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《American journal of human genetics》2022,109(8):1500-1519
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Luca Comai Kirk R Amundson Benny Ordoez Xin Zhao Guilherme Tomaz Braz Jiming Jiang Isabelle M Henry 《Genetics》2021,219(3)
Large-scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1 Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a nonreciprocal translocation between chromosomes (chr.) 7 and 8 resulted in a 5–3 copy number change affecting several Mb at the respective chromosome tips. In cv. “Alca Tarma,” the terminal arm of chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping. 相似文献
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Mohammed Uddin Brianna K. Unda Vickie Kwan Nicholas T. Holzapfel Sean H. White Leon Chalil Marc Woodbury-Smith Karen S. Ho Erin Harward Nadeem Murtaza Biren Dave Giovanna Pellecchia Lia D’Abate Thomas Nalpathamkalam Sylvia Lamoureux John Wei Marsha Speevak James Stavropoulos Karun K. Singh 《American journal of human genetics》2018,102(2):278-295
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Meiying Cai Yanting Que Meihuan Chen Min Zhang Hailong Huang Liangpu Xu Na Lin 《Journal of cellular and molecular medicine》2023,27(16):2354-2361
Shortened foetal femur length (FL) is a common abnormal phenotype that often causes anxiety in pregnant women, and standard clinical treatments remain unavailable. We investigated the clinical characteristics, genetic aetiology and obstetric pregnancy outcomes of foetuses with short FL and provided a reference for perinatal management of such cases. Chromosomal microarray analysis was used to analyse the copy number variations (CNV) in short FL foetuses. Of the 218 foetuses with short FL, 33 foetuses exhibited abnormal CNVs, including 19 with pathogenic CNVs and 14 with variations of uncertain clinical significance. Of the 19 foetuses with pathogenic CNVs, four had aneuploidy, 14 had deletions/duplications, and one had pathogenic uniparental diploidy. The 7q11.23 microdeletion was detected in three foetuses. The severity of short FL was not associated with the rate of pathogenic CNVs. The duration of short FL for the intrauterine ultrasound phenotype in foetuses carrying a pathogenic CNV was independent of the gestational age. Further, maternal age was not associated with the incidence of foetal pathogenic CNVs. Adverse pregnancy outcomes occurred in 77 cases, including termination of pregnancy in 63 cases, postnatal dwarfed foetuses with intellectual disability in 11 cases, and three deaths within 3 months of birth. Pathogenic CNVs closely related to foetal short FL were identified, among which the 7q11.23 microdeletion was highly associated with short FL development. This study provides a reference for the perinatal management of foetuses with short FL. 相似文献
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人类第五染色体5q13.3带区一新基因的分子克隆初报 总被引：2，自引：0，他引：2
人类第五染色体５ｑ１３．３带区是毛发样白血病、ｒｅｆａｃｔｏｒｙ白血病、骨髓增生不良综合征、卵巢癌、肺癌等恶性肿瘤的共同畸变区域,表明该区域可能存在一个或多个同恶性肿瘤发生有关的基因（癌基因或抑癌基因）．克隆这些有关基因并进一步鉴定,对于阐明恶性肿瘤的发病机理,进而应用于基因治疗具有重要的理论和实践意义．本文报道位于该区域的一个新基因的ｃＤＮＡ克隆及在人体不同组织表达的初步结果． 相似文献
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Joseph Scarborough Flavia Mueller Ulrike Weber‐Stadlbauer Juliet Richetto Urs Meyer 《Genes, Brain & Behavior》2019,18(4)
Hemizygous microdeletion at the chromosomal locus 22q11.2 is a copy number variation with strong genetic linkage to schizophrenia and related disorders. This association, along with its phenotypic overlap with the 22q11.2 microdeletion syndrome, has motivated the establishment of Df[h22q11]/+ mice, in which the human 22q11.2 orthologous region is deleted. Previous investigations using this model showed the presence of reduced prepulse inhibition (PPI) of the acoustic startle reflex, a form of sensorimotor gating known to be impaired in a number of psychiatric disorders. Concomitantly to reduced PPI, however, Df[h22q11]/+ mice are also characterized by a robust increase in baseline startle reactivity, which may complicate or confound the interpretation of PPI. Therefore, the present study re‐examined the relationship between acoustic startle reactivity and PPI in this mouse model. We found that while PPI is reduced in Df[h22q11]/+ mice when using its relative indexation (ie, % PPI), this deficit is no longer apparent when using the absolute quantification, that is, the direct comparison between pulse‐alone and prepulse‐plus‐pulse conditions with successively increasing prepulse intensities. We further identified marked negative correlations between % PPI and startle reactivity in Df[h22q11]/+ mice. Moreover, when stratifying Df[h22q11]/+ mice into subgroups displaying low‐ and high‐startle reactivity, only the latter subgroup displayed a significant reduction in % PPI. Collectively, our data suggest that alterations in baseline startle reactivity can confound the outcomes and interpretation of PPI in this mouse model of the human 22q11.2 microdeletion syndrome. 相似文献
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拷贝数变异(Copy number variation, CNV)是染色体上发生的一种微结构变异, 已引起越来越多研究者的关注。本课题组前期已获得猪13号染色体上的32个CNV区域(CNV region, CNVR), 为了发掘CNVR内的基因信息, 文章在线检索了上述CNVR内的基因并进行基因本体(Gene Ontology)分析。结果共发现236个基因, 其中有注释基因169个, 主要参与蛋白质水解、细胞粘附、大分子降解等生物过程。为了探索这些基因拷贝数变异的遗传规律, 文章选择RCAN1(Regulators of calcineurin 1)基因为候选基因, 利用QPCR方法在莱芜猪群中检测了该基因的拷贝数, 并分析了CNV在莱芜猪3个家系中的遗传规律。结果表明, RCAN1基因在莱芜猪群体中存在拷贝数的缺失、重复现象, 其拷贝数变异的遗传规律符合孟德尔遗传方式。 相似文献
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Kathie Y Sun Daniel Oreper Sarah A Schoenrock Rachel McMullan Paola Giusti-Rodríguez Vasyl Zhabotynsky Darla R Miller Lisa M Tarantino Fernando Pardo-Manuel de Villena William Valdar 《Genetics》2021,218(1)
Female mammals are functional mosaics of their parental X-linked gene expression due to X chromosome inactivation (XCI). This process inactivates one copy of the X chromosome in each cell during embryogenesis and that state is maintained clonally through mitosis. In mice, the choice of which parental X chromosome remains active is determined by the X chromosome controlling element (Xce), which has been mapped to a 176-kb candidate interval. A series of functional Xce alleles has been characterized or inferred for classical inbred strains based on biased, or skewed, inactivation of the parental X chromosomes in crosses between strains. To further explore the function structure basis and location of the Xce, we measured allele-specific expression of X-linked genes in a large population of F1 females generated from Collaborative Cross (CC) strains. Using published sequence data and applying a Bayesian “Pólya urn” model of XCI skew, we report two major findings. First, inter-individual variability in XCI suggests mouse epiblasts contain on average 20–30 cells contributing to brain. Second, CC founder strain NOD/ShiLtJ has a novel and unique functional allele, Xceg, that is the weakest in the Xce allelic series. Despite phylogenetic analysis confirming that NOD/ShiLtJ carries a haplotype almost identical to the well-characterized C57BL/6J (Xceb), we observed unexpected patterns of XCI skewing in females carrying the NOD/ShiLtJ haplotype within the Xce. Copy number variation is common at the Xce locus and we conclude that the observed allelic series is a product of independent and recurring duplications shared between weak Xce alleles. 相似文献
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Nicholas Ho Hui Peng Chelsea Mayoh Pei Y. Liu Bernard Atmadibrata Glenn M. Marshall 《Cell cycle (Georgetown, Tex.)》2018,17(6):749-758
Neuroblastoma, the most common solid tumour in early childhood, is characterized by very frequent chromosomal copy number variations (CNVs). While chromosome 2p amplification, 17q gain, 1p and 11q deletion in human neuroblastoma tissues are well-known, the exact frequencies and boundaries of the chromosomal CNVs have not been delineated. We analysed the publicly available single nucleotide polymorphism (SNP) array data which were originally generated by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative, defined the frequencies and boundaries of chromosomes 2p11.2 – 2p25.3 amplification, 17q11.1-17q25.3 gain, 1p13.3-1p36.33 deletion and 11q13.3-11q25 deletion in neuroblastoma tissues, and identified chromosome 7q14.1 (Chr7:38254795-38346971) and chromosome 14q11.2 (Chr14:21637401-22024617) deletion in blood and bone marrow samples from neuroblastoma patients, but not in tumour tissues. Kaplan Meier analysis showed that double deletion of Chr7q14.1 and Chr14q11.2 correlated with poor prognosis in MYCN gene amplified neuroblastoma patients. In conclusion, the oncogenes amplified or gained and tumour suppressor genes deleted within the boundaries of chromosomal CNVs in tumour tissues should be studied for their roles in tumourigenesis and as therapeutic targets. Focal deletions of Chr7q14.1 and Chr14q11.2 together in blood and bone marrow samples from neuroblastoma patients can be used as a marker for poorer prognosis and more aggressive therapies. 相似文献
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Cyclins are key regulators of cell cycle progression. Previous studies have shown that cyclin genes in plants can be divided into 10 groups. However, because those studies only focused on genes from two well-known model plants (i.e., Arabidopsis thaliana (L.) Heynh. and Oryza sativa L.), it remains unclear whether the 10 groups are reasonably defined. In this study, by analyzing the genomes of 10 representative plants (Chlamydomonas reinhardtii P. A. Dang, Physcomitrella patens(Hedw.) Bruch & Schimp., Selaginella moellendorffii Hieron., Picea abies (L.) H. Karst., Amborella trichopoda Baill., A. thaliana, Populus trichocarpa Torr. & A. Gray ex Hook., Vitis vinifera L., O. sativa, and Sorghum bicolor (L.) Moench), we estimated the phylogenetic relationships of plant cyclins and investigated their evolutionary patterns. We confirmed that plant cyclins can be classified into 10 groups, although only eight ancestral genes may have existed in the most recent common ancestor of extant green plants. We also found that, due to the frequent occurrences of gene duplication events, several groups have expanded extensively in seed plants and, particularly, flowering plants, so that multiple genes belonging to different subgroups are present in a species. Reconciliation of the evolutionary histories of these groups and subgroups further led to the identification of evolutionarily highly conserved and rapidly duplicating gene lineages. These results will guide the classification and nomenclature of plant cyclins and help understand the conservativeness and variation in their functions. 相似文献
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Lora McClain Anna M. Segreti Sharon Nau Patricia Shaw David N. Finegold Lisa A. Pan David G. Peters 《Genes, Brain & Behavior》2020,19(5)
Major depressive disorder (MDD) affects approximately 15 million Americans. Approximately 2 million of these are classified as being refractory to treatment (TR‐MDD). Because of the lack of available therapies for TR‐MDD, and the high risk of suicide, there is interest in identifying new treatment modalities and diagnostic methods. Understanding of the impact of genomic copy number variation in the etiology of a variety of neuropsychiatric phenotypes is increasing. Low copy repeat elements at 15q13.3 facilitate non‐allelic homologous recombination, resulting in recurrent copy number variants (CNVs). Numerous reports have described association between microdeletions in this region and a variety of neuropsychiatric phenotypes, with CHRNA7 implicated as a candidate gene. However, the pathogenicity of 15q13.3 duplications is less clear. As part of an ongoing study, in which we have identified a number of metabolomic anomalies in spinal fluid from TR‐MDD patients, we also evaluated genomic copy number variation in patients (n = 125) and controls (n = 26) via array‐based copy number genomic hybridization (CGH); the case frequency was compared with frequencies reported in a prior study as well as a larger population‐sized cohort. We identified five TR‐MDD patients with microduplications involving CHRNA7. CHRNA7 duplications are the most common CNVs identified by clinical CGH in this cohort. Therefore, this study provides insight into the potential involvement of CHRNA7 duplications in the etiology of TR‐MDD and informs those involved with care of affected individuals. 相似文献