Standards and Guidelines for Genetic Variant Interpretation

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Wang, D., Scalici, A., Wang, Y., Lin, H., Pitsillides, A., Heard-Costa, N., Cruchaga, C., Ziegemeier, E., Bis, J. C., Fornage, M., Boerwinkle, E., De Jager, P. L., Wijsman, E., Dupuis, J., Renton, A. E., Seshadri, S., Goate, A. M., DeStefano, A. L., & Peloso, G. M. (2025). Frequency of variants in Mendelian Alzheimer’s disease genes within the Alzheimer’s Disease Sequencing Project. Journal of Alzheimer’s Disease. https://doi.org/10.1177/13872877251320375
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Ellis, C. A., Ottman, R., Epstein, M. P., Berkovic, S. F., & Oliver, K. L. (2025). Phenotypic heterogeneity in familial epilepsies is influenced by polygenic risk for generalized and focal epilepsies. Epilepsia. Portico. https://doi.org/10.1111/epi.18348
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Vialle, R. A., de Paiva Lopes, K., Li, Y., Ng, B., Schneider, J. A., Buchman, A. S., Wang, Y., Farfel, J. M., Barnes, L. L., Wingo, A. P., Wingo, T. S., Seyfried, N. T., De Jager, P. L., Gaiteri, C., Tasaki, S., & Bennett, D. A. (2025). Structural variants linked to Alzheimer’s disease and other common age-related clinical and neuropathologic traits. Genome Medicine, 17(1). https://doi.org/10.1186/s13073-025-01444-6
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Hodgson, A. K. O., Baxandall, L., Aiyedun, D., Li, A., Au, P. Y. B., Bain, J. M., Gillentine, M. A., Goel, H., Kline, A. D., Ricupero, C. L., Sánchez‐Carpintero, R., Seward, E. P., Sidlow, R., Wilson, S. A., & Balasubramanian, M. (2025). Expanding the Phenotypic Spectrum of HNRNPU‐Related Disorder, Documenting the First Familial Presentation and Comprehensive Review. American Journal of Medical Genetics Part A. Portico. https://doi.org/10.1002/ajmg.a.64013
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Cornejo‐Olivas, M., Griswold, A. J., Saldarriaga‐Mayo, A., Mena, P. R., Rodriguez, R. S., Adams, L. D., Whitehead, P. L., Isasi, R., Illanes‐Manrique, M., Sarapura‐Castro, E., Rajabli, F., McInerney, K. F., Milla‐Neyra, K., Manrique‐Enciso, C., Beecham, G. W., Castro‐Suarez, S., George‐Hyslop, P. S., Araujo‐Aliaga, I., Cuccaro, M. L., … Pericak‐Vance, M. A. (2024). A novel stop‐gain SORL1 mutation from Amerindian background in a Peruvian family with Alzheimer’s Disease of the PeADI Study. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.090818
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Mena, P. R., Zaman, A. F., Faber, K. M., Adams, L. D., Inciute, J. D., Whitehead, P. L., Foroud, T. M., Reyes‐Dumeyer, D., Kuzma, A. B., Nicaretta, H. I., Naj, A. C., Martin, E. R., Dalgard, C. L., Schellenberg, G. D., Wang, L., Mayeux, R., Vardarajan, B. N., Vance, J. M., Cuccaro, M. L., … Pericak‐Vance, M. A. (2024). The Alzheimer’s Disease Sequencing Project – Discovery, Discovery Extension and Follow Up Study (ADSP‐FUS): APOE genotype status and demographic characteristics across datasets. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.092629
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Lee, W., Choi, S. H., Shea, M. G., Cheng, P., Dombroski, B. A., Pitsillides, A. N., Heard‐Costa, N. L., Wang, H., Bulekova, K., Kuzma, A. B., Leung, Y. Y., Farrell, J. J., Lin, H., Kunkle, B. W., Naj, A., Blue, E. E., Nusetor, F., Wang, D., Boerwinkle, E., … Peloso, G. M. (2024). Association of common and rare variants with Alzheimer’s disease in more than 13,000 diverse individuals with whole‐genome sequencing from the Alzheimer’s Disease Sequencing Project. Alzheimer’s & Dementia. Portico. https://doi.org/10.1002/alz.14283
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Bickell, N. A., May, B., Havrylchuk, I., John, J., Lin, S., Tao, A., Yagnik, R., & Tatonetti, N. P. (2024). Implementation of a rule-based algorithm to find patients eligible for cancer clinical trials. JAMIA Open, 7(4). https://doi.org/10.1093/jamiaopen/ooae131
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Hainsworth, A. H., Blackburn, T. P., Bradshaw, E. M., Elahi, F. M., Gorelick, P. B., Isaacs, J. D., Wallin, A., & Williams, S. C. (2024). The promise of molecular science in brain health. What breakthroughs are anticipated in the next 20 years? Cerebral Circulation - Cognition and Behavior, 7, 100364. https://doi.org/10.1016/j.cccb.2024.100364
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Sudnawa, K. K., Pini, N., Li, W., Kanner, C. H., Ryu, J., Calamia, S., Bain, J. M., Goldman, S., Montes, J., Shen, Y., & Chung, W. K. (2024). Clinical characteristics, longitudinal adaptive functioning, and association with electroencephalogram activity in PPP2R5D‐related neurodevelopmental disorder. Clinical Genetics. Portico. https://doi.org/10.1111/cge.14612
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Schrauwen, I., Rajendran, Y., Acharya, A., Öhman, S., Arvio, M., Paetau, R., Siren, A., Avela, K., Granvik, J., Leal, S. M., Määttä, T., Kokkonen, H., & Järvelä, I. (2024). Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-62009-y
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Malamon, J. S., Farrell, J. J., Xia, L. C., Dombroski, B. A., Das, R. G., Way, J., Kuzma, A. B., Valladares, O., Leung, Y. Y., Scanlon, A. J., Lopez, I. A. B., Brehony, J., Worley, K. C., Zhang, N. R., Wang, L.-S., Farrer, L. A., Schellenberg, G. D., Lee, W.-P., & Vardarajan, B. N. (2024). A comparative study of structural variant calling in WGS from Alzheimer’s disease families. Life Science Alliance, 7(5), e202302181. https://doi.org/10.26508/lsa.202302181
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Xicota, L., Cosentino, S., Vardarajan, B., Mayeux, R., Perls, T. T., Andersen, S. L., Zmuda, J. M., Thyagarajan, B., Yashin, A., Wojczynski, M. K., Krinsky‐McHale, S., Handen, B. L., Christian, B. T., Head, E., Mapstone, M. E., Schupf, N., Lee, J. H., & Barral, S. (2024). Whole genome‐wide sequence analysis of long‐lived families (Long‐Life Family Study) identifies MTUS2 gene associated with late‐onset Alzheimer’s disease. Alzheimer’s & Dementia, 20(4), 2670–2679. Portico. https://doi.org/10.1002/alz.13718
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Kanner, C. H., Uher, D., Zreibe, K., Beard, G., Patterson, M., Harris, M., Doerger, J., Calamia, S., Chung, W. K., & Montes, J. (2024). Validation of a modified version of the gross motor function measure in PPPR5D related neurodevelopmental disorder. Orphanet Journal of Rare Diseases, 19(1). https://doi.org/10.1186/s13023-024-03067-3
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Duyzend, M. H., Cacheiro, P., Jacobsen, J. O. B., Giordano, J., Brand, H., Wapner, R. J., Talkowski, M. E., Robinson, P. N., & Smedley, D. (2024). Improving prenatal diagnosis through standards and aggregation. Prenatal Diagnosis, 44(4), 454–464. Portico. https://doi.org/10.1002/pd.6522
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Gargano, M. A., Matentzoglu, N., Coleman, B., Addo-Lartey, E. B., Anagnostopoulos, A. V., Anderton, J., Avillach, P., Bagley, A. M., Bakštein, E., Balhoff, J. P., Baynam, G., Bello, S. M., Berk, M., Bertram, H., Bishop, S., Blau, H., Bodenstein, D. F., Botas, P., Boztug, K., … Robinson, P. N. (2023). The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Research, 52(D1), D1333–D1346. https://doi.org/10.1093/nar/gkad1005
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Reich, C., Ostropolets, A., Ryan, P., Rijnbeek, P., Schuemie, M., Davydov, A., Dymshyts, D., & Hripcsak, G. (2024). OHDSI Standardized Vocabularies—a large-scale centralized reference ontology for international data harmonization. Journal of the American Medical Informatics Association, 31(3), 583–590. https://doi.org/10.1093/jamia/ocad247
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Zhuo, X., Aggarwal, V., & Liao, J. (2024). P641: Application of AlphaMissense prediction to pathogenicity classification of missense variants from clinical exome sequencing. Genetics in Medicine Open, 2, 101547. https://doi.org/10.1016/j.gimo.2024.101547
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Chung, W., Ziegler, A., Koval-Burt, C., Kay, D., Suchy, S., Bergtrup, A., Langley, K., Amendola, L., Boyd, B., Bradley, J., Brandt, T., Cohen, L., Coffey, A., Devaney, J., Dygulska, B., Friedman, B., Fuleihan, R., Gyimah, A., Hernan, R., … Caggana, M. (2024). O35: Feasibility of expanded newborn screening using genome sequencing for early actionable conditions in a diverse city. Genetics in Medicine Open, 2, 101369. https://doi.org/10.1016/j.gimo.2024.101369
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Deignan, J. L., Aggarwal, V., Bale, A. E., Bellissimo, D. B., Booker, J. K., Cao, Y., Crooks, K. R., Deak, K. L., Del Gaudio, D., Funke, B., Hoppman, N. L., Horner, V., Hufnagel, R. B., Jackson-Cook, C., Koduru, P., Leung, M. L., Li, S., Liu, P., Luo, M., … Williams, E. S. (2024). The challenges and opportunities of offering and integrating training in clinical molecular genetics and clinical cytogenetics: A survey of LGG Fellowship Program Directors. Genetics in Medicine Open, 2, 101820. https://doi.org/10.1016/j.gimo.2024.101820
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Spector, E., Andersen, E., Herriges, J., Higgins, A., Levy, B., Matyakhina, L., Martin, C., Pineda-Alvarez, D., Shao, L., Shetty, S., Vaags, A., Thorland, E., Kang, S.-H., Lowther, C., McMullan, D., & Riggs, E. (2024). P576: Recalibration of scoring metrics to assess the pathogenicity of constitutional copy number variants (CNVs)*. Genetics in Medicine Open, 2, 101482. https://doi.org/10.1016/j.gimo.2024.101482
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Kowanda, M., Smith, R. S., Lundy, J., Kentros, C., Kleinman, E., Walsh, L. K., Schratt, G., Taylor, C., & Chung, W. (2024). P612: Improvement of variant reclassification in genetic neurodevelopmental conditions: Simons Searchlight research registry. Genetics in Medicine Open, 2, 101518. https://doi.org/10.1016/j.gimo.2024.101518
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Broeckel, U., Iqbal, M. A., Levy, B., Sahajpal, N., Nagy, P. L., Scharer, G., Rodriguez, V., Bossler, A., Stence, A., Skinner, C., Skinner, S. A., Kolhe, R., & Stevenson, R. (2024). Detection of Constitutional Structural Variants by Optical Genome Mapping. The Journal of Molecular Diagnostics, 26(3), 213–226. https://doi.org/10.1016/j.jmoldx.2023.12.003
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Karyn Roberts, Eileen Chaves, Adolfo Ariza, Vidhu Thaker, Chi Cho, Helen Binns (2024). P565: Exploring genetic testing for rare disorders of obesity: Experience and perspectives of pediatric weight management providers. Genetics in Medicine Open, Volume 2, Supplement 1, https://doi.org/10.1016/j.gimo.2024.101464
 

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Heilmann, R., Pfalzer, A., Bichell, T. J., Terala, A., Campbell, A., Taatjes, D., Ghoumid, J., Grueter, C., Bain, J., Strich, R., Dias, V., Sokorai, K., Seaver, N., Sexton, K., & Boychuck, K. (2024). The MED13L Foundation strategic research plan: a roadmap to the future. Therapeutic Advances in Rare Disease, 5. https://doi.org/10.1177/26330040241290252
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Stefanucci, L., Collins, J., Sims, M. C., Barrio-Hernandez, I., Sun, L., Burren, O. S., Perfetto, L., Bender, I., Callahan, T. J., Fleming, K., Guerrero, J. A., Hermjakob, H., Martin, M. J., Stephenson, J., Paneerselvam, K., Petrovski, S., Porras, P., Robinson, P. N., Wang, Q., … Vuckovic, D. (2023). The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants. Blood, 142(24), 2055–2068. https://doi.org/10.1182/blood.2023020118
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Kong, X.-F., Bogyo, K., Kapoor, S., Shea, P. R., Groopman, E. E., Thomas-Wilson, A., Cocchi, E., Milo Rasouly, H., Zheng, B., Sun, S., Zhang, J., Martinez, M., Vittorio, J. M., Dove, L. M., Marasa, M., Wang, T. C., Verna, E. C., Worman, H. J., Gharavi, A. G., … Wattacheril, J. (2023). The diagnostic yield of exome sequencing in liver diseases from a curated gene panel. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-42202-1
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Rehm, H. L., Alaimo, J. T., Aradhya, S., Bayrak-Toydemir, P., Best, H., Brandon, R., Buchan, J. G., Chao, E. C., Chen, E., Clifford, J., Cohen, A. S. A., Conlin, L. K., Das, S., Davis, K. W., del Gaudio, D., Del Viso, F., DiVincenzo, C., Eisenberg, M., Guidugli, L., … Rehm, H. (2023). The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change. Genetics in Medicine, 25(12), 100947. https://doi.org/10.1016/j.gim.2023.100947
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Slavotinek, A., Rego, S., Sahin-Hodoglugil, N., Kvale, M., Lianoglou, B., Yip, T., Hoban, H., Outram, S., Anguiano, B., Chen, F., Michelson, J., Cilio, R. M., Curry, C., Gallagher, R. C., Gardner, M., Kuperman, R., Mendelsohn, B., Sherr, E., Shieh, J., … Norton, M. E. (2023). Diagnostic yield of pediatric and prenatal exome sequencing in a diverse population. Npj Genomic Medicine, 8(1). https://doi.org/10.1038/s41525-023-00353-0
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Columbia Affiliation
Callahan, T. J., Stefanski, A. L., Wyrwa, J. M., Zeng, C., Ostropolets, A., Banda, J. M., Baumgartner, W. A., Boyce, R. D., Casiraghi, E., Coleman, B. D., Collins, J. H., Deakyne Davies, S. J., Feinstein, J. A., Lin, A. Y., Martin, B., Matentzoglu, N. A., Meeker, D., Reese, J., Sinclair, J., … Kahn, M. G. (2023). Ontologizing health systems data at scale: making translational discovery a reality. Npj Digital Medicine, 6(1). https://doi.org/10.1038/s41746-023-00830-x
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Thompson, J. L. P., Karaa, A., Pham, H., Yeske, P., Krischer, J., Xiao, Y., Long, Y., Kramer, A., Dimmock, D., Holbert, A., Gorski, C., Engelstad, K. M., Buchsbaum, R., Rosales, X. Q., & Hirano, M. (2023). The evolution of the mitochondrial disease diagnostic odyssey. Orphanet Journal of Rare Diseases, 18(1). https://doi.org/10.1186/s13023-023-02754-x
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Bosch, E., Popp, B., Güse, E., Skinner, C., van der Sluijs, P. J., Maystadt, I., Pinto, A. M., Renieri, A., Bruno, L. P., Granata, S., Marcelis, C., Baysal, Ö., Hartwich, D., Holthöfer, L., Isidor, B., Cogne, B., Wieczorek, D., Capra, V., Scala, M., … Vasileiou, G. (2023). Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals. Genetics in Medicine, 25(11), 100950. https://doi.org/10.1016/j.gim.2023.100950
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Myers, S. J., Yuan, H., Perszyk, R. E., Zhang, J., Kim, S., Nocilla, K. A., Allen, J. P., Bain, J. M., Lemke, J. R., Lal, D., Benke, T. A., & Traynelis, S. F. (2023). Classification of missense variants in the N-methyl-d-aspartate receptor GRIN gene family as gain- or loss-of-function. Human Molecular Genetics, 32(19), 2857–2871. https://doi.org/10.1093/hmg/ddad104
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Hays, T., Hernan, R., Disco, M., Griffin, E. L., Goldshtrom, N., Vargas, D., Krishnamurthy, G., Bomback, M., Rehman, A. U., Wilson, A. T., Guha, S., Phadke, S., Okur, V., Robinson, D., Felice, V., Abhyankar, A., Jobanputra, V., & Chung, W. K. (2023). Implementation of Rapid Genome Sequencing for Critically Ill Infants With Complex Congenital Heart Disease. Circulation: Genomic and Precision Medicine, 16(5), 415–420. https://doi.org/10.1161/circgen.122.004050
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Fecho, K., Bizon, C., Issabekova, T., Moxon, S., Thessen, A. E., Abdollahi, S., Baranzini, S. E., Belhu, B., Byrd, W. E., Chung, L., Crouse, A., Duby, M. P., Ferguson, S., Foksinska, A., Forero, L., Friedman, J., Gardner, V., Glusman, G., … Hadlock, J. (2023). An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges. Journal of Clinical and Translational Science, 7(1). https://doi.org/10.1017/cts.2023.619
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Schreidah, C. M., Reynolds, G. B., Fahmy, L. M., Carvajal, R. D., Vermeer, M. H., Whittaker, S., Pe’er, I., & Geskin, L. J. (2023). Scoping review of genetic databases for rare dermatologic diseases: Opportunity for artificial intelligence and machine learning. JAAD International, 12, 24–31. https://doi.org/10.1016/j.jdin.2023.02.017
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Abul-Husn, N. S., Marathe, P. N., Kelly, N. R., Bonini, K. E., Sebastin, M., Odgis, J. A., Abhyankar, A., Brown, K., Di Biase, M., Gallagher, K. M., Guha, S., Ioele, N., Okur, V., Ramos, M. A., Rodriguez, J. E., Rehman, A. U., Thomas-Wilson, A., Edelmann, L., Zinberg, R. E., … Gelb, B. D. (2023). Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients. Genetics in Medicine, 25(9), 100880. https://doi.org/10.1016/j.gim.2023.100880
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Lowther, C., Valkanas, E., Giordano, J. L., Wang, H. Z., Currall, B. B., O’Keefe, K., Pierce-Hoffman, E., Kurtas, N. E., Whelan, C. W., Hao, S. P., Weisburd, B., Jalili, V., Fu, J., Wong, I., Collins, R. L., Zhao, X., Austin-Tse, C. A., Evangelista, E., Lemire, G., … Talkowski, M. E. (2023). Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. The American Journal of Human Genetics, 110(9), 1454–1469. https://doi.org/10.1016/j.ajhg.2023.07.010
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Baker, B. H., Zhang, S., Simon, J. M., McLarnan, S. M., Chung, W. K., & Pearson, B. L. (2023). Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Frontiers in Neuroscience, 17. https://doi.org/10.3389/fnins.2023.1106573
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Calame, D. G., Guo, T., Wang, C., Garrett, L., Jolly, A., Dawood, M., Kurolap, A., Henig, N. Z., Fatih, J. M., Herman, I., Du, H., Mitani, T., Becker, L., Rathkolb, B., Gerlini, R., Seisenberger, C., Marschall, S., Hunter, J. V., Gerard, A., … Lupski, J. R. (2023). Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. The American Journal of Human Genetics, 110(8), 1394–1413. https://doi.org/10.1016/j.ajhg.2023.06.013
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Hussain, A., Acharya, A., Bharadwaj, T., Genomics, U. O. W. C. F. M., Leal, S. M., Khaliq, A., Mir, A., & Schrauwen, I. (2023). A Novel Variant in VPS13B Underlying Cohen Syndrome. BioMed Research International, 2023(1). Portico. https://doi.org/10.1155/2023/9993801
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Spillmann, R. C., Tan, Q. K.-G., Reuter, C., Schoch, K., Kohler, J., Bonner, D., Zastrow, D., Alkelai, A., Baugh, E., Cope, H., Marwaha, S., Wheeler, M. T., Bernstein, J. A., Shashi, V., Acosta, M. T., Adam, M., Adams, D. R., Alvey, J., Amendola, L., … Zuchner, S. (2023). A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genetics in Medicine, 25(4), 100353. https://doi.org/10.1016/j.gim.2022.12.001
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Columbia Affiliation
Linder, J. E., Allworth, A., Bland, H. T., Caraballo, P. J., Chisholm, R. L., Clayton, E. W., Crosslin, D. R., Dikilitas, O., DiVietro, A., Esplin, E. D., Forman, S., Freimuth, R. R., Gordon, A. S., Green, R., Harden, M. V., Holm, I. A., Jarvik, G. P., Karlson, E. W., Labrecque, S., … Peterson, J. F. (2023). Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genetics in Medicine, 25(4), 100006. https://doi.org/10.1016/j.gim.2023.100006
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Sheppard, S. E., Bryant, L., Wickramasekara, R. N., Vaccaro, C., Robertson, B., Hallgren, J., Hulen, J., Watson, C. J., Faundes, V., Duffourd, Y., Lee, P., Simon, M. C., de la Cruz, X., Padilla, N., Flores-Mendez, M., Akizu, N., Smiler, J., Pellegrino Da Silva, R., Li, D., … Stessman, H. A. F. (2023). Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice. Science Advances, 9(10). https://doi.org/10.1126/sciadv.ade1463
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Iqbal, M. A., Broeckel, U., Levy, B., Skinner, S., Sahajpal, N. S., Rodriguez, V., Stence, A., Awayda, K., Scharer, G., Skinner, C., Stevenson, R., Bossler, A., Nagy, P. L., & Kolhe, R. (2023). Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases. The Journal of Molecular Diagnostics, 25(3), 175–188. https://doi.org/10.1016/j.jmoldx.2022.12.005
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Timmins, G. T., Wynn, J., Saami, A. M., Espinal, A., & Chung, W. K. (2022). Diverse Parental Perspectives of the Social and Educational Needs for Expanding Newborn Screening through Genomic Sequencing. Public Health Genomics, 25(5–6), 185–192. Portico. https://doi.org/10.1159/000526382
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Ganapathi, M., Thomas-Wilson, A., Buchovecky, C., Dharmadhikari, A., Barua, S., Lee, W., Ruan, M. Z. C., Soucy, M., Ragi, S., Tanaka, J., Clark, L. N., Naini, A. B., Liao, J., Mansukhani, M., Tsang, S., & Jobanputra, V. (2022). Clinical exome sequencing for inherited retinal degenerations at a tertiary care center. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-13026-2
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