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Items: 22

1.

Comprehensive Genomic Analysis of Metastatic Mucinous Urethral Adenocarcinoma Guides Precision Oncology Treatment: Targetable EGFR Amplification Leading to Successful Treatment With Erlotinib.

Bryce AH, Borad MJ, Egan JB, Condjella RM, Liang WS, Fonseca R, McCullough AE, Hunt KS, Ritacca NR, Barrett MT, Patel MD, Young SW, Silva AC, Ho TH, Halfdanarson TR, Stanton ML, Cheville J, Swanson S, Schneider DE, McWilliams RR, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Cuyugan L, McDonald J, Adkins J, Mastrian SD, Von Hoff DD, Craig DW, Stewart AK, Carpten JD.

Clin Genitourin Cancer. 2017 Aug;15(4):e727-e734. doi: 10.1016/j.clgc.2016.11.001. Epub 2016 Dec 1. No abstract available.

2.

Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers.

Borad MJ, Egan JB, Condjella RM, Liang WS, Fonseca R, Ritacca NR, McCullough AE, Barrett MT, Hunt KS, Champion MD, Patel MD, Young SW, Silva AC, Ho TH, Halfdanarson TR, McWilliams RR, Lazaridis KN, Ramanathan RK, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Cuyugan L, McDonald J, Adkins J, Mastrian SD, Valdez R, Jaroszewski DE, Von Hoff DD, Craig DW, Stewart AK, Carpten JD, Bryce AH.

Sci Rep. 2016 Dec 23;6(1):25. doi: 10.1038/s41598-016-0021-4.

3.

Novel pathogenic variants and genes for myopathies identified by whole exome sequencing.

Hunter JM, Ahearn ME, Balak CD, Liang WS, Kurdoglu A, Corneveaux JJ, Russell M, Huentelman MJ, Craig DW, Carpten J, Coons SW, DeMello DE, Hall JG, Bernes SM, Baumbach-Reardon L.

Mol Genet Genomic Med. 2015 Jul;3(4):283-301. doi: 10.1002/mgg3.142. Epub 2015 Apr 8.

4.

A Frame-Shift Mutation in CAV1 Is Associated with a Severe Neonatal Progeroid and Lipodystrophy Syndrome.

Schrauwen I, Szelinger S, Siniard AL, Kurdoglu A, Corneveaux JJ, Malenica I, Richholt R, Van Camp G, De Both M, Swaminathan S, Turk M, Ramsey K, Craig DW, Narayanan V, Huentelman MJ.

PLoS One. 2015 Jul 15;10(7):e0131797. doi: 10.1371/journal.pone.0131797. eCollection 2015.

5.

A De Novo Mutation in TEAD1 Causes Non-X-Linked Aicardi Syndrome.

Schrauwen I, Szelinger S, Siniard AL, Corneveaux JJ, Kurdoglu A, Richholt R, De Both M, Malenica I, Swaminathan S, Rangasamy S, Kulkarni N, Bernes S, Buchhalter J, Ramsey K, Craig DW, Narayanan V, Huentelman MJ.

Invest Ophthalmol Vis Sci. 2015 Jun;56(6):3896-904. doi: 10.1167/iovs.14-16261.

PMID:
26091538
6.

Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.

Szelinger S, Malenica I, Corneveaux JJ, Siniard AL, Kurdoglu AA, Ramsey KM, Schrauwen I, Trent JM, Narayanan V, Huentelman MJ, Craig DW.

PLoS One. 2014 Dec 12;9(12):e113036. doi: 10.1371/journal.pone.0113036. eCollection 2014.

7.

Alzheimer's disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes.

Sekar S, McDonald J, Cuyugan L, Aldrich J, Kurdoglu A, Adkins J, Serrano G, Beach TG, Craig DW, Valla J, Reiman EM, Liang WS.

Neurobiol Aging. 2015 Feb;36(2):583-91. doi: 10.1016/j.neurobiolaging.2014.09.027. Epub 2014 Oct 2.

8.

Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer.

Shanmugam V, Ramanathan RK, Lavender NA, Sinari S, Chadha M, Liang WS, Kurdoglu A, Izatt T, Christoforides A, Benson H, Phillips L, Baker A, Murray C, Hostetter G, Von Hoff DD, Craig DW, Carpten JD.

BMC Med Genomics. 2014 Jun 18;7:36. doi: 10.1186/1755-8794-7-36.

9.

Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma.

Borad MJ, Champion MD, Egan JB, Liang WS, Fonseca R, Bryce AH, McCullough AE, Barrett MT, Hunt K, Patel MD, Young SW, Collins JM, Silva AC, Condjella RM, Block M, McWilliams RR, Lazaridis KN, Klee EW, Bible KC, Harris P, Oliver GR, Bhavsar JD, Nair AA, Middha S, Asmann Y, Kocher JP, Schahl K, Kipp BR, Barr Fritcher EG, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Phillips L, McDonald J, Adkins J, Mastrian SD, Placek P, Watanabe AT, Lobello J, Han H, Von Hoff D, Craig DW, Stewart AK, Carpten JD.

PLoS Genet. 2014 Feb 13;10(2):e1004135. doi: 10.1371/journal.pgen.1004135. eCollection 2014 Feb.

10.

Simultaneous characterization of somatic events and HPV-18 integration in a metastatic cervical carcinoma patient using DNA and RNA sequencing.

Liang WS, Aldrich J, Nasser S, Kurdoglu A, Phillips L, Reiman R, McDonald J, Izatt T, Christoforides A, Baker A, Craig C, Egan JB, Chase DM, Farley JH, Bryce AH, Stewart AK, Borad MJ, Carpten JD, Craig DW, Monk BJ.

Int J Gynecol Cancer. 2014 Feb;24(2):329-38. doi: 10.1097/IGC.0000000000000049.

11.

A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges.

Weiss GJ, Liang WS, Demeure MJ, Kiefer JA, Hostetter G, Izatt T, Sinari S, Christoforides A, Aldrich J, Kurdoglu A, Phillips L, Benson H, Reiman R, Baker A, Marsh V, Von Hoff DD, Carpten JD, Craig DW.

PLoS One. 2013 Oct 30;8(10):e76438. doi: 10.1371/journal.pone.0076438. eCollection 2013.

12.

Long insert whole genome sequencing for copy number variant and translocation detection.

Liang WS, Aldrich J, Tembe W, Kurdoglu A, Cherni I, Phillips L, Reiman R, Baker A, Weiss GJ, Carpten JD, Craig DW.

Nucleic Acids Res. 2014 Jan;42(2):e8. doi: 10.1093/nar/gkt865. Epub 2013 Sep 25.

13.

In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue.

Hjelm BE, Salhia B, Kurdoglu A, Szelinger S, Reiman RA, Sue LI, Beach TG, Huentelman MJ, Craig DW.

Hum Mol Genet. 2013 Sep 1;22(17):3534-46. doi: 10.1093/hmg/ddt208. Epub 2013 May 10.

14.

Extramedullary myeloma whole genome sequencing reveals novel mutations in Cereblon, proteasome subunit G2 and the glucocorticoid receptor in multi drug resistant disease.

Egan JB, Kortuem KM, Kurdoglu A, Izatt T, Aldrich J, Reiman R, Phillips L, Baker A, Shi CX, Schmidt J, Liang WS, Craig DW, Carpten JD, Stewart AK.

Br J Haematol. 2013 Jun;161(5):748-51. doi: 10.1111/bjh.12291. Epub 2013 Mar 11. No abstract available.

15.

Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities.

Craig DW, O'Shaughnessy JA, Kiefer JA, Aldrich J, Sinari S, Moses TM, Wong S, Dinh J, Christoforides A, Blum JL, Aitelli CL, Osborne CR, Izatt T, Kurdoglu A, Baker A, Koeman J, Barbacioru C, Sakarya O, De La Vega FM, Siddiqui A, Hoang L, Billings PR, Salhia B, Tolcher AW, Trent JM, Mousses S, Von Hoff D, Carpten JD.

Mol Cancer Ther. 2013 Jan;12(1):104-16. doi: 10.1158/1535-7163.MCT-12-0781. Epub 2012 Nov 19.

16.

Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing.

Liang WS, Craig DW, Carpten J, Borad MJ, Demeure MJ, Weiss GJ, Izatt T, Sinari S, Christoforides A, Aldrich J, Kurdoglu A, Barrett M, Phillips L, Benson H, Tembe W, Braggio E, Kiefer JA, Legendre C, Posner R, Hostetter GH, Baker A, Egan JB, Han H, Lake D, Stites EC, Ramanathan RK, Fonseca R, Stewart AK, Von Hoff D.

PLoS One. 2012;7(10):e43192. doi: 10.1371/journal.pone.0043192. Epub 2012 Oct 10.

17.

Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma.

Weiss GJ, Liang WS, Izatt T, Arora S, Cherni I, Raju RN, Hostetter G, Kurdoglu A, Christoforides A, Sinari S, Baker AS, Metpally R, Tembe WD, Phillips L, Von Hoff DD, Craig DW, Carpten JD.

PLoS One. 2012;7(5):e37029. doi: 10.1371/journal.pone.0037029. Epub 2012 May 23.

18.

Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides.

Egan JB, Shi CX, Tembe W, Christoforides A, Kurdoglu A, Sinari S, Middha S, Asmann Y, Schmidt J, Braggio E, Keats JJ, Fonseca R, Bergsagel PL, Craig DW, Carpten JD, Stewart AK.

Blood. 2012 Aug 2;120(5):1060-6. doi: 10.1182/blood-2012-01-405977. Epub 2012 Apr 23.

19.

Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer.

Szelinger S, Kurdoglu A, Craig DW.

Methods Mol Biol. 2011;700:89-104. doi: 10.1007/978-1-61737-954-3_7.

PMID:
21204029
20.

Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum.

Lu YK, Marden J, Han M, Swingley WD, Mastrian SD, Chowdhury SR, Hao J, Helmy T, Kim S, Kurdoglu AA, Matthies HJ, Rollo D, Stothard P, Blankenship RE, Bauer CE, Touchman JW.

BMC Genomics. 2010 May 25;11:325. doi: 10.1186/1471-2164-11-325.

21.

The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus.

Sattley WM, Madigan MT, Swingley WD, Cheung PC, Clocksin KM, Conrad AL, Dejesa LC, Honchak BM, Jung DO, Karbach LE, Kurdoglu A, Lahiri S, Mastrian SD, Page LE, Taylor HL, Wang ZT, Raymond J, Chen M, Blankenship RE, Touchman JW.

J Bacteriol. 2008 Jul;190(13):4687-96. doi: 10.1128/JB.00299-08. Epub 2008 Apr 25.

22.

Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.

Swingley WD, Chen M, Cheung PC, Conrad AL, Dejesa LC, Hao J, Honchak BM, Karbach LE, Kurdoglu A, Lahiri S, Mastrian SD, Miyashita H, Page L, Ramakrishna P, Satoh S, Sattley WM, Shimada Y, Taylor HL, Tomo T, Tsuchiya T, Wang ZT, Raymond J, Mimuro M, Blankenship RE, Touchman JW.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2005-10. doi: 10.1073/pnas.0709772105. Epub 2008 Feb 5.

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