Publications & Pre-Prints

The UMGC develops novel genomic approaches through research & development in our Innovation Lab and also in collaboration with clients.

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2021

Effect of losartan on hospitalized patients with COVID-19-induced lung injury: A randomized clinical trial

Michael A. Puskarich, Nicholas E. Ingraham, Lisa H Merck, Brian E Driver, David A. Wacker, Lauren Page Black, Alan E. Jones, Courtney V. Fletcher, Andrew M. South, Andrew C. Nelson, Thomas A Murray, Christopher J. Tignanelli, Christopher Lewandowski, Joseph Farhat, Justin L. Benoit, Dana Byrne, Alex Hall, Ronald A. Reilkoff, Michelle H. Biros, Kartik Cherabuddi, Jeffrey G. Chipman, Timothy W. Schacker, Tyler Bold, Kenneth Beckman, Ryan Langlois, Matthew T. Aliota, Faheem W. Guirgis, James Galbriath, Margaret Beyer, Chas Salmen, Brian Roberts, David Wright, Helen T. Voelker, Joseph S. Koopmeiners

medRxiv doi:10.1101/2021.08.25.21262623. 2021 Aug 28.

CLAMP regulates Zygotic Genome Activation in Drosophila embryos

Megan M Colonnetta, Juan E Abrahante, Paul Schedl, Daryl M Gohl, Girish Deshpande

Genetics. iyab107. 2021 August 09.

Saliva testing is accurate for early-stage and presymptomatic COVID-19

Abigail J. Johnson, Shannon Zhou, Suzie L. Hoops, Benjamin Hillmann, Matthew Schomaker, Robyn Kincaid, Jerry Daniel, Kenneth Beckman, Daryl M. Gohl, Sophia Yohe, Dan Knights, Andrew C. Nelson

Microbiology Spectrum. 9(1) e00086-21. 2021 July 14.

Biological Aging Predicts Vulnerability to COVID-19 Severity in UK Biobank Participants

Kuo CL, Pilling LC, Atkins JL, Masoli JAH, Delgado J, Tignanelli C, Kuchel GA, Melzer D, Beckman KB, Levine ME

J Gerontol A Biol Sci Med Sci. 2021 Jul 13;76(8):e133-e141.

Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing

Morgan E. Meissner, Emily J. Julik, Jonathan P. Badalamenti, William G. Arndt, Lauren J. Mills, Louis M. Mansky

Viruses. 13(7),1338. 2021 July 11. 

Neither Donor nor Recipient Mitochondrial Haplotypes Are Associated with Unrelated Donor Transplant Outcomes: A Validation Study from the CIBMTR

Logan G. Spector, Stephen R. Spellman, Bharat Thyagarajan, Kenneth B. Beckman, Cody Hoffmann, John Garbe, Theresa Hahn, Lara Sucheston-Campbell, Michaela Richardson, Todd E. De For, Jakub Tolar, Michael R.Verneris

Transplantation and Cellular Therapy. doi: 10.1016/j.jtct.2021.06.019. 2021 June 23. 

Dissecting and tuning primer editing by proofreading polymerases

Daryl M Gohl, Benjamin Auch, Amanda Certano, Brice LeFrançois, Anne Bouevitch, Evgueni Doukhanine, Christina Fragel, Jean Macklaim, Emily Hollister, John Garbe, Kenneth B Beckman

Nucleic Acids Research. 2021 14 June, gkab471.

Prediction of false positive SARS-CoV-2 molecular results in a high-throughput open platform system

Ryan John Martinez, Nathan Pankratz, Matthew Schomaker, Jerry Daniel, Kenneth Beckman, Amy BethKarger, Bharat Thyagarajan, Patricia Ferreri, Sophia Louise Yohe, Andrew Cook Nelson

The Journal of Molecular Diagnostics. Available online 8 June 2021.

Low frequency variants associated with leukocyte telomere length in the Singapore Chinese population

Xuling Chang, Resham L Gurung, Ling Wang, Aizhen Jin, Zheng Li, Renwei Wang, Kenneth B Beckman, Jennifer Adams-Haduch, Wee Yang Meah, Kar Seng Sim, Weng Khong Lim, Sonia Davila, Patrick Tan, Jing Xian Teo, Khung Keong Yeo, Yiamunaa M, Sylvia Liu, Su Chi Lim, Jianjun Liu, Rob M van Dam, Yechiel Friedlander, Woon-Puay Koh, Jian-Min Yuan, Chiea Chuen Khor, Chew-Kiat Heng, Rajkumar Dorajoo

Commun Biol. 2021 May 3;4(1):519. 

Leukocyte telomere length, cancer incidence and all-cause mortality among Chinese adults: Singapore Chinese Health Study

Hamed Samavat, Hung N Luu, Kenneth B Beckman, Aizhen Jin, Renwei Wang, Woon-Puay Koh, Jian-Min Yuan

Int J Cancer. 2021 Jan 15;148(2):352-362.

2020

A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2

Daryl M Gohl, John Garbe, Patrick Grady, Jerry Daniel, Ray H B Watson, Benjamin Auch, Andrew Nelson, Sophia Yohe, Kenneth B Beckman

Nucleic Acids Research. 2020 Dec 4;21(1):863.

Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma

Lauren J Mills, Milcah C Scott, Pankti Shah, Anne R Cunanan, Archana Deshpande, Benjamin Auch, Bridget Curtin, Kenneth B Beckman, Logan G Spector, Aaron L Sarver, Subbaya Subramanian, Todd A Richmond, Jaime F Modiano

Bone. 2020 Oct 27;115716. Online ahead of print. 

Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

Jessica K. Fiege, Joshua M. Thiede, Hezkiel Nanda, William E. Matchett, Patrick J. Moore, Noe Rico Montanari, Beth K. Thielen, Jerry Daniel, Emma Stanley, Ryan C. Hunter, Vineet D. Menachery, Steven S. Shen, Tyler D. Bold, Ryan A. Langlois

bioRxiv 343954. 2020 Oct 19.

Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung

Christopher L Seiler, J Ung Min Song, Delshanee Kotandeniya, Jianji Chen, Thomas J Y Kono, Qiyuan Han, Mathia Colwell, Benjamin Auch, Aaron L Sarver, Pramod Upadhyaya, Yanan Ren, Christopher Faulk, Silvio De Flora, Sebastiano La Maestra, Yue Chen, Fekadu Kassie, Natalia Y Tretyakova

Sci Rep. 2020 Jul 9;10(1):11290. 

Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer

Yingming Li, Rendong Yang, Christine M Henzler, Yeung Ho, Courtney Passow, Benjamin Auch, Suzanne Carreira, Daniel Nava Rodrigues, Claudia Bertan, Tae Hyun Hwang, David A Quigley, Ha X Dang, Colm Morrissey, Michael Frase, Stephen R Plymate, Christopher A Maher, Felix Y Feng, Johann S de Bono, Scott M Dehm

Clin Cancer Res. 2020 Apr 15;26(8):1965-1976.

2019

Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii

Nardini L, Holm I, Pain A, Bischoff E, Gohl DM, Zongo S, Guelbeogo W, Sagnon N, Vernick KD & Riehle MM.

Scientific Reports. 2019 Oct 24. 9(1):15275.


Association between mitochondrial genetic variation and breast cancer risk: The Multiethnic Cohort

Li Y, Giorgi E, Beckman KB, Caberto C, Kazma R, Lum-Jones A, Haiman C, Marchand L, Stram D, Saxena R, Cheng I.

PLos One. 2019 Oct 2. 14(10):e0222284.


Identification of Target Genes Mediated by Two-Component Regulators of Staphylococcus aureus Using RNA-Seq Technology

Lei T, Yang J, Becker AD, Ji Y.

Methods Mol Biol. 2019 Sept 16. 2020, 2069:125-138.


Genome projects in invasion biology

McCartney MA, Mallez S, Gohl DM.

Conservation Genetics. 2019 Sept 11. 20 (6):1201-1222.


Stress responses, M2 macrophages, and a distinct microbial signature in fatal intestinal acute graft-vesus-host disease

Holtan S, Shabaneh A, Betts B, Rashidi A, MacMillan M, Ustun C, Amin K, Vaughn B, Howard J, Khoruts A, Arora M, DeFor T, Johnson D, Blazar B, Weisdorf D, Wang J.

JCI Insight. 2019 Aug 8. 4(17):e129762.


Performance of gene expression analyses using de novo assembled transcripts in polyploid species.

Chen LY, Morales-Briones DF, Passow CN, Ya Y.

Bioinformatics. 2019 Aug 10. pii: btz620.


Long-term tolerance of islet allografts in nonhuman primates induced by apoptotic donor leukocytes.

Singh A, Ramachandran S, Graham ML, Daneshmandi S, Heller D, Suarez-Pinzon WL, Balamurugan AN, Ansite JD, Wilhelm JJ, Yang A, Zhang Y, Palani NP, Abrahante JE, Burlak C, Miller SD, Luo X, Hering BJ.

Nat Commun. 2019 Aug 2;10(1):3495.


The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research.

McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan S, Sone ED, Koren S, Silverstein KAT, Beckman KB, Gohl DM.

bioRxiv 696732. 2019 July 9.


Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification.

Gohl DM, Magli A, Garbe J, Becker A, Johnson DM, Anderson S, Auch B, Billstein B, Froehling E, McDevitt SL, Beckman KB.

Genome Biol. 2019 Apr 29;20(1):85.


Loci for human leukocyte telomere length in the Singaporean Chinese population and transethnic genetic studies.

Dorajoo R, Chang X, Gurung RL, Li Z, Wang L, Wang R, Beckman KB, Adams-Haduch J, M Y, Liu S, Meah WY, Sim KS, Lim SC, Friedlander Y, Liu J, van Dam RM, Yuan JM, Koh WP, Khor CC, Heng CK.

Nat Commun. 2019 Jun 6;10(1):2491.


Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory.

Hartman P, Beckman K, Silverstein K, Yohe S, Schomaker M, Henzler C, Onsongo G, Lam HC, Munro S, Daniel J, Billstein B, Deshpande A, Hauge A, Mroz P, Lee W, Holle J, Wiens K, Karnuth K, Kemmer T, Leary M, Michel S, Pohlman L, Thayanithy V, Nelson A, Bower M, Thyagarajan B.

Mol Genet Metab Rep. 2019 Mar 1;19:100464.


Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways.

Minato Y, Gohl DM, Thiede JM, Chacón JM, Harcombe WR, Maruyama F, Baughn AD.

mSystems. 2019 Jun 25;4(4). pii: e00070-19.


Resequencing Study Confirms Host Defense and Cell Senescence Gene Variants Contribute to the Risk of Idiopathic Pulmonary Fibrosis.

Moore C et al (including Beckman KB).

Am J Respir Crit Care Med. 2019 Apr 29.

2018

Evaluating the Information Content of Shallow Shotgun Metagenomics.

Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D.

mSystems. 2018 Nov 13;3(6). pii: e00069-18.


Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF.

Dale JL, Beckman KB, Willett JLE, Nilson JL, Palani NP, Baller JA, Hauge A, Gohl DM, Erickson R, Manias DA, Sadowsky MJ, Dunny GM.

mSystems. 2018 Sep 11;3(5). pii: e00062-18.


Optimization of a microfluidics-based next generation sequencing assay for clinical oncology diagnostics.

Henzler C, Schomaker M, Yang R, Lambert AP, LaRue R, Kincaid R, Beckman K, Kemmer T, Wilson J, Yohe S, Thyagarajan B, Nelson AC.

Ann Transl Med. 2018 May;6(9):162.


Leukocyte telomere length in relation to risk of lung adenocarcinoma incidence: Findings from the Singapore Chinese Health Study.

Yuan JM, Beckman KB, Wang R, Bull C, Adams-Haduch J, Huang JY, Jin A, Opresko P, Newman AB, Zheng YL, Fenech M, Koh WP.

Int J Cancer. 2018 Jun 1;142(11):2234-2243.


EditR: A Method to Quantify Base Editing from Sanger Sequencing.

Kluesner MG, Nedveck DA, Lahr WS, Garbe JR, Abrahante JE, Webber BR, Moriarity BS.

CRISPR J. 2018 Jun;1:239-250.

2016

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies.

Gohl DM, Vangay P, Garbe J, MacLean A, Hauge A, Becker A, Gould TJ, Clayton JB, Johnson TJ, Hunter R, Knights D, Beckman KB.

Nat Biotechnol. 2016 Sep;34(9):942-9.


Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

Fingerlin TE, Zhang W, Yang IV, Ainsworth HC, Russell PH, Blumhagen RZ, Schwarz MI, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch DA, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Murphy E, Smith K, McKean D, Pedersen BS, Talbert J, Powers J, Markin CR, Beckman KB, Lathrop M, Freed B, Langefeld CD, Schwartz DA.

BMC Genet. 2016 Jun 7;17(1):74.


No Association between the Mitochondrial Genome and Prostate Cancer Risk: The Multiethnic Cohort.

Giorgi EE, Li Y, Caberto CP, Beckman KB, Lum-Jones A, Haiman CA, Le Marchand L, Stram DO, Saxena R, Cheng I.

Cancer Epidemiol Biomarkers Prev. 2016 Jun;25(6):1001-3.


Toward clinical genomics in everyday medicine: perspectives and recommendations.

Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush J, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC.

Expert Rev Mol Diagn. 2016;16(5):521-32.

2017

The ecological landscape of microbiome science.

>Gohl DM.

 

Nat Biotechnol. 2017 Nov;35(11):1047-1049.


Single-Strand Consensus Sequencing Reveals that HIV Type but not Subtype Significantly Impacts Viral Mutation Frequencies and Spectra.

Rawson JMO, Gohl DM, Landman SR, Roth ME, Meissner ME, Peterson TS, Hodges JS, Beckman KB, Mansky LM.

J Mol Biol. 2017 Jul 21;429(15):2290-2307.


Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells.

Winterhoff BJ, Maile M, Mitra AK, Sebe A, Bazzaro M, Geller MA, Abrahante JE, Klein M, Hellweg R, Mullany SA, Beckman K, Daniel J, Starr TK.

Gynecol Oncol. 2017 Mar;144(3):598-606.


Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome.

Belda E, Coulibaly B, Fofana A, Beavogui AH, Traore SF, Gohl DM, Vernick KD, Riehle MM.

Sci Rep. 2017 Jun 12;7(1):3241.

2015

Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery.

Baldwin EA, Walther-Antonio M, MacLean AM, Gohl DM, Beckman KB, Chen J, White B, Creedon DJ, Chia N.

PeerJ. 2015 Nov 26;3:e1398.


Association of Genes, Pathways, and Haplogroups of the Mitochondrial Genome with the Risk of Colorectal Cancer: The Multiethnic Cohort.

Li Y, Beckman KB, Caberto C, Kazma R, Lum-Jones A, Haiman CA, Le Marchand L, Stram DO, Saxena R, Cheng I.

PLoS One. 2015 Sep 4;10(9):e0136796.


mRNA 3‘-UTR shortening is a molecular signature of mTORC1 activation.

Chang JW, Zhang W, Yeh HS, de Jong EP, Jun S, Kim KH, Bae SS, Beckman K, Hwang TH, Kim KS, Kim DH, Griffin TJ, Kuang R, Yong J.

Nat Commun. 2015 Jun 15;6:7218.


Next generation sequencing in endocrine practice.

Forlenza GP, Calhoun A, Beckman KB, Halvorsen T, Hamdoun E, Zierhut H, Sarafoglou K, Polgreen LE, Miller BS, Nathan B, Petryk A.

Mol Genet Metab. 2015 Jun-Jul;115(2-3):61-71.


Clinical validation of targeted next-generation sequencing for inherited disorders.

Yohe S, Hauge A, Bunjer K, Kemmer T, Bower M, Schomaker M, Onsongo G, Wilson J, Erdmann J, Zhou Y, Deshpande A, Spears MD, Beckman K, Silverstein KA, Thyagarajan B.

Arch Pathol Lab Med. 2015 Feb;139(2):204-10.

2014

Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25.

Fejerman L, Ahmadiyeh N, Hu D, Huntsman S, Beckman KB, Caswell JL, Tsung K, John EM, Torres-Mejia G, Carvajal-Carmona L, Echeverry MM, Tuazon AM, Ramirez C; COLUMBUS Consortium, Gignoux CR, Eng C, Gonzalez-Burchard E, Henderson B, Le Marchand L, Kooperberg C, Hou L, Agalliu I, Kraft P, Lindström S, Perez-Stable EJ, Haiman CA, Ziv E.

Nat Commun. 2014 Oct 20;5:5260.


Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

Onsongo G, Erdmann J, Spears MD, Chilton J, Beckman KB, Hauge A, Yohe S, Schomaker M, Bower M, Silverstein KA, Thyagarajan B.

BMC Res Notes. 2014 May 23;7:314.


Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D.

Genome Res. 2014 Jan;24(1):14-24.


Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing.

Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, MacKinnon DF, Notes L, Schweizer B, Furman D, Montgomery SB, Urban AE, Koller D, Levinson DF.

Mol Psychiatry. 2014 Dec;19(12):1267-74.


Transcriptomic analysis of Staphylococcus aureus using microarray and advanced next-generation RNA-seq technologies.

Lei T, Becker A, Ji Y.

Methods Mol Biol. 2014;1085:213-29.


Identification of a new target of miR-16, Vacuolar Protein Sorting 4a.

Adhikari N, Guan W, Capaldo B, Mackey AJ, Carlson M, Ramakrishnan S, Walek D, Gupta M, Mitchell A, Eckman P, John R, Ashley E, Barton PJ, Hall JL.

PLoS One. 2014 Jul 17;9(7):e101509.


Vascular biomechanical properties in mice with smooth muscle specific deletion of Ndst1.

Adhikari N, Billaud M, Carlson M, Lake SP, Montaniel KR, Staggs R, Guan W, Walek D, Desir S, Isakson BE, Barocas VH, Hall JL.

Mol Cell Biochem. 2014 Jan;385(1-2):225-38.


Fed state prior to hemorrhagic shock and polytrauma in a porcine model results in altered liver transcriptomic response.

Determan C Jr, Anderson R, Becker A, Witowski N, Lusczek E, Mulier K, Beilman GJ.

PLoS One. 2014 Jun 17;9(6):e100088.

2013

Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.

Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Cogan JD, Mason WR, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Smith K, McKean D, Pedersen BS, Talbert J, Kidd RN, Markin CR, Beckman KB, Lathrop M, Schwarz MI, Schwartz DA.

Nat Genet. 2013 Jun;45(6):613-20.


Genetic and environmental predictors of serum 25-hydroxyvitamin D concentrations among middle-aged and elderly Chinese in Singapore.

Robien K, Butler LM, Wang R, Beckman KB, Walek D, Koh WP, Yuan JM.

Br J Nutr. 2013 Feb 14;109(3):493-502.