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1.
Ceska Gynekol ; 86(3): 220-234, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34192880

RESUMO

BACKGROUND: Radiation therapy plays a leading role in the treatment of prostate cancer, but the emergence of radioresistant forms of this disease dictates the need for a personalized ap-proach based on the data from genetic and epigenetic markers. Such markers include the copy number variation as well as gene and microRNA expression. PURPOSE: The aim of the study was to validate the list of potential predictors of radioresistance of prostate tumor cells in a model experiment based on the determination of gene copy number variation, gene transcriptional activity and microRNA expression. MATERIAL AND METHODS: The study used a PC-3 prostate cancer cell culture. The determination of the relative copy number variation and expression of 32 genes (BRCA1, BRCA2, PTEN, CASP3, CASP8, BAX, BCL2, CASP9, P53, MDM2, AKT1, ATM, BRIP1, CDK1, CDKN1B, CCND1, CCND3, FGFR2, KU70, RAD50, RAP80, Rif1, RNF168, TopBP1, HIST, H2AX, EXO1, XRCC4, RBBP8, EP300, LIG4, C-FLIP), as well as 15 microRNAs (let-7, miR15a/ 16, miR-17, miR-18a, miR-21, miR-24, miR-26b, miR-99a, miR-100, miR-101, miR-106a, miR-663a, miR-143, miR-145) was performed using the real-time quantitative polymerase chain reaction method. It was found that daily irradiation of PC-3 cells on a Novalis TX linear accelerator at doses of 6 and 7 Gy for 5 days leads to a significant decrease in the total number of cells and the number of viable cells. Nevertheless, after 5 days of irradiation, about 15% of the initial number of prostate tumor cells retained their viability, which is due to their special genetic and epigenetic characteristics: increased copy number and expression of genes BRCA2, CDK1, CDKN1B, H2AX, RAD50, XRCC4, RBBP8 and EP300 and reduced copy number and expression of CCND3, TP53, and BCL2 genes, as well as differential expression of six microRNAs (hsa-miR-18a-5p, hsa-miR-24-5p, hsa-miR-99a-5p, hsa-miR-100-5p, hsa-miR-145-5p, hsa-let-7a-3p). CONCLUSION: This study enabled to identify genetic and epigenetic markers of prostate tumor cells resistance to radiation therapy.


Assuntos
MicroRNAs , Neoplasias da Próstata , Variações do Número de Cópias de DNA , Epigênese Genética , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , MicroRNAs/genética , Neoplasias da Próstata/genética
2.
Nat Commun ; 12(1): 4132, 2021 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-34226556

RESUMO

Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits - Equalizers - that buffer copy-number variation at the single-cell level. Equalizers couple a transcriptional negative feedback loop with post-transcriptional incoherent feedforward control. Computational modeling suggests that the combination of these two topologies enables Equalizers to operate over a wide range of plasmid copy numbers. We demonstrate experimentally that Equalizers outperform other gene dosage compensation topologies and produce as low cell-to-cell variation as chromosomally integrated genes. We also show that episome-encoded Equalizers enable the rapid generation of extrachromosomal cell lines with stable and uniform expression. Overall, Equalizers are simple and versatile devices for homogeneous gene expression and can facilitate the engineering of synthetic circuits that function reliably in every cell.


Assuntos
Variações do Número de Cópias de DNA , Dosagem de Genes , Regulação da Expressão Gênica , Animais , Linhagem Celular , Expressão Gênica , MicroRNAs , Plasmídeos , Transfecção
3.
Int J Mol Sci ; 22(11)2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34198843

RESUMO

Vitreoretinal lymphoma (VRL) is an uncommon eye malignancy, and VRLs of T cell origin are rare. They are difficult to treat, and their molecular underpinnings, including actionable genomic alterations, remain to be elucidated. At present, vitreous fluid liquid biopsies represent a valuable VRL sample for molecular analysis to study VRLs. In this study, we report the molecular diagnostic workup of a rare case of bilateral T cell VRL and characterize its genomic landscape, including identification of potentially targetable alterations. Using next-generation sequencing of vitreous-derived DNA with a pan-cancer 126-gene panel, we found a copy number gain of BRAF and copy number loss of tumor suppressor DNMT3A. To the best of our knowledge, this represents the first exploration of the T cell VRL cancer genome and supports vitreous liquid biopsy as a suitable approach for precision oncology treatments.


Assuntos
DNA (Citosina-5-)-Metiltransferases/genética , Linfoma de Células T/genética , Proteínas Proto-Oncogênicas B-raf/genética , Neoplasias da Retina/genética , Biomarcadores Tumorais/genética , Variações do Número de Cópias de DNA/genética , Regulação Neoplásica da Expressão Gênica/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Biópsia Líquida , Linfoma de Células T/patologia , Masculino , Pessoa de Meia-Idade , Proteínas de Neoplasias/genética , Neoplasias da Retina/patologia , Corpo Vítreo/metabolismo , Corpo Vítreo/patologia
4.
BMC Gastroenterol ; 21(1): 284, 2021 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-34247571

RESUMO

BACKGROUND: Gastrointestinal adenocarcinoma (GIAD) has caused a serious disease burden globally. Targeted therapy for the transforming growth factor beta (TGF-ß) signaling pathway is becoming a reality. However, the molecular characterization of TGF-ß associated signatures in GIAD requires further exploration. METHODS: Multi-omics data were collected from TCGA and GEO database. A pivotal unsupervised clustering for TGF-ß level was performed by distinguish status of TGF-ß associated genes. We analyzed differential mRNAs, miRNAs, proteins gene mutations and copy number variations in both clusters for comparison. Enrichment of pathways and gene sets were identified in each type of GIAD. Then we performed differential mRNA related drug response by collecting data from GDSC. At last, a summarized deep neural network for TGF-ß status and GIADs was constracted. RESULTS: The TGF-ßhigh group had a worse prognosis in overall GIAD patients, and had a worse prognosis trend in gastric cancer and colon cancer specifically. Signatures (including mRNA and proteins) of the TGF-ßhigh group is highly correlated with EMT. According to miRNA analysis, miR-215-3p, miR-378a-5p, and miR-194-3p may block the effect of TGF-ß. Further genomic analysis showed that TGF-ßlow group had more genomic changes in gastric cancer, such as TP53 mutation, EGFR amplification, and SMAD4 deletion. And drug response dataset revealed tumor-sensitive or tumor-resistant drugs corresponding to TGF-ß associated mRNAs. Finally, the DNN model showed an excellent predictive effect in predicting TGF-ß status in different GIAD datasets. CONCLUSIONS: We provide molecular signatures associated with different levels of TGF-ß to deepen the understanding of the role of TGF-ß in GIAD and provide potential drug possibilities for therapeutic targets in different levels of TGF-ß in GIAD.


Assuntos
Adenocarcinoma , MicroRNAs , Preparações Farmacêuticas , Adenocarcinoma/tratamento farmacológico , Adenocarcinoma/genética , Variações do Número de Cópias de DNA , Humanos , MicroRNAs/genética , Fator de Crescimento Transformador beta/genética
5.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-34203883

RESUMO

Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.


Assuntos
Proteínas de Transporte/genética , Distrofias de Cones e Bastonetes/genética , Oftalmopatias Hereditárias/genética , Estudos de Associação Genética , Predisposição Genética para Doença , Mutação/genética , Distrofias Retinianas/genética , Adulto , Idoso , Criança , Pontos de Quebra do Cromossomo , Simulação por Computador , Distrofias de Cones e Bastonetes/fisiopatologia , Variações do Número de Cópias de DNA/genética , Eletrorretinografia , Oftalmopatias Hereditárias/fisiopatologia , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo , Distrofias Retinianas/fisiopatologia
6.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-34203967

RESUMO

A substantial proportion of subjects with autosomal recessive retinitis pigmentosa (arRP) or Usher syndrome type II (USH2) lacks a genetic diagnosis due to incomplete USH2A screening in the early days of genetic testing. These cases lack eligibility for optimal genetic counseling and future therapy. USH2A defects are the most frequent cause of USH2 and are also causative in individuals with arRP. Therefore, USH2A is an important target for genetic screening. The aim of this study was to assess unscreened or incompletely screened and unexplained USH2 and arRP cases for (likely) pathogenic USH2A variants. Molecular inversion probe (MIP)-based sequencing was performed for the USH2A exons and their flanking regions, as well as published deep-intronic variants. This was done to identify single nucleotide variants (SNVs) and copy number variants (CNVs) in 29 unscreened or partially pre-screened USH2 and 11 partially pre-screened arRP subjects. In 29 out of these 40 cases, two (likely) pathogenic variants were successfully identified. Four of the identified SNVs and one CNV were novel. One previously identified synonymous variant was demonstrated to affect pre-mRNA splicing. In conclusion, genetic diagnoses were obtained for a majority of cases, which confirms that MIP-based sequencing is an effective screening tool for USH2A. Seven unexplained cases were selected for future analysis with whole genome sequencing.


Assuntos
Análise Custo-Benefício , Éxons/genética , Proteínas da Matriz Extracelular/genética , Sondas Moleculares/metabolismo , Sítios de Splice de RNA/genética , Retinite Pigmentosa/genética , Análise de Sequência de DNA , Síndromes de Usher/genética , Sequência de Bases , Variações do Número de Cópias de DNA/genética , Deleção de Genes , Humanos , Polimorfismo de Nucleotídeo Único/genética , Retinite Pigmentosa/economia , Síndromes de Usher/economia
7.
Yi Chuan ; 43(7): 665-679, 2021 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-34284982

RESUMO

Glioblastoma (GBM) is the most common primary intracranial tumor with extremely high malignancy and poor prognosis. In order to identify the GBM prognostic biomarkers and establish a prognostic model, we analyzed the expression profile data of GBM in The Cancer Genome Atlas (TCGA) database as the experimental group. First, we identified the differentially expressed genes of different survival periods among the GBM patients. The GISTIC software and Kaplan Meier (KM) survival curve were used to analyze the copy number variation of GBM to identify the survival-associated amplified gene (SAG). We selected the intersection genes of up-regulated ones in short survival group and SAG, performed univariate Cox regression and iterative Lasso regression with them to identify the important candidate genes and establish a prognostic model. Based on the model, the prognostic score was calculated. The patients were divided into high-risk and low-risk groups according to the median prognostic score. Meanwhile ROC curve was used to evaluate the validity of the model, applying the KM survival analysis of the high-risk and low-risk groups. Multivariate Cox regression analysis was used to determine the independence of the prognostic score. All the data were verified with three external datasets: GEO GSE16011, CGGA, and Rembrandt. The results showed that differential expression analysis of different survival periods of GBM identified 426 up-regulated genes and 65 down-regulated genes in the TCGA GBM dataset. The intersection of up-regulated genes in short survival group and SAG yielded 47 genes. After the screening, the six-gene combination (EN2,PPBP,LRRC61,SEL1L3,CPA4,DDIT4L) prognostic model was finally determined. The area under ROC curve of the model in TCGA experimental group and three external validation group were all greater than 0.6, even reaching 0.912. KM analysis showed that the prognosis of the high-risk and low-risk groups was significant different (P<0.05). In the multivariate Cox regression analysis, the six-gene prognostic score was an independent factor influencing the prognosis of GBM patients (P<0.05). In summary, this study established a prognostic model of six-gene (EN2,PPBP,LRRC61,SEL1L3,CPA4,DDIT4L) for GBM. This six-gene model has good predictive ability and could be used as an independent prognostic marker for GBM patients.


Assuntos
Neoplasias Encefálicas , Glioblastoma , Proteínas Adaptadoras de Transdução de Sinal , Neoplasias Encefálicas/genética , Variações do Número de Cópias de DNA , Regulação Neoplásica da Expressão Gênica , Glioblastoma/genética , Humanos , Prognóstico
8.
BMC Bioinformatics ; 22(1): 374, 2021 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-34284719

RESUMO

BACKGROUND: As exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number variants (CNVs) often get overlooked or obscured by under-powered data collection. Many groups have developed methodology for detecting CNVs from ES, but existing methods often perform poorly for small CNVs and rely on large numbers of samples not always available to clinical laboratories. Furthermore, methods often rely on Bayesian approaches requiring user-defined priors in the setting of insufficient prior knowledge. This report first demonstrates the benefit of multiplexed exome capture (pooling samples prior to capture), then presents a novel detection algorithm, mcCNV ("multiplexed capture CNV"), built around multiplexed capture. RESULTS: We demonstrate: (1) multiplexed capture reduces inter-sample variance; (2) our mcCNV method, a novel depth-based algorithm for detecting CNVs from multiplexed capture ES data, improves the detection of small CNVs. We contrast our novel approach, agnostic to prior information, with the the commonly-used ExomeDepth. In a simulation study mcCNV demonstrated a favorable false discovery rate (FDR). When compared to calls made from matched genome sequencing, we find the mcCNV algorithm performs comparably to ExomeDepth. CONCLUSION: Implementing multiplexed capture increases power to detect single-exon CNVs. The novel mcCNV algorithm may provide a more favorable FDR than ExomeDepth. The greatest benefits of our approach derive from (1) not requiring a database of reference samples and (2) not requiring prior information about the prevalance or size of variants.


Assuntos
Variações do Número de Cópias de DNA , Exoma , Algoritmos , Teorema de Bayes , Exoma/genética , Sequenciamento de Nucleotídeos em Larga Escala , Sequenciamento Completo do Exoma
9.
Aging (Albany NY) ; 13(12): 16287-16315, 2021 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-34230220

RESUMO

N6-methyladenosine (m6A) RNA methylation is associated with malignant tumor progression and is modulated by various m6A RNA methylation regulator proteins. However, its role in endometrial cancer is unclear. In this work, we analyzed sequence, copy number variation, and clinical data obtained from the TCGA database. Expression was validated using real-time quantitative polymerase chain reaction and immunohistochemistry. Changes in m6A RNA methylation regulators were closely related to the clinicopathological stage and prognosis of endometrial cancer. In particular, ZC3H13, YTHDC1, and METTL14 were identified as potential markers for endometrial cancer diagnosis and prognosis. The TIMER algorithm indicated that immune cell infiltration correlated with changes in ZC3H13, YTHDC1, and METTL14 expression. Meanwhile, ZC3H13 or YTHDC1 knockdown promoted the proliferation and invasion of endometrial cancer cells. Through gene enrichment analysis, we constructed a regulatory network in order to explore the potential molecular mechanism involving ZC3H13, YTHDC1, and METTL14. Virtual screening predicted interactions of potential therapeutic compounds with METTL14 and YTHDC1. These findings advance the understanding of RNA epigenetic modifications in endometrial cancer while identifying m6A regulators associated with immune infiltration, prognosis, and potential treatment strategies.


Assuntos
Adenosina/análogos & derivados , Neoplasias do Endométrio/genética , Neoplasias do Endométrio/imunologia , Linfócitos do Interstício Tumoral/imunologia , Adenosina/metabolismo , Linhagem Celular Tumoral , Proliferação de Células/genética , Variações do Número de Cópias de DNA/genética , Intervalo Livre de Doença , Neoplasias do Endométrio/patologia , Feminino , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Ligantes , Metilação , Pessoa de Meia-Idade , Simulação de Acoplamento Molecular , Mutação/genética , Invasividade Neoplásica , Proteínas de Neoplasias/metabolismo , Prognóstico , Modelos de Riscos Proporcionais , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Bibliotecas de Moléculas Pequenas/farmacologia , Bibliotecas de Moléculas Pequenas/uso terapêutico , Microambiente Tumoral/imunologia
10.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(7): 613-619, 2021 Jul 10.
Artigo em Chinês | MEDLINE | ID: mdl-34247362

RESUMO

Genomic disorders caused by pathogenic copy number variation (pCNV) have proven to underlie a significant proportion of birth defects. With technological advance, improvement of bioinformatics analysis procedure, and accumulation of clinical data, non-invasive prenatal screening of pCNV (NIPS-pCNV) by high-throughput sequencing of maternal plasma cell-free DNA has been put to use in clinical settings. Specialized standards for clinical application of NIPS-pCNV are required. Based on the discussion, 10 pCNV-associated diseases with well-defined conditions and 5 common chromosomal aneuploidy syndromes are recommended as the target of screening in this consensus. Meanwhile, a standardized procedure for NIPS-pCNV is also provided, which may facilitate propagation of this technique in clinical settings.


Assuntos
Ácidos Nucleicos Livres , Variações do Número de Cópias de DNA , Aneuploidia , Ácidos Nucleicos Livres/genética , Consenso , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Gravidez , Diagnóstico Pré-Natal
11.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(7): 647-651, 2021 Jul 10.
Artigo em Chinês | MEDLINE | ID: mdl-34247369

RESUMO

OBJECTIVE: To explore the genetic etiology for a fetus with congenital orofacial cleft. METHODS: Single nucleotide polymorphism microarray (SNP array) was carried out on skin tissues sampled from the fetus following induced abortion for the detection of copy number variation (CNVs). Pathogenicity of the candidate gene was validated through experiment. RESULTS: SNP array revealed that the fetus has carried a hemizygous 9.23Mb deletion at Xq21.31-q22.1(91 063 807-100 293 555), which was inherited from its mother. The region contained 13 OMIM genes and 1 ncRNA coding gene(MIR548M). Inhibiting of the expression of the MIR548M gene in oral epithelial celllines has resulted in up-regulation of the expression of SUMO1 gene which was known to involve in the pathogenesis of orofacial cleft. CONCLUSION: Dosage insufficiency of the MIR548M gene may underlie the etiology of orofacial cleft in this fetus.


Assuntos
Fenda Labial , Fissura Palatina , MicroRNAs , Fenda Labial/genética , Fissura Palatina/genética , Variações do Número de Cópias de DNA/genética , Feminino , Feto , Humanos , MicroRNAs/genética , Polimorfismo de Nucleotídeo Único , Gravidez , Proteína SUMO-1
12.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(7): 659-662, 2021 Jul 10.
Artigo em Chinês | MEDLINE | ID: mdl-34247372

RESUMO

OBJECTIVE: To analyze the prenatal diagnosis, parental verification and pregnancy outcome of 6 fetuses with 22q11.2 microdeletion syndrome. METHODS: Copy number variation sequencing (CNV-seq)and chromosomal microarray analysis (CMA) were carried out for the fetuses. RESULTS: The fetuses were found to harbor 2.54-3.2 Mb microdeletions of the 22q11.2 region, among which one was maternally inherited and one was paternally inherited. Two parents opted to continue with the pregnancy, and 4 chose induced labor. One fetus was found to have tetralogy of Fallot, while two carrier parents and one fetus appeared to have normal phenotype. CONCLUSION: 22q11.2 microdeletions identified upon prenatal diagnosis should be treated carefully, with ultrasonic scan and parental verification taken into account.


Assuntos
Variações do Número de Cópias de DNA , Diagnóstico Pré-Natal , Feminino , Feto , Humanos , Análise em Microsséries , Gravidez , Resultado da Gravidez , Ultrassonografia Pré-Natal
13.
BMC Genomics ; 22(1): 531, 2021 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-34253178

RESUMO

BACKGROUND: CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. RESULTS: Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. CONCLUSION: For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments.


Assuntos
Variações do Número de Cópias de DNA , Genoma , Animais , Bovinos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Fenótipo , Polimorfismo de Nucleotídeo Único
14.
Front Cell Infect Microbiol ; 11: 683423, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34249776

RESUMO

Drug-resistant Plasmodium vivax malaria impedes efforts to control, eliminate, and ultimately eradicate malaria in Southeast Asia. P. vivax resistance to antifolate drugs derives from point mutations in specific parasite genes, including the dihydropteroate synthase (pvdhps), dihydrofolate reductase (pvdhfr), and GTP cyclohydrolase I (pvgch1) genes. This study aims to investigate the prevalence and spread of drug resistance markers in P. vivax populating the China-Myanmar border. Blood samples were collected from symptomatic patients with acute P. vivax infection. Samples with single-clone P. vivax infections were sequenced for pvdhps and pvdhfr genes and genotyped for 6 flanking microsatellite markers. Copy number variation in the pvgch1 gene was also examined. Polymorphisms were observed in six different codons of the pvdhps gene (382, 383, 512, 549, 553, and 571) and six different codons of the pvdhfr gene (13, 57, 58, 61, 99, 117) in two study sites. The quadruple mutant haplotypes 57I/L/58R/61M/117T of pvdhfr gene were the most common (comprising 76% of cases in Myitsone and 43.7% of case in Laiza). The double mutant haplotype 383G/553G of pvdhps gene was also prevalent at each site (40.8% and 31%). Microsatellites flanking the pvdhfr gene differentiated clinical samples from wild type and quadruple mutant genotypes (F ST= 0.259-0.3036), as would be expected for a locus undergoing positive selection. The lack of copy number variation of pvgch1 suggests that SP-resistant P. vivax may harbor alternative mechanisms to secure sufficient folate.


Assuntos
Antimaláricos , Antagonistas do Ácido Fólico , Migrantes , Antimaláricos/farmacologia , China , Variações do Número de Cópias de DNA , Resistência a Medicamentos/genética , Antagonistas do Ácido Fólico/farmacologia , Humanos , Mutação , Mianmar , Plasmodium vivax/genética , Proteínas de Protozoários/genética , Tetra-Hidrofolato Desidrogenase/genética
15.
Zhonghua Yu Fang Yi Xue Za Zhi ; 55(7): 827-834, 2021 Jul 06.
Artigo em Chinês | MEDLINE | ID: mdl-34304418

RESUMO

Objective: To evaluate the utility of whole-exome sequencing (WES) in early diagnosis for children with language delay/disorder. Methods: Children with language delay/disorder who were admitted to the Department of Health Care, Children's Hospital Affiliated to the Capital Pediatric Institute from January 2019 to December 2020 were analyzed retrospectively. Based on informed consent, the peripheral blood of the children and their parents was collected for WES. Combining the clinical phenotypes of the children, the candidate variants, including single nucleotide variants (SNVs) and copy number variations (CNVs), were selected for validation and family segregation analysis using Sanger sequencing, real-time PCR or CNV-Seq. The pathogenicity of variants was evaluated based on ACMG guideline following with finial genetic diagnosis. Based on whether genetic diagnosis was achieved or not, 125 children with comprehensive examination of the Children Neuropsychological and Behavioral Scale(CNBS-R2016) were sub-grouped (positive/negative group), and the total scores and the detailed scores of five developmental sections (gross motor, fine motor, adaptive ability, language and social behavior ability) between two subgroups were compared. Results: A total of 165 children with language delay/disorder were recruited, including 109 males and 56 females. The ratio of boys to girls was 1.95∶1.The age of the children was (3.2±1.2) years old, the median age was 3.0 years. 45 children carry disease-related pathogenic/likely pathogenic variants, including 36 SNVs and 9 CNVs. The genetic diagnostic yield of this cohort was 27.3% (45/165). The inheritance analysis for core family members showed de novo variant accounted for 86% of genetic diagnosis (31/36). The positive diagnosis rate in girls was 45% (25/56), which was significantly higher than that in boys (18.3%, 20/109, χ²=12.171, P<0.05). There was no significant difference in the rate of positive diagnosis among all age groups (χ²=4.349, P>0.05). Interestingly, the scores of gross motors of positive group were significantly lower than that of negative group (61.5 vs. 69.4, t=-2.610, P<0.05). Otherwise, no significant difference was seen between two groups(t=-0.933, -1.298, -0.114, -0.214, all P>0.05). Conclusions: Language delay/disorder has complex genetic heterogeneity. WES has important application value in early etiological diagnosis for children with language delay/disorder.


Assuntos
Variações do Número de Cópias de DNA , Transtornos do Desenvolvimento da Linguagem , Criança , Pré-Escolar , Diagnóstico Precoce , Feminino , Humanos , Transtornos do Desenvolvimento da Linguagem/diagnóstico , Transtornos do Desenvolvimento da Linguagem/genética , Masculino , Estudos Retrospectivos , Sequenciamento Completo do Exoma
16.
BMC Bioinformatics ; 22(1): 360, 2021 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-34217219

RESUMO

BACKGROUND: Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using Copy Number Aberrations (CNAs). Nowadays ITH can be assessed at the highest possible resolution using single-cell DNA (scDNA) sequencing technology. Additionally, single-cell CNA (scCNA) profiles from multiple samples of the same tumor can in principle be exploited to study the spatial distribution of subclones within a tumor mass. However, since the technology required to generate large scDNA sequencing datasets is relatively recent, dedicated analytical approaches are still lacking. RESULTS: We present PhyliCS, the first tool which exploits scCNA data from multiple samples from the same tumor to estimate whether the different clones of a tumor are well mixed or spatially separated. Starting from the CNA data produced with third party instruments, it computes a score, the Spatial Heterogeneity score, aimed at distinguishing spatially intermixed cell populations from spatially segregated ones. Additionally, it provides functionalities to facilitate scDNA analysis, such as feature selection and dimensionality reduction methods, visualization tools and a flexible clustering module. CONCLUSIONS: PhyliCS represents a valuable instrument to explore the extent of spatial heterogeneity in multi-regional tumour sampling, exploiting the potential of scCNA data.


Assuntos
Variações do Número de Cópias de DNA , Neoplasias , Análise por Conglomerados , Heterogeneidade Genética , Humanos , Análise de Sequência de DNA , Análise de Célula Única
17.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(6): 573-576, 2021 Jun 10.
Artigo em Chinês | MEDLINE | ID: mdl-34096029

RESUMO

OBJECTIVE: To determine the chromosomal karyotype of a fetus with copy number variation (CNV) of the X chromosome signaled by non-invasive prenatal testing (NIPT). METHODS: NIPT was performed on the peripheral blood sample taken from the pregnant women. Amniotic fluid and cord blood samples were subjected to conventional G banded karyotyping, and were further analyzed by high-throughput sequencing for chromosome microdeletion/microduplication. The results were then verified by fluorescence in situ hybridization (FISH) on metaphase cells. RESULTS: The NIPT test of pregnant women suggested low risk for 21-trisomy, 18-trisomy, and 13-trisomy, whilst indicated the number of chromosome X to be low. The G banded karyotype of the amniotic fluid and cord blood cells was 46,XX. The result of high-throughput sequencing chromosome microdeletion/microduplication detection was seq[hg19](X)× 1, (Y)× 2. FISH showed a clear red signal at each end of a whole chromosome, and a green signal on the other chromosome, with a karyotype of 46,X,ish idic(Y) (q11.23) (SRY++, DXZ1+). C banding showed that there is a dense and a slightly loose centromere at both ends of the Y chromosome, and the parachromatin region was missing. The karyotype of amniotic fluid and cord blood cells was finally determined to be 46,X, pus idic(Y) (q11.23). CONCLUSION: For chromosome anomalies suggested by auxiliary report of NIPT, conventional karyotyping combined with high-throughput sequencing for chromosome microdeletion/microduplication should be adopted for the prevention and reduction of the rate of chromosome microdeletion/microduplication syndromes.


Assuntos
Variações do Número de Cópias de DNA , Diagnóstico Pré-Natal , Aberrações Cromossômicas , Feminino , Humanos , Hibridização in Situ Fluorescente , Gravidez , Cromossomo X
18.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(6): 577-580, 2021 Jun 10.
Artigo em Chinês | MEDLINE | ID: mdl-34096030

RESUMO

OBJECTIVE: To explore the cause of abortion and strategy of prenatal diagnosis for pregnant women with high risk for chromosomal abnormalities by using copy number variation sequencing (CNV-seq) and short tandem repeats (STR) analysis. METHODS: A total of 36 samples were collected, including amniotic fluid, abortion tissue, whole blood, chorionic villi and umbilical cord blood. CNV-seq and STR analysis were carried out to detect microdeletions, microduplications, chromosomal aneuploidies, mosaicisms and triploidies. RESULTS: Among all samples, 1 was detected with 4p15.1p16.3 and 14q11.1q22.1 duplication, 1 was detected with 19p13.3 deletion, 8 were detected with chromosomal aneuploidies, 4 were detected with mosaicisms, two were detected with triploidies. No definite pathogenic CNVs were detected in 20 samples, which yielded a positive detection rate of 44.44%. CONCLUSION: As a high-throughput detection method, CNV-seq has the advantages of rapidity, simplicity and high accuracy. It may suit prenatal diagnosis and analysis of abortion factors in combination with STR analysis.


Assuntos
Aborto Espontâneo , Variações do Número de Cópias de DNA , Aborto Espontâneo/genética , Feminino , Humanos , Cariotipagem , Repetições de Microssatélites , Gravidez , Diagnóstico Pré-Natal
19.
BMC Genomics ; 22(1): 419, 2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34090344

RESUMO

BACKGROUND: Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies are ideal to identify tumor sub-clones, they remain expensive and in contrast to single cell RNA-seq (scRNA-seq) methods are more limited in the data they generate. However, CNV data can be inferred from scRNA-seq and bulk RNA-seq, for which several tools have been developed, including inferCNV, CaSpER, and HoneyBADGER. Inferences regarding tumor clonality from CNV data (and other sources) are frequently visualized using phylogenetic plots, which previously required time-consuming and error-prone, manual analysis. RESULTS: Here, we present Uphyloplot2, a python script that generates phylogenetic plots directly from inferred RNA-seq data, or any Newick formatted dendrogram file. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/ . CONCLUSIONS: Uphyloplot2 is an easy-to-use tool to generate phylogenetic plots to depict tumor clonality from scRNA-seq data and other sources.


Assuntos
Variações do Número de Cópias de DNA , Análise de Célula Única , Perfilação da Expressão Gênica , Filogenia , RNA-Seq , Análise de Sequência de RNA , Software
20.
Medicina (Kaunas) ; 57(5)2021 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-34063545

RESUMO

Background and Objectives: Mycosis fungoides (MF) and large plaque parapsoriasis (LPP) evolution provide intriguing data and are the cause of numerous debates. The diagnosis of MF and LPP is associated with confusion and imprecise definition. Copy number alterations (CNAs) may play an essential role in the genesis of cancer out of genes expression dysregulation. Objectives: Due to the heterogeneity of MF and LPP and the scarcity of the cases, there are an exceedingly small number of studies that have identified molecular changes in these pathologies. We aim to identify and compare DNA copy number alterations and gene expression changes between MF and LPP to highlight the similarities and the differences between these pathologies. Materials and Methods: The patients were prospectively selected from University Clinic of Dermatology and Venereology Timișoara, Romania. From fresh frozen skin biopsies, we extracted DNA using single nucleotide polymorphism (SNP) data. The use of SNP array for copy number profiling is a promising approach for genome-wide analysis. Results: After reviewing each group, we observed that the histograms generated for chromosome 1-22 were remarkably similar and had a lot of CNAs in common, but also significant differences were seen. Conclusions: This study took a step forward in finding out the differences and similarities between MF and LPP, for a more specific and implicitly correct approach of the case. The similarity between these two pathologies in terms of CNAs is striking, emphasizing once again the difficulty of approaching and differentiating them.


Assuntos
Micose Fungoide , Parapsoríase , Dermatopatias , Neoplasias Cutâneas , DNA , Variações do Número de Cópias de DNA/genética , Humanos , Micose Fungoide/genética , Parapsoríase/genética , Romênia , Neoplasias Cutâneas/genética
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