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Items: 25

1.

Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small-Cell Lung Cancer.

Chang H, Sasson A, Srinivasan S, Golhar R, Greenawalt DM, Geese WJ, Green G, Zerba K, Kirov S, Szustakowski J.

Mol Diagn Ther. 2019 Aug;23(4):507-520. doi: 10.1007/s40291-019-00408-y.

2.

STK11/LKB1 Mutations and PD-1 Inhibitor Resistance in KRAS-Mutant Lung Adenocarcinoma.

Skoulidis F, Goldberg ME, Greenawalt DM, Hellmann MD, Awad MM, Gainor JF, Schrock AB, Hartmaier RJ, Trabucco SE, Gay L, Ali SM, Elvin JA, Singal G, Ross JS, Fabrizio D, Szabo PM, Chang H, Sasson A, Srinivasan S, Kirov S, Szustakowski J, Vitazka P, Edwards R, Bufill JA, Sharma N, Ou SI, Peled N, Spigel DR, Rizvi H, Aguilar EJ, Carter BW, Erasmus J, Halpenny DF, Plodkowski AJ, Long NM, Nishino M, Denning WL, Galan-Cobo A, Hamdi H, Hirz T, Tong P, Wang J, Rodriguez-Canales J, Villalobos PA, Parra ER, Kalhor N, Sholl LM, Sauter JL, Jungbluth AA, Mino-Kenudson M, Azimi R, Elamin YY, Zhang J, Leonardi GC, Jiang F, Wong KK, Lee JJ, Papadimitrakopoulou VA, Wistuba II, Miller VA, Frampton GM, Wolchok JD, Shaw AT, Jänne PA, Stephens PJ, Rudin CM, Geese WJ, Albacker LA, Heymach JV.

Cancer Discov. 2018 Jul;8(7):822-835. doi: 10.1158/2159-8290.CD-18-0099. Epub 2018 May 17.

3.

Comparative analysis of primary versus relapse/refractory DLBCL identifies shifts in mutation spectrum.

Greenawalt DM, Liang WS, Saif S, Johnson J, Todorov P, Dulak A, Enriquez D, Halperin R, Ahmed A, Saveliev V, Carpten J, Craig D, Barrett JC, Dougherty B, Zinda M, Fawell S, Dry JR, Byth K.

Oncotarget. 2017 Jun 15;8(59):99237-99244. doi: 10.18632/oncotarget.18502. eCollection 2017 Nov 21.

4.

Rational Selection of Syngeneic Preclinical Tumor Models for Immunotherapeutic Drug Discovery.

Mosely SI, Prime JE, Sainson RC, Koopmann JO, Wang DY, Greenawalt DM, Ahdesmaki MJ, Leyland R, Mullins S, Pacelli L, Marcus D, Anderton J, Watkins A, Coates Ulrichsen J, Brohawn P, Higgs BW, McCourt M, Jones H, Harper JA, Morrow M, Valge-Archer V, Stewart R, Dovedi SJ, Wilkinson RW.

Cancer Immunol Res. 2017 Jan;5(1):29-41. doi: 10.1158/2326-6066.CIR-16-0114. Epub 2016 Dec 6.

5.

A multigene mutation classification of 468 colorectal cancers reveals a prognostic role for APC.

Schell MJ, Yang M, Teer JK, Lo FY, Madan A, Coppola D, Monteiro AN, Nebozhyn MV, Yue B, Loboda A, Bien-Willner GA, Greenawalt DM, Yeatman TJ.

Nat Commun. 2016 Jun 15;7:11743. doi: 10.1038/ncomms11743.

6.

Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.

Knowles JW, Xie W, Zhang Z, Chennamsetty I, Assimes TL, Paananen J, Hansson O, Pankow J, Goodarzi MO, Carcamo-Orive I, Morris AP, Chen YD, Mäkinen VP, Ganna A, Mahajan A, Guo X, Abbasi F, Greenawalt DM, Lum P, Molony C, Lind L, Lindgren C, Raffel LJ, Tsao PS; RISC (Relationship between Insulin Sensitivity and Cardiovascular Disease) Consortium; EUGENE (European Network on Functional Genomics of Type Diabetes) Study; GUARDIAN (Genetics UndeRlying DIAbetes in HispaNics) Consortium; SAPPHIRe (Stanford Asian and Pacific Program for Hypertension and Insulin Resistance) Study, Schadt EE, Rotter JI, Sinaiko A, Reaven G, Yang X, Hsiung CA, Groop L, Cordell HJ, Laakso M, Hao K, Ingelsson E, Frayling TM, Weedon MN, Walker M, Quertermous T.

J Clin Invest. 2016 Jan;126(1):403. doi: 10.1172/JCI85921. Epub 2016 Jan 4. No abstract available.

7.

Co-evolution of somatic variation in primary and metastatic colorectal cancer may expand biopsy indications in the molecular era.

Kim R, Schell MJ, Teer JK, Greenawalt DM, Yang M, Yeatman TJ.

PLoS One. 2015 May 14;10(5):e0126670. doi: 10.1371/journal.pone.0126670. eCollection 2015.

8.

Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.

Knowles JW, Xie W, Zhang Z, Chennamsetty I, Assimes TL, Paananen J, Hansson O, Pankow J, Goodarzi MO, Carcamo-Orive I, Morris AP, Chen YD, Mäkinen VP, Ganna A, Mahajan A, Guo X, Abbasi F, Greenawalt DM, Lum P, Molony C, Lind L, Lindgren C, Raffel LJ, Tsao PS; RISC (Relationship between Insulin Sensitivity and Cardiovascular Disease) Consortium; EUGENE2 (European Network on Functional Genomics of Type 2 Diabetes) Study; GUARDIAN (Genetics UndeRlying DIAbetes in HispaNics) Consortium; SAPPHIRe (Stanford Asian and Pacific Program for Hypertension and Insulin Resistance) Study, Schadt EE, Rotter JI, Sinaiko A, Reaven G, Yang X, Hsiung CA, Groop L, Cordell HJ, Laakso M, Hao K, Ingelsson E, Frayling TM, Weedon MN, Walker M, Quertermous T.

J Clin Invest. 2015 Apr;125(4):1739-51. doi: 10.1172/JCI74692. Epub 2015 Mar 23. Erratum in: J Clin Invest. 2016 Jan;126(1):403. Chennemsetty, Indumathi [corrected to Chennamsetty, Indumathi].

9.

Weight loss after gastric bypass is associated with a variant at 15q26.1.

Hatoum IJ, Greenawalt DM, Cotsapas C, Daly MJ, Reitman ML, Kaplan LM.

Am J Hum Genet. 2013 May 2;92(5):827-34. doi: 10.1016/j.ajhg.2013.04.009.

10.

Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets.

Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, Wang IM, Dai H, Bruss MD, Lum PY, Zhou YP, Kemp DM, Kendziorski C, Yandell BS, Attie AD, Schadt EE, Zhu J.

PLoS Genet. 2012;8(12):e1003107. doi: 10.1371/journal.pgen.1003107. Epub 2012 Dec 6.

11.

Inverse regulation of inflammation and mitochondrial function in adipose tissue defines extreme insulin sensitivity in morbidly obese patients.

Qatanani M, Tan Y, Dobrin R, Greenawalt DM, Hu G, Zhao W, Olefsky JM, Sears DD, Kaplan LM, Kemp DM.

Diabetes. 2013 Mar;62(3):855-63. doi: 10.2337/db12-0399. Epub 2012 Dec 6.

12.

Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility Loci for type 2 diabetes mellitus.

Greenawalt DM, Sieberts SK, Cornelis MC, Girman CJ, Zhong H, Yang X, Guinney J, Qi L, Hu FB.

Am J Epidemiol. 2012 Sep 1;176(5):423-30. doi: 10.1093/aje/kws123. Epub 2012 Aug 2.

13.

Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.

Fox CS, Liu Y, White CC, Feitosa M, Smith AV, Heard-Costa N, Lohman K; GIANT Consortium; MAGIC Consortium; GLGC Consortium, Johnson AD, Foster MC, Greenawalt DM, Griffin P, Ding J, Newman AB, Tylavsky F, Miljkovic I, Kritchevsky SB, Launer L, Garcia M, Eiriksdottir G, Carr JJ, Gudnason V, Harris TB, Cupples LA, Borecki IB.

PLoS Genet. 2012;8(5):e1002695. doi: 10.1371/journal.pgen.1002695. Epub 2012 May 10.

14.

Dissecting cis regulation of gene expression in human metabolic tissues.

Dobrin R, Greenawalt DM, Hu G, Kemp DM, Kaplan LM, Schadt EE, Emilsson V.

PLoS One. 2011;6(8):e23480. doi: 10.1371/journal.pone.0023480. Epub 2011 Aug 31.

15.

Heritability of the weight loss response to gastric bypass surgery.

Hatoum IJ, Greenawalt DM, Cotsapas C, Reitman ML, Daly MJ, Kaplan LM.

J Clin Endocrinol Metab. 2011 Oct;96(10):E1630-3. doi: 10.1210/jc.2011-1130. Epub 2011 Aug 10.

16.

A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort.

Greenawalt DM, Dobrin R, Chudin E, Hatoum IJ, Suver C, Beaulaurier J, Zhang B, Castro V, Zhu J, Sieberts SK, Wang S, Molony C, Heymsfield SB, Kemp DM, Reitman ML, Lum PY, Schadt EE, Kaplan LM.

Genome Res. 2011 Jul;21(7):1008-16. doi: 10.1101/gr.112821.110. Epub 2011 May 20.

17.

Pretreatment transcriptional profiling for predicting response to neoadjuvant chemoradiotherapy in rectal adenocarcinoma.

Brettingham-Moore KH, Duong CP, Greenawalt DM, Heriot AG, Ellul J, Dow CA, Murray WK, Hicks RJ, Tjandra J, Chao M, Bui A, Joon DL, Thomas RJ, Phillips WA.

Clin Cancer Res. 2011 May 1;17(9):3039-47. doi: 10.1158/1078-0432.CCR-10-2915. Epub 2011 Jan 11.

18.

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.

Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, Lango Allen H, Lindgren CM, Luan J, Mägi R, Randall JC, Vedantam S, Winkler TW, Qi L, Workalemahu T, Heid IM, Steinthorsdottir V, Stringham HM, Weedon MN, Wheeler E, Wood AR, Ferreira T, Weyant RJ, Segrè AV, Estrada K, Liang L, Nemesh J, Park JH, Gustafsson S, Kilpeläinen TO, Yang J, Bouatia-Naji N, Esko T, Feitosa MF, Kutalik Z, Mangino M, Raychaudhuri S, Scherag A, Smith AV, Welch R, Zhao JH, Aben KK, Absher DM, Amin N, Dixon AL, Fisher E, Glazer NL, Goddard ME, Heard-Costa NL, Hoesel V, Hottenga JJ, Johansson A, Johnson T, Ketkar S, Lamina C, Li S, Moffatt MF, Myers RH, Narisu N, Perry JR, Peters MJ, Preuss M, Ripatti S, Rivadeneira F, Sandholt C, Scott LJ, Timpson NJ, Tyrer JP, van Wingerden S, Watanabe RM, White CC, Wiklund F, Barlassina C, Chasman DI, Cooper MN, Jansson JO, Lawrence RW, Pellikka N, Prokopenko I, Shi J, Thiering E, Alavere H, Alibrandi MT, Almgren P, Arnold AM, Aspelund T, Atwood LD, Balkau B, Balmforth AJ, Bennett AJ, Ben-Shlomo Y, Bergman RN, Bergmann S, Biebermann H, Blakemore AI, Boes T, Bonnycastle LL, Bornstein SR, Brown MJ, Buchanan TA, Busonero F, Campbell H, Cappuccio FP, Cavalcanti-Proença C, Chen YD, Chen CM, Chines PS, Clarke R, Coin L, Connell J, Day IN, den Heijer M, Duan J, Ebrahim S, Elliott P, Elosua R, Eiriksdottir G, Erdos MR, Eriksson JG, Facheris MF, Felix SB, Fischer-Posovszky P, Folsom AR, Friedrich N, Freimer NB, Fu M, Gaget S, Gejman PV, Geus EJ, Gieger C, Gjesing AP, Goel A, Goyette P, Grallert H, Grässler J, Greenawalt DM, Groves CJ, Gudnason V, Guiducci C, Hartikainen AL, Hassanali N, Hall AS, Havulinna AS, Hayward C, Heath AC, Hengstenberg C, Hicks AA, Hinney A, Hofman A, Homuth G, Hui J, Igl W, Iribarren C, Isomaa B, Jacobs KB, Jarick I, Jewell E, John U, Jørgensen T, Jousilahti P, Jula A, Kaakinen M, Kajantie E, Kaplan LM, Kathiresan S, Kettunen J, Kinnunen L, Knowles JW, Kolcic I, König IR, Koskinen S, Kovacs P, Kuusisto J, Kraft P, Kvaløy K, Laitinen J, Lantieri O, Lanzani C, Launer LJ, Lecoeur C, Lehtimäki T, Lettre G, Liu J, Lokki ML, Lorentzon M, Luben RN, Ludwig B; MAGIC, Manunta P, Marek D, Marre M, Martin NG, McArdle WL, McCarthy A, McKnight B, Meitinger T, Melander O, Meyre D, Midthjell K, Montgomery GW, Morken MA, Morris AP, Mulic R, Ngwa JS, Nelis M, Neville MJ, Nyholt DR, O'Donnell CJ, O'Rahilly S, Ong KK, Oostra B, Paré G, Parker AN, Perola M, Pichler I, Pietiläinen KH, Platou CG, Polasek O, Pouta A, Rafelt S, Raitakari O, Rayner NW, Ridderstråle M, Rief W, Ruokonen A, Robertson NR, Rzehak P, Salomaa V, Sanders AR, Sandhu MS, Sanna S, Saramies J, Savolainen MJ, Scherag S, Schipf S, Schreiber S, Schunkert H, Silander K, Sinisalo J, Siscovick DS, Smit JH, Soranzo N, Sovio U, Stephens J, Surakka I, Swift AJ, Tammesoo ML, Tardif JC, Teder-Laving M, Teslovich TM, Thompson JR, Thomson B, Tönjes A, Tuomi T, van Meurs JB, van Ommen GJ, Vatin V, Viikari J, Visvikis-Siest S, Vitart V, Vogel CI, Voight BF, Waite LL, Wallaschofski H, Walters GB, Widen E, Wiegand S, Wild SH, Willemsen G, Witte DR, Witteman JC, Xu J, Zhang Q, Zgaga L, Ziegler A, Zitting P, Beilby JP, Farooqi IS, Hebebrand J, Huikuri HV, James AL, Kähönen M, Levinson DF, Macciardi F, Nieminen MS, Ohlsson C, Palmer LJ, Ridker PM, Stumvoll M, Beckmann JS, Boeing H, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Collins FS, Cupples LA, Smith GD, Erdmann J, Froguel P, Grönberg H, Gyllensten U, Hall P, Hansen T, Harris TB, Hattersley AT, Hayes RB, Heinrich J, Hu FB, Hveem K, Illig T, Jarvelin MR, Kaprio J, Karpe F, Khaw KT, Kiemeney LA, Krude H, Laakso M, Lawlor DA, Metspalu A, Munroe PB, Ouwehand WH, Pedersen O, Penninx BW, Peters A, Pramstaller PP, Quertermous T, Reinehr T, Rissanen A, Rudan I, Samani NJ, Schwarz PE, Shuldiner AR, Spector TD, Tuomilehto J, Uda M, Uitterlinden A, Valle TT, Wabitsch M, Waeber G, Wareham NJ, Watkins H; Procardis Consortium, Wilson JF, Wright AF, Zillikens MC, Chatterjee N, McCarroll SA, Purcell S, Schadt EE, Visscher PM, Assimes TL, Borecki IB, Deloukas P, Fox CS, Groop LC, Haritunians T, Hunter DJ, Kaplan RC, Mohlke KL, O'Connell JR, Peltonen L, Schlessinger D, Strachan DP, van Duijn CM, Wichmann HE, Frayling TM, Thorsteinsdottir U, Abecasis GR, Barroso I, Boehnke M, Stefansson K, North KE, McCarthy MI, Hirschhorn JN, Ingelsson E, Loos RJ.

Nat Genet. 2010 Nov;42(11):937-48. doi: 10.1038/ng.686. Epub 2010 Oct 10.

19.

Common body mass index-associated variants confer risk of extreme obesity.

Cotsapas C, Speliotes EK, Hatoum IJ, Greenawalt DM, Dobrin R, Lum PY, Suver C, Chudin E, Kemp D, Reitman M, Voight BF, Neale BM, Schadt EE, Hirschhorn JN, Kaplan LM, Daly MJ; GIANT Consortium.

Hum Mol Genet. 2009 Sep 15;18(18):3502-7. doi: 10.1093/hmg/ddp292. Epub 2009 Jun 24. Erratum in: Hum Mol Genet. 2010 Sep 15;19(18):3690-1.

20.

Genetic structures of copy number variants revealed by genotyping single sperm.

Luo M, Cui X, Fredman D, Brookes AJ, Azaro MA, Greenawalt DM, Hu G, Wang HY, Tereshchenko IV, Lin Y, Shentu Y, Gao R, Shen L, Li H.

PLoS One. 2009;4(4):e5236. doi: 10.1371/journal.pone.0005236. Epub 2009 Apr 22.

21.

High-throughput genotyping of single nucleotide polymorphisms with high sensitivity.

Li H, Wang HY, Cui X, Luo M, Hu G, Greenawalt DM, Tereshchenko IV, Li JY, Chu Y, Gao R.

Methods Mol Biol. 2007;396:281-94.

PMID:
18025699
22.

Pretreatment gene expression profiles can be used to predict response to neoadjuvant chemoradiotherapy in esophageal cancer.

Duong C, Greenawalt DM, Kowalczyk A, Ciavarella ML, Raskutti G, Murray WK, Phillips WA, Thomas RJ.

Ann Surg Oncol. 2007 Dec;14(12):3602-9. Epub 2007 Sep 26.

PMID:
17896157
23.

Gene expression profiling of esophageal cancer: comparative analysis of Barrett's esophagus, adenocarcinoma, and squamous cell carcinoma.

Greenawalt DM, Duong C, Smyth GK, Ciavarella ML, Thompson NJ, Tiang T, Murray WK, Thomas RJ, Phillips WA.

Int J Cancer. 2007 May 1;120(9):1914-21.

24.

AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays.

Hu G, Wang HY, Greenawalt DM, Azaro MA, Luo M, Tereshchenko IV, Cui X, Yang Q, Gao R, Shen L, Li H.

Nucleic Acids Res. 2006;34(17):e116. Epub 2006 Sep 18.

25.

Strong correlation between meiotic crossovers and haplotype structure in a 2.5-Mb region on the long arm of chromosome 21.

Greenawalt DM, Cui X, Wu Y, Lin Y, Wang HY, Luo M, Tereshchenko IV, Hu G, Li JY, Chu Y, Azaro MA, Decoste CJ, Chimge NO, Gao R, Shen L, Shih WJ, Lange K, Li H.

Genome Res. 2006 Feb;16(2):208-14. Epub 2005 Dec 29.

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