwards, the use of DNA probes to visualise sequences on individual chromosomes (fluorescent in-situ hybridisation - FISH) revolutionised the study of cytogenetics. Following single colour experiments, more fluorochromes were added, culminating in a 24 colour assay that could distinguish all human chromosomes. Interphase cytogenetics (the detection of chromosome copy number in interphase nuclei) soon followed, however 24 colour experiments are hampered for this application as mixing fluorochromes to produce secondary colours produces images that are not easily distinguishable from overlapping signals. This study reports the development and use of a novel protocol, new fast hybridising FISH probes, and a bespoke image capture system for the assessment of chromosome copy number in interphase nuclei. The multicolour probe sets can be used individually or in sequential hybridisation layers to assess ploidy of all 24 human chromosomes in the same nucleus. Applications of this technique are in the investigation of chromosome copy number and the assessment of nuclear organisation for a range of different cell types including human sperm, cancer cells and preimplantation embryos.

The assessment of array comparative genomic hybridization in complex karyotype analyses.

Molecular-cytogenetic methods were used to analyse and specify complex genome rearrangements in malignant cells. Twelve samples of bone marrow cells were collected from patients with myelodysplastic syndromes (MDS). The complex karyotypes were examined by multicolour fluorescence in situ hybridization (mFISH), high-resolution multicolour banding (mBAND) and array comparative genomic hybridization (aCGH). For aCGH, DNA was isolated from fixed bone marrow cells in methanol and acetic acid and amplified by whole-genome amplification. Three samples were analysed by the oligonucleotide array NimbleGen on the basis of full service. BAC-based Haematochips (BlueGnome) were used for the other nine samples. Sensitivity and detection limits of both methods were compared. The results obtained by mFISH/mBAND were in most cases confirmed by the microarray technique. aCGH detected 43 unbalanced chromosomal changes that were also identified by classical cytogenetics and FISH. Moreover, aCGH discovered 14 additional changes. Cryptic amplifications and deletions were characterized with a resolution of 0.5 Mb. In one bone marrow sample with suspected monosomy 5 detected by conventional cytogenetic analysis, aCGH revealed a 22.3 Mb region of chromosome 5 inserted in another autosome within the complex karyotype. Amplified DNA was successfully used for aCGH in 11 out of 12 cases, improving resolution of unbalanced chromosomal aberrations. The combination of both approaches brought more detailed description of complex karyotypes and is highly recommended.

A support vector machine classifier for recognizing mitotic subphases using high-content screening data.

High-content screening studies of mitotic checkpoints are important for identifying cancer targets and developing novel cancer-specific therapies. A crucial step in such a study is to determine the stage of cell cycle. Due to the overwhelming number of cells assayed in a high-content screening experiment and the multiple factors that need to be taken into consideration for accurate determination of mitotic subphases, an automated classifier is necessary. In this article, the authors describe in detail a support vector machine (SVM) classifier that they have implemented to recognize various mitotic subphases. In contrast to previous studies to recognize subcellular patterns, they used only low-resolution cell images and a few parameters that can be calculated inexpensively with off-the-shelf image-processing software. The performance of the SVM was evaluated with a cross-validation method and was shown to be comparable to that of a human expert.

Analysis of RNA recovery and gene expression in the epidermis using non-invasive tape stripping.

BACKGROUND: The recovery of RNA from the upper epidermis by tape stripping yields variable RNA mass but has not been evaluated for its dependence on anatomical location. Gene expression at different body locations and the origin of RNA recovered by tape stripping have not been investigated. OBJECTIVES: To characterize the recovery of RNA from different anatomical locations by tape stripping; to correlate the recovery of RNA and removal of barrier by tape stripping, as assayed by transepidermal water loss; and to investigate gene expression in the upper epidermis at different body locations. METHODS: Twelve subjects were tape stripped at 15 body locations. RNA mass was evaluated and gene expression assayed. Subjects were tape stripped 4, 8 and 12 times on the upper back and transepidermal water loss and RNA recovery assayed. RESULTS: Ranked by median RNA recovery, the following order was observed: mastoid>forehead>chest>upper back>mid back>cheek>lower back>deltoid>forearm>abdomen>ventral thigh>inner arm>shin>dorsal thigh>lower leg. Expression of the housekeeping gene mRNAs is found to be uniform and reproducible while IL-8 and TNFalpha mRNAs are expressed in different quantities both at different body sites within an individual and between individuals at a specific anatomical site. Data show a significant and high correlation between the number of tapes used to strip a site and transepidermal water loss but no strong correlation between transepidermal water loss and RNA recovery or number of tapes used to strip a site and RNA recovery. CONCLUSIONS: Subjects and anatomical location are shown to be significantly different for the ability to recover RNA by tape stripping. We hypothesize that RNA recovered by tape strip is not derived from corneocytes but from cells associated with the stratum corneum.

Trisomia parcial del cromosoma 6(q27): presentación de un caso / Partial trisomy of chromosome 6(q27): a case report

Presentamos un caso de un paciente de sexo masculino de 5 meses de edad, múltiple malformado. Mediante técnicas de citogenética clásica y bandeamiento G, se determino, trisomía parcial del brazo largo del cromosoma 6, (dup parcial 6 (q27). Una enfermedad cromosómica extremadamente rara, por lo que se busco una relación con otros casos similares reportados y la probable acción de los genes involucrados en esta región para la expresión de los signos clínicos reportados.

Microdissection techniques for cancer analysis.

One difficulty in studying molecular changes of tumours has been the inability to isolate DNA and RNA from a homogeneous cell population. The combination of several new technologies should help overcome these hurdles. Microdissection is a technique for rapid and easy procurement of a pure cellular subpopulation away from its complex tissue milieu. Laser-assisted microdissection has recently been identified as a quick, simple and effective method by which microdissection of complex tissue specimens can be routinely performed for molecular analysis. With the advent of laser microdissection, cDNA libraries can be developed from pure cells obtained directly from stained neoplastic tissue, and microarrays of thousands of genes can now be used to examine gene expression in microdissected tumour tissue samples. This review will concentrate on the application of different microdissection techniques in the area of cancer research.

Simple technique of codenaturation and fluorescence in situ hybridization with probes in a microcamera.

We describe a rapid, precise and economical method of performing fluorescence in situ hybridization with probes in a microcamera, without chemical risk for the operator caused by the use of formamide. The application has been tried on metaphase spreads and interphase nuclei from peripheral blood or bone marrow cultures and on formalin-fixed, paraffin-embedded tissue.

Actualización de síndrome de Down en el Instituto de Genética / Review about Down syndrome in the genetics institute

El presente documento contiene información sobre los aspectos más relevalentes que engloban a la cromosomopatía más frecuente, el Síndrome de Down (SD). Enfatizamos en la importancia de corroborar el diagnóstico clínico con el diagnóstico. Con el fin de tener una idea más concreta de la realidad actual en cuanto al SD en nuestro medio, se mencionan los resultados arciales del estudio de prevalencia de enfermedades genéticas en el Instituto de Genética (IG), obtenidos de expedientes de los pacientes correspondientes al periodo de enero de 1998 a dicembre de 2001, con cariotipo compatible con SD, periodo durante el cual se atenderon 89 casos de SD. la edad de derivación para el diagnóstico citogenético se realizó antes de primer año de vida en un75 por ciento. El número de casos fue similar para ambos sexos, el 85.9 porciento de los casos corresponden ala ciudad de La Paz y el 58 porciento de los casos corresponden a madres mayores de 34 años. el porcentaje de presentación de las características fenotípicas es variable en el SD. La alteracion cromosómica más frecuente es a trisomía libre (96,6 porciento). Los datos nacionales permitieron argumentar el proqué se debe realziar el diagnóstico precoz, la importancia del manejo integral y multidisciplinario de los pacientes con SD, la obligación ético moral que tiene el profesional médico de brindar la posibilidad de asesoramiento genético a los padres, familias y el establecer el seguimiento adecuado del paciente. Conclusiones y Recmendaicones: Para realziar el diagnóstico adecuado del Sd y su posterior manejo es imprescindible el estudio citogenético precoz. el manejo inadecuado y e tardío o inexistente diagnóstico citogenético dsminuye las oportunidades de pacientes con sociedad coadyuvando a una mejora calidad de vida del individuo y la familia.

Molecular cytogenetics: unraveling of the genetic composition of individual cells by fluorescence in situ hybridization and digital imaging microscopy.

Molecular biology techniques allow the unraveling of the genetic alterations that cause or accompany malignant disease. Since tumors are often heterogeneous, biochemical analysis of tissue homogenates is of limited diagnostic value. This paper gives examples of methods that are presently operational to analyze the genetic composition of individual cells. They are based on fluorescence in situ hybridization (FISH) and digital imaging microscopy. First, the current status of indirect and direct FISH staining methods with respect to probe labeling, detection sensitivity, multiplicity, and DNA resolution is summarized. Microscope hardware as well as charge-coupled device (CCD) cameras required for FISH analysis are then described. Applications potentially important for the analysis of urological malignancies, such as the automated enumeration of chromosomal abnormalities (counting of dots in interphase cells) and high-resolution DNA mapping on highly extended chromatin, are described in detail. Finally, the limitations of the present methodology and its future prospects are discussed.

Evaluation of a metaphase chromosome finder: potential application to chromosome-based radiation dosimetry.

An automated metaphase chromosome finder is described which combines a microscope, state-of-the-art computer technology and a simple decision-making algorithm. A microscope slide is systematically scanned under computer control and the location of each positive 'signal' placed into memory for later recall and review by a human operator. The software identifies two events, positives (the presence of a 'signal') and negatives (the absence of a 'signal'). The performance of the metaphase finder was evaluated using receiver operating characteristic curve analysis. At the optimum decision threshold, the detection rates for true positives (metaphase spreads) was about 74%, false positives (type I error) about 6%, and false negatives (type II error) about 26%. The overall accuracy, which accounts for differences in the sensitivity of the detector to positive and negative events, was 89.4% (+/- 0.01%; standard error of the mean, n = 8). Potential applications to radiation dosimetry are discussed.

A high resolution chromosome image processor for study purposes, NIRS-1000:CHROMO STUDY, and algorithm developing to classify radiation induced aberrations.

Since 1989 we have promoted a project to develop an automated scoring system of radiation induced chromosome aberrations. As a first step, a high resolution image processing system for study purposes, NIRS-1000:CHROMO STUDY, has been developed. It is composed of: (1) CHROMO MARKER whose main purpose is to mark on images to make image data base, (2) CHROMO ALGO whose purpose is algorithm development, and (3) METAPHASE RANKER whose purposes are metaphase finding and ranking with a high power objective lens. However, METAPHASE RANKER is presently under development. The system utilizes a high definition video system so as to realize the best spatial resolution that is achievable with an optical microscope using an objective lens (x 100, numerical aperture 1.4). The video camera has 1024 effective scan lines to realize 0.1 microns sampling on a specimen. The system resolution achieved on the hard copy is less than 0.3 microns on a specimen. A preliminary algorithm has been developed to classify the aberrations on the system using projection information of gray level. The preliminary test results on excellent 10 metaphases show that the correct classification ratio is 92.7%, that the detection rate of the aberrations is 83.3% and that the false positive rate is 6.1%.

Application of laser optical tweezers in immunology and molecular genetics.

Optical tweezers, based on a compact diode pumped Nd:YAG laser providing 350 mW at 1,064 nm coupled into a Zeiss IM 35 microscope, were used to sort CD4+ T cells into a capillary for further mechanical handling and to establish contact between single human natural killer (NK) cells and human erythroleukemia cells (K562) as targets. After contact and a lag phase of a few tens of seconds, the target cell starts to change its morphology and membrane blebbing occurs. The kinetics of the attack of the NK cell on K562 cells is not straightforward but governed by temporal oscillations in the shape of the target cell (zeosis). In a second application, the optical tweezers are combined with a UV laser microbeam based on a pulsed UV laser and with flow cytometry and sorting. With the pulsed laser, segments of sorted chromosome 1 of the chinese hamster karyotype (CHV 79) can be easily micro-dissected and subsequently collected using the optical tweezers. This allows preparation of a few hundred chromosome segments per day without mechanical contact and in an absolutely sterile way and thus may provide an interesting basic technique in any type of genome sequencing project.