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For: Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. ACTA ACUST UNITED AC 2014;30:2843-51. [PMID: 24974202 DOI: 10.1093/bioinformatics/btu356] [Citation(s) in RCA: 576] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Number Cited by Other Article(s)
101
Zhao Y, Yang Z, Zhang Z, Yin M, Chu S, Tong Z, Qin Y, Zha L, Fang Q, Yuan Y, Huang L, Peng H. The first chromosome-level Fallopia multiflora genome assembly provides insights into stilbene biosynthesis. HORTICULTURE RESEARCH 2023;10:uhad047. [PMID: 37213683 PMCID: PMC10194901 DOI: 10.1093/hr/uhad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/07/2023] [Indexed: 05/23/2023]
102
Olson ND, Wagner J, Dwarshuis N, Miga KH, Sedlazeck FJ, Salit M, Zook JM. Variant calling and benchmarking in an era of complete human genome sequences. Nat Rev Genet 2023:10.1038/s41576-023-00590-0. [PMID: 37059810 DOI: 10.1038/s41576-023-00590-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2023] [Indexed: 04/16/2023]
103
Song A, Su J, Wang H, Zhang Z, Zhang X, Van de Peer Y, Chen F, Fang W, Guan Z, Zhang F, Wang Z, Wang L, Ding B, Zhao S, Ding L, Liu Y, Zhou L, He J, Jia D, Zhang J, Chen C, Yu Z, Sun D, Jiang J, Chen S, Chen F. Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum. Nat Commun 2023;14:2021. [PMID: 37037808 PMCID: PMC10085997 DOI: 10.1038/s41467-023-37730-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/29/2023] [Indexed: 04/12/2023]  Open
104
Li Q, Zhao L, Zeng Y, Kuang Y, Guan Y, Chen B, Xu S, Tang B, Wu L, Mao X, Sun X, Shi J, Xu P, Diao F, Xue S, Bao S, Meng Q, Yuan P, Wang W, Ma N, Song D, Xu B, Dong J, Mu J, Zhang Z, Fan H, Gu H, Li Q, He L, Jin L, Wang L, Sang Q. Large-scale analysis of de novo mutations identifies risk genes for female infertility characterized by oocyte and early embryo defects. Genome Biol 2023;24:68. [PMID: 37024973 PMCID: PMC10080761 DOI: 10.1186/s13059-023-02894-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/01/2023] [Indexed: 04/08/2023]  Open
105
Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023;33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
106
Zhao S, Mekbib KY, van der Ent MA, Allington G, Prendergast A, Chau JE, Smith H, Shohfi J, Ocken J, Duran D, Furey CG, Le HT, Duy PQ, Reeves BC, Zhang J, Nelson-Williams C, Chen D, Li B, Nottoli T, Bai S, Rolle M, Zeng X, Dong W, Fu PY, Wang YC, Mane S, Piwowarczyk P, Fehnel KP, See AP, Iskandar BJ, Aagaard-Kienitz B, Kundishora AJ, DeSpenza T, Greenberg ABW, Kidanemariam SM, Hale AT, Johnston JM, Jackson EM, Storm PB, Lang SS, Butler WE, Carter BS, Chapman P, Stapleton CJ, Patel AB, Rodesch G, Smajda S, Berenstein A, Barak T, Erson-Omay EZ, Zhao H, Moreno-De-Luca A, Proctor MR, Smith ER, Orbach DB, Alper SL, Nicoli S, Boggon TJ, Lifton RP, Gunel M, King PD, Jin SC, Kahle KT. Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.532837. [PMID: 36993588 PMCID: PMC10055230 DOI: 10.1101/2023.03.18.532837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
107
Kim H, Suyama M. Genome-wide identification of copy neutral loss of heterozygosity reveals its possible association with spatial positioning of chromosomes. Hum Mol Genet 2023;32:1175-1183. [PMID: 36349694 PMCID: PMC10026252 DOI: 10.1093/hmg/ddac278] [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: 09/08/2022] [Revised: 10/17/2022] [Accepted: 11/02/2022] [Indexed: 11/10/2022]  Open
108
Zhai Y, Bardel C, Vallée M, Iwaz J, Roy P. Performance comparisons between clustering models for reconstructing NGS results from technical replicates. Front Genet 2023;14:1148147. [PMID: 37007945 PMCID: PMC10060969 DOI: 10.3389/fgene.2023.1148147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023]  Open
109
Population Structure and Genetic Diversity Analysis of “Yufen 1” H Line Chickens Using Whole-Genome Resequencing. Life (Basel) 2023;13:life13030793. [PMID: 36983948 PMCID: PMC10059704 DOI: 10.3390/life13030793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]  Open
110
Revisiting mutagenesis at non-B DNA motifs in the human genome. Nat Struct Mol Biol 2023;30:417-424. [PMID: 36914796 DOI: 10.1038/s41594-023-00936-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/03/2023] [Indexed: 03/16/2023]
111
Sezmis AL, Woods LC, Peleg AY, McDonald MJ. Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations of Acinetobacter Baylyi. Mol Biol Evol 2023;40:msad028. [PMID: 36788632 PMCID: PMC9985319 DOI: 10.1093/molbev/msad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/17/2022] [Accepted: 01/27/2023] [Indexed: 02/16/2023]  Open
112
Fan S, Spence JP, Feng Y, Hansen MEB, Terhorst J, Beltrame MH, Ranciaro A, Hirbo J, Beggs W, Thomas N, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi A, Folkunang C, Meskel DW, Belay G, Song YS, Tishkoff SA. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell 2023;186:923-939.e14. [PMID: 36868214 PMCID: PMC10568978 DOI: 10.1016/j.cell.2023.01.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
113
Sekino M, Hashimoto K, Nakamichi R, Yamamoto M, Fujinami Y, Sasaki T. Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome. Mol Ecol 2023;32:2945-2963. [PMID: 36855846 DOI: 10.1111/mec.16908] [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: 07/13/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023]
114
Zhi Y, Wang D, Zhang K, Wang Y, Geng W, Chen B, Li H, Li Z, Tian Y, Kang X, Liu X. Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds. Animals (Basel) 2023;13:753. [PMID: 36830540 PMCID: PMC9952073 DOI: 10.3390/ani13040753] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023]  Open
115
Pfeilsticker TR, Jones RC, Steane DA, Vaillancourt RE, Potts BM. Molecular insights into the dynamics of species invasion by hybridisation in Tasmanian eucalypts. Mol Ecol 2023;32:2913-2929. [PMID: 36807951 DOI: 10.1111/mec.16892] [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: 08/29/2022] [Revised: 11/26/2022] [Accepted: 01/26/2023] [Indexed: 02/22/2023]
116
Di Marco F, Spitaleri A, Battaglia S, Batignani V, Cabibbe AM, Cirillo DM. Advantages of long- and short-reads sequencing for the hybrid investigation of the Mycobacterium tuberculosis genome. Front Microbiol 2023;14:1104456. [PMID: 36819039 PMCID: PMC9932330 DOI: 10.3389/fmicb.2023.1104456] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023]  Open
117
Martin CA, Sheppard EC, Illera JC, Suh A, Nadachowska-Brzyska K, Spurgin LG, Richardson DS. Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird. Mol Ecol 2023;32:1972-1989. [PMID: 36704917 DOI: 10.1111/mec.16865] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
118
Yin X, Yang D, Zhao Y, Yang X, Zhou Z, Sun X, Kong X, Li X, Wang G, Duan Y, Yang Y, Yang Y. Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies. PLANT COMMUNICATIONS 2023;4:100427. [PMID: 36056558 PMCID: PMC9860189 DOI: 10.1016/j.xplc.2022.100427] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/30/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
119
Hari A, Zhou Q, Gonzaludo N, Harting J, Scott SA, Qin X, Scherer S, Sahinalp SC, Numanagić I. An efficient genotyper and star-allele caller for pharmacogenomics. Genome Res 2023;33:61-70. [PMID: 36657977 PMCID: PMC9977157 DOI: 10.1101/gr.277075.122] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/12/2022] [Indexed: 01/20/2023]
120
Bai H, Zhang X, Bush WS. Pharmacogenomic and Statistical Analysis. Methods Mol Biol 2023;2629:305-330. [PMID: 36929083 DOI: 10.1007/978-1-0716-2986-4_14] [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: 03/18/2023]
121
Gu Y, Zhou Y, Ju S, Liu X, Zhang Z, Guo J, Gao J, Zang J, Sun H, Chen Q, Wang J, Xu J, Xu Y, Chen Y, Guo Y, Dai J, Ma H, Wang C, Jin G, Li C, Xia Y, Shen H, Yang Y, Guo X, Hu Z. Multi-omics profiling visualizes dynamics of cardiac development and functions. Cell Rep 2022;41:111891. [PMID: 36577384 DOI: 10.1016/j.celrep.2022.111891] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/14/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022]  Open
122
Saad M, El-Menyar A, Kunji K, Ullah E, Al Suwaidi J, Kullo IJ. Validation of Polygenic Risk Scores for Coronary Heart Disease in a Middle Eastern Cohort Using Whole Genome Sequencing. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022;15:e003712. [PMID: 36252120 PMCID: PMC9770120 DOI: 10.1161/circgen.122.003712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/04/2022] [Indexed: 12/24/2022]
123
Khera AV, Wang M, Chaffin M, Emdin CA, Samani NJ, Schunkert H, Watkins H, McPherson R, Elosua R, Boerwinkle E, Ardissino D, Butterworth AS, Di Angelantonio E, Naheed A, Danesh J, Chowdhury R, Krumholz HM, Sheu WHH, Rich SS, Rotter JI, Chen YDI, Gabriel S, Lander ES, Saleheen D, Kathiresan S. Gene Sequencing Identifies Perturbation in Nitric Oxide Signaling as a Nonlipid Molecular Subtype of Coronary Artery Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022;15:e003598. [PMID: 36215124 PMCID: PMC9771961 DOI: 10.1161/circgen.121.003598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/24/2022] [Indexed: 12/24/2022]
124
Robinson KG, Marsh AG, Lee SK, Hicks J, Romero B, Batish M, Crowgey EL, Shrader MW, Akins RE. DNA Methylation Analysis Reveals Distinct Patterns in Satellite Cell-Derived Myogenic Progenitor Cells of Subjects with Spastic Cerebral Palsy. J Pers Med 2022;12:jpm12121978. [PMID: 36556199 PMCID: PMC9780849 DOI: 10.3390/jpm12121978] [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: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]  Open
125
Xie HB, Yan C, Adeola AC, Wang K, Huang CP, Xu MM, Qiu Q, Yin X, Fan CY, Ma YF, Yin TT, Gao Y, Deng JK, Okeyoyin AO, Oluwole OO, Omotosho O, Okoro VMO, Omitogun OG, Dawuda PM, Olaogun SC, Nneji LM, Ayoola AO, Sanke OJ, Luka PD, Okoth E, Lekolool I, Mijele D, Bishop RP, Han J, Wang W, Peng MS, Zhang YP. African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments. Mol Biol Evol 2022;39:6840307. [PMID: 36413509 PMCID: PMC9733430 DOI: 10.1093/molbev/msac256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]  Open
126
Understanding Mendelian errors in SNP arrays data using a Gochu Asturcelta pig pedigree: genomic alterations, family size and calling errors. Sci Rep 2022;12:19686. [PMID: 36385499 PMCID: PMC9668983 DOI: 10.1038/s41598-022-24340-0] [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: 04/25/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]  Open
127
von Seth J, van der Valk T, Lord E, Sigeman H, Olsen RA, Knapp M, Kardailsky O, Robertson F, Hale M, Houston D, Kennedy E, Dalén L, Norén K, Massaro M, Robertson BC, Dussex N. Genomic trajectories of a near-extinction event in the Chatham Island black robin. BMC Genomics 2022;23:747. [PMID: 36357860 PMCID: PMC9647977 DOI: 10.1186/s12864-022-08963-1] [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: 06/17/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022]  Open
128
Lee J, Lee J, Jeon S, Lee J, Jang I, Yang JO, Park S, Lee B, Choi J, Choi BO, Gee HY, Oh J, Jang IJ, Lee S, Baek D, Koh Y, Yoon SS, Kim YJ, Chae JH, Park WY, Bhak JH, Choi M. A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population. Exp Mol Med 2022;54:1862-1871. [PMID: 36323850 PMCID: PMC9628380 DOI: 10.1038/s12276-022-00871-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022]  Open
129
Woerner AE, Mandape S, Kapema KB, Duque TM, Smuts A, King JL, Crysup B, Wang X, Huang M, Ge J, Budowle B. Optimized variant calling for estimating kinship. Forensic Sci Int Genet 2022;61:102785. [DOI: 10.1016/j.fsigen.2022.102785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/07/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022]
130
Ferreira JC, Alshamali F, Pereira L, Fernandes V. Characterization of Arabian Peninsula whole exomes: Contributing to the catalogue of human diversity. iScience 2022;25:105336. [DOI: 10.1016/j.isci.2022.105336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/01/2022] [Accepted: 10/10/2022] [Indexed: 11/24/2022]  Open
131
Lee KS, Seo J, Lee CK, Shin S, Choi Z, Min S, Yang JH, Kwon WS, Yun W, Park MR, Choi JR, Chung HC, Lee ST, Rha SY. Analytical and Clinical Validation of Cell-Free Circulating Tumor DNA Assay for the Estimation of Tumor Mutational Burden. Clin Chem 2022;68:1519-1528. [DOI: 10.1093/clinchem/hvac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/21/2022] [Indexed: 11/12/2022]
132
Hlaváč V, Holý P, Václavíková R, Rob L, Hruda M, Mrhalová M, Černaj P, Bouda J, Souček P. Whole-exome sequencing of epithelial ovarian carcinomas differing in resistance to platinum therapy. Life Sci Alliance 2022;5:5/12/e202201551. [PMID: 36229065 PMCID: PMC9574568 DOI: 10.26508/lsa.202201551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]  Open
133
Kelly JB, Carlson DE, Low JS, Thacker RW. Novel trends of genome evolution in highly complex tropical sponge microbiomes. MICROBIOME 2022;10:164. [PMID: 36195901 PMCID: PMC9531527 DOI: 10.1186/s40168-022-01359-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
134
Zhou X, Feliciano P, Shu C, Wang T, Astrovskaya I, Hall JB, Obiajulu JU, Wright JR, Murali SC, Xu SX, Brueggeman L, Thomas TR, Marchenko O, Fleisch C, Barns SD, Snyder LG, Han B, Chang TS, Turner TN, Harvey WT, Nishida A, O'Roak BJ, Geschwind DH, Michaelson JJ, Volfovsky N, Eichler EE, Shen Y, Chung WK. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nat Genet 2022;54:1305-1319. [PMID: 35982159 PMCID: PMC9470534 DOI: 10.1038/s41588-022-01148-2] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 06/28/2022] [Indexed: 12/16/2022]
135
Castaneda-Garcia C, Iyer V, Nsengimana J, Trower A, Droop A, Brown KM, Choi J, Zhang T, Harland M, Newton-Bishop JA, Bishop DT, Adams DJ, Iles MM, Robles-Espinoza CD. Defining novel causal SNPs and linked phenotypes at melanoma-associated loci. Hum Mol Genet 2022;31:2845-2856. [PMID: 35357426 PMCID: PMC9433725 DOI: 10.1093/hmg/ddac074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022]  Open
136
Bouzinier MA, Etin D, Trifonov SI, Evdokimova VN, Ulitin V, Shen J, Kokorev A, Ghazani AA, Chekaluk Y, Albertyn Z, Giersch A, Morton CC, Abraamyan F, Bendapudi PK, Sunyaev S, Undiagnosed Diseases Network, Brigham Genomic Medicine, SEQuencing A Baby For An Optimal Outcome, Quantori, Krier JB. AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease. J Biomed Inform 2022;133:104174. [PMID: 35998814 DOI: 10.1016/j.jbi.2022.104174] [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: 10/27/2021] [Revised: 07/23/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022]
137
Majeed A, Johar P, Raina A, Salgotra RK, Feng X, Bhat JA. Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding. Front Genet 2022;13:944501. [PMID: 36003337 PMCID: PMC9393495 DOI: 10.3389/fgene.2022.944501] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/28/2022] [Indexed: 12/26/2022]  Open
138
Brucato N, André M, Hudjashov G, Mondal M, Cox MP, Leavesley M, Ricaut FX. Chronology of natural selection in Oceanian genomes. iScience 2022;25:104583. [PMID: 35880026 PMCID: PMC9308150 DOI: 10.1016/j.isci.2022.104583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022]  Open
139
Di Santo LN, Hoban S, Parchman TL, Wright JW, Hamilton JA. Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation. Mol Ecol 2022;31:4622-4639. [PMID: 35822858 DOI: 10.1111/mec.16615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
140
Exome sequencing analysis of Japanese autism spectrum disorder case-control sample supports an increased burden of synaptic function-related genes. Transl Psychiatry 2022;12:265. [PMID: 35811316 PMCID: PMC9271461 DOI: 10.1038/s41398-022-02033-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 01/16/2023]  Open
141
Giorgashvili E, Reichel K, Caswara C, Kerimov V, Borsch T, Gruenstaeudl M. Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow Endemic Calligonum bakuense. FRONTIERS IN PLANT SCIENCE 2022;13:779830. [PMID: 35874012 PMCID: PMC9296850 DOI: 10.3389/fpls.2022.779830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
142
Lefouili M, Nam K. The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species. Sci Rep 2022;12:11331. [PMID: 35790846 PMCID: PMC9256665 DOI: 10.1038/s41598-022-15563-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 06/27/2022] [Indexed: 11/09/2022]  Open
143
Zhao Y, Zhang K, Pan H, Wang Y, Zhou X, Xiang Y, Xu Q, Sun Q, Tan J, Yan X, Li J, Guo J, Tang B, Liu Z. Genetic Analysis of Six Transmembrane Protein Family Genes in Parkinson's Disease in a Large Chinese Cohort. Front Aging Neurosci 2022;14:889057. [PMID: 35860667 PMCID: PMC9289399 DOI: 10.3389/fnagi.2022.889057] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022]  Open
144
Wang RJ, Raveendran M, Harris RA, Murphy WJ, Lyons LA, Rogers J, Hahn MW. De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations. Mol Biol Evol 2022;39:msac147. [PMID: 35771663 PMCID: PMC9290555 DOI: 10.1093/molbev/msac147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
145
Patel AP, Dron JS, Wang M, Pirruccello JP, Ng K, Natarajan P, Lebo M, Ellinor PT, Aragam KG, Khera AV. Association of Pathogenic DNA Variants Predisposing to Cardiomyopathy With Cardiovascular Disease Outcomes and All-Cause Mortality. JAMA Cardiol 2022;7:723-732. [PMID: 35544052 PMCID: PMC9096692 DOI: 10.1001/jamacardio.2022.0901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
146
Agrawal S, Wang M, Klarqvist MDR, Smith K, Shin J, Dashti H, Diamant N, Choi SH, Jurgens SJ, Ellinor PT, Philippakis A, Claussnitzer M, Ng K, Udler MS, Batra P, Khera AV. Inherited basis of visceral, abdominal subcutaneous and gluteofemoral fat depots. Nat Commun 2022;13:3771. [PMID: 35773277 PMCID: PMC9247093 DOI: 10.1038/s41467-022-30931-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 12/11/2022]  Open
147
Chen P, Tan Z, Qiu A, Yin S, Zhou Y, Dong Z, Qiu Y, Xu J, Li K, Dong L, Shek HT, Liu J, Yeung EHK, Gao B, Cheung KMC, To MKT. Patient-reported outcomes in a Chinese cohort of osteogenesis imperfecta unveil psycho-physical stratifications associated with clinical manifestations. Orphanet J Rare Dis 2022;17:249. [PMID: 35765008 PMCID: PMC9238011 DOI: 10.1186/s13023-022-02394-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/11/2022] [Indexed: 11/10/2022]  Open
148
Herzig AF, Ciullo M, Leutenegger AL, Perdry H. Moment estimators of relatedness from low-depth whole-genome sequencing data. BMC Bioinformatics 2022;23:254. [PMID: 35751014 PMCID: PMC9233360 DOI: 10.1186/s12859-022-04795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/09/2022] [Indexed: 11/29/2022]  Open
149
Lee S, Hong S, Woo J, Lee JH, Kim K, Kim L, Park K, Jung J. RDscan: A New Method for Improving Germline and Somatic Variant Calling Based on Read Depth Distribution. J Comput Biol 2022;29:987-1000. [PMID: 35749140 DOI: 10.1089/cmb.2021.0269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
150
Cai C, Yin Z, Liu A, Wang H, Zeng S, Wang Z, Qiu H, Li S, Zhou J, Wang M. Identifying Rare Genetic Variants of Immune Mediators as Risk Factors for Autism Spectrum Disorder. Genes (Basel) 2022;13:1098. [PMID: 35741860 PMCID: PMC9223212 DOI: 10.3390/genes13061098] [Citation(s) in RCA: 6] [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] [Received: 05/27/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/30/2022]  Open
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