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For: Ho SS, Urban AE, Mills RE. Structural variation in the sequencing era. Nat Rev Genet 2020;21:171-189. [PMID: 31729472 PMCID: PMC7402362 DOI: 10.1038/s41576-019-0180-9] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Hemstrom W, Grummer JA, Luikart G, Christie MR. Next-generation data filtering in the genomics era. Nat Rev Genet 2024;25:750-767. [PMID: 38877133 DOI: 10.1038/s41576-024-00738-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
2
Behera S, Belyeu JR, Chen X, Paulin LF, Nguyen NQH, Newman E, Mahmoud M, Menon VK, Qi Q, Joshi P, Marcovina S, Rossi M, Roller E, Han J, Onuchic V, Avery CL, Ballantyne CM, Rodriguez CJ, Kaplan RC, Muzny DM, Metcalf GA, Gibbs RA, Yu B, Boerwinkle E, Eberle MA, Sedlazeck FJ. Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk. BMC Med Genomics 2024;17:255. [PMID: 39449055 DOI: 10.1186/s12920-024-02024-0] [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: 05/24/2024] [Accepted: 10/07/2024] [Indexed: 10/26/2024]  Open
3
Trinh J, Schaake S, Gabbert C, Lüth T, Cowley SA, Fienemann A, Ullrich KK, Klein C, Seibler P. Optical genome mapping of structural variants in Parkinson's disease-related induced pluripotent stem cells. BMC Genomics 2024;25:980. [PMID: 39425080 PMCID: PMC11490025 DOI: 10.1186/s12864-024-10902-1] [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: 09/04/2024] [Accepted: 10/14/2024] [Indexed: 10/21/2024]  Open
4
Parmar JM, Laing NG, Kennerson ML, Ravenscroft G. Genetics of inherited peripheral neuropathies and the next frontier: looking backwards to progress forwards. J Neurol Neurosurg Psychiatry 2024;95:992-1001. [PMID: 38744462 PMCID: PMC11503175 DOI: 10.1136/jnnp-2024-333436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
5
Ma C, Shi X, Li X, Zhang YP, Peng MS. Comprehensive evaluation and guidance of structural variation detection tools in chicken whole genome sequence data. BMC Genomics 2024;25:970. [PMID: 39415108 PMCID: PMC11481438 DOI: 10.1186/s12864-024-10875-1] [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: 11/06/2023] [Accepted: 10/08/2024] [Indexed: 10/18/2024]  Open
6
Ferreira MR, Carratto TMT, Frontanilla TS, Bonadio RS, Jain M, de Oliveira SF, Castelli EC, Mendes-Junior CT. Advances in forensic genetics: Exploring the potential of long read sequencing. Forensic Sci Int Genet 2024;74:103156. [PMID: 39427416 DOI: 10.1016/j.fsigen.2024.103156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 10/04/2024] [Accepted: 10/06/2024] [Indexed: 10/22/2024]
7
Wu L, Yi W, Yao S, Xie S, Peng R, Zhang J, Tan W. mRNA-Based Cancer Vaccines: Advancements and Prospects. NANO LETTERS 2024. [PMID: 39375146 DOI: 10.1021/acs.nanolett.4c03296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
8
Dunn T, Zook JM, Holt JM, Narayanasamy S. Jointly benchmarking small and structural variant calls with vcfdist. Genome Biol 2024;25:253. [PMID: 39358801 PMCID: PMC11446017 DOI: 10.1186/s13059-024-03394-5] [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: 03/23/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024]  Open
9
Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol 2024;42:1571-1580. [PMID: 38168980 PMCID: PMC11217151 DOI: 10.1038/s41587-023-02024-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
10
Karageorgiou C, Gokcumen O, Dennis MY. Deciphering the role of structural variation in human evolution: a functional perspective. Curr Opin Genet Dev 2024;88:102240. [PMID: 39121701 PMCID: PMC11485010 DOI: 10.1016/j.gde.2024.102240] [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: 03/30/2024] [Revised: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]
11
Zhang Z, Zhang J, Kang L, Qiu X, Xu S, Xu J, Guo Y, Niu Z, Niu B, Bi A, Zhao X, Xu D, Wang J, Yin C, Lu F. Structural variation discovery in wheat using PacBio high-fidelity sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;120:687-698. [PMID: 39239888 DOI: 10.1111/tpj.17011] [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: 01/14/2024] [Revised: 08/09/2024] [Accepted: 08/22/2024] [Indexed: 09/07/2024]
12
Zheng Y, Shang X. FindCSV: a long-read based method for detecting complex structural variations. BMC Bioinformatics 2024;25:315. [PMID: 39342151 PMCID: PMC11439270 DOI: 10.1186/s12859-024-05937-w] [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: 03/24/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024]  Open
13
Rubio-Alarcón C, Stelloo E, Vessies DCL, Erve IV, Mekkes NJ, Swennenhuis J, Lakbir S, van Bree EJ, Tijssen M, Diemen PDV, Lanfermeijer M, Linders T, van den Broek D, Punt CJA, Heringa J, Meijer GA, Abeln S, Feitsma H, Fijneman RJA. High Prevalence of Chromosomal Rearrangements and LINE Retrotranspositions Detected in Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Tissue. J Mol Diagn 2024:S1525-1578(24)00206-X. [PMID: 39332629 DOI: 10.1016/j.jmoldx.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/04/2024] [Accepted: 08/23/2024] [Indexed: 09/29/2024]  Open
14
Su KJ, Qiu C, Greenbaum J, Zhang X, Liu A, Liu Y, Luo Z, Mungasavalli Gnanesh SS, Tian Q, Zhao LJ, Shen H, Deng HW. Genomic structural variations link multiple genes to bone mineral density in a multi-ethnic cohort study: Louisiana osteoporosis study. J Bone Miner Res 2024;39:1474-1485. [PMID: 39167757 PMCID: PMC11425707 DOI: 10.1093/jbmr/zjae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/11/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]
15
Mascher M, Jayakodi M, Shim H, Stein N. Promises and challenges of crop translational genomics. Nature 2024:10.1038/s41586-024-07713-5. [PMID: 39313530 DOI: 10.1038/s41586-024-07713-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/13/2024] [Indexed: 09/25/2024]
16
Vilkaite G, Vogel J, Mattsson-Carlgren N. Integrating amyloid and tau imaging with proteomics and genomics in Alzheimer's disease. Cell Rep Med 2024;5:101735. [PMID: 39293391 DOI: 10.1016/j.xcrm.2024.101735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/28/2024] [Accepted: 08/20/2024] [Indexed: 09/20/2024]
17
Boyanton BL, Zarate YA, Broadfoot BG, Kelly T, Crawford BD. NR3C2 microdeletions-an underrecognized cause of pseudohypoaldosteronism type 1A: a case report and literature review. Lab Med 2024;55:640-644. [PMID: 38493321 DOI: 10.1093/labmed/lmae005] [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] [Indexed: 03/18/2024]  Open
18
Köroğlu Ç, Chen P, Traurig M, Altok S, Bogardus C, Baier LJ. De Novo Genome Assemblies From Two Indigenous Americans from Arizona Identify New Polymorphisms in Non-Reference Sequences. Genome Biol Evol 2024;16:evae188. [PMID: 39190003 PMCID: PMC11384899 DOI: 10.1093/gbe/evae188] [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: 11/08/2023] [Revised: 05/17/2024] [Accepted: 08/22/2024] [Indexed: 08/28/2024]  Open
19
Engelbrecht E, Rodriguez OL, Watson CT. Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024;213:651-662. [PMID: 39007649 PMCID: PMC11333172 DOI: 10.4049/jimmunol.2400131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024]
20
Tang X, Berger MF, Solit DB. Precision oncology: current and future platforms for treatment selection. Trends Cancer 2024;10:781-791. [PMID: 39030146 DOI: 10.1016/j.trecan.2024.06.009] [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: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/21/2024]
21
Tsai CY, Hsu JSJ, Chen PL, Wu CC. Implementing next-generation sequencing for diagnosis and management of hereditary hearing impairment: a comprehensive review. Expert Rev Mol Diagn 2024;24:753-765. [PMID: 39194060 DOI: 10.1080/14737159.2024.2396866] [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: 06/14/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
22
Ren J, Gao Z, Lu Y, Li M, Hong J, Wu J, Wu D, Deng W, Xi D, Chong Y. Application of GWAS and mGWAS in Livestock and Poultry Breeding. Animals (Basel) 2024;14:2382. [PMID: 39199916 PMCID: PMC11350712 DOI: 10.3390/ani14162382] [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: 06/18/2024] [Revised: 08/04/2024] [Accepted: 08/15/2024] [Indexed: 09/01/2024]  Open
23
Nikjoo H, Rahmanian S, Taleei R. Modelling DNA damage-repair and beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024;190:1-18. [PMID: 38754703 DOI: 10.1016/j.pbiomolbio.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/27/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024]
24
Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, Schatz MC. Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Annu Rev Genomics Hum Genet 2024;25:77-104. [PMID: 38663087 PMCID: PMC11451085 DOI: 10.1146/annurev-genom-021623-081639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
25
Yuan N, Jia P. Comprehensive assessment of long-read sequencing platforms and calling algorithms for detection of copy number variation. Brief Bioinform 2024;25:bbae441. [PMID: 39256200 PMCID: PMC11387058 DOI: 10.1093/bib/bbae441] [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: 02/01/2024] [Revised: 07/09/2024] [Accepted: 08/25/2024] [Indexed: 09/12/2024]  Open
26
Sund KL, Liu J, Lee J, Garbe J, Abdelhamed Z, Maag C, Hallinan B, Wu SW, Sperry E, Deshpande A, Stottmann R, Smolarek TA, Dyer LM, Hestand MS. Long-read sequencing and optical genome mapping identify causative gene disruptions in noncoding sequence in two patients with neurologic disease and known chromosome abnormalities. Am J Med Genet A 2024:e63818. [PMID: 39041659 DOI: 10.1002/ajmg.a.63818] [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: 03/07/2024] [Revised: 06/12/2024] [Accepted: 07/07/2024] [Indexed: 07/24/2024]
27
Junjun R, Zhengqian Z, Ying W, Jialiang W, Yongzhuang L. A comprehensive review of deep learning-based variant calling methods. Brief Funct Genomics 2024;23:303-313. [PMID: 38366908 DOI: 10.1093/bfgp/elae003] [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: 12/01/2023] [Revised: 01/14/2024] [Accepted: 01/18/2023] [Indexed: 02/18/2024]  Open
28
Liu Z, Xie Z, Li M. Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data. Genome Biol 2024;25:188. [PMID: 39010145 PMCID: PMC11247875 DOI: 10.1186/s13059-024-03324-5] [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: 06/27/2023] [Accepted: 06/26/2024] [Indexed: 07/17/2024]  Open
29
Jia H, Tan S, Cai Y, Guo Y, Shen J, Zhang Y, Ma H, Zhang Q, Chen J, Qiao G, Ruan J, Zhang YE. Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes. Nat Commun 2024;15:5644. [PMID: 38969648 PMCID: PMC11226609 DOI: 10.1038/s41467-024-49992-6] [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: 11/01/2023] [Accepted: 06/20/2024] [Indexed: 07/07/2024]  Open
30
Qiao G, Xu P, Guo T, He X, Yue Y, Yang B. Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data. J Anim Breed Genet 2024;141:403-414. [PMID: 38247268 DOI: 10.1111/jbg.12846] [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: 11/08/2022] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
31
Shim Y, Koo YK, Shin S, Lee ST, Lee KA, Choi JR. Comparison of Optical Genome Mapping With Conventional Diagnostic Methods for Structural Variant Detection in Hematologic Malignancies. Ann Lab Med 2024;44:324-334. [PMID: 38433573 PMCID: PMC10961627 DOI: 10.3343/alm.2023.0339] [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: 08/31/2023] [Revised: 11/21/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024]  Open
32
Niu J, Wang W, Wang Z, Chen Z, Zhang X, Qin Z, Miao L, Yang Z, Xie C, Xin M, Peng H, Yao Y, Liu J, Ni Z, Sun Q, Guo W. Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing. Genome Biol 2024;25:171. [PMID: 38951917 PMCID: PMC11218387 DOI: 10.1186/s13059-024-03315-6] [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: 01/31/2024] [Accepted: 06/18/2024] [Indexed: 07/03/2024]  Open
33
Sun W, Xiong D, Ouyang J, Xiao X, Jiang Y, Wang Y, Li S, Xie Z, Wang J, Tang Z, Zhang Q. Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia. Nat Commun 2024;15:5048. [PMID: 38871723 DOI: 10.1038/s41467-024-49376-w] [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: 06/06/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024]  Open
34
Pan C, Reinert K. Leaf: an ultrafast filter for population-scale long-read SV detection. Genome Biol 2024;25:155. [PMID: 38872200 PMCID: PMC11170821 DOI: 10.1186/s13059-024-03297-5] [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: 11/28/2022] [Accepted: 06/04/2024] [Indexed: 06/15/2024]  Open
35
Knief U, Müller IA, Stryjewski KF, Metzler D, Sorenson MD, Wolf JBW. Evolution of Chromosomal Inversions across an Avian Radiation. Mol Biol Evol 2024;41:msae092. [PMID: 38743589 PMCID: PMC11152452 DOI: 10.1093/molbev/msae092] [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: 01/08/2024] [Revised: 04/05/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]  Open
36
Thomas M, Mackes N, Preuss-Dodhy A, Wieland T, Bundschus M. Assessing Privacy Vulnerabilities in Genetic Data Sets: Scoping Review. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2024;5:e54332. [PMID: 38935957 PMCID: PMC11165293 DOI: 10.2196/54332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 06/29/2024]
37
Schrauwen I, Rajendran Y, Acharya A, Öhman S, Arvio M, Paetau R, Siren A, Avela K, Granvik J, Leal SM, Määttä T, Kokkonen H, Järvelä I. Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci Rep 2024;14:11239. [PMID: 38755281 PMCID: PMC11099145 DOI: 10.1038/s41598-024-62009-y] [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: 01/04/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]  Open
38
Chen Q, Wu B, Li C, Ding L, Huang S, Wang J, Zhao J. Deciphering male influence in gynogenetic Pengze crucian carp (Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations. Front Genet 2024;15:1392110. [PMID: 38784042 PMCID: PMC11111978 DOI: 10.3389/fgene.2024.1392110] [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: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024]  Open
39
Yang X, Zheng G, Jia P, Wang S, Ye K. Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae008. [PMID: 38862430 PMCID: PMC11425056 DOI: 10.1093/gpbjnl/qzae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 06/13/2024]
40
Elfman J, Goins L, Heller T, Singh S, Wang YH, Li H. Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction. Nucleic Acids Res 2024;52:4409-4421. [PMID: 38587197 PMCID: PMC11077074 DOI: 10.1093/nar/gkae258] [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: 12/17/2022] [Accepted: 03/27/2024] [Indexed: 04/09/2024]  Open
41
Yang L, Yin H, Bai L, Yao W, Tao T, Zhao Q, Gao Y, Teng J, Xu Z, Lin Q, Diao S, Pan Z, Guan D, Li B, Zhou H, Zhou Z, Zhao F, Wang Q, Pan Y, Zhang Z, Li K, Fang L, Liu GE. Mapping and functional characterization of structural variation in 1060 pig genomes. Genome Biol 2024;25:116. [PMID: 38715020 PMCID: PMC11075355 DOI: 10.1186/s13059-024-03253-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 04/19/2024] [Indexed: 05/12/2024]  Open
42
Schloissnig S, Pani S, Rodriguez-Martin B, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, Asparuhova M, Hunt S, Rausch T, Marschall T, Korbel JO. Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590093. [PMID: 38659906 PMCID: PMC11042266 DOI: 10.1101/2024.04.18.590093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
43
Du ZZ, He JB, Jiao WB. A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biol 2024;25:91. [PMID: 38589937 PMCID: PMC11003132 DOI: 10.1186/s13059-024-03239-1] [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: 07/19/2023] [Accepted: 04/04/2024] [Indexed: 04/10/2024]  Open
44
Rivas-González I, Tung J. A multi-million-year natural experiment: Comparative genomics on a massive scale and its implications for human health. Evol Med Public Health 2024;12:67-70. [PMID: 38601345 PMCID: PMC11005778 DOI: 10.1093/emph/eoae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/18/2024] [Indexed: 04/12/2024]  Open
45
David G, Bertolotti A, Layer R, Scofield D, Hayward A, Baril T, Burnett HA, Gudmunds E, Jensen H, Husby A. Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations. Genome Biol Evol 2024;16:evae049. [PMID: 38489588 PMCID: PMC11018544 DOI: 10.1093/gbe/evae049] [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: 11/29/2022] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024]  Open
46
Hujoel MLA, Handsaker RE, Sherman MA, Kamitaki N, Barton AR, Mukamel RE, Terao C, McCarroll SA, Loh PR. Protein-altering variants at copy number-variable regions influence diverse human phenotypes. Nat Genet 2024;56:569-578. [PMID: 38548989 PMCID: PMC11018521 DOI: 10.1038/s41588-024-01684-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: 06/23/2023] [Accepted: 02/08/2024] [Indexed: 04/09/2024]
47
Li X, Liu Q, Fu C, Li M, Li C, Li X, Zhao S, Zheng Z. Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption. J Genet Genomics 2024;51:394-406. [PMID: 38056526 DOI: 10.1016/j.jgg.2023.11.005] [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: 07/14/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
48
Wang S, Lin J, Jia P, Xu T, Li X, Liu Y, Xu D, Bush SJ, Meng D, Ye K. De novo and somatic structural variant discovery with SVision-pro. Nat Biotechnol 2024:10.1038/s41587-024-02190-7. [PMID: 38519720 DOI: 10.1038/s41587-024-02190-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
49
Lesack KJ, Wasmuth JD. The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data. PeerJ 2024;12:e17101. [PMID: 38500526 PMCID: PMC10946394 DOI: 10.7717/peerj.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024]  Open
50
Helal AA, Saad BT, Saad MT, Mosaad GS, Aboshanab KM. Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data. Sci Rep 2024;14:6160. [PMID: 38486064 PMCID: PMC10940726 DOI: 10.1038/s41598-024-56604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024]  Open
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