scholarly journals Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 441
Author(s):  
LiJuan Li ◽  
Peng Yang ◽  
ShuYue Shi ◽  
ZiJing Zhang ◽  
QiaoTing Shi ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Molecular Genetic ◽  
Copy Number Variant ◽  
Copy Number Variations ◽  
Individual Growth ◽  
Nucleotide Polymorphisms ◽  
Number Variation ◽  
Normal Copy Number

Extensive research has been carried out regarding the correlation between the growth traits of livestock and genetic polymorphisms, including single nucleotide polymorphisms and copy number variations (CNV). The purpose of this study was to analyze the CNV and its genetic effects of the Opn4 gene in 284 Guizhou goats (Guizhou black goat: n = 186, Guizhou white goat: n = 98). We used qPCR to detect the CNV of the Opn4 gene in Guizhou goats, and the classification results were correlated with the corresponding individual growth traits by SPSS software. The results showed that the Opn4 gene had a superior effect on growth traits with multiple copy variants in Guizhou black goats, and there was a significant correlation between copy number variation sites and body length traits. Contrary to the former conclusion, in Guizhou white goats, individuals with the Normal copy number type showed superior growth traits and copy number variant sites were significantly associated with body weight traits. Therefore, the CNV of the Opn4 gene can be used as a candidate molecular genetic marker to improve goat growth traits, speeding up the breeding process of goat elite varieties.

Application of Copy Number Variation Sequencing in Genetic Analysis of Miscarriages in Early and Middle Pregnancy

2020 ◽  
Vol 160 (11-12) ◽  
pp. 634-642
Author(s):  
Shiqiang Luo ◽  
Xingyuan Chen ◽  
Tizhen Yan ◽  
Jiaolian Ya ◽  
Zehui Xu ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
High Throughput ◽  
Copy Number ◽  
High Throughput Sequencing ◽  
Chromosomal Abnormalities ◽  
Pregnancy Termination ◽  
Mendelian Inheritance ◽  
Copy Number Variations ◽  
Abnormal Chromosome ◽  
Number Variation

High-throughput sequencing based on copy number variation (CNV-seq) is commonly used to detect chromosomal abnormalities. This study identifies chromosomal abnormalities in aborted embryos/fetuses in early and middle pregnancy and explores the application value of CNV-seq in determining the causes of pregnancy termination. High-throughput sequencing was used to detect chromosome copy number variations (CNVs) in 116 aborted embryos in early and middle pregnancy. The detection data were compared with the Database of Genomic Variants (DGV), the Database of Chromosomal Imbalance and Phenotype in Humans using Ensemble Resources (DECIPHER), and the Online Mendelian Inheritance in Man (OMIM) database to determine the CNV type and the clinical significance. High-throughput sequencing results were successfully obtained in 109 out of 116 specimens, with a detection success rate of 93.97%. In brief, there were 64 cases with abnormal chromosome numbers and 23 cases with CNVs, in which 10 were pathogenic mutations and 13 were variants of uncertain significance. An abnormal chromosome number is the most important reason for embryo termination in early and middle pregnancy, followed by pathogenic chromosome CNVs. CNV-seq can quickly and accurately detect chromosome abnormalities and identify microdeletion and microduplication CNVs that cannot be detected by conventional chromosome analysis, which is convenient and efficient for genetic etiology diagnosis in miscarriage.

scholarly journals Carcinosarcoma of the prostate: case report with molecular and histological characterization

2018 ◽  
Vol 33 (4) ◽  
pp. 540-544 ◽  
Author(s):  
Samanta Salvi ◽  
Valentina Casadio ◽  
Filippo Martignano ◽  
Giorgia Gurioli ◽  
Maria Maddalena Tumedei ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Copy Number Variations ◽  
Molecular Characteristics ◽  
Glutathione S Transferase ◽  
Molecular Alterations ◽  
Positive Expression ◽  
Molecular Pattern ◽  
Programmed Death ◽  
Number Variation

Background: We report a case of prostatic carcinosarcoma, a rare variant of prostatic cancer, which is composed of a mixture of epithelial and mesenchymal components with a generally poor outcome. Aims and methods: We aim to identify molecular alterations, in particular copy number variations of AR and c -MYC genes, methylation and expression of glutathione S-transferase P1 (GSTP1), programmed death-ligand 1 (PD-L1), AR, and phosphorylated AR expression. Results: We found a distinct molecular pattern between adenocarcinoma and carcinosarcoma, which was characterized by high AR copy number variation gain; positive expression of PD-L1, AR, and phosphorylated AR; low espression of GSTP1 in epithelial component. The sarcomatoid component had a lower gain of the AR gene, and no expression of PD-L1, AR, phosphorylated AR, or GSTP1. Both components had a gain of c-MYC copy number variation. Conclusions: Our findings suggest that carcinosarcoma has specific molecular characteristics that could be indicative for early diagnosis and treatment selection.

Effect of copy number variation of PLA2G2A gene to growth traits in Chinese cattle

Gene ◽  
2021 ◽  
pp. 146014
Author(s):  
Peng Yang ◽  
Cuicui Cai ◽  
Mengxiao Niu ◽  
Xian Liu ◽  
Hongli Wang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Chinese Cattle ◽  
Number Variation

Association analysis of KMT2D copy number variation as a positional candidate for growth traits

Gene ◽  
2020 ◽  
Vol 753 ◽  
pp. 144799
Author(s):  
Jie Cheng ◽  
Rui Jiang ◽  
Yu Yang ◽  
Xiukai Cao ◽  
Yongzhen Huang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Association Analysis ◽  
Copy Number ◽  
Growth Traits ◽  
Positional Candidate ◽  
Number Variation

Novel copy number variation of the KLF3 gene is associated with growth traits in beef cattle

Gene ◽  
2019 ◽  
Vol 680 ◽  
pp. 99-104 ◽  
Author(s):  
Jia-Wei Xu ◽  
Li Zheng ◽  
Li-Juan Li ◽  
Yu-fei Yao ◽  
He Hua ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Number Variation

scholarly journals Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 688 ◽  
Author(s):  
Ziting Feng ◽  
Xinyu Li ◽  
Jie Cheng ◽  
Rui Jiang ◽  
Ruolan Huang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Association Analysis ◽  
Copy Number ◽  
Growth Traits ◽  
Gansu Province ◽  
Genomic Variation ◽  
Association Analyses ◽  
Qinghai Province ◽  
Real Time Quantitative Pcr ◽  
Number Variation

Copy number variation (CNV) is a type of genomic variation with an important effect on animal phenotype. We found that the PIGY gene contains a 3600 bp copy number variation (CNV) region located in chromosome 6 of sheep (Oar_v4.0 36,121,601–36,125,200 bp). This region overlaps with multiple quantitative trait loci related to phenotypes like muscle density and carcass weight. Therefore, in this study, the copy number variation of the PIGY gene was screened in three Chinese sheep breeds, namely, Chaka sheep (CKS, May of 2018, Wulan County, Qinghai Province, China), Hu sheep (HS, May of 2015, Mengjin County, Henan Province, China), and small-tailed Han sheep (STHS, May of 2016, Yongjing, Gansu Province, China). Association analyses were performed on the presence of CNV and sheep body size traits. We used real-time quantitative PCR (qPCR) to detect the CNV for association analysis. According to the results, the loss-type CNV was more common than other types in the three breeds (global average: loss = 61.5%, normal = 17.5%, and gain = 21.0%). The association analysis also showed significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of the cannon bone of sheep. Sheep with gain-type CNV had better growth traits than those with other types. The results indicate a clear relationship between the PIGY gene CNV and growth traits of sheep, suggesting the use of CNV as a new molecular breeding marker.

scholarly journals Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1008 ◽  
Author(s):  
Fei Ge ◽  
Congjun Jia ◽  
Min Chu ◽  
Chunnian Liang ◽  
Ping Yan
Keyword(s):  
Body Weight ◽  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Quantitative Polymerase Chain Reaction ◽  
The Body ◽  
Gene Copy ◽  
Common Source ◽  
Economic Traits ◽  
Number Variation

Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.

scholarly journals Population genetics of immune-related multilocus copy number variation in Native Americans

2017 ◽  
Vol 14 (128) ◽  
pp. 20170057 ◽  
Author(s):  
Luciana W. Zuccherato ◽  
Silvana Schneider ◽  
Eduardo Tarazona-Santos ◽  
Robert J. Hardwick ◽  
Douglas E. Berg ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Native American ◽  
Native Americans ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genomic Variation ◽  
Population Subdivision ◽  
Nucleotide Polymorphisms ◽  
Number Variation

While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy–Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f , which quantifies the departure of homozygosity from the Hardy–Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1 , FCGR3A , FCGR3B and FCGR2C ) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.

scholarly journals Phenome-wide burden of copy number variation in UK Biobank

2019 ◽  
Author(s):  
Matthew Aguirre ◽  
Manuel Rivas ◽  
James Priest
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Significant Proportion ◽  
High Body Mass Index ◽  
Population Level ◽  
Copy Number Variations ◽  
Uk Biobank ◽  
Number Variation ◽  
Artery Disease ◽  
The Uk

AbstractCopy number variations (CNV) represent a significant proportion of the genetic differences between individuals and many CNVs associate causally with syndromic disease and clinical outcomes. Here, we characterize the landscape of copy number variation and their phenome-wide effects in a sample of 472,228 array-genotyped individuals from the UK Biobank. In addition to population-level selection effects against genic loci conferring high-mortality, we describe genetic burden from syndromic and previously uncharacterized CNV loci across nearly 2,000 quantitative and dichotomous traits, with separate analyses for common and rare classes of variation. Specifically, we highlight the effects of CNVs at two well-known syndromic loci 16p11.2 and 22q11.2, as well as novel associations at 9p23, in the context of acute coronary artery disease and high body mass index. Our data constitute a deeply contextualized portrait of population-wide burden of copy number variation, as well as a series of known and novel dosage-mediated genic associations across the medical phenome.

scholarly journals Frequency of CDK2 , CCNE1 Copy Number Variation in Acral Melanoma and Implications for CDK Inhibitor in Targeted Therapy

2020 ◽  
Author(s):  
Xiaowen Wu ◽  
Junya Yan ◽  
Jiayi Yu ◽  
Jinyu Yu ◽  
Zhiyuan Cheng ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Targeted Therapy ◽  
Copy Number Variation ◽  
Copy Number ◽  
Melanoma Cells ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Cdk Inhibitor ◽  
Acral Melanoma ◽  
Number Variation

Abstract Background: Acral melanoma have a high frequency of cell cycle-related gene copy number variation. However, the status and clinical significance of CNVs of CDK 2 and CCNE1 have not been fully elucidated. Methods: A total of 490 acral melanoma samples were examined for CNVs of CDK 2 and CCNE1 using QuantiGenePlex DNA Assay. Correlations of CDK2 and CCNE1 CNVs to clinicopathologic features and prognosis of acral melanoma were evaluated.The sensitivity of cell lines and cell-derived xenograft (CDX) containing CCNE1 CNVs to CDK inhibitor AT7519,Dinaciclib and proteasome inhibitor Bortezomib were also analyzed. Results: Among the 490 samples,140 cases, 139 cases and 39 cases respectively showed CDK2 gain (28.5%), CCNE1 gain (28.3%) and CDK2 gain plus CCNE1 gain (8.0%).The median progression-free survival (PFS) time for acral patients with CCNE1 gain was significantly shorter than that for patients without CCNE1 gain (17.0 versus 27.0 months; P =0.002). Furthermore, CCNE1 gain was an independent prognostic factor for patients receiving chemotherapy. The pan-CDK inhibitor AT7519 could inhibit the cell proliferation, induce apoptosis and cause cell cycle arrest in G2 phase of acral melanoma cells and inhibit the tumor growth of CDX with CCNE1 gain. Dinaciclib and Bortezomib showed CCNE1 copy number independent inhibitory effects on the proliferation of melanoma cells. Conclusions: CDK2 and CCNE1 copy number variations were frequent in acral melanoma and CCNE1 gain may be a useful biomarker to predict the outcome of receiving chemotherapy in patients with acral melanoma. In addition, our study provides a basis for the use of CDK inhibitor in the treatment of acral melanoma. Keywords: acral melanoma, targeted therapy, CDK2 , CCNE1 , copy number variation

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