RCytoGPS: An R Package for Reading and Visualizing Cytogenetics Data

Summary Cytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology. Availability and Implementation Freely available at https://CRAN.R-project.org/package=RCytoGPS. The code for the underlying CytoGPS software can be found at https://github.com/i2-wustl/CytoGPS. Supplementary information There is no supplementary data.

FISH-Based Karyotype Analyses of Four Dracaena Species

The genus <i>Dracaena</i> is the main source of dragon’s blood, which is a plant resin and has been used as traditional medicine since ancient times in different civilizations. However, the chromosome numbers and karyotypes present in this genus remain poorly understood. In this study, fluorescence in situ hybridization (FISH) using oligonucleotide probes for ribosomal DNAs (5S and 45S rDNA) and telomeric repeats (TTTAGGG)₃ was applied to analyze 4 related species: <i>Dracaena terniflora</i> Roxb., <i>Dracaena cambodiana</i> Pierre ex Gagnep., Aizong (<i>Dracaena</i> sp.), and <i>Dracaena cochinchinensis</i> (Lour.) S.C. Chen. In all 4 species, both 5S and 45S rDNA showed hybridization signals in the paracentromeric region of a pair of chromosomes; the sizes of the 45S rDNA signals were larger than those of the 5S rDNA. Importantly, the telomeric repeat signals were located in the telomeric regions of almost all chromosomes. The results indicated that the chromosome number of all 4 <i>Dracaena</i> species is 2n = 40, and the lengths of the mitotic metaphase chromosomes range from 0.99 to 2.98 μm. Our results provide useful cytogenetic information, which will be beneficial to future studies in genome structure of the genus <i>Dracaena</i>.

Orcein and DAPI-stained karyotype analysis of Alocasia macrorrhizos (L.) G. Don

Karyotype analyses are required for the identification, characterization, and genetic improvement of any organism. Alocasia macrorrhizos (L.) G. Don. was investigated cytogenetically to determine the karyotypic features. Complex chromocenter type, of interphase nuclei, and gradient type of prophase chromosomes were found in this study. Alocasia macrorrhizos was found to possesses 2n=28 chromosomes. The total length of the 2n chromosome complement was recorded as 98.83±1.39 μm. The range of chromosomal length was 2.50±0.10-4.70±0.10 μm. A gradual decrease in chromosomal length was observed. The total form (TF%) value was found to be 43.58%, Karyotype symmetry index (Syi %) was 77.00 % and karyotype asymmetry index (AsK %) was 56.66%. The centromeric formula was 18m+4sm+2ac, representing asymmetric karyotype. In DAPI banding, the 1.48% positive banded region indicates the lower amount of AT rich repeats in this material. Therefore, Alocasia macrorrhizos could be authentically characterized through karyotype analysis. J. Bangladesh Acad. Sci. 45(1); 27-35: June 2021

Elevated mature monocytes in bone marrow accompanied with a higher IPSS-R score predicts a poor prognosis in myelodysplastic syndromes

Background Myelodysplastic syndromes (MDS) is a group of heterogeneous myeloid clonal diseases originating from hematopoietic stem cells. Clinically, elevated mature monocyte in bone marrow is often observed, but its clinical value still remains unclear. Methods We retrospectively analyzed a cohort of 216 MDS patients to explore the prognostic value of the percentage of mature monocyte in bone marrow (PMMBM). All patients were divided into elevated PMMBM group and the normal group by 6% PMMBM as the cut-off value. Results Our results showed that PMMBM> 6% was associated with inferior overall survival (OS) (P = 0.026) along with higher-risk IPSS-R (P = 0.025) and higher frequency of IDH2 mutation (P = 0.007). Multivariate analyses showed that besides older age (> 60 years) for OS, gender (male) for OS, lower neutrophil count (< 0.8 × 109/L) for OS, higher bone marrow blast percentage (> 5%) for OS and LFS, poorer karyotype for OS, elevated PMMBM was also an independent adverse prognostic factor for OS in MDS (P < 0.0001) but not for LFS (P = 0.736). Conclusions These findings indicate that increased PMMBM may assists Revised International Prognostic Scoring System (IPSS-R) to predict a poor outcome and provide a novel evaluation factor for MDS patients especially when their karyotype analyses fail.

Karyotype analysis and chromosome number for two Cirsium taxa (Asteraceae) in Iran

Cirsium Mill. contains more than 250 species in the world mainly distributed in the Northern hemisphere. Different chromosome numbers with different ploidy levels were reported in this genus. In this study, karyotype details and chromosome numbers were established for two Cirsium taxa in Iran. C. ciliatum subsp. szovitsii and C. echinus had the mitotic chromosome numbers of 2n = 2x = 34. Karyotype analyses showed that chromosomes were generally metacentric and sub-metacentric. In C. echinus, Lowshan population had the longest chromosome (19.10 µm) and Heyran Canyon population (4.73 µm) the shortest one while in C. ciliatum, the longest chromosome was observed in Urmia to Salmas population (14.67 µm) and the shortest one (4.71 µm) in Doshanlu population. Total haploid chromosome length ranged from 275.29 to 376.42 µm in populations studied. Both taxa were grouped in 2B class. B-chromosomes were recorded for two taxa studied too. Chromosome type, mitotic chromosome numbers and occurrence of B-chromosomes were in agreement with previous results (Albers, Pröbsting, 1998; Lövkvist, Hultgård, 1999; Yüksel et al., 2013; Yildiz et al., 2016).

RCytoGPS: An R Package for Reading and Visualizing Cytogenetics Data

SummaryCytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology.Availability and ImplementationFreely available at https://CRAN.R-project.org/package=RCytoGPSSupplementary informationSupplementary data are available at Bioinformatics online.

Elevated mature monocytes in bone marrow accompanied with a higher IPSS-R score predicts a poor prognosis in myelodysplastic syndromes

Background: Myelodysplastic syndromes (MDS) is a group of heterogeneousmyeloid clonal diseases originating from hematopoietic stem cells. Clinically, elevated mature monocyte is often observed, but its clinical value still remains unclear.Methods: We retrospectively analyzed a cohort of 235 MDS patients to explore the prognostic value of the percentage of mature monocyte in bone marrow (PMMBM). All patients were divided into elevated PMMBM group and the normal group by 6% PMMBM as the cut-off value. Results: Our results showed that PMMBM>6% was associated with inferior overall survival (OS) (P=0.007) and leukemia-free survival (LFS) (P=0.016) along with higher Revised International Prognostic Scoring System (IPSS-R) score (P<0.0001) and higher frequency of IDH2 mutation (P=0.001). Multivariate analyses showed that besides older age (>60 years), lower hemoglobin level (<10 g/dl), higher bone marrow blast percentage (>5%), poorer karyotype, elevated PMMBM was also an independent adverse prognostic factor for OS in MDS (P=0.049). Conclusions: These findings indicate that increased PMMBM accompanied with a higher IPSS-R score may predict a poor outcome and provide a novel evaluation factor for MDS patients especially when their karyotype analyses fail.

The highly rearranged karyotype of the hangingfly Bittacus sinicus (Mecoptera, Bittacidae): the lowest chromosome number in the order

Cytogenetic features of the hangingfly Bittacus sinicus Issiki, 1931 were investigated for the first time using C-banding and DAPI (4',6-diamidino-2-phenylindole) staining. The karyotype analyses show that the male B. sinicus possesses the lowest chromosome number (2n = 15) ever observed in Mecoptera, and an almost symmetric karyotype with MCA (Mean Centromeric Asymmetry) of 12.55 and CVCL (Coefficient of Variation of Chromosome Length) of 19.78. The chromosomes are either metacentric or submetacentric with their sizes decreasing gradually. Both the C-banding and DAPI+ patterns detect intermediate heterochromatin on the pachytene bivalents of B. sinicus, definitely different from the heterochromatic segment at one bivalent terminal of other bittacids studied previously. The male meiosis of B. sinicus is chiasmate with two chiasmata in metacentric bivalents and one in the submetacentric bivalent. The sex determination mechanism is X0(♂), which is likely plesiomorphic in Bittacidae. Two alternative scenarios of karyotype origin and evolution in Bittacus Latreille, 1805 are discussed.

Towards New Approaches to Evaluate Dynamic Mosaicism in Ring Chromosome 13 Syndrome

Individuals with ring chromosome 13 may show characteristics observed in a deletion syndrome and could present a set of dismorphies along with intellectual disability, according to chromosomal segments involved in the genetic imbalance. Nevertheless, ring anomalies likewise is called “dynamic mosaicism”, phenomena triggered by the inner instability concerning the ring structure, thus leading to the establishment of different cell clones with secondary aberrations. Phenotypic features, such as growth failure and other anomalies in patients with this condition have been associated with an inherent ring chromosome mitotic instability, while recent studies offer evidence on a role played by the differential loss of genes implicated in development. Here, we observed similar mosaicism rates and specific gene loss profile among three individuals with ring chromosome 13 using GTW-banding karyotype analyses along with FISH and CGH-array approaches. Karyotypes results were: patient 1—r(13)(p13q32.3), patient 2—r(13)(p11q33.3), and patient 3—r(13)(p12q31.1). Array-CGH has revealed qualitative genetic differences among patients in this study and it was elusive in precise chromosomal loss statement, ranging from 13 Mb, 6.8 Mb, and 30 Mb in size. MIR17HG and ZIC2 loss was observed in a patient with digital anomalies, severe growth failure, microcephaly and corpus callosum agenesis while hemizygotic EFNB2 gene loss was identified in two patients, one of them with microphtalmia. According to these findings, it can be concluded that specific hemizygotic loss of genes related to development, more than dynamic mosaicism, may be causative of congenital anomalies shown in patients with ring 13 chromosome.

31 Building a functional annotation of the equine genome

The molecular determination of complex traits related to animal production, health, and performance remains elusive. In response, an international effort (Functional Annotation of ANimal Genomes, or FAANG) was initiated with the goal of identifying functional elements of the genome across domestic animal species. Toward this goal, the equine FAANG community has developed a biobank of over 80 tissues, four fluid types, and nine microbiome samples collected from two adult Thoroughbred mares as a resource for functional annotation of the horse genome. Full clinical phenotyping and careful histologic evaluation was performed on each tissue to allow for correlation of any observed pathologies and cell composition with sequencing results. Whole-genome sequencing (WGS) of each horse is complete as is RNA-sequencing (mRNA and smRNA) and analysis from eight prioritized tissues (liver, lung, hoof lamina, heart, longissimus dorsi muscle, ovary, parietal cortex, and adipose) as well as from 30 additional tissues sequenced with support from members of the community (known as the “Adopt-a-tissue” initiative). All sequencing data are now publicly available. Chromatin shearing and antibody concentrations have been optimized for ChIP-seq to characterize the major histone modification marks (H3K4me1, H3K4me3, H3K27me3, H3K27ac) in the eight prioritized tissues and spleen. Data collection and analyses are nearly complete. Assays to identify genomic insulators denoted by CCCTC-binding sites are also underway as is optimization of ATAC-seq, to characterize open chromatin in select tissues. The biobank’s use has extended to include chromatin run-on and sequencing (ChRO-seq) assays allowing for a novel comparison with ChIP-seq peaks. Further extensions of the biobank include keratinocyte cell culture, centromere mapping, karyotype analyses, methylation profiles, and microbiome characterization. These data provide a valuable baseline of genome function in the healthy, adult Thoroughbred mare and will allow for an improved understanding of and continuing research on tissue-, developmental-, and disease-associated genome regulation.