Publications

1. Mistry NA, Roellinger SE, Manninen MC, Gandham M, Koganti T, Balan J, Basu S, Blake EJ, Tandale PP, Holdren MA, Hoenig MF, Urban RM, Veith RL, Kendzior MC, Wang C, Gupta S, Shen W. Variant Detection in 3' Exons of PMS2 Using Exome Sequencing Data. J Mol Diagn. 2024 Sep; 26 (9):843-850 Epub 2024 June 24
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2. Jobanputra V, Schroeder B, Rehm HL, Shen W, Spiteri E, Nakouzi G, Taylor S, Marshall CR, Meng L, Kingsmore SF, Ellsworth K, Ashley E, Taft RJ, Medical Genome Initiative. Advancing access to genome sequencing for rare genetic disorders: recent progress and call to action. NPJ Genom Med. 2024 Mar 27; 9 (1):23
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3. Shen W, Rehm HL, Alaimo JT, Aradhya S, Bayrak-Toydemir P, Best H, Brandon R, Buchan JG, Chao EC, Chen E, Clifford J, Cohen ASA, Conlin LK, Das S, Davis KW, Del Gaudio D, Del Viso F, DiVincenzo C, Eisenberg M, Guidugli L, Hammer MB, Harrison SM, Hatchell KE, Dyer LH, Hoang LU, Holt JM, Jobanputra V, Karbassi ID, Kearney HM, Kelly MA, Kelly JM, Kluge ML, Komala T, Kruszka P, Lau L, Lebo MS, Marshall CR, McKnight D, McWalter K, Meng Y, Nagan N, Neckelmann CS, Neerman N, Niu Z, Paolillo VK, Paolucci SA, Perry D, Pesaran T, Radtke K, Rasmussen KJ, Retterer K, Saunders CJ, Spiteri E, Stanley C, Szuto A, Taft RJ, Thiffault I, Thomas BC, Thomas-Wilson A, Thorpe E, Tidwell TJ, Towne MC, Zouk H, Medical Genome Initiative Steering Committee. The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change. Genet Med. 2023 Dec; 25 (12):100947 Epub 2023 July 30
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4. Shen W, Sellers HL, Choate LA, Stein MI, Tandale PP, Tan J, Setlem R, Sakai Y, Fadra N, Sosa C, McClelland SP, Barnett SS, Rasmussen KJ, Runke CK, Smoley SA, Tillmans LS, Marcou CA, Rowsey RA, Thorland EC, Boczek NJ, Kearney HM. Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders. J Mol Diagn. 2023 Jul; 25(7):524-531. Epub 2023 Apr 23.
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5. Sheppard SE, Bryant L, Wickramasekara RN, Vaccaro C, Robertson B, Hallgren J, Hulen J, Watson CJ, Faundes V, Duffourd Y, Lee P, Simon MC, de la Cruz X, Padilla N, Flores-Mendez M, Akizu N, Smiler J, Pellegrino Da Silva R, Li D, March M, Diaz-Rosado A, Peixoto de Barcelos I, Choa ZX, Lim CY, Dubourg C, Journel H, Demurger F, Mulhern M, Akman C, Lippa N, Andrews M, Baldridge D, Constantino J, van Haeringen A, Snoeck-Streef I, Chow P, Hing A, Graham JM Jr, Au M, Faivre L, Shen W, Mao R, Palumbos J, Viskochil D, Gahl W, Tifft C, Macnamara E, Hauser N, Miller R, Maffeo J, Afenjar A, Doummar D, Keren B, Arn P, Macklin-Mantia S, Meerschaut I, Callewaert B, Reis A, Zweier C, Brewer C, Saggar A, Smeland MF, Kumar A, Elmslie F, Deshpande C, Nizon M, Cogne B, van Ierland Y, Wilke M, van Slegtenhorst M, Koudijs S, Chen JY, Dredge D, Pier D, Wortmann S, Kamsteeg EJ, Koch J, Haynes D, Pollack L, Titheradge H, Ranguin K, Denomme-Pichon AS, Weber S, Perez de la Fuente R, Sanchez Del Pozo J, Lezana Rosales JM, Joset P, Steindl K, Rauch A, Mei D, Mari F, Guerrini R, Lespinasse J, Tran Mau-Them F, Philippe C, Dauriat B, Raymond L, Moutton S, Cueto-Gonzalez AM, Tan TY, Mignot C, Grotto S, Renaldo F, Drivas TG, Hennessy L, Raper A, Parenti I, Kaiser FJ, Kuechler A, Busk OL, Islam L, Siedlik JA, Henderson LB, Juusola J, Person R, Schnur RE, Vitobello A, Banka S, Bhoj EJ, Stessman HAF. Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice. Sci Adv. 2023 Mar 10; 9 (10):eade1463
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6. Choate LA, Jiang L, Stein MI, Shen W, Baughn LB, Peterson JF. Detection of an MN1::ETV6 Gene Fusion in a Case of Acute Myeloid Leukemia with Erythroid Differentiation: A Case Report and Review of the Literature. Case Rep Hematol. 2023; 2023:9771388 Epub 2023 July 03
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7. Gupta S, Sukov WR, Vanderbilt CM, Shen W, Herrera-Hernandez L, Lohse CM, Thompson RH, Boorjian SA, Leibovich BC, Jimenez RE, Cheville JC. A contemporary guide to chromosomal copy number profiling in the diagnosis of renal cell carcinoma. Urol Oncol. 2022 Dec; 40 (12):512-524 Epub 2021 June 04
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8. Helman G, Zarekiani P, Tromp SAM, Andrews A, Botto LD, Bonkowsky JL, Chassevent A, Giorgio E, Pippucci T, Wei S, Shen W, Smith-Hicks C, Vaula G, Willemsen MAAP, Schimmel M, Vollert K, Shimizu F, Kanda T, Lynch M, Roscioli T, Taft RJ, Simons C, Bugiani M, Kuijpers TW, van der Knaap MS. Heterozygous NOTCH1 Variants Cause CNS Immune Activation and Microangiopathy. Ann Neurol. 2022 Nov; 92 (5):895-901 Epub 2022 Aug 20
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9. Hu C, Susswein LR, Roberts ME, Yang H, Marshall ML, Hiraki S, Berkofsky-Fessler W, Gupta S, Shen W, Dunn CA, Huang H, Na J, Domchek SM, Yadav S, Monteiro ANA, Polley EC, Hart SN, Hruska KS, Couch FJ. Classification of BRCA2 Variants of Uncertain Significance (VUS) Using an ACMG/AMP Model Incorporating a Homology-Directed Repair (HDR) Functional Assay. Clin Cancer Res. 2022 Sep 01; 28(17):3742-3751.
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10. Zimmerman Zuckerman E, Thompson JA, Schneider AR, Campion MB, Johns JJ, Stier TJ, Peterson LM, Ward AM, Blommel JH, Gnanaolivu RD, Lauer KP, Sivasankaran G, Balan J, Dasari S, Sakai Y, Marcou CA, Zheng G, Halling KC, Shen W, Viswanatha DS, Niu Z. Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures. SLAS Technol. 2022 Jun; 27 (3):214-218 Epub 2021 Nov 26
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11. Gupta S, Farooq A, Rowsey RA, Rahman MA, Shen W, Herrera-Hernandez L, Raghunathan A, Thompson RH, Boorjian SA, Leibovich BC, Cheville JC, Jimenez RE. Cytogenetics of spermatocytic tumors with a discussion of gain of chromosome 12p in anaplastic variants. Hum Pathol. 2022 Jun; 124:85-95 Epub 2022 Apr 01
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12. Gupta S, Lohse CM, Rowsey R, McCarthy MR, Shen W, Herrera-Hernandez L, Boorjian SA, Houston Thompson R, Jimenez RE, Leibovich BC, Cheville JC. Renal Neoplasia in Polycystic Kidney Disease: An Assessment of Tuberous Sclerosis Complex-associated Renal Neoplasia and PKD1/TSC2 Contiguous Gene Deletion Syndrome. Eur Urol. 2022 Mar; 81 (3):229-233 Epub 2021 Dec 06
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13. Gupta S, Erickson LA, Lohse CM, Shen W, Pitel BA, Knight SM, Halling KC, Herrera-Hernandez L, Boorjian SA, Thompson RH, Leibovich BC, Jimenez RE, Cheville JC. Assessment of Risk of Hereditary Predisposition in Patients With Melanoma and/or Mesothelioma and Renal Neoplasia. JAMA Netw Open. 2021 Nov 1; 4 (11):e2132615 Epub 2021 Nov 01
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14. Freitag CE, Sukov WR, Bryce AH, Berg JV, Vanderbilt CM, Shen W, Smadbeck JB, Greipp PT, Ketterling RP, Jenkins RB, Herrera-Hernandez L, Costello BA, Thompson RH, Boorjian SA, Leibovich BC, Jimenez RE, Murphy SJ, Vasmatzis G, Cheville JC, Gupta S. Assessment of isochromosome 12p and 12p abnormalities in germ cell tumors using fluorescence in situ hybridization, single-nucleotide polymorphism arrays, and next-generation sequencing/mate-pair sequencing. Hum Pathol. 2021 Jun; 112:20-34 Epub 2021 Mar 31
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15. Shen W, Flores-Daboub J, Viskochil D, Dugan SL, Best HD, Mao R. Detecting mosaic variants in patients with somatic overgrowth syndromes using cell-free circulating DNA and deep sequencing. J Med Genet. 2020 Nov; 57 (11):794-796 Epub 2020 Jan 28
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16. McGlaughon JL, Pasquali M, Wallace K, Ross J, Senol-Cosar O, Shen W, Weaver MA, Feigenbaum A, Lyon E, Enns GM, Mao R, Baudet HG. Assessing the strength of evidence for genes implicated in fatty acid oxidation disorders using the ClinGen clinical validity framework. Mol Genet Metab. 2019 Sep - Oct; 128 (1-2):122-128 Epub 2019 July 18
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17. Wooderchak-Donahue WL, Akay G, Whitehead K, Briggs E, Stevenson DA, O'Fallon B, Velinder M, Farrell A, Shen W, Bedoukian E, Skrabann CM, Antaya RJ, Henderson K, Pollak J, Treat J, Day R, Jacher JE, Hannibal M, Bontempo K, Marth G, Bayrak-Toydemir P, McDonald J. Phenotype of CM-AVM2 caused by variants in EPHB4: how much overlap with hereditary hemorrhagic telangiectasia (HHT)? Genet Med. 2019 Sep; 21 (9):2007-2014 Epub 2019 Feb 14
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18. Burrage LC, Reynolds JJ, Baratang NV, Phillips JB, Wegner J, McFarquhar A, Higgs MR, Christiansen AE, Lanza DG, Seavitt JR, Jain M, Li X, Parry DA, Raman V, Chitayat D, Chinn IK, Bertuch AA, Karaviti L, Schlesinger AE, Earl D, Bamshad M, Savarirayan R, Doddapaneni H, Muzny D, Jhangiani SN, Eng CM, Gibbs RA, Bi W, Emrick L, Rosenfeld JA, Postlethwait J, Westerfield M, Dickinson ME, Beaudet AL, Ranza E, Huber C, Cormier-Daire V, Shen W, Mao R, Heaney JD, Orange JS, Bertola D, Yamamoto GL, Baratela WAR, Butler MG, Ali A, Adeli M, Cohn DH, Krakow D, Jackson AP, Lees M, Offiah AC, Carlston CM, Carey JC, Stewart GS, Bacino CA, Campeau PM, Lee B, University of Washington Center for Mendelian Genomics//Undiagnosed Diseases Network. Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes. Am J Hum Genet. 2019 Mar 7; 104 (3):422-438 Epub 2019 Feb 14
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19. Shen W, Krautscheid P, Rutz AM, Bayrak-Toydemir P, Dugan SL. De novo loss-of-function variants of ASH1L are associated with an emergent neurodevelopmental disorder. Eur J Med Genet. 2019 Jan; 62 (1):55-60 Epub 2018 May 22
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20. Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R, ClinGen Inborn Errors of Metabolism Working Group. Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene. Hum Mutat. 2018 Nov; 39 (11):1569-1580
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21. Shen W, Paxton CN, Szankasi P, Longhurst M, Schumacher JA, Frizzell KA, Sorrells SM, Clayton AL, Jattani RP, Patel JL, Toydemir R, Kelley TW, Xu X. Detection of genome-wide copy number variants in myeloid malignancies using next-generation sequencing. J Clin Pathol. 2018 Apr; 71 (4):372-378 Epub 2017 Dec 02
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22. Shen W, Heeley JM, Carlston CM, Acuna-Hidalgo R, Nillesen WM, Dent KM, Douglas GV, Levine KL, Bayrak-Toydemir P, Marcelis CL, Shinawi M, Carey JC. The spectrum of DNMT3A variants in Tatton-Brown-Rahman syndrome overlaps with that in hematologic malignancies. Am J Med Genet A. 2017 Nov; 173 (11):3022-3028 Epub 2017 Sept 21
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23. Patel JL, Schumacher JA, Frizzell K, Sorrells S, Shen W, Clayton A, Jattani R, Kelley TW. Coexisting and cooperating mutations in NPM1-mutated acute myeloid leukemia. Leuk Res. 2017 May; 56:7-12 Epub 2017 Jan 23
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24. Shen W, Szankasi P, Sederberg M, Schumacher J, Frizzell KA, Gee EP, Patel JL, South ST, Xu X, Kelley TW. Concurrent detection of targeted copy number variants and mutations using a myeloid malignancy next generation sequencing panel allows comprehensive genetic analysis using a single testing strategy. Br J Haematol. 2016 Apr; 173 (1):49-58 Epub 2016 Jan 05
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25. Matynia AP, Szankasi P, Shen W, Kelley TW. Molecular genetic biomarkers in myeloid malignancies. Arch Pathol Lab Med. 2015 May; 139 (5):594-601 Epub 2014 Aug 25
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26. Babcock DT, Shen W, Ganetzky B. A neuroprotective function of NSF1 sustains autophagy and lysosomal trafficking in Drosophila. Genetics. 2015 Feb; 199 (2):511-22 Epub 2014 Dec 17
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27. Shen W, Henry AG, Paumier KL, Li L, Mou K, Dunlop J, Berger Z, Hirst WD. Inhibition of glucosylceramide synthase stimulates autophagy flux in neurons. J Neurochem. 2014 Jun; 129 (5):884-94 Epub 2014 Mar 03
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28. Singh R, Phillips MJ, Kuai D, Meyer J, Martin JM, Smith MA, Perez ET, Shen W, Wallace KA, Capowski EE, Wright LS, Gamm DM. Functional analysis of serially expanded human iPS cell-derived RPE cultures. Invest Ophthalmol Vis Sci. 2013 Oct 17; 54(10):6767-78.
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29. Singh R, Shen W, Kuai D, Martin JM, Guo X, Smith MA, Perez ET, Phillips MJ, Simonett JM, Wallace KA, Verhoeven AD, Capowski EE, Zhang X, Yin Y, Halbach PJ, Fishman GA, Wright LS, Pattnaik BR, Gamm DM. iPS cell modeling of Best disease: insights into the pathophysiology of an inherited macular degeneration. Hum Mol Genet. 2013 Feb 01; 22(3):593-607. Epub 2012 Nov 08.
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30. Paumier KL, Sukoff Rizzo SJ, Berger Z, Chen Y, Gonzales C, Kaftan E, Li L, Lotarski S, Monaghan M, Shen W, Stolyar P, Vasilyev D, Zaleska M, D Hirst W, Dunlop J. Behavioral characterization of A53T mice reveals early and late stage deficits related to Parkinson's disease. PLoS One. 2013; 8 (8):e70274 Epub 2013 Aug 01
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31. Li L, Nadanaciva S, Berger Z, Shen W, Paumier K, Schwartz J, Mou K, Loos P, Milici AJ, Dunlop J, Hirst WD. Human A53T alpha-synuclein causes reversible deficits in mitochondrial function and dynamics in primary mouse cortical neurons. PLoS One. 2013; 8 (12):e85815 Epub 2013 Dec 31
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32. Phillips MJ, Wallace KA, Dickerson SJ, Miller MJ, Verhoeven AD, Martin JM, Wright LS, Shen W, Capowski EE, Percin EF, Perez ET, Zhong X, Canto-Soler MV, Gamm DM. Blood-derived human iPS cells generate optic vesicle-like structures with the capacity to form retinal laminae and develop synapses. Invest Ophthalmol Vis Sci. 2012 Apr 18; 53(4):2007-19.
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33. Shen W, Ganetzky B. Nibbling away at synaptic development. Autophagy. 2010 Jan; 6 (1):168-9 Epub 2010 Jan 13
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34. Shen W, Ganetzky B. Autophagy promotes synapse development in Drosophila. J Cell Biol. 2009 Oct 5; 187 (1):71-9 Epub 2009 Sept 28
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