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  • 2020-2022  (5)
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  • 1
    Publikationsdatum: 2020-04-29
    Beschreibung: Aneuploidy is the leading contributor to pregnancy loss, congenital anomalies, and in vitro fertilization (IVF) failure in humans. Although most aneuploid conceptions are thought to originate from meiotic division errors in the female germline, quantitative studies that link the observed phenotypes to underlying error mechanisms are lacking. In this study, we developed a mathematical modeling framework to quantify the contribution of different mechanisms of erroneous chromosome segregation to the production of aneuploid eggs. Our model considers the probabilities of all possible chromosome gain/loss outcomes that arise from meiotic errors, such as nondisjunction (NDJ) in meiosis I and meiosis II, and premature separation of sister chromatids (PSSC) and reverse segregation (RS) in meiosis I. To understand the contributions of different meiotic errors, we fit our model to aneuploidy data from 11,157 blastocyst-stage embryos. Our best-fitting model captures several known features of female meiosis, for instance, the maternal age effect on PSSC. More importantly, our model reveals previously undescribed patterns, including an increased frequency of meiosis II errors among eggs affected by errors in meiosis I. This observation suggests that the occurrence of NDJ in meiosis II is associated with the ploidy status of an egg. We further demonstrate that the model can be used to identify IVF patients who produce an extreme number of aneuploid embryos. The dynamic nature of our mathematical model makes it a powerful tool both for understanding the relative contributions of mechanisms of chromosome missegregation in human female meiosis and for predicting the outcomes of assisted reproduction.
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2020-09-24
    Beschreibung: Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic qPCR, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including fifteen first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and forty losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defence, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation, but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.
    Digitale ISSN: 1759-6653
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2020-07-27
    Print ISSN: 1465-6906
    Digitale ISSN: 1474-760X
    Thema: Biologie
    Publiziert von BioMed Central
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2020-01-01
    Beschreibung: Macaques are the most widely used non-human primates in biomedical research. The genetic divergence between these animal models is responsible for their phenotypic differences in response to certain diseases. However, the macaque single nucleotide polymorphism resources mainly focused on rhesus macaque (Macaca mulatta), which hinders the broad research and biomedical application of other macaques. In order to overcome these limitations, we constructed a database named MACSNVdb that focuses on the interspecies genetic diversity among macaque genomes. MACSNVdb is a web-enabled database comprising ~74.51 million high-quality non-redundant single nucleotide variants (SNVs) identified among 20 macaque individuals from six species groups (muttla, fascicularis, sinica, arctoides, silenus, sylvanus). In addition to individual SNVs, MACSNVdb also allows users to browse and retrieve groups of user-defined SNVs. In particular, users can retrieve non-synonymous SNVs that may have deleterious effects on protein structure or function within macaque orthologs of human disease and drug-target genes. Besides position, alleles and flanking sequences, MACSNVdb integrated additional genomic information including SNV annotations and gene functional annotations. MACSNVdb will facilitate biomedical researchers to discover molecular mechanisms of diverse responses to diseases as well as primatologist to perform population genetic studies. We will continue updating MACSNVdb with newly available sequencing data and annotation to keep the resource up to date. Database URL: http://big.cdu.edu.cn/macsnvdb/
    Digitale ISSN: 1758-0463
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2021-03-31
    Beschreibung: Summary As the next-generation sequencing technology becomes broadly applied, genomics and transcriptomics are becoming more commonly used in both research and clinical settings. However, proteomics is still an obstacle to be conquered. For most peptide search programs in proteomics, a standard reference protein database is used. Because of the thousands of coding DNA variants in each individual, a standard reference database does not provide perfect match for many proteins/peptides of an individual. A personalized reference database can improve the detection power and accuracy for individual proteomics data. To connect genomics and proteomics, we designed a Python package PrecisionProDB that is specialized for generating a personized protein database for proteomics applications. PrecisionProDB supports multiple popular file formats and reference databases, and can generate a personized database in minutes. To demonstrate the application of PrecisionProDB, we generated human population-specific reference protein databases with PrecisionProDB, which improves the number of identified peptides by 0.34% on average. In addition, by incorporating cell line-specific variants into the protein database, we demonstrated a 0.71% improvement for peptide identification in the Jurkat cell line. With PrecisionProDB and these datasets, researchers and clinicians can improve their peptide search performance by adopting the more representative protein database or adding population and individual-specific proteins to the search database with minimum increase of efforts. Availabilityand implementation PrecisionProDB and pre-calculated protein databases are freely available at https://github.com/ATPs/PrecisionProDB and https://github.com/ATPs/PrecisionProDB_references. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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