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1.
Arch Gynecol Obstet ; 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38955819

RESUMO

PURPOSE: This is a retrospective comparative study. We aimed to analyze the results of karyotype and chromosomal microarray analysis (CMA) of amniotic fluid across different gestational weeks and evaluate the clinical value in prenatal diagnosis, particularly in the late pregnancies. METHODS: Samples from 580 pregnant women of 18-23 weeks of gestation (mid-gestation group) and 196 pregnant women of 24-32 weeks of gestation (late group) were performed both standard G-band karyotype analysis and CMA. RESULTS: Among the 580 pregnant women in the routine group, the most common indications were positive Down's screening (213/580, 36.7%), followed by advanced maternal age (196/580, 33.8%); while fetal structural anomalies on ultrasonography were the top reason for amniocentesis in the late group (56/196, 28.6%). In the routine group, the total detection rate was 12.1% (70/580), of which 4.1% (24/580) were identified by karyotype analysis and 11.2% (65/580) by CMA. The total detection rate was 15.3% (30/196) in the late group, of which 5.1% (10/196) were detected by karyotype analysis, and 14.3% (28/196) by CMA. CONCLUSION: Karyotype analysis and CMA are complementary in detecting chromosomal abnormalities. Amniotic cavity puncture in the karyotype analysis in 18-23 weeks of gestation and 24-32 weeks of gestation is safe and effective, more obvious effect on the latter.

2.
Genome Biol Evol ; 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38946297

RESUMO

Schoenoplectus tabernaemontani (C. C. Gmelin) Palla is a typical macrophyte in diverse wetland ecosystems. This species holds great potential in decontamination applications and carbon sequestration. Previous studies have shown that this species may have experienced recent polyploidization. This would make S. tabernaemontani a unique model to study the processes and consequences of whole genome duplications in the context of the well-documented holocentric chromosomes and dysploidy events in Cyperaceae. However, the inference was not completely solid because it lacked homology information which is essential to ascertain polyploidy. We present here the first chromosome-level genome assembly for S.tabernaemontani. By combining ONT long-reads and Illumina short-reads, plus chromatin conformation via the Hi-C method, we assembled a genome spanning 507.96 Mb, with 99.43% of Hi-C data accurately mapped to the assembly. The assembly contig N50 value was 3.62 Mb. The overall BUSCO score was 94.40%. About 68.94% of the genome was comprised of repetitive elements. 36994 protein-coding genes were predicted and annotated. Long terminal repeat retrotransposons (LTR-rts) accounted for approximate 26.99% of the genome, surpassing the content observed in most sequenced Cyperid genomes. Our well-supported haploid assembly comprised 21 pseudochromosomes, each harboring putative holocentric centromeres. Our findings corroborated a karyotype of 2n=2X=42. We also confirmed a recent whole genome duplication (WGD) occurring after the divergence between Schoenoplecteae and Bolboschoeneae. Our genome assembly expands the scope of sequenced genomes within the Cyperaceae family, encompassing the fifth genus. It also provides research resources on Cyperid evolution and wetland conservation.

3.
Comp Cytogenet ; 18: 105-122, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38966326

RESUMO

Recently, hypotheses regarding the evolutionary patterns of ribosomal genes in ant chromosomes have been under discussion. One of these hypotheses proposes a relationship between chromosomal location and the number of rDNA sites, suggesting that terminal locations facilitate the dispersion of rDNA clusters through ectopic recombination during meiosis, while intrachromosomal locations restrict them to a single chromosome pair. Another hypothesis suggests that the multiplication of rDNA sites could be associated with an increase in the chromosome number in Hymenoptera due to chromosomal fissions. In this study, we physically mapped rDNA sites in 15 new ant species and also reviewed data on rDNA available since the revision by Teixeira et al. (2021a). Our objectives were to investigate whether the new data confirm the relationship between chromosomal location and the number of rDNA sites, and whether the increase in the chromosome number is significant in the dispersion of rDNA clusters in ant karyotypes. Combining our new data with all information on ant cytogenetics published after 2021, 40 new species and nine new genera were assembled. Most species exhibited intrachromosomal rDNA sites on a single chromosome pair, while three species showed these genes in terminal regions of multiple chromosome pairs. On one hand, the hypothesis that the chromosomal location of rDNA clusters may facilitate the dispersion of rDNA sites in the ant genome, as previously discussed, was strengthened, but, on the other hand, the hypothesis of chromosomal fission as the main mechanism for dispersion of ribosomal genes in ants is likely to be refuted. Furthermore, in certain genera, the location of rDNA sites remained similar among the species studied, whereas in others, the distribution of these genes showed significant variation between species, suggesting a more dynamic chromosomal evolution.

4.
IJU Case Rep ; 7(4): 329-332, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38966769

RESUMO

Introduction: 17α-Hydroxylase deficiency is a very rare disease reported to be associated with a risk of gonadal malignancy. We herein report a rare case of seminoma in a 46, XY patient with 17α-hydroxylase deficiency. Case presentation: A 52-year-old woman presented with a 9-cm pelvic tumor. At age 14, she had been identified as having the XY karyotype and 17α-hydroxylase deficiency. However, she was not informed and did not consult the urology department. Laparoscopic gonadectomy was performed at the latest consultation, and seminoma was diagnosed. Conclusion: This is the third reported case of testicular tumor and the first of germ cell tumor in a 46, XY patient with 17α-hydroxylase deficiency. Given the rarity and the risk of gonadal malignancy associated with 17α-hydroxylase deficiency, the involvement of multidisciplinary specialists and prophylactic gonadectomy is considered crucial in its management.

5.
Comp Cytogenet ; 18: 97-103, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38948005

RESUMO

The current study analyzed the chromosomal karyotype of Quasipaaspinosa David, 1875 from Hunan Province, China. The karyotype, C-banding, BrdU-banding pattern were characterized using direct preparation of bone-marrow cells and hemocyte cultures. The findings indicated that Q.spinosa was a diploid species (2n = 26) that lacked heteromorphic chromosomes and secondary constrictions. C-banding analysis revealed an abundance of positive signals in the centromere regions, while the BrdU-banding pattern showed three phases in both male and female, occurring consistently and in chronological sequence during S-phase. Notably, there was no asynchronous replication in the late phase. This study enhanced our understanding of the karyotypic structure of Q.spinosa by conventional cytogenetic techniques, thus providing essential scientific insights into the cytogenetics of Q.spinosa.

6.
BMC Vet Res ; 20(1): 298, 2024 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-38971779

RESUMO

BACKGROUND: Sex chromosome abnormalities associated with disorders of sexual development (DSD) are rarely described in cats, mainly due to the lack of chromossome studies that precisely reveal the condition. Genetic approaches are therefore required in order to detect sex chromossomes abnormalities as variations in the number and structure of chromosomes, or the presence of a second cell line as mosaicim or chimerism. CASE PRESENTATION: A male Shorthair cryptorchid cat was presented with clinical signs of anorexia, tenesmus and hyperthermia. Ultrasonography revealed a fluid-filled structure, with approximately 1 cm in diameter, adjacent to the descending colon. Computed tomography evidenced a tubular structure, ventral to the descending colon and caudal to the bladder, which extended cranially, through two branches. Histopathological evaluation confirmed the presence of two atrophic uterine horns and one hypoplastic testicle with epididymis at the end of one of the uterine horns. The end of the other uterine horn was attached to a structure composed by a mass of adipocytes. Cytogenetic analysis revealed a mosaic 37,X/38,XY karyotype. The two cell lines were found in 15% and 85% of the lymphocytes, respectively. Genetic analysis confirmed the presence of SRY and ZFY genes in blood and hair bulbs, and revealed a marked reduction in SRY expression in the testicle. Additionally, this case presented exceptionally rare features, such as a Leydig' cell tumour and a chronic endometritis in both uterine horns. CONCLUSIONS: Complete imaging workup, cytogenetic analysis and SRY gene expression should be systematically realized, in order to properly classify disorders of sexual development (DSD) in cats.


Assuntos
Doenças do Gato , Cariótipo , Mosaicismo , Animais , Gatos , Masculino , Doenças do Gato/genética , Doenças do Gato/patologia , Doenças do Gato/diagnóstico por imagem , Transtornos do Desenvolvimento Sexual/veterinária , Transtornos do Desenvolvimento Sexual/genética , Transtornos do Desenvolvimento Sexual/patologia
7.
Genes (Basel) ; 15(6)2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38927599

RESUMO

The sex chromosomes of skinks are usually poorly differentiated and hardly distinguished by cytogenetic methods. Therefore, identifying sex chromosomes in species lacking easily recognizable heteromorphic sex chromosomes is necessary to fully understand sex chromosome diversity. In this paper, we employed cytogenetics, sex quantification of genes, and transcriptomic approaches to characterize the sex chromosomes in Plestiodon elegans. Cytogenetic examination of metaphases revealed a diploid number of 2n = 26, consisting of 12 macrochromosomes and 14 microchromosomes, with no significant heteromorphic chromosome pairs, speculating that the sex chromosomes may be homomorphic or poorly differentiated. The results of the sex quantification of genes showed that Calumenin (calu), COPI coat complex subunit γ 2 (copg2), and Smoothened (smo) were at half the dose in males as in females, suggesting that they are on the X chromosome. Transcriptomic data analysis from the gonads yielded the excess expression male-specific genes (n = 16), in which five PCR molecular markers were developed. Restricting the observed heterozygosity to males suggests the presence of homomorphic sex chromosomes in P. elegans, XX/XY. This is the first breakthrough in the study of the sex chromosomes of Plestiodon.


Assuntos
Transcriptoma , Animais , Masculino , Feminino , Transcriptoma/genética , Cromossomos Sexuais/genética , Cromossomo X/genética , Gônadas/metabolismo , Análise Citogenética/métodos
8.
Genes (Basel) ; 15(6)2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38927657

RESUMO

Chromosomal translocations can result in phenotypic effects of varying severity, depending on the position of the breakpoints and the rearrangement of genes within the interphase nucleus of the translocated chromosome regions. Balanced translocations are often asymptomatic phenotypically and are typically detected due to a decrease in fertility resulting from issues during meiosis. Robertsonian translocations are among the most common chromosomal abnormalities, often asymptomatic, and can persist in the population as a normal polymorphism. We serendipitously discovered a Robertsonian translocation between chromosome 21 and chromosome 22, which is inherited across three generations without any phenotypic effect, notably only in females. In situ hybridization with alpha-satellite DNAs revealed the presence of both centromeric sequences in the translocated chromosome. The reciprocal translocation resulted in a partial deletion of the short arm of both chromosomes 21, and 22, with the ribosomal RNA genes remaining present in the middle part of the new metacentric chromosome. The rearrangement did not cause alterations to the long arm. The spread of an asymptomatic heterozygous chromosomal polymorphism in a population can lead to mating between heterozygous individuals, potentially resulting in offspring with a homozygous chromosomal configuration for the anomaly they carry. This new karyotype may not produce phenotypic effects in the individual who presents it. The frequency of karyotypes with chromosomal rearrangements in asymptomatic heterozygous form in human populations is likely underestimated, and molecular karyotype by array Comparative Genomic Hybridization (array-CGH) analysis does not allow for the identification of this type of chromosomal anomaly, making classical cytogenetic analysis the preferred method for obtaining clear results on a karyotype carrying a balanced rearrangement.


Assuntos
Cromossomos Humanos Par 21 , Cromossomos Humanos Par 22 , Translocação Genética , Humanos , Cromossomos Humanos Par 21/genética , Cromossomos Humanos Par 22/genética , Hibridização in Situ Fluorescente , Cariótipo , Cariotipagem , Fenótipo , Translocação Genética/genética
9.
Cancers (Basel) ; 16(12)2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38927962

RESUMO

Current CLL guidelines recommend a two parallel cultures assessment using TPA and IL2+DSP30 mitogens for complex karyotype (CK) detection. Studies comparing both mitogens for CK identification in the same cohort are lacking. We analyzed the global performance, CK detection, and concordance in the complexity assessment of two cytogenetic cultures from 255 CLL patients. IL2+DSP30 identified more altered karyotypes than TPA (50 vs. 39%, p = 0.031). Moreover, in 71% of those abnormal by both, IL2+DSP30 identified more abnormalities and/or abnormal metaphases. CK detection was similar for TPA and IL2+DSP30 (10% vs. 11%). However, 11/33 CKs (33%) were discordant, mainly due to the detection of a normal karyotype or no metaphases in the other culture. Patients requiring treatment within 12 months after sampling (active CLL) displayed significantly more CKs than those showing a stable disease (55% vs. 12%, p < 0.001). Disease status did not impact cultures' concordance (κ index: 0.735 and 0.754 for stable and active). Although CK was associated with shorter time to first treatment (TTFT) using both methods, IL2+DSP30 displayed better accuracy than TPA for predicting TTFT (C-index: 0.605 vs. 0.580, respectively). In summary, the analysis of two parallel cultures is the best option to detect CKs in CLL. Nonetheless, IL2+DSP30 could be prioritized above TPA to optimize cytogenetic assessment in clinical practice.

10.
Ann Hematol ; 103(7): 2337-2346, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38849603

RESUMO

High hyperdiploid karyotype with ≥ 49 chromosomes (which will be referred to as HHK) is rare in acute myeloid leukemia (AML). The European leukemia network (ELN) excluded those harboring only numerical changes (with ≥ 3 chromosome gains) from CK and listed them in the intermediate risk group, while the UK National Cancer Research Institute Adult Leukaemia Working Group classification defined ≥ 4 unrelated chromosome abnormalities as the cutoff for a poorer prognosis. Controversies occurred among studies on the clinical outcome of HHK AML, and their molecular characteristics remained unstudied. We identified 1.31% (133/10,131) HHK cases within our center, among which 48 cases only had numerical changes (NUM), 42 had ELN defined adverse abnormalities (ADV) and 43 had other structural abnormalities (STR). Our study demonstrated that: (1) No statistical significance for overall survival (OS) was observed among three cytogenetic subgroups (NUM, STR and ADV) and HHK AML should be assigned to the adverse cytogenetic risk group. (2) The OS was significantly worse in HHK AML with ≥ 51 chromosomes compared with those with 49-50 chromosomes. (3) The clinical characteristics were similar between NUM and STR group compared to ADV group. The former two groups had higher white blood cell counts and blasts, lower platelet counts, and mutations associated with signaling, while the ADV group exhibited older age, higher chromosome counts, higher percentage of myelodysplastic syndrome (MDS) history, and a dominant TP53 mutation.


Assuntos
Leucemia Mieloide Aguda , Mutação , Proteína Supressora de Tumor p53 , Humanos , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/mortalidade , Leucemia Mieloide Aguda/diagnóstico , Pessoa de Meia-Idade , Feminino , Masculino , Adulto , Idoso , Proteína Supressora de Tumor p53/genética , China/epidemiologia , Prognóstico , Adolescente , Adulto Jovem , Idoso de 80 Anos ou mais , Aberrações Cromossômicas , Cariótipo , Taxa de Sobrevida , Cariotipagem
11.
Cureus ; 16(5): e60264, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38872687

RESUMO

Trisomy 13, also known as Patau syndrome, is a widely congenital anomaly syndrome characterized by microphthalmia, cleft lip, and palate, microcephaly with a sloping forehead, congenital heart disease, and polydactyly of the limbs. Patau syndrome is identified either prenatally or postnatally. Its survival rate is low, and most of the patients die even before their first year of life. The risk of trisomy 13 is higher in women of advanced maternal age. Brain and cardiovascular abnormalities are typically the primary factors contributing to the syndrome's poor prognosis. We report a case of a male newborn born at full term from a first-degree consanguineous marriage. Upon initial inspection, the patient had classic dysmorphic features, including low-set ears, a cleft lip and palate, a short neck, bilateral anophthalmia, and polydactyly of the limbs. After chromosomal analysis, the diagnosis was made, and a trisomy 13 was discovered.

12.
BMC Genomics ; 25(1): 599, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38877397

RESUMO

BACKGROUND: Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, ß- and γ-subfamilies, while α- and ß-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. RESULTS: We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 ß- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. CONCLUSIONS: For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and ß-tubulins.


Assuntos
Evolução Molecular , Genoma de Planta , Família Multigênica , Filogenia , Tubulina (Proteína) , Tubulina (Proteína)/genética , Brassicaceae/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Sintenia , Regulação da Expressão Gênica de Plantas , Duplicação Gênica , Íntrons/genética , Éxons/genética
14.
Animals (Basel) ; 14(11)2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38891755

RESUMO

We present a comparative chromosome study of several taxa of the Malagasy ground geckos of the Paroedura bastardi and P. picta species groups. We employed a preliminary molecular analysis using a trait of the mitochondrial 16S rRNA gene (of about 570 bp) to assess the taxonomic status of the samples studied and a cytogenetic analysis with standard karyotyping (5% Giemsa solution), silver staining (Ag-NOR staining) and sequential C-banding (C-banding + Giemsa and + fluorochromes). Our results show that all the taxa studied of the P. bastardi group (P. ibityensis, P. rennerae and P. cf. guibeae) have a similar karyotype composed of 2n = 34 chromosomes, with two metacentric pairs (1 and 3) and all other pairs being acrocentric. Chromosome diversification in the P. bastardi group was mainly linked to the diversification of heteromorphic sex chromosome systems (ZZ/ZW) in P. ibityensis and P. rennerae, while no heteromorphic sex chromosome pair was found in P. cf. guibeae. The two taxa investigated of the P. picta species group (here named P. picta and P. cf. picta based on molecular data) showed the same chromosome number of 2n = 36, mostly acrocentric elements, but differed in the number of metacentric elements, probably as a result of an inversion at chromosome pair 2. We highlight that the genus Paroedura is characterized by the independent diversification of heterogametic sex chromosomes in different evolutionary lineages and, similarly to other phylogenetically related gecko genera, by a progressive formation of a biarmed element by means of tandem fusions and inversions of distinct pairs.

15.
Front Genet ; 15: 1387724, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38846960

RESUMO

Fetal chromosomal abnormalities are the main cause of adverse pregnancy outcomes and are the focus of invasive prenatal diagnosis. Recent studies have demonstrated that various techniques have distinct advantages. Achieving high-resolution and effective prenatal chromosomal abnormality diagnosis requires a multi-technology integration strategy. Based on retrospective samples from a single center, we propose that integrating CNV-seq and karyotype analysis is an effective strategy for prenatal diagnosis of chromosomal abnormalities. In this study, 13.80% of the pregnant women (347/2514) were found to have likely pathogenic or pathogenic fetal chromosomal abnormalities using this integrated approach. Among these cases, 53.89% (187/347) had consistent chromosomal abnormalities detected by both CNV-seq and karyotyping analysis, while 19.02% (66/347) and 27.09% (94/347) of cases were diagnosed solely by CNV-seq or karyotyping, respectively. Fetal chromosomal abnormalities were identified in 18.39% of samples with abnormal ultrasound, which was significantly higher than the percentage found in samples with normal ultrasound (p < 0.001). Samples with multiple ultrasound abnormalities and single-indicator ultrasound abnormalities such as nasal bone dysplasia, renal dysplasia, or echogenic fetal bowel also had higher rates of chromosomal abnormalities (p < 0.05) compared to normal samples. Analyzing samples with Trio family data (N = 521) revealed that about 94% of variants of uncertain significance were inherited from parents and were non-pathogenic. Overall, integrating CNV-seq and karyotype analysis is an effective strategy for prenatal diagnosis of chromosomal abnormalities. This study provides valuable insights for correlating prenatal screening indicators with chromosomal abnormalities.

16.
J Pediatr (Rio J) ; 2024 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-38823786

RESUMO

OBJECTIVE: It was to verify the association between the definition of sex of rearing and, clinical and cytogenetic features among patients with genital ambiguity referred without a sex assignment. METHODS: The sample consisted of 133 patients with genital ambiguity seen at a single reference service. These patients did not have a defined social sex at the first consultation and their etiological diagnosis was obtained during follow-up. RESULTS: A total of 133 cases were included, 74 of which were reared as males and 59 as females. No correlation was found between the year of birth and the year of the first consultation with the definition of sex of rearing. However, the definition of sex of rearing was associated with age at the first consultation, severity of genital ambiguity, presence of palpable gonad(s), presence of uterus on ultrasound, karyotype, and diagnosis. Palpable gonad(s), more virilized genitalia, absence of a uterus on ultrasound, 46, XY karyotype, or a karyotype with sex chromosome abnormalities emerged as strong predictors for defining male sex. All 77 (58 %) patients over 18 years old had a gender identity in accordance with the sex of rearing; though 9 of 77 (12 %) had homo or bisexual orientation, especially girls with Congenital Adrenal Hyperplasia. CONCLUSIONS: Clinical and cytogenetic data were strongly associated with the definition of the sex of rearing of children with genital ambiguity referred to a DSD center without sex assignment. Management in a specialized center allows the establishment of a gender identity in accordance with the sex of rearing.

17.
Front Genet ; 15: 1396530, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38903758

RESUMO

The karyotype of an organism is the set of gross features that characterize the way the genome is packaged into separate chromosomes. It has been known for decades that different taxonomic groups often have distinct karyotypic features, but whether selective forces act to maintain these differences over evolutionary timescales is an open question. In this paper we analyze a database of karyotype features and sperm head morphology in 103 mammal species with spatulate sperm heads and 90 sauropsid species (birds and non-avian reptiles) with vermiform heads. We find that mammal species with a larger head area have more chromosomes, while sauropsid species with longer heads have a wider range of chromosome lengths. These results remain significant after controlling for genome size, so sperm head morphology is the relevant variable. This suggest that post-copulatory sexual selection, by acting on sperm head shape, can influence genome architecture.

18.
Methods Mol Biol ; 2825: 79-111, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38913304

RESUMO

Cytogenetic analysis has traditionally focused on the clonal chromosome aberrations, or CCAs, and considered the large number of diverse non-clonal chromosome aberrations, or NCCAs, as insignificant noise. Our decade-long karyotype evolutionary studies have unexpectedly demonstrated otherwise. Not only the baseline of NCCAs is associated with fuzzy inheritance, but the frequencies of NCCAs can also be used to reliably measure genome or chromosome instability (CIN). According to the Genome Architecture Theory, CIN is the common driver of cancer evolution that can unify diverse molecular mechanisms, and genome chaos, including chromothripsis, chromoanagenesis, and polypoidal giant nuclear and micronuclear clusters, and various sizes of chromosome fragmentations, including extrachromosomal DNA, represent some extreme forms of NCCAs that play a key role in the macroevolutionary transition. In this chapter, the rationale, definition, brief history, and current status of NCCA research in cancer are discussed in the context of two-phased cancer evolution and karyotype-coded system information. Finally, after briefly describing various types of NCCAs, we call for more research on NCCAs in future cytogenetics.


Assuntos
Aberrações Cromossômicas , Neoplasias , Humanos , Neoplasias/genética , Instabilidade Cromossômica , Análise Citogenética/métodos , Cariotipagem/métodos
19.
Methods Mol Biol ; 2825: 113-124, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38913305

RESUMO

Optical genome mapping (OGM) has generated excitement following decades of research and development. Now, commercially available technical platforms have been used to compare various other cytogenetic and cytogenomic technologies, including karyotype, microarrays, and DNA sequencing, with impressive results. In this chapter, using OGM as a case study, we advocate for a new trend in future cytogenomics, emphasizing the power of machine automation to deliver higher-quality cytogenomic data. By briefly discussing OGM, along with its major advantages and limitations, we underscore the importance of karyotype-based genomic research, from both a theoretical framework and a new technology perspective. We also call for the encouragement of further technological platform development for the future of cytogenetics and cytogenomics.


Assuntos
Mapeamento Cromossômico , Genômica , Humanos , Genômica/métodos , Mapeamento Cromossômico/métodos
20.
Methods Mol Biol ; 2825: 3-37, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38913301

RESUMO

The promises of the cancer genome sequencing project, combined with various -omics technologies, have raised questions about the importance of cancer cytogenetic analyses. It is suggested that DNA sequencing provides high resolution, speed, and automation, potentially replacing cytogenetic testing. We disagree with this reductionist prediction. On the contrary, various sequencing projects have unexpectedly challenged gene theory and highlighted the importance of the genome or karyotype in organizing gene network interactions. Consequently, profiling the karyotype can be more meaningful than solely profiling gene mutations, especially in cancer where karyotype alterations mediate cellular macroevolution dominance. In this chapter, recent studies that illustrate the ultimate importance of karyotype in cancer genomics and evolution are briefly reviewed. In particular, the long-ignored non-clonal chromosome aberrations or NCCAs are linked to genome or chromosome instability, genome chaos is linked to genome reorganization under cellular crisis, and the two-phased cancer evolution reconciles the relationship between genome alteration-mediated punctuated macroevolution and gene mutation-mediated stepwise microevolution. By further synthesizing, the concept of karyotype coding is discussed in the context of information management. Altogether, we call for a new era of cancer cytogenetics and cytogenomics, where an array of technical frontiers can be explored further, which is crucial for both basic research and clinical implications in the cancer field.


Assuntos
Aberrações Cromossômicas , Genômica , Neoplasias , Humanos , Neoplasias/genética , Genômica/métodos , Análise Citogenética/métodos , Citogenética/métodos , Cariotipagem/métodos , Mutação
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