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Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition.
Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL; University of Washington Center for Mendelian Genomics (UW-CMG), Undiagnosed Diseases Network (UDN); Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. Vollger MR, et al. Among authors: wenger am. bioRxiv [Preprint]. 2023 Sep 27:2023.09.26.559521. doi: 10.1101/2023.09.26.559521. bioRxiv. 2023. PMID: 37808736 Free PMC article. Preprint.
Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort.
Cheung WA, Johnson AF, Rowell WJ, Farrow E, Hall R, Cohen ASA, Means JC, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Truong TK, Schwendinger-Schreck C, Yoo B, Johnston JJ, Gibson M, Evrony G, Rizzo WB, Thiffault I, Younger ST, Curran T, Wenger AM, Grundberg E, Pastinen T. Cheung WA, et al. Among authors: wenger am. Nat Commun. 2023 May 29;14(1):3090. doi: 10.1038/s41467-023-38782-1. Nat Commun. 2023. PMID: 37248219 Free PMC article.
Comprehensive de novo mutation discovery with HiFi long-read sequencing.
Kucuk E, van der Sanden BPGH, O'Gorman L, Kwint M, Derks R, Wenger AM, Lambert C, Chakraborty S, Baybayan P, Rowell WJ, Brunner HG, Vissers LELM, Hoischen A, Gilissen C. Kucuk E, et al. Among authors: wenger am. Genome Med. 2023 May 8;15(1):34. doi: 10.1186/s13073-023-01183-6. Genome Med. 2023. PMID: 37158973 Free PMC article.
Characterization and visualization of tandem repeats at genome scale.
Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Dolzhenko E, et al. Nat Biotechnol. 2024 Jan 2. doi: 10.1038/s41587-023-02057-3. Online ahead of print. Nat Biotechnol. 2024. PMID: 38168995
A multi-platform reference for somatic structural variation detection.
Espejo Valle-Inclan J, Besselink NJM, de Bruijn E, Cameron DL, Ebler J, Kutzera J, van Lieshout S, Marschall T, Nelen M, Priestley P, Renkens I, Roemer MGM, van Roosmalen MJ, Wenger AM, Ylstra B, Fijneman RJA, Kloosterman WP, Cuppen E. Espejo Valle-Inclan J, et al. Among authors: wenger am. Cell Genom. 2022 Jun 8;2(6):100139. doi: 10.1016/j.xgen.2022.100139. eCollection 2022 Jun 8. Cell Genom. 2022. PMID: 36778136 Free PMC article.
The complete sequence of a human Y chromosome.
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. Rhie A, et al. Among authors: wenger am. Nature. 2023 Sep;621(7978):344-354. doi: 10.1038/s41586-023-06457-y. Epub 2023 Aug 23. Nature. 2023. PMID: 37612512 Free PMC article.
Benchmarking challenging small variants with linked and long reads.
Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, Schatz MC, Narzisi G, Byrska-Bishop M, Clarke W, Evani US, Markello C, Shafin K, Zhou X, Sidow A, Bansal V, Ebert P, Marschall T, Lansdorp P, Hanlon V, Mattsson CA, Barrio AM, Fiddes IT, Xiao C, Fungtammasan A, Chin CS, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM. Wagner J, et al. Among authors: wenger am. Cell Genom. 2022 May;2(5):100128. doi: 10.1016/j.xgen.2022.100128. Cell Genom. 2022. PMID: 36452119 Free PMC article.
Approaches to long-read sequencing in a clinical setting to improve diagnostic rate.
Sanford Kobayashi E, Batalov S, Wenger AM, Lambert C, Dhillon H, Hall RJ, Baybayan P, Ding Y, Rego S, Wigby K, Friedman J, Hobbs C, Bainbridge MN. Sanford Kobayashi E, et al. Among authors: wenger am. Sci Rep. 2022 Oct 9;12(1):16945. doi: 10.1038/s41598-022-20113-x. Sci Rep. 2022. PMID: 36210382 Free PMC article.
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.
Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, McLean CY, Nattestad M, Chang PC, Carroll A. Baid G, et al. Among authors: wenger am. Nat Biotechnol. 2023 Feb;41(2):232-238. doi: 10.1038/s41587-022-01435-7. Epub 2022 Sep 1. Nat Biotechnol. 2023. PMID: 36050551
49 results