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Kafi Z, Masoudi AA, Torshizi RV, Ehsani A. Copy number variations affecting growth curve parameters in a crossbred chicken population. Gene 2024; 927:148710. [PMID: 38901536 DOI: 10.1016/j.gene.2024.148710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/01/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Copy number variations (CNVs) are key structural variations in the genome and may contribute to phenotypic differences. In this study, we used a F2 chicken population created from reciprocal crossing between fast-growing Arian broiler line and Urmia native chickens. The chickens were genotyped by 60 K SNP BeadChip, and PennCNV algorithm was used to detect genome-wide CNVs. The growth curve parameters of W0, k, L, Wf, Wi, ti and average GR were used as phenotypic data. The association between CNV and growth curve parameters was carried out using the CNVRanger R/Bioconductor package. Five CNV regions (CNVRs) were chosen for the validation experiment using qPCR. Gene enrichment analysis was done using WebGestalt. The STRING database was used to search for significant pathways. The results identified 966 CNVs and 600 CNVRs including 468 gains, 67 losses, and 65 both events on autosomal chromosomes. Validation of the CNVRs obtained from the qPCR assay were 79 % consistent with the prediction by PennCNV. A total of 43 significant CNVs were obtained for the seven growth curve parameters. The 416 genes annotated for significant CNVs. Six genes out of 416 genes were most related to growth curve parameters. These genes were LCP2, Dock2, CD80, CYFIP1, NIPA1 and NIPA2. Some of these genes in their biological process were associated with the growth, reproduction and development of cells or organs that ultimately lead to the growth of the body. The results of the study could pave the way for better understanding the molecular process of CNVs and growth curve parameters in birds.
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Affiliation(s)
- Zeinab Kafi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Alireza Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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2
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Lotfizadeh F, Masoudi AA, Vaez Torshizi R, Emrani H. Genome-wide association study of copy number variations with shank traits in a F 2 crossbred chicken population. Anim Genet 2024; 55:559-574. [PMID: 38764135 DOI: 10.1111/age.13447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/21/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
Copy number variations (CNVs) are large-scale changes in the DNA sequence that can affect the genetic structure and phenotype of an organism. The purpose of this study was to investigate the existing CNVs and their associations with the shank diameter (ShD) and shank length (ShL) traits using data from an F2 crossbred chicken population. To carry out the study, 312 chickens were genotyped using the Illumina 60k SNP Beadchip. The shank traits of the birds were measured from day 1 to 12 weeks of age. penncnv and cnvruler tools were used to find copy numbers and regions with copy number changes (CNVR), respectively. The CNVRanger package was used to perform a genome-wide association study between shank traits and CNVs. Gene ontology research in CNVRs was carried out using the david database. In this investigation, 966 CNVs and 606 regions with copy number changes were discovered. The copy number states and variations were randomly distributed along the length of the autosomal chromosomes. Weeks 1-4, 9 and 12 of growth revealed a significant association of copy number variations with shank traits, false discovery rate (FDR-corrected p-value < 0.01), and the majority of CNVs that were statistically significant were found on chromosomes 1-3. These CNV segments are nearby genes such as KCNJ12, FGF6 and MYF5, which are fundamental to growth and development. In addition, gene set analyses revealed terms related to muscle physiology, regulation of cellular processes and potassium channels.
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Affiliation(s)
- Fateme Lotfizadeh
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Hossein Emrani
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
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3
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Zhao C. Genome wide association study gateway-transitioning variants from association to causality in complex diseases. Sleep 2024; 47:zsae116. [PMID: 38752386 DOI: 10.1093/sleep/zsae116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024] Open
Affiliation(s)
- Chen Zhao
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, Germany
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4
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Gupta H, Sharma S, Gilyazova I, Satyamoorthy K. Molecular tools are crucial for malaria elimination. Mol Biol Rep 2024; 51:555. [PMID: 38642192 DOI: 10.1007/s11033-024-09496-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
The eradication of Plasmodium parasites, responsible for malaria, is a daunting global public health task. It requires a comprehensive approach that addresses symptomatic, asymptomatic, and submicroscopic cases. Overcoming this challenge relies on harnessing the power of molecular diagnostic tools, as traditional methods like microscopy and rapid diagnostic tests fall short in detecting low parasitaemia, contributing to the persistence of malaria transmission. By precisely identifying patients of all types and effectively characterizing malaria parasites, molecular tools may emerge as indispensable allies in the pursuit of malaria elimination. Furthermore, molecular tools can also provide valuable insights into parasite diversity, drug resistance patterns, and transmission dynamics, aiding in the implementation of targeted interventions and surveillance strategies. In this review, we explore the significance of molecular tools in the pursuit of malaria elimination, shedding light on their key contributions and potential impact on public health.
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Affiliation(s)
- Himanshu Gupta
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Sonal Sharma
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Irina Gilyazova
- Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, 450054, Russia
- Bashkir State Medical University, Ufa, 450008, Russia
| | - Kapaettu Satyamoorthy
- SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur, Dharwad, 580009, Karnataka, India
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Higgins J, Osorio-Guarín JA, Olave-Achury C, Toloza-Moreno DL, Enriquez A, Di Palma F, Yockteng R, De Vega JJ. Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages. ANNALS OF BOTANY 2024; 133:349-364. [PMID: 38097270 PMCID: PMC11005773 DOI: 10.1093/aob/mcad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation. METHODS We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination. RESULTS In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties. CONCLUSIONS We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.
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Affiliation(s)
- Janet Higgins
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Jaime Andrés Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
| | | | - Deisy Lisseth Toloza-Moreno
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
| | - Ayda Enriquez
- Centro de Investigación Palmira, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Palmira, Colombia
| | | | - Roxana Yockteng
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
- Muséum National d’Histoire Naturelle, UMR-CNRS 7205, Paris, France
| | - Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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Kumar H, Panigrahi M, G Strillacci M, Sonejita Nayak S, Rajawat D, Ghildiyal K, Bhushan B, Dutt T. Detection of genome-wide copy number variation in Murrah buffaloes. Anim Biotechnol 2023; 34:3783-3795. [PMID: 37381739 DOI: 10.1080/10495398.2023.2227670] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom® Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts.
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Affiliation(s)
- Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Maria G Strillacci
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | | | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, India
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Xu Z, Wang X, Song X, An Q, Wang D, Zhang Z, Ding X, Yao Z, Wang E, Liu X, Ru B, Xu Z, Huang Y. Association between the copy number variation of CCSER1 gene and growth traits in Chinese Capra hircus (goat) populations. Anim Biotechnol 2023; 34:1377-1383. [PMID: 35108172 DOI: 10.1080/10495398.2022.2025818] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Recently, Coiled-coil serine-rich protein 1 (CCSER1) gene is reported to be related to economic traits in livestock, and become a hotspot. In our study, we detected CCSER1 gene CNV in 693 goats from six breeds (GZB, GZW, AN, BH, HG, TH) by quantitative real-time PCR (qPCR) and the association analysis between the types of CNV and growth traits. Then, CCSER1 gene expression pattern was discovered in seven tissues from NB goats. Our results showed that the CCSER1 gene copy numbers were distributed differently in the aforementioned six breeds. The type of CCSER1 gene CNV was significantly associated with body weight and heart girth traits in GZW goat, in which individuals with deletion type were dominant in body weight trait (P < 0.05), while the normal type individuals were more advantageous in heart girth trait (P < 0.01); and there was a significant association with heart girth in TH goat (P < 0.05), which normal type was the dominant one. The expression profile revealed that CCSER1 gene has the highest level in the lung, followed by the small intestine and heart. In conclusion, our result is dedicated to an in-depth study of the novel CCSER1 gene CNV site and to provide essential information for Chinese goats molecular selective breeding in the future.
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Affiliation(s)
- Zijie Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Xingya Song
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou, People's Republic of China
| | - Dahui Wang
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xiaoting Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
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Pajuste FD, Remm M. GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads. Sci Rep 2023; 13:17765. [PMID: 37853040 PMCID: PMC10584998 DOI: 10.1038/s41598-023-44636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Genomes exhibit large regions with segmental copy number variation, many of which include entire genes and are multiallelic. We have developed a computational method GeneToCN that counts the frequencies of gene-specific k-mers in FASTQ files and uses this information to infer copy number of the gene. We validated the copy number predictions for amylase genes (AMY1, AMY2A, AMY2B) using experimental data from digital droplet PCR (ddPCR) on 39 individuals and observed a strong correlation (R = 0.99) between GeneToCN predictions and experimentally determined copy numbers. An additional validation on FCGR3 genes showed a higher concordance for FCGR3A compared to two other methods, but reduced accuracy for FCGR3B. We further tested the method on three different genomic regions (SMN, NPY4R, and LPA Kringle IV-2 domain). Predicted copy number distributions of these genes in a set of 500 individuals from the Estonian Biobank were in good agreement with the previously published studies. In addition, we investigated the possibility to use GeneToCN on sequencing data generated by different technologies by comparing copy number predictions from Illumina, PacBio, and Oxford Nanopore data of the same sample. Despite the differences in variability of k-mer frequencies, all three sequencing technologies give similar predictions with GeneToCN.
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Affiliation(s)
- Fanny-Dhelia Pajuste
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia.
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia
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Arias KD, Gutiérrez JP, Fernández I, Álvarez I, Goyache F. Copy Number Variation Regions Differing in Segregation Patterns Span Different Sets of Genes. Animals (Basel) 2023; 13:2351. [PMID: 37508128 PMCID: PMC10376189 DOI: 10.3390/ani13142351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta pig breed was subjected to enrichment and functional annotation analyses to ascertain their functional independence and importance. Enrichment analyses allowed us to annotate 1018 and 351 candidate genes within the bounds of the segregating and non-segregating CNVRs, respectively. The information retrieved suggested that the candidate genes spanned by segregating and non-segregating CNVRs were functionally independent. Functional annotation analyses allowed us to identify nine different significantly enriched functional annotation clusters (ACs) in segregating CNVR candidate genes mainly involved in immunity and regulation of the cell cycle. Up to five significantly enriched ACs, mainly involved in reproduction and meat quality, were identified in non-segregating CNVRs. The current analysis fits with previous reports suggesting that segregating CNVRs would explain performance at the population level, whereas non-segregating CNVRs could explain between-individuals differences in performance.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
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Salehian-Dehkordi H, Huang JH, Pirany N, Mehrban H, Lv XY, Sun W, Esmailizadeh A, Lv FH. Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep. Genes (Basel) 2023; 14:1256. [PMID: 37372436 PMCID: PMC10298528 DOI: 10.3390/genes14061256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.
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Affiliation(s)
- Hosein Salehian-Dehkordi
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Jia-Hui Huang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
| | - Nasrollah Pirany
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Hossein Mehrban
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Xiao-Yang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 76169-14111, Iran
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
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11
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Sun T, Pei S, Liu Y, Hanif Q, Xu H, Chen N, Lei C, Yue X. Whole genome sequencing of simmental cattle for SNP and CNV discovery. BMC Genomics 2023; 24:179. [PMID: 37020271 PMCID: PMC10077681 DOI: 10.1186/s12864-023-09248-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUD The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity. RESULTS In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility. CONCLUSIONS In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.
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Affiliation(s)
- Ting Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Shengwei Pei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Yangkai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
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12
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López-López D, Roldán G, Fernández-Rueda JL, Bostelmann G, Carmona R, Aquino V, Perez-Florido J, Ortuño F, Pita G, Núñez-Torres R, González-Neira A, Peña-Chilet M, Dopazo J. A crowdsourcing database for the copy-number variation of the Spanish population. Hum Genomics 2023; 17:20. [PMID: 36894999 PMCID: PMC9997023 DOI: 10.1186/s40246-023-00466-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/25/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. RESULTS Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/ . CONCLUSION SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.
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Affiliation(s)
- Daniel López-López
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Gema Roldán
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Jose L Fernández-Rueda
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Gerrit Bostelmann
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Rosario Carmona
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Virginia Aquino
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Javier Perez-Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Francisco Ortuño
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Department of Computer Architecture and Computer Technology, University of Granada, 18071, Granada, Spain
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Rocío Núñez-Torres
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - María Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain. .,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain. .,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain. .,FPS/ELIXIR-ES, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.
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13
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Zhang H, Alarcon C, Cavallari LH, Nutescu E, Carvill GL, Perera MA, Hernandez W. Genomewide Association Study Identifies Copy Number Variants Associated With Warfarin Dose Response and Risk of Venous Thromboembolism in African Americans. Clin Pharmacol Ther 2023; 113:624-633. [PMID: 36507737 PMCID: PMC11238476 DOI: 10.1002/cpt.2820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The anticoagulant warfarin is commonly used to control and prevent thrombotic disorders, such as venous thromboembolism (VTE), which disproportionately afflicts African Americans. Despite the importance of copy number variants (CNVs), few studies have focused on characterizing and understanding their role in drug response and disease risk among African Americans. In this study, we conduct the first genome-wide analysis of CNVs to more comprehensively account for the contribution of genetic variation in warfarin dose requirement and VTE risk among African Americans. We used hidden Markov models to detect CNVs from high-throughput single-nucleotide polymorphism arrays for 340 African American participants in the International Warfarin Pharmacogenetics Consortium. We identified 11,570 CNVs resulting in 2,038 copy number variable regions (CNVRs) and found 3 CNVRs associated with warfarin dose requirement and 3 CNVRs associated with VTE risk in African Americans. CNVRs 1q31.2del and 6q14.1del were associated with increased warfarin dose requirement (β = 11.18 and 4.94, respectively; Pemp = < 0.002); CNVR 19p13.31del was associated with decreased warfarin dose requirement (β = -1.41, Pemp = 0.0004); CNVRs (2p22.1del and 5q35.1-q35.2del) were found to be associated with increased risk of VTE (odds ratios (ORs) = 1.88 and 14.9, respectively; Pemp ≤0.02); and CNVR 10q26.12del was associated with a decreased risk of VTE (OR = 0.6; Pemp = 0.05). Modeling of the 10q26.12del in HepG2 cells revealed that this deletion results in decreased fibrinogen gene expression, decreased fibrinogen and WDR11 protein levels, and decreased secretion of fibrinogen into the extracellular matrix. We found robust evidence that CNVRs could contribute to warfarin dose requirement and risk of VTE in African Americans and for 10q26.3del describe a possible pathogenic mechanism.
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Affiliation(s)
- Honghong Zhang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Cristina Alarcon
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Larisa H. Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Edith Nutescu
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois, USA
| | - Gemma L. Carvill
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Minoli A. Perera
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Wenndy Hernandez
- Section of Cardiology, University of Chicago, Chicago, Illinois, USA
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14
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Peripolli E, Stafuzza NB, Machado MA, do Carmo Panetto JC, do Egito AA, Baldi F, da Silva MVGB. Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data. Anim Genet 2023; 54:254-270. [PMID: 36740987 DOI: 10.1111/age.13298] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/13/2021] [Accepted: 01/13/2023] [Indexed: 02/07/2023]
Abstract
Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome-wide assessment of copy number variations (CNVs) based on whole-genome re-sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS-UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75-2.07-fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA-DQB, BOLA-DQA5, CD1A, β-defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy-related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.
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Affiliation(s)
- Elisa Peripolli
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | | | | | | | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
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15
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Sánchez S, Juárez U, Domínguez J, Molina B, Barrientos R, Martínez-Hernández A, Carnevale A, Grether-González P, Mayen DG, Villarroel C, Lieberman E, Yokoyama E, Del Castillo V, Torres L, Frias S. Frequent copy number variants in a cohort of Mexican-Mestizo individuals. Mol Cytogenet 2023; 16:2. [PMID: 36631885 PMCID: PMC9835318 DOI: 10.1186/s13039-022-00631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The human genome presents variation at distinct levels, copy number variants (CNVs) are DNA segments of variable lengths that range from several base pairs to megabases and are present at a variable number of copies in human genomes. Common CNVs have no apparent influence on the phenotype; however, some rare CNVs have been associated with phenotypic traits, depending on their size and gene content. CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. Nevertheless, this default reference is inadequate when the samples analysed are from people from Mexico, since population with a Hispanic genetic background are minimally represented. In this work, we describe the variation in the frequencies of four common CNVs in Mexican-Mestizo individuals. RESULTS In a cohort of 147 unrelated Mexican-Mestizo individuals, we found that the common CNVs 2p11.2 (99.6%), 8p11.22 (54.5%), 14q32.33 (100%), and 15q11.2 (71.1%) appeared with unexpectedly high frequencies when contrasted with the HapMap reference (ChAS). Yet, while when comparing to an ethnically related reference population, these differences were significantly reduced or even disappeared. CONCLUSION The findings in this work contribute to (1) a better description of the CNVs characteristics of the Mexican Mestizo population and enhance the knowledge of genome variation in different ethnic groups. (2) emphasize the importance of contrasting CNVs identified in studied individuals against a reference group that-as best as possible-share the same ethnicity while keeping this relevant information in mind when conducting CNV studies at the population or clinical level.
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Affiliation(s)
- Silvia Sánchez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises Juárez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Julieta Domínguez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Bertha Molina
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Rehotbevely Barrientos
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Angélica Martínez-Hernández
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Alessandra Carnevale
- grid.452651.10000 0004 0627 7633Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Patricia Grether-González
- grid.419218.70000 0004 1773 5302Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología, Ciudad de Mexico, México ,grid.413678.fPresent Address: Centro Médico ABC, Campus Santa Fe, Ciudad de Mexico, México
| | - Dora Gilda Mayen
- Unidad de Genética Aplicada. Hospital Ángeles Lomas, Huixquilucan, Edo. de México México
| | - Camilo Villarroel
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Esther Lieberman
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Emiy Yokoyama
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Victoria Del Castillo
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Leda Torres
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Sara Frias
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
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16
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Zhang Z, Peng M, Wen Y, Chai Y, Liang J, Yang P, Liu X, Li J, Huang Y, Li L, Huang W, Qi Z, Yang G, Chen F, Shi Q, Li Z, Ru B, Lei C, Wang E, Huang Y. Copy number variation of
EIF4A2
loci related to phenotypic traits in Chinese cattle. Vet Med Sci 2022; 8:2147-2156. [PMID: 36052549 PMCID: PMC9514498 DOI: 10.1002/vms3.875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science Henan Academy of Agricultural Sciences Zhengzhou Henan People's Republic of China
| | - Mengyang Peng
- College of Animal Science and Technology Northwest A&F University Yangling Shaanxi People's Republic of China
| | - Yifan Wen
- College of Animal Science and Technology Northwest A&F University Yangling Shaanxi People's Republic of China
| | - Yanan Chai
- Institute of Animal Husbandry and Veterinary Science Henan Academy of Agricultural Sciences Zhengzhou Henan People's Republic of China
| | - Juntong Liang
- College of Animal Science and Technology Northwest A&F University Yangling Shaanxi People's Republic of China
| | - Peng Yang
- College of Animal Science and Technology Northwest A&F University Yangling Shaanxi People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station Zhengzhou Henan People's Republic of China
| | - Jungang Li
- Jiaxian Animal Husbandry Bureau Jiaxian Henan People's Republic of China
| | - Yajun Huang
- Jiaxian Animal Husbandry Bureau Jiaxian Henan People's Republic of China
| | - Lijuan Li
- Jiaxian Animal Husbandry Bureau Jiaxian Henan People's Republic of China
| | - Weihong Huang
- Jiaxian Animal Husbandry Bureau Jiaxian Henan People's Republic of China
| | - Zengfang Qi
- Jiaxian Animal Husbandry Bureau Jiaxian Henan People's Republic of China
| | - Guojie Yang
- Jiaxian Animal Husbandry Bureau Jiaxian Henan People's Republic of China
| | - Fuying Chen
- Institute of Animal Husbandry and Veterinary Science Henan Academy of Agricultural Sciences Zhengzhou Henan People's Republic of China
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science Henan Academy of Agricultural Sciences Zhengzhou Henan People's Republic of China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station Zhengzhou Henan People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station Zhengzhou Henan People's Republic of China
| | - Chuzhao Lei
- Institute of Animal Husbandry and Veterinary Science Henan Academy of Agricultural Sciences Zhengzhou Henan People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science Henan Academy of Agricultural Sciences Zhengzhou Henan People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology Northwest A&F University Yangling Shaanxi People's Republic of China
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17
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Mountford HS, Braden R, Newbury DF, Morgan AT. The Genetic and Molecular Basis of Developmental Language Disorder: A Review. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9050586. [PMID: 35626763 PMCID: PMC9139417 DOI: 10.3390/children9050586] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 04/12/2022] [Indexed: 01/05/2023]
Abstract
Language disorders are highly heritable and are influenced by complex interactions between genetic and environmental factors. Despite more than twenty years of research, we still lack critical understanding of the biological underpinnings of language. This review provides an overview of the genetic landscape of developmental language disorders (DLD), with an emphasis on the importance of defining the specific features (the phenotype) of DLD to inform gene discovery. We review the specific phenotype of DLD in the genetic literature, and the influence of historic variation in diagnostic inclusion criteria on researchers' ability to compare and replicate genotype-phenotype studies. This review provides an overview of the recently identified gene pathways in populations with DLD and explores current state-of-the-art approaches to genetic analysis based on the hypothesised architecture of DLD. We will show how recent global efforts to unify diagnostic criteria have vastly increased sample size and allow for large multi-cohort metanalyses, leading the identification of a growing number of contributory loci. We emphasise the important role of estimating the genetic architecture of DLD to decipher underlying genetic associations. Finally, we explore the potential for epigenetics and environmental interactions to further unravel the biological basis of language disorders.
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Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Ruth Braden
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Angela T. Morgan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
- Correspondence:
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18
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Prokop JW, Jdanov V, Savage L, Morris M, Lamb N, VanSickle E, Stenger CL, Rajasekaran S, Bupp CP. Computational and Experimental Analysis of Genetic Variants. Compr Physiol 2022; 12:3303-3336. [PMID: 35578967 DOI: 10.1002/cphy.c210012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics has grown exponentially over the last decade. Common variants are associated with physiological changes through statistical strategies such as Genome-Wide Association Studies (GWAS) and quantitative trail loci (QTL). Rare variants are associated with diseases through extensive filtering tools, including population genomics and trio-based sequencing (parents and probands). However, the genomic associations require follow-up analyses to narrow causal variants, identify genes that are influenced, and to determine the physiological changes. Large quantities of data exist that can be used to connect variants to gene changes, cell types, protein pathways, clinical phenotypes, and animal models that establish physiological genomics. This data combined with bioinformatics including evolutionary analysis, structural insights, and gene regulation can yield testable hypotheses for mechanisms of genomic variants. Molecular biology, biochemistry, cell culture, CRISPR editing, and animal models can test the hypotheses to give molecular variant mechanisms. Variant characterizations can be a significant component of educating future professionals at the undergraduate, graduate, or medical training programs through teaching the basic concepts and terminology of genetics while learning independent research hypothesis design. This article goes through the computational and experimental analysis strategies of variant characterization and provides examples of these tools applied in publications. © 2022 American Physiological Society. Compr Physiol 12:3303-3336, 2022.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Vladislav Jdanov
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Lane Savage
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA.,Office of Research, Spectrum Health, Grand Rapids, Michigan, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Medical Genetics, Spectrum Health, Grand Rapids, Michigan, USA
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19
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Gu C, Gao H, Li K, Dai X, Yang Z, Li R, Wen C, He Y. Copy Number Variation Analysis of Euploid Pregnancy Loss. Front Genet 2022; 13:766492. [PMID: 35401693 PMCID: PMC8984164 DOI: 10.3389/fgene.2022.766492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/24/2022] [Indexed: 12/30/2022] Open
Abstract
Objectives: Copy number variant (CNV) is believed to be the potential genetic cause of pregnancy loss. However, CNVs less than 3 Mb in euploid products of conceptions (POCs) remain largely unexplored. The aim of this study was to investigate the features of CNVs less than 3 Mb in POCs and their potential clinical significance in pregnancy loss/fetal death.Methods: CNV data were extracted from a cohort in our institution and 19 peer-reviewed publications, and only those CNVs less than 3 Mb detected in euploid pregnancy loss/fetal death were included. We conducted a CNV map to analyze the distribution of CNVs in chromosomes using R packages karyoploteR_1.10.5. Gene names and annotated gene types covered by those CNVs were mined from the human Release 19 reference genome file and GENECODE database. We assessed the expression patterns and the consequences of murine knock-out of those genes using TiGER and Mouse Genome Informatics (MGI) databases. Functional enrichment and pathway analysis for genes in CNVs were performed using clusterProfiler V3.12.0.Result: Breakpoints of 564 CNVs less than 3 Mb were obtained from 442 euploid POCs, with 349 gains and 185 losses. The CNV map showed that CNVs were distributed in all chromosomes, with the highest frequency detected in chromosome 22 and the lowest frequency in chromosome Y, and CNVs showed a higher density in the pericentromeric and sub-telomeric regions. A total of 5,414 genes mined from the CNV regions (CNVRs), Gene Ontology (GO), and pathway analysis showed that the genes were significantly enriched in multiple terms, especially in sensory perception, membrane region, and tight junction. A total of 995 protein-coding genes have been reported to present mammalian phenotypes in MGI, and 276 of them lead to embryonic lethality or abnormal embryo/placenta in knock-out mouse models. CNV located at 19p13.3 was the most common CNV of all POCs.Conclusion: CNVs less than 3 Mb in euploid POCs distribute unevenly in all chromosomes, and a higher density was seen in the pericentromeric and sub-telomeric regions. The genes in those CNVRs are significantly enriched in biological processes and pathways that are important to embryonic/fetal development. CNV in 19p13.3 and the variations of ARID3A and FSTL3 might contribute to pregnancy loss.
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Affiliation(s)
- Chongjuan Gu
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huan Gao
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Kuanrong Li
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xinyu Dai
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhao Yang
- West China Hospital, Sichuan University, Chengdu, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Canliang Wen
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yaojuan He
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Yaojuan He,
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20
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Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Li X, Ding X, Liu L, Yang P, Yao Z, Lei C, Chen H, Huang Y, Liu W. Copy number variation of bovine DYNC1I2 gene is associated with body conformation traits in chinese beef cattle. Gene 2021; 810:146060. [PMID: 34740731 DOI: 10.1016/j.gene.2021.146060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022]
Abstract
Previous, studies have shown that the dynein transporter compound has a role in diseases such as intellectual disability and cerebral malformations. However, the study of CNV in DYNC1I2 gene has not been reported. Q-PCR and data association analysis were used for DYNC1I2 gene copy in this study. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for DYNC1I2 gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. Association analysis indicate that CNV of DYNC1I2 gene showed a positive effect in cattle growth: in XN cattle, individuals with deletion types showed better performance on height at hip cross (P < 0.05); individuals with duplication types have better performance on body length (P < 0.05) in PN cattle; individuals with deletion types was significantly correlated with chest width and Hucklebone width (P < 0.05) in QC cattle; individuals with duplication types in Yunling cattle were better than the normal types, and there was a significant correlation between copy number variant and chest depth (P < 0.05). The results showed that CNV markers closely related to cattle production traits were detected at DNA level, which could be used as an important candidate molecular marker for marker-assisted selection of growth traits in Chinese cattle, and provided a new research basis for genetics and breeding of Chinese beef cattle.
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Affiliation(s)
- Xinmiao Li
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang 830052, People's Republic of China; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Xiaoting Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Lingling Liu
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang 830052, People's Republic of China.
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Wujun Liu
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang 830052, People's Republic of China.
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22
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Yu QY, Lu TP, Hsiao TH, Lin CH, Wu CY, Tzeng JY, Hsiao CK. An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data. Front Genet 2021; 12:709555. [PMID: 34567069 PMCID: PMC8456116 DOI: 10.3389/fgene.2021.709555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic studies have been a major approach to elucidating disease etiology and to exploring potential targets for treatments of many complex diseases. Statistical analyses in these studies often face the challenges of multiplicity, weak signals, and the nature of dependence among genetic markers. This situation becomes even more complicated when multi-omics data are available. To integrate the data from different platforms, various integrative analyses have been adopted, ranging from the direct union or intersection operation on sets derived from different single-platform analysis to complex hierarchical multi-level models. The former ignores the biological relationship between molecules while the latter can be hard to interpret. We propose in this study an integrative approach that combines both single nucleotide variants (SNVs) and copy number variations (CNVs) in the same genomic unit to co-localize the concurrent effect and to deal with the sparsity due to rare variants. This approach is illustrated with simulation studies to evaluate its performance and is applied to low-density lipoprotein cholesterol and triglyceride measurements from Taiwan Biobank. The results show that the proposed method can more effectively detect the collective effect from both SNVs and CNVs compared to traditional methods. For the biobank analysis, the identified genetic regions including the gene VNN2 could be novel and deserve further investigation.
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Affiliation(s)
- Qi-You Yu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ching-Heng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Yun Wu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, United States.,Department of Statistics, University of Pennsylvania, Philadelphia, PA, United States
| | - Jung-Ying Tzeng
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States
| | - Chuhsing Kate Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
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23
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Lange M, Begolli R, Giakountis A. Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. Noncoding RNA 2021; 7:47. [PMID: 34449663 PMCID: PMC8395730 DOI: 10.3390/ncrna7030047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.
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Affiliation(s)
- Marios Lange
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
- Institute for Fundamental Biomedical Research, B.S.R.C “Alexander Fleming”, 34 Fleming Str., 16672 Vari, Greece
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24
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Chen BB, Yan JH, Zheng J, Peng HW, Cai XL, Pan XT, Li HQ, Hong QZ, Peng XE. Copy number variation in the CES1 gene and the risk of non-alcoholic fatty liver in a Chinese Han population. Sci Rep 2021; 11:13984. [PMID: 34234263 PMCID: PMC8263572 DOI: 10.1038/s41598-021-93549-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
A recent genome-wide copy number variations (CNVs) scan identified a 16q12.2 deletion that included the carboxylesterase 1 (CES1) gene, which is important in the metabolism of fatty acids and cholesterol. We aimed to investigate whether CES1 CNVs was associated with susceptibility to non-alcoholic fatty liver disease (NAFLD) in a Chinese Han population. A case-control study was conducted among 303 patients diagnosed with NAFLD and 303 age (± 5) and sex-matched controls from the Affiliated Nanping First Hospital of Fujian Medical University in China. The copy numbers of CES1 were measured using TaqMan quantitative real-time polymerase chain reaction (qPCR) and serum CES1 was measured using enzyme-linked immunosorbent assays. The Chi-squared test and a logistic regression model were used to evaluate the association between CES1 CNVs and NAFLD susceptibility. The distribution of CES1 CNVs showed a higher frequency of CNVs loss (< 2) among patients; however, the difference was not significant (P = 0.05). After controlling for other known or suspected risk factors for NAFLD, CES1 CNVs loss was significantly associated with greater risk of NAFLD (adjusted OR = 2.75, 95% CI 1.30-5.85, P = 0.01); while CES1 CNVs gain (> 2) was not. There was a suggestion of an association between increased CES1 serum protein levels and CNVs losses among cases, although this was not statistically significant (P = 0.07). Copy number losses (< 2) of CES1 contribute to susceptibility to NAFLD in the Chinese Han population.
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Affiliation(s)
- Bing Bing Chen
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China.,Department of Hospital Infection Control, First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China
| | - Jian Hui Yan
- Department of Infectious Disease, The Second Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Jing Zheng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China
| | - He Wei Peng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China
| | - Xiao Ling Cai
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China
| | - Xin Ting Pan
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China
| | - Hui Quan Li
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China
| | - Qi Zhu Hong
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China
| | - Xian-E Peng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, 350122, China. .,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fujian, China.
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25
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Fotoukkiaii SM, Wybouw N, Kurlovs AH, Tsakireli D, Pergantis SA, Clark RM, Vontas J, Van Leeuwen T. High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest. PLoS Genet 2021; 17:e1009422. [PMID: 34153029 PMCID: PMC8248744 DOI: 10.1371/journal.pgen.1009422] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/01/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022] Open
Abstract
Chemical control strategies are driving the evolution of pesticide resistance in pest populations. Understanding the genetic mechanisms of these evolutionary processes is of crucial importance to develop sustainable resistance management strategies. The acaricide pyflubumide is one of the most recently developed mitochondrial complex II inhibitors with a new mode of action that specifically targets spider mite pests. In this study, we characterize the molecular basis of pyflubumide resistance in a highly resistant population of the spider mite Tetranychus urticae. Classical genetic crosses indicated that pyflubumide resistance was incompletely recessive and controlled by more than one gene. To identify resistance loci, we crossed the resistant population to a highly susceptible T. urticae inbred strain and propagated resulting populations with and without pyflubumide exposure for multiple generations in an experimental evolution set-up. High-resolution genetic mapping by a bulked segregant analysis approach led to the identification of three quantitative trait loci (QTL) linked to pyflubumide resistance. Two QTLs were found on the first chromosome and centered on the cytochrome P450 CYP392A16 and a cluster of CYP392E6-8 genes. Comparative transcriptomics revealed a consistent overexpression of CYP392A16 and CYP392E8 in the experimental populations that were selected for pyflubumide resistance. We further corroborated the involvement of CYP392A16 in resistance by in vitro functional expression and metabolism studies. Collectively, these experiments uncovered that CYP392A16 N-demethylates the toxic carboxamide form of pyflubumide to a non-toxic compound. A third QTL coincided with cytochrome P450 reductase (CPR), a vital component of cytochrome P450 metabolism. We show here that the resistant population harbors three gene copies of CPR and that this copy number variation is associated with higher mRNA abundance. Together, we provide evidence for detoxification of pyflubumide by cytochrome P450s that is likely synergized by gene amplification of CPR. Our understanding of the causal genetic variants that drive the evolution of quantitative traits, such as polygenic pesticide resistance, remains very limited. Here, we followed a high-resolution genetic mapping approach to localize the genetic variants that cause pyflubumide resistance in the two-spotted spider mite Tetranychus urticae. Three well-supported QTL were uncovered and pointed towards a major role for cytochrome P450-mediated detoxification. Cis-regulatory variation for cytochrome P450s was observed, and in vitro cytochrome P450 experiments showed that pyflubumide was metabolized into a non-toxic derivate. A third QTL centered on cytochrome P450 reductase (CPR), which is required for cytochrome P450 activity, and is amplified in pyflubumide resistant populations. Our results indicate that pyflubumide resistance is mediated by cytochrome P450 detoxification that is enhanced by gene amplification at the CPR locus.
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Affiliation(s)
- Seyedeh Masoumeh Fotoukkiaii
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Nicky Wybouw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Terrestrial Ecology Unit, Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Andre H. Kurlovs
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Dimitra Tsakireli
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Heraklion, Crete, Greece
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | | | - Richard M. Clark
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States of America
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Heraklion, Crete, Greece
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- * E-mail:
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26
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Chandramohan R, Kakkar N, Roy A, Parsons DW. reconCNV: interactive visualization of copy number data from high-throughput sequencing. Bioinformatics 2021; 37:1164-1167. [PMID: 32821910 DOI: 10.1093/bioinformatics/btaa746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/21/2020] [Accepted: 08/17/2020] [Indexed: 12/30/2022] Open
Abstract
SUMMARY Copy number variation (CNV) is an important category of unbalanced structural rearrangement. While methods for detecting CNV in high-throughput targeted sequencing have become increasingly sophisticated, dedicated tools for interactive and dynamic visualization of CNV from these data are still lacking. We describe reconCNV, a tool that produces an interactive and annotated web-based dashboard for viewing and summarizing CNVs detected in next-generation sequencing (NGS) data. reconCNV is designed to work with delimited result files from most NGS CNV callers with minor adjustments to the configuration file. The reconCNV output is an HTML file that is viewable on any modern web browser, requires no backend server, and can be readily appended to existing analysis pipelines. In addition to a standard CNV track for visualizing relative fold change and absolute copy number, the tool includes an auxiliary variant allele fraction track for visualizing underlying allelic imbalance and loss of heterozygosity. A feature to mask assay-specific technical artifacts and a direct HTML link out to the UCSC Genome Browser are also included to augment the reviewer experience. By providing a light-weight plugin for interactive visualization to existing NGS CNV pipelines, reconCNV can facilitate efficient NGS CNV visualization and interpretation in both research and clinical settings. AVAILABILITY AND IMPLEMENTATION The source code and documentation including a tutorial can be accessed at https://github.com/rghu/reconCNV as well as a Docker image at https://hub.docker.com/repository/docker/raghuc1990/reconcnv. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Nipun Kakkar
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Angshumoy Roy
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - D Williams Parsons
- Department of Molecular and Human Genetics, Houston, TX 77030, USA
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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27
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Nandolo W, Mészáros G, Wurzinger M, Banda LJ, Gondwe TN, Mulindwa HA, Nakimbugwe HN, Clark EL, Woodward-Greene MJ, Liu M, Liu GE, Van Tassell CP, Rosen BD, Sölkner J. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics 2021; 22:398. [PMID: 34051743 PMCID: PMC8164248 DOI: 10.1186/s12864-021-07703-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8677 duplications) were identified, corresponding to an overall average of 1393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07703-1.
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Affiliation(s)
- Wilson Nandolo
- University of Natural Resources and Life Sciences, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria Wurzinger
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Liveness J Banda
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK
| | - M Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.,National Agricultural Library, USDA-ARS, Beltsville, MD, USA
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
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28
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Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Mol Ecol 2021; 30:2710-2723. [PMID: 33955064 DOI: 10.1111/mec.15936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023]
Abstract
A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.
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Affiliation(s)
- Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Alexander Suh
- School of Biological Sciences - Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Inês Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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29
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Huang X, Ruan G, Sun P. Estrogen-related receptor alpha copy number variation is associated with ovarian cancer histological grade. J Obstet Gynaecol Res 2021; 47:1878-1883. [PMID: 33751740 DOI: 10.1111/jog.14741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/27/2021] [Accepted: 02/20/2021] [Indexed: 11/27/2022]
Abstract
AIM Copy number variations (CNVs) are related to the genetic and phenotypic diversity of cancers and identifying genetic alterations could improve treatment strategies. Here, we used The Cancer Genome Atlas (TCGA) to explore associations between estrogen-related receptor alpha (ESRRA) CNVs and histological grade in patients with ovarian cancer (OC). METHODS Gene expression data and clinical information of 620 OC patients were obtained from The Cancer Genome Atlas)TCGA and associations between ESRRA CNVs and clinical characteristics were evaluated. Multivariate logistic regression analyses to obtain odds ratios (ORs) using a 95% confidence interval (CI) were performed, adjusting for race, age, histological grade, and tumor size. RESULTS ESRRA CNVs were associated with histological grade (OR 0.6235 [95% CI, 0.3593-0.8877]; p < 0.05) and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) CNVs (OR -0.6298 [95% CI, -0.9011 to -0.3585]; p < 0.05). In multivariate analyses, ESRRA CNVs remained significantly associated with histological grade (OR 0.6492 [95% CI, 0.3549-0.9435]; p < 0.05) and PPARGC1A CNVs (OR -0.6236 [95% CI, -0.9269 to 0.3203]; p < 0.05). CONCLUSION There was a significant association between ESRRA CNVs in patients with OC and histological grade of the cancer.
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Affiliation(s)
- Xiqi Huang
- Laboratory of Gynecologic Oncology, Fujian Provincial Maternity and Children's Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Guanyu Ruan
- Laboratory of Gynecologic Oncology, Fujian Provincial Maternity and Children's Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Key Laboratory of Women and Children's Critical Diseases Research, Fujian Provincial Maternity and Children's Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Pengming Sun
- Laboratory of Gynecologic Oncology, Fujian Provincial Maternity and Children's Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Key Laboratory of Women and Children's Critical Diseases Research, Fujian Provincial Maternity and Children's Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
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30
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Vasilyev SA, Skryabin NA, Kashevarova AA, Tolmacheva EN, Savchenko RR, Vasilyeva OY, Lopatkina ME, Zarubin AA, Fishman VS, Belyaeva EO, Filippova MO, Shorina AR, Maslennikov AB, Shestovskikh OL, Gayner TA, Čulić V, Vulić R, Nazarenko LP, Lebedev IN. Differential DNA Methylation of the IMMP2L Gene in Families with Maternally Inherited 7q31.1 Microdeletions is Associated with Intellectual Disability and Developmental Delay. Cytogenet Genome Res 2021; 161:105-119. [PMID: 33849037 DOI: 10.1159/000514491] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/18/2021] [Indexed: 11/19/2022] Open
Abstract
Most copy number variations (CNVs) in the human genome display incomplete penetrance with unknown underlying mechanisms. One such mechanism may be epigenetic modification, particularly DNA methylation. The IMMP2L gene is located in a critical region for autism susceptibility on chromosome 7q (AUTS1). The level of DNA methylation was assessed by bisulfite sequencing of 87 CpG sites in the IMMP2L gene in 3 families with maternally inherited 7q31.1 microdeletions affecting the IMMP2L gene alone. Bisulfite sequencing revealed comparable levels of DNA methylation in the probands, healthy siblings without microdeletions, and their fathers. In contrast, a reduced DNA methylation index and increased IMMP2L expression were observed in lymphocytes from the healthy mothers compared with the probands. A number of genes were upregulated in the healthy mothers compared to controls and downregulated in probands compared to mothers. These genes were enriched in components of the ribosome and electron transport chain, as well as oxidative phosphorylation and various degenerative conditions. Differential expression in probands and mothers with IMMP2L deletions relative to controls may be due to compensatory processes in healthy mothers with IMMP2L deletions and disturbances of these processes in probands with intellectual disability. The results suggest a possible partial compensation for IMMP2L gene haploinsufficiency in healthy mothers with the 7q31.1 microdeletion by reducing the DNA methylation level. Differential DNA methylation of intragenic CpG sites may affect the phenotypic manifestation of CNVs and explain the incomplete penetrance of chromosomal microdeletions.
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Affiliation(s)
- Stanislav A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Nikolay A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Renata R Savchenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Maria E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Alexei A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Veniamin S Fishman
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russian Federation
| | - Elena O Belyaeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Miroslava O Filippova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Asia R Shorina
- Novosibirsk City Clinical Hospital, Novosibirsk, Russian Federation
| | | | | | - Tatyana A Gayner
- Group of Companies "Center of New Medical Technologies,", Novosibirsk, Russian Federation.,Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russian Federation
| | - Vida Čulić
- Gynecology and Obstetrics Private Outpatient Clinic, Split, Croatia
| | - Robert Vulić
- Gynecology and Obstetrics Private Outpatient Clinic, Split, Croatia
| | - Lyudmila P Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
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31
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Copy number variation: Characteristics, evolutionary and pathological aspects. Biomed J 2021; 44:548-559. [PMID: 34649833 PMCID: PMC8640565 DOI: 10.1016/j.bj.2021.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) were the subject of extensive research in the past years. They are common features of the human genome that play an important role in evolution, contribute to population diversity, development of certain diseases, and influence host–microbiome interactions. CNVs have found application in the molecular diagnosis of many diseases and in non-invasive prenatal care, but their full potential is only emerging. CNVs are expected to have a tremendous impact on screening, diagnosis, prognosis, and monitoring of several disorders, including cancer and cardiovascular disease. Here, we comprehensively review basic definitions of the term CNV, outline mechanisms and factors involved in CNV formation, and discuss their evolutionary and pathological aspects. We suggest a need for better defined distinguishing criteria and boundaries between known types of CNVs.
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32
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Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
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33
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Binversie EE, Baker LA, Engelman CD, Hao Z, Moran JJ, Piazza AM, Sample SJ, Muir P. Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture. PLoS One 2020; 15:e0244075. [PMID: 33382735 PMCID: PMC7774950 DOI: 10.1371/journal.pone.0244075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Anterior cruciate ligament (ACL) rupture is an important condition of the human knee. Second ruptures are common and societal costs are substantial. Canine cranial cruciate ligament (CCL) rupture closely models the human disease. CCL rupture is common in the Labrador Retriever (5.79% prevalence), ~100-fold more prevalent than in humans. Labrador Retriever CCL rupture is a polygenic complex disease, based on genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers. Dissection of genetic variation in complex traits can be enhanced by studying structural variation, including copy number variants (CNVs). Dogs are an ideal model for CNV research because of reduced genetic variability within breeds and extensive phenotypic diversity across breeds. We studied the genetic etiology of CCL rupture by association analysis of CNV regions (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were called from SNPs using three different programs (PennCNV, CNVPartition, and QuantiSNP). After quality control, CNV calls were combined to create CNVRs using ParseCNV and an association analysis was performed. We found no strong effect CNVRs but found 46 small effect (max(T) permutation P<0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were deletions and 21 were duplications. Of the 46 CCL rupture associated CNVRs, we identified 39 unique regions. Thirty four were identified by a single calling algorithm, 3 were identified by two calling algorithms, and 2 were identified by all three algorithms. For 42 of the associated CNVRs, frequency in the population was <10% while 4 occurred at a frequency in the population ranging from 10–25%. Average CNVR length was 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were associated with case status. CNVRs did not overlap previous canine CCL rupture risk loci identified by GWAS. Associated CNVRs contained 152 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using pathway analysis, a cluster of 19 homeobox domain transcript regulator genes was associated with CCL rupture (P = 6.6E-13). This gene cluster influences cranial-caudal body pattern formation during embryonic limb development. Clustered genes were found in 3 CNVRs on chromosome 14 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion CNVRs, the association was strengthened (P = 8.7E-16). This study suggests a component of the polygenic risk of CCL rupture in Labrador Retrievers is associated with small effect CNVs and may include aspects of stifle morphology regulated by homeobox domain transcript regulator genes.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lauren A. Baker
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Corinne D. Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zhengling Hao
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John J. Moran
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander M. Piazza
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susannah J. Sample
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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34
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Cheng YH, Liu CFJ, Yu YH, Jhou YT, Fujishima M, Tsai IJ, Leu JY. Genome plasticity in Paramecium bursaria revealed by population genomics. BMC Biol 2020; 18:180. [PMID: 33250052 PMCID: PMC7702705 DOI: 10.1186/s12915-020-00912-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. Results We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. Conclusions We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments. Supplementary information The online version contains supplementary material available at 10.1186/s12915-020-00912-2.
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Affiliation(s)
- Yu-Hsuan Cheng
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Chien-Fu Jeff Liu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yen-Hsin Yu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Masahiro Fujishima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan
| | - Isheng Jason Tsai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan. .,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
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35
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Bhatia S, Egri-Nagy A, Serdoz S, Praeger CE, Gebhardt V, Francis A. A Path-Deformation Framework for Determining Weighted Genome Rearrangement Distance. Front Genet 2020; 11:1035. [PMID: 33193592 PMCID: PMC7542183 DOI: 10.3389/fgene.2020.01035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022] Open
Abstract
Measuring the distance between two bacterial genomes under the inversion process is usually done by assuming all inversions to occur with equal probability. Recently, an approach to calculating inversion distance using group theory was introduced, and is effective for the model in which only very short inversions occur. In this paper, we show how to use the group-theoretic framework to establish minimal distance for any weighting on the set of inversions, generalizing previous approaches. To do this we use the theory of rewriting systems for groups, and exploit the Knuth–Bendix algorithm, the first time this theory has been introduced into genome rearrangement problems. The central idea of the approach is to use existing group theoretic methods to find an initial path between two genomes in genome space (for instance using only short inversions), and then to deform this path to optimality using a confluent system of rewriting rules generated by the Knuth–Bendix algorithm.
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Affiliation(s)
- Sangeeta Bhatia
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia
| | - Attila Egri-Nagy
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia
| | - Stuart Serdoz
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia
| | - Cheryl E Praeger
- School of Physics, Mathematics, and Computing, University of Western Australia, Perth, WA, Australia
| | - Volker Gebhardt
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia
| | - Andrew Francis
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia
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36
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Das S, Choubey S. Tunability enhancement of gene regulatory motifs through competition for regulatory protein resources. Phys Rev E 2020; 102:052410. [PMID: 33327198 DOI: 10.1103/physreve.102.052410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/12/2020] [Indexed: 11/07/2022]
Abstract
Gene regulatory networks (GRNs) orchestrate the spatiotemporal levels of gene expression, thereby regulating various cellular functions ranging from embryonic development to tissue homeostasis. Some patterns called "motifs" recurrently appear in the GRNs. Owing to the prevalence of these motifs they have been subjected to much investigation, both in the context of understanding cellular decision making and engineering synthetic circuits. Mounting experimental evidence suggests that (1) the copy number of genes associated with these motifs varies, and (2) proteins produced from these genes bind to decoy binding sites on the genome as well as promoters driving the expression of other genes. Together, these two processes engender competition for protein resources within a cell. To unravel how competition for protein resources affects the dynamical properties of regulatory motifs, we propose a simple kinetic model that explicitly incorporates copy number variation (CNV) of genes and decoy binding of proteins. Using quasi-steady-state approximations, we theoretically investigate the transient and steady-state properties of three of the commonly found motifs: Autoregulation, toggle switch, and repressilator. While protein resource competition alters the timescales to reach the steady state for all these motifs, the dynamical properties of the toggle switch and repressilator are affected in multiple ways. For toggle switch, the basins of attraction of the known attractors are dramatically altered if one set of proteins binds to decoys more frequently than the other, an effect which gets suppressed as the copy number of the toggle switch is enhanced. For repressilators, protein sharing leads to an emergence of oscillation in regions of parameter space that were previously nonoscillatory. Intriguingly, both the amplitude and frequency of oscillation are altered in a nonlinear manner through the interplay of CNV and decoy binding. Overall, competition for protein resources within a cell provides an additional layer of regulation of gene regulatory motifs.
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Affiliation(s)
- Swetamber Das
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden, Germany
| | - Sandeep Choubey
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden, Germany
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37
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Oneda B, Sirleto P, Baldinger R, Taralczak M, Joset P, Zweier M, Niedrist D, Azzarello-Burri S, Britschgi C, Breymann C, Ochsenbein-Kölble N, Burkhardt T, Wisser J, Zimmermann R, Steindl K, Rauch A. Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing. Eur J Obstet Gynecol Reprod Biol 2020; 252:19-29. [PMID: 32619881 DOI: 10.1016/j.ejogrb.2020.05.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT. STUDY DESIGN We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up. RESULTS A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality. CONCLUSION When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Christian Britschgi
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | | | - Nicole Ochsenbein-Kölble
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Josef Wisser
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Roland Zimmermann
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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38
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Mountford HS, Bishop DVM, Thompson PA, Simpson NH, Newbury DF. Copy number variation burden does not predict severity of neurodevelopmental phenotype in children with a sex chromosome trisomy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:256-266. [PMID: 32452638 DOI: 10.1002/ajmg.c.31791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022]
Abstract
Sex chromosome trisomies (SCTs) (XXX, XXY, and XYY karyotypes) are associated with an elevated risk of neurodevelopmental disorders. The range of severity of the phenotype is substantial. We considered whether this variable outcome was related to the presence of copy number variants (CNVs)-stretches of duplicated or deleted DNA. A sample of 125 children with an SCT were compared with 181 children of normal karyotype who had been given the same assessments. First, we compared the groups on measures of overall CNV burden: number of CNVs, total span of CNVs, and likely functional impact (probability of loss-of-function intolerance, pLI, summed over CNVs). Differences between groups were small relative to within-group variance and not statistically significant on overall test. Next, we considered whether a measure of general neurodevelopmental impairment was predicted by pLI summed score, SCT versus comparison group, or the interaction between them. There was a substantial effect of SCT/comparison status but the pLI score was not predictive of outcomes in either group. We conclude that variable presence of CNVs is not a likely explanation for the wide phenotypic variation in children with SCTs. We discuss methodological challenges of testing whether CNVs are implicated in causing neurodevelopmental problems.
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Affiliation(s)
- Hayley S Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
| | - Dorothy V M Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Paul A Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Nuala H Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
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39
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Goshu HA, Xiaoyun W, Chu M, Pengjia B, Xue Zhi D, Yan P. Novel copy number variations of the CHRM3 gene associated with gene expression and growth traits in Chinese Datong yak (Bos grunniens). JOURNAL OF APPLIED ANIMAL RESEARCH 2020. [DOI: 10.1080/09712119.2020.1753750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Habtamu Abera Goshu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
- Oromia Agricultural Research Institute, Bako Agricultural Research Center, Bako, Ethiopia
| | - Wu Xiaoyun
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Bao Pengjia
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Ding Xue Zhi
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
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40
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Falque M, Jebreen K, Paux E, Knaak C, Mezmouk S, Martin OC. CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data. Genetics 2020; 214:561-576. [PMID: 31882400 PMCID: PMC7054022 DOI: 10.1534/genetics.119.302881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are used widely for detecting quantitative trait loci, or for searching for causal variants of diseases. Nevertheless, structural variations such as copy-number variants (CNVs) represent a large part of natural genetic diversity, and contribute significantly to trait variation. Numerous methods and softwares based on different technologies (amplicons, CGH, tiling, or SNP arrays, or sequencing) have already been developed to detect CNVs, but they bypass a wealth of information such as genotyping data from segregating populations, produced, e.g., for QTL mapping. Here, we propose an original method to both detect and genetically map CNVs using mapping panels. Specifically, we exploit the apparent heterozygous state of duplicated loci: peaks in appropriately defined genome-wide allelic profiles provide highly specific signatures that identify the nature and position of the CNVs. Our original method and software can detect and map automatically up to 33 different predefined types of CNVs based on segregation data only. We validate this approach on simulated and experimental biparental mapping panels in two maize populations and one wheat population. Most of the events found correspond to having just one extra copy in one of the parental lines, but the corresponding allelic value can be that of either parent. We also find cases with two or more additional copies, especially in wheat, where these copies locate to homeologues. More generally, our computational tool can be used to give additional value, at no cost, to many datasets produced over the past decade from genetic mapping panels.
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Affiliation(s)
- Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Kamel Jebreen
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
- Department of Mathematics, An-Najah National University, Nablus, Palestine
| | - Etienne Paux
- Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France
| | | | | | - Olivier C Martin
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Review of Preferential Suspicious Genes in Microtia Patients Through Various Approaches. J Craniofac Surg 2020; 31:538-541. [PMID: 31977690 DOI: 10.1097/scs.0000000000006244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recently, an increasing trend of the birth prevalence of anotia/microtia is observed in China, contributed by changes of social environment and lifestyle. There seems to be no major breakthroughs in exact pathogenesis of microtia, though the research results related to molecular genetics unceasingly appear. In this review, the authors focus on the results of various research methods which the authors regard as the preferential suspicious gene pool to facilitate the exploration of the pathogenic genes of microtia, knowing that the mechanism of microtia is very complicated. The advantages and limitations of these various approaches will also be systematically delineated. The authors believe that this review will give a deep insight in the genetic research of microtia and help plastic surgeons manage congenital microtia more effectively.
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Liu G, Ruan G, Huang M, Chen L, Sun P. Genome-wide DNA copy number profiling and bioinformatics analysis of ovarian cancer reveals key genes and pathways associated with distinct invasive/migratory capabilities. Aging (Albany NY) 2020; 12:178-192. [PMID: 31895688 PMCID: PMC6977652 DOI: 10.18632/aging.102608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
Ovarian cancer (OC) metastasis presents major hurdles that must be overcome to improve patient outcomes. Recent studies have demonstrated copy number variations (CNVs) frequently contribute to alterations in oncogenic drivers. The present study used a CytoScan HD Array to analyse CNVs and loss of heterozygosity (LOH) in the entire genomes of 6 OC patients and human OC cell lines to determine the genetic target events leading to the distinct invasive/migratory capacities of OC. The results showed that LOH at Xq11.1 and Xp21.1 and gains at 8q21.13 were novel, specific CNVs. Ovarian cancer-related CNVs were then screened by bioinformatics analysis. In addition, transcription factors-target gene interactions were predicted with information from PASTAA analysis. As a result, six genes (i.e., GAB2, AKT1, EGFR, COL6A3, UGT1A1 and UGT1A8) were identified as strong candidates by integrating the above data with gene expression and clinical outcome data. In the transcriptional regulatory network, 4 known cancer-related transcription factors (TFs) interacted with 6 CNV-driven genes. The protein/DNA arrays revealed 3 of these 4 TFs as potential candidate gene-related transcription factors in OC. We then demonstrated that these six genes can serve as potential biomarkers for OC. Further studies are required to elucidate the pathogenesis of OC.
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Affiliation(s)
- GuiFen Liu
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - GuanYu Ruan
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - MeiMei Huang
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - LiLi Chen
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
| | - PengMing Sun
- Laboratory of Gynaecologic Oncology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China.,Department of Gynaecology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, China
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Selvaraju V, Venkatapoorna CMK, Babu JR, Geetha T. Salivary Amylase Gene Copy Number Is Associated with the Obesity and Inflammatory Markers in Children. Diabetes Metab Syndr Obes 2020; 13:1695-1701. [PMID: 32547131 PMCID: PMC7245430 DOI: 10.2147/dmso.s251359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/29/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We have recently shown that the copy number of salivary amylase (AMY1) gene was significantly decreased, and the obesity-related salivary biomarkers resistin, MCP-1, TNF-α, IL-6, and CRP were significantly increased in overweight/obese children compared to normal weight. This study aimed to evaluate the association of AMY1 copy number variant (CNV) with obesity and inflammatory markers. Seventy-six participants aged between 6 and 10 years have participated, and the saliva samples were collected along with the anthropometric measurements. METHODS AMY1 copy number was analyzed by 3D digital PCR, and obesity-related biomarkers were performed with a Bioplex multiplex analyzer. RESULTS The mean AMY1 copy number was higher in normal weight (7.90 ± 0.38) compared to the overweight/obese group (6.20 ± 0.29). The association of AMY1 CNV with obesity and inflammatory markers showed significant negative correlation [CRP, β = -0.238 (p < 0.05); resistin, β = -0.25 (p < 0.05); MCP-1, β = -0.304 (p < 0.01)] except for complement factor D, TNF α and IL-6. The anti-inflammatory cytokine, IL-10 reported a positive correlation with AMY1 copy number with a β = 0.268 (p < 0.05). The multivariable model adjusted with age and gender depicted a similar correlation with obesity markers. CONCLUSION Our results report that AMY1 CNV is associated with obesity and inflammatory biomarkers in children's saliva sample.
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Affiliation(s)
- Vaithinathan Selvaraju
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
| | | | - Jeganathan R Babu
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL, USA
| | - Thangiah Geetha
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL, USA
- Correspondence: Thangiah Geetha Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA Tel +1 334 844 7418Fax +1 334 844 3268 Email
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Abstract
Copy number variants (CNVs) refer to the loss or gain of copies of a genomic DNA region. While some CNVs may play a role in species evolution by enriching the diversity of an organism, CNVs may also be linked to certain diseases such as neurological disorders, early onset obesity, and cancer. CNVs may affect gene expression by direct overlap of the genic region or by an indirect effect where the CNV is located outside the gene location. These indirect CNV regions may contain regulatory elements such as transcription enhancers or repressors as well as regulators such as miRNAs which may work at the level of transcription or translation. Danio rerio (zebrafish) is an excellent model organism for CNV studies. Zebrafish genomes contain a large amount of variation with 14.6% of the zebrafish reference genome found to be copy number variable. This level of variation is more than four times the percentage of reference genome sequence covered by similarly common CNVs in humans. It is this high level of variation that makes zebrafish interesting to investigate the effects of CNV on gene expression. Additionally, zebrafish share 70% of genetic similarities with humans, and 84% of genes associated with human disease are also found in zebrafish. Expressive quantitative trait loci (eQTL) analysis may be used in zebrafish to explore how CNVs may affect gene expression in both a direct and indirect manner. eQTL analysis may be performed for cis associations with a 1-Mb (megabase) window upstream and downstream from the transcription probe midpoint to CGH midpoint. Trans associations (variants that are located beyond the 1-Mb window of the gene either on the same chromosome as the gene or on a different chromosome) may be investigated as well through eQTL analysis; however, trans associations require more tests to be performed than cis associations, which limits power to detect associations. Pairwise associations between each pair of copy number variant and gene will be investigated separately from the same individual using Spearman rank correlations with significant associations found being followed with a multi-test correction technique to assess significance of those CNV gene expression associations. An association between a CNV to a gene expression phenotype should be considered significant only if the p value from the analysis of the observed data is lower than the 0.001 tail threshold from a distribution of the minimal p values (which are found from all comparisons for a given gene from 10,000 permutations of the expression phenotypes). Associations between CNVs and genes may be found to be direct or indirect as well as positive (increased copy number-increased expression) or negative (increased copy number-decreased expression, decreased copy number-increased expression). Ongoing analyses with these associations will investigate the impact of CNVs on gene functionality including immune function and potential disease susceptibility.
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Sun T, Hanif Q, Chen H, Lei C, Dang R. Copy Number Variations of Four Y-Linked Genes in Swamp Buffaloes. Animals (Basel) 2019; 10:ani10010031. [PMID: 31877875 PMCID: PMC7023270 DOI: 10.3390/ani10010031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/18/2019] [Indexed: 12/25/2022] Open
Abstract
Simple Summary The amplification of the male-specific region of the Y chromosome was a unique phenomenon during mammalian sex chromosome evolution. The Y-linked copy number variations of many species have been confirmed. However, the Y-linked copy number variations (CNVs) in water buffalo are still unknown. In this study, we investigated the copy number variations of four Y-linked genes (SRY, UTY, DBY, and OFD1Y) in buffalo. Our results showed that UTY was a single-copy gene in buffalo, while DBY, OFD1Y, and SRY exhibited copy number variations in buffalo. Abstract Copy number variation (CNV), a significant source of genetic diversity in the mammalian Y chromosome, is associated with the development of many complex phenotypes, such as spermatogenesis and male fertility. The contribution of Y-linked CNVs has been studied in various species, however, water buffalo has not been explored in this area and the genetic information still remains unknown. The aim of the current study was to investigate the CNVs of four Y-linked genes, including, sex determining Region of Y-Chromosome (SRY), ubiquitously transcribed tetratricopeptide repeat gene protein on the chromosome Y (UTY), DEAD-box helicase 3 Y-linked (DDX3Y, also known as DBY), and oral-facial-digital syndrome 1 Y-linked (OFD1Y) in 254 swamp buffaloes from 15 populations distributed across China, Vietnam, and Laos using quantitative real-time PCR (qPCR). Our results revealed the prevalence of a single-copy UTY gene in buffaloes. The DBY and OFD1Y represented CNVs among and within different buffalo breeds. The SRY showed CNVs only in Vietnamese and Laotian buffaloes. In conclusion, this study indicated that DBY, OFD1Y, and SRY showed CNVs, while the UTY was a single-copy gene in swamp buffaloes.
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Affiliation(s)
- Ting Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad 577, Pakistan
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
- Correspondence: ; Tel.: +86-153-8862-7637
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Oliynyk RT. Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective. Int J Mol Sci 2019; 20:E5013. [PMID: 31658652 PMCID: PMC6834143 DOI: 10.3390/ijms20205013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
With the accumulation of scientific knowledge of the genetic causes of common diseases and continuous advancement of gene-editing technologies, gene therapies to prevent polygenic diseases may soon become possible. This study endeavored to assess population genetics consequences of such therapies. Computer simulations were used to evaluate the heterogeneity in causal alleles for polygenic diseases that could exist among geographically distinct populations. The results show that although heterogeneity would not be easily detectable by epidemiological studies following population admixture, even significant heterogeneity would not impede the outcomes of preventive gene therapies. Preventive gene therapies designed to correct causal alleles to a naturally-occurring neutral state of nucleotides would lower the prevalence of polygenic early- to middle-age-onset diseases in proportion to the decreased population relative risk attributable to the edited alleles. The outcome would manifest differently for late-onset diseases, for which the therapies would result in a delayed disease onset and decreased lifetime risk; however, the lifetime risk would increase again with prolonging population life expectancy, which is a likely consequence of such therapies. If the preventive heritable gene therapies were to be applied on a large scale, the decreasing frequency of risk alleles in populations would reduce the disease risk or delay the age of onset, even with a fraction of the population receiving such therapies. With ongoing population admixture, all groups would benefit over generations.
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Affiliation(s)
- Roman Teo Oliynyk
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand.
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand.
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Ma YL, Wen YF, Cao XK, Cheng J, Huang YZ, Ma Y, Hu LY, Lei CZ, Qi XL, Cao H, Chen H. Copy number variation (CNV) in the IGF1R gene across four cattle breeds and its association with economic traits. Arch Anim Breed 2019; 62:171-179. [PMID: 31807627 PMCID: PMC6852844 DOI: 10.5194/aab-62-171-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
The insulin-like growth factor 1 receptor (IGF1R) plays a vital role in
immunomodulation and muscle and bone growth. The copy number variation (CNV) is
believed to the reason for many complex phenotypic variations. In
this paper, we statistically analyzed the copy number and the expression
profiling in different tissue types of the IGF1R gene using the
422 samples from four Chinese beef cattle breeds, and the mRNA of
IGF1R was widely expressed in nine tissue types of adult cattle (heart,
liver, kidney, muscle, fat, stomach, spleen, lung and testis). Results of CNV and growth traits indicated that the IGF1R CNV
was significantly associated with body weight and body height of Jinnan (JN)
cattle and was significantly associated with body height and hucklebone width
of Qinchuan (QC) cattle, making IGF1R CNV a promising molecular
marker to improve meat production in beef cattle breeding. Bioinformatics
predictions show that the CNV region is highly similar to the human genome,
and there are a large number of transcription factors, DNase I hypersensitive
sites, and high levels of histone acetylation, suggesting that this region may
play a role in transcriptional regulation, providing directions for further
study of the role of bovine CNV and economic traits.
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Affiliation(s)
- Yi-Lei Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Yi-Fan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Xiu-Kai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Jie Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, 464000, P. R. China
| | - Lin-Yong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810001, P. R. China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan, 463700, P. R. China
| | - Hui Cao
- Shaanxi Kingbull Animal Husbandry Co. Ltd., Yangling, Shaanxi, 712100, P. R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, P. R. China
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Ahmed P H, V V, More RP, Viswanath B, Jain S, Rao MS, Mukherjee O. INDEX-db: The Indian Exome Reference Database (Phase I). J Comput Biol 2019; 26:225-234. [PMID: 30615482 PMCID: PMC6441288 DOI: 10.1089/cmb.2018.0199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Deep sequencing-based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. Confirming how these identified variants contribute to specific disease conditions, across human populations, poses the next challenge. Differential selection pressure may impact the frequency of genetic variations, and thus detection of association with disease conditions, across populations. To understand genotype to phenotype correlations, it thus becomes important to first understand the spectrum of genetic variation within a population by creating a reference map. In this study, we report the development of phase I of a new database of genetic variations called INDian EXome database (INDEX-db), from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanisms at clinical, genetic, and cellular levels.
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Affiliation(s)
- Husayn Ahmed P
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
| | - Vidhya V
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Ravi Prabhakar More
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Mahendra S. Rao
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Odity Mukherjee
- Address correspondence to: Dr. Odity Mukherjee, Investigator & Chief Technologist, Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bellary Road, Bengaluru–560065, Karnataka, India
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Goshu HA, Chu M, Xiaoyun W, Pengjia B, Zhi DX, Yan P. Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds. Mol Genet Genomics 2019; 294:549-561. [DOI: 10.1007/s00438-018-01530-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/29/2018] [Indexed: 12/22/2022]
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Khan M, Fadaie Z, Cornelis SS, Cremers FPM, Roosing S. Identification and Analysis of Genes Associated with Inherited Retinal Diseases. Methods Mol Biol 2019; 1834:3-27. [PMID: 30324433 DOI: 10.1007/978-1-4939-8669-9_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inherited retinal diseases (IRDs) display a very high degree of clinical and genetic heterogeneity, which poses challenges in finding the underlying defects in known IRD-associated genes and in identifying novel IRD-associated genes. Knowledge on the molecular and clinical aspects of IRDs has increased tremendously in the last decade. Here, we outline the state-of-the-art techniques to find the causative genetic variants, with special attention for next-generation sequencing which can combine molecular diagnostics and retinal disease gene identification. An important aspect is the functional assessment of rare variants with RNA and protein effects which can only be predicted in silico. We therefore describe the in vitro assessment of putative splice defects in human embryonic kidney cells. In addition, we outline the use of stem cell technology to generate photoreceptor precursor cells from patients' somatic cells which can subsequently be used for RNA and protein studies. Finally, we outline the in silico methods to interpret the causality of variants associated with inherited retinal disease and the registry of these variants.
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Affiliation(s)
- Mubeen Khan
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zeinab Fadaie
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stéphanie S Cornelis
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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