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Structural variation across 138,134 samples in the TOPMed consortium.
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Jun G, et al. Among authors: shen h. Res Sq [Preprint]. 2023 Feb 3:rs.3.rs-2515453. doi: 10.21203/rs.3.rs-2515453/v1. Res Sq. 2023. PMID: 36778386 Free PMC article. Preprint.
Fully resolved assembly of Cryptosporidium parvum.
Menon VK, Okhuysen PC, Chappell CL, Mahmoud M, Mahmoud M, Meng Q, Doddapaneni H, Vee V, Han Y, Salvi S, Bhamidipati S, Kottapalli K, Weissenberger G, Shen H, Ross MC, Hoffman KL, Cregeen SJ, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Menon VK, et al. Among authors: shen h. Gigascience. 2022 Feb 15;11:giac010. doi: 10.1093/gigascience/giac010. Gigascience. 2022. PMID: 35166336 Free PMC article.
Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism.
Chander V, Mahmoud M, Hu J, Dardas Z, Grochowski CM, Dawood M, Khayat MM, Li H, Li S, Jhangiani S, Korchina V, Shen H, Weissenberger G, Meng Q, Gingras MC, Muzny DM, Doddapaneni H, Posey JE, Lupski JR, Sabo A, Murdock DR, Sedlazeck FJ, Gibbs RA. Chander V, et al. Among authors: shen h. Hum Mutat. 2022 Dec;43(12):2033-2053. doi: 10.1002/humu.24461. Epub 2022 Sep 24. Hum Mutat. 2022. PMID: 36054313 Free PMC article.
Structural variation across 138,134 samples in the TOPMed consortium.
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Jun G, et al. Among authors: shen h. bioRxiv [Preprint]. 2023 Jan 25:2023.01.25.525428. doi: 10.1101/2023.01.25.525428. bioRxiv. 2023. PMID: 36747810 Free PMC article. Preprint.
Closing the gap: Solving complex medically relevant genes at scale.
Mahmoud M, Harting J, Corbitt H, Chen X, Jhangiani SN, Doddapaneni H, Meng Q, Han T, Lambert C, Zhang S, Baybayan P, Henno G, Shen H, Hu J, Han Y, Riegler C, Metcalf G, Henno G, Chinn IK, Eberle MA, Kingan S, Farinholt T, Carvalho CMB, Gibbs RA, Kronenberg Z, Muzny D, Sedlazeck FJ. Mahmoud M, et al. Among authors: shen h. medRxiv [Preprint]. 2024 Mar 18:2024.03.14.24304179. doi: 10.1101/2024.03.14.24304179. medRxiv. 2024. PMID: 38562723 Free PMC article. Preprint.
A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus.
Pellerin D, Del Gobbo GF, Couse M, Dolzhenko E, Nageshwaran SK, Cheung WA, Xu IRL, Dicaire MJ, Spurdens G, Matos-Rodrigues G, Stevanovski I, Scriba CK, Rebelo A, Roth V, Wandzel M, Bonnet C, Ashton C, Agarwal A, Peter C, Hasson D, Tsankova NM, Dewar K, Lamont PJ, Laing NG, Renaud M, Houlden H, Synofzik M, Usdin K, Nussenzweig A, Napierala M, Chen Z, Jiang H, Deveson IW, Ravenscroft G, Akbarian S, Eberle MA, Boycott KM, Pastinen T; All of Us Research Program Long Read Working Group; Brais B, Zuchner S, Danzi MC. Pellerin D, et al. Nat Genet. 2024 Jul;56(7):1366-1370. doi: 10.1038/s41588-024-01808-5. Epub 2024 Jun 27. Nat Genet. 2024. PMID: 38937606 Free PMC article.
Somatic mutations affect key pathways in lung adenocarcinoma.
Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Ding L, et al. Among authors: shen h. Nature. 2008 Oct 23;455(7216):1069-75. doi: 10.1038/nature07423. Nature. 2008. PMID: 18948947 Free PMC article.
Phenotypic and protein localization heterogeneity associated with AHDC1 pathogenic protein-truncating alleles in Xia-Gibbs syndrome.
Khayat MM, Li H, Chander V, Hu J, Hansen AW, Li S, Traynelis J, Shen H, Weissenberger G, Stossi F, Johnson HL, Lupski JR, Posey JE, Sabo A, Meng Q, Murdock DR, Wangler M, Gibbs RA. Khayat MM, et al. Among authors: shen h. Hum Mutat. 2021 May;42(5):577-591. doi: 10.1002/humu.24190. Epub 2021 Mar 6. Hum Mutat. 2021. PMID: 33644933 Free PMC article.
Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.
Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, Wang Q, Shen H, Holder M, Villasana D, Nazareth LV, Cree A, Courtney L, Veizer J, Kotkiewicz H, Cho TJ, Koutseva N, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Hughes JF, et al. Among authors: shen h. Nature. 2012 Feb 22;483(7387):82-6. doi: 10.1038/nature10843. Nature. 2012. PMID: 22367542 Free PMC article.
Phenotypic expansion in KIF1A-related dominant disorders: A description of novel variants and review of published cases.
Montenegro-Garreaud X, Hansen AW, Khayat MM, Chander V, Grochowski CM, Jiang Y, Li H, Mitani T, Kessler E, Jayaseelan J, Shen H, Gezdirici A, Pehlivan D, Meng Q, Rosenfeld JA, Jhangiani SN, Madan-Khetarpal S, Scott DA, Abarca-Barriga H, Trubnykova M, Gingras MC, Muzny DM, Posey JE, Liu P, Lupski JR, Gibbs RA. Montenegro-Garreaud X, et al. Among authors: shen h. Hum Mutat. 2020 Dec;41(12):2094-2104. doi: 10.1002/humu.24118. Epub 2020 Oct 8. Hum Mutat. 2020. PMID: 32935419 Free PMC article. Review.
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