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Items: 27

1.

A machine learning approach for somatic mutation discovery.

Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA Jr, Jones S, Sausen M, Velculescu VE, Angiuoli SV.

Sci Transl Med. 2018 Sep 5;10(457). pii: eaar7939. doi: 10.1126/scitranslmed.aar7939.

2.

Direct detection of early-stage cancers using circulating tumor DNA.

Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, Anagnostou V, Fiksel J, Cristiano S, Papp E, Speir S, Reinert T, Orntoft MW, Woodward BD, Murphy D, Parpart-Li S, Riley D, Nesselbush M, Sengamalay N, Georgiadis A, Li QK, Madsen MR, Mortensen FV, Huiskens J, Punt C, van Grieken N, Fijneman R, Meijer G, Husain H, Scharpf RB, Diaz LA Jr, Jones S, Angiuoli S, ├śrntoft T, Nielsen HJ, Andersen CL, Velculescu VE.

Sci Transl Med. 2017 Aug 16;9(403). pii: eaan2415. doi: 10.1126/scitranslmed.aan2415.

PMID:
28814544
3.

Clinical study of genomic drivers in pancreatic ductal adenocarcinoma.

Barrett MT, Deiotte R, Lenkiewicz E, Malasi S, Holley T, Evers L, Posner RG, Jones T, Han H, Sausen M, Velculescu VE, Drebin J, O'Dwyer P, Jameson G, Ramanathan RK, Von Hoff DD.

Br J Cancer. 2017 Aug 8;117(4):572-582. doi: 10.1038/bjc.2017.209. Epub 2017 Jul 18.

4.

The Effect of Preservative and Temperature on the Analysis of Circulating Tumor DNA.

Parpart-Li S, Bartlett B, Popoli M, Adleff V, Tucker L, Steinberg R, Georgiadis A, Phallen J, Brahmer J, Azad N, Browner I, Laheru D, Velculescu VE, Sausen M, Diaz LA Jr.

Clin Cancer Res. 2017 May 15;23(10):2471-2477. doi: 10.1158/1078-0432.CCR-16-1691. Epub 2016 Nov 8.

5.

Whole-Exome Sequencing of Salivary Gland Mucoepidermoid Carcinoma.

Kang H, Tan M, Bishop JA, Jones S, Sausen M, Ha PK, Agrawal N.

Clin Cancer Res. 2017 Jan 1;23(1):283-288. doi: 10.1158/1078-0432.CCR-16-0720. Epub 2016 Jun 23.

6.

Genomic and Immunological Tumor Profiling Identifies Targetable Pathways and Extensive CD8+/PDL1+ Immune Infiltration in Inflammatory Breast Cancer Tumors.

Hamm CA, Moran D, Rao K, Trusk PB, Pry K, Sausen M, Jones S, Velculescu VE, Cristofanilli M, Bacus S.

Mol Cancer Ther. 2016 Jul;15(7):1746-56. doi: 10.1158/1535-7163.MCT-15-0353. Epub 2016 Apr 19.

7.

Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.

Rettig EM, Talbot CC Jr, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Ling S, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N.

Cancer Prev Res (Phila). 2016 Apr;9(4):265-74. doi: 10.1158/1940-6207.CAPR-15-0316. Epub 2016 Feb 9. Erratum in: Cancer Prev Res (Phila). 2018 Apr;11(4):249.

8.

The genomic landscape of response to EGFR blockade in colorectal cancer.

Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Lupo B, Sausen M, Phallen J, Hruban CA, Tokheim C, Niknafs N, Nesselbush M, Lytle K, Sassi F, Cottino F, Migliardi G, Zanella ER, Ribero D, Russolillo N, Mellano A, Muratore A, Paraluppi G, Salizzoni M, Marsoni S, Kragh M, Lantto J, Cassingena A, Li QK, Karchin R, Scharpf R, Sartore-Bianchi A, Siena S, Diaz LA Jr, Trusolino L, Velculescu VE.

Nature. 2015 Oct 8;526(7572):263-7. doi: 10.1038/nature14969. Epub 2015 Sep 30.

9.

Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients.

Sausen M, Phallen J, Adleff V, Jones S, Leary RJ, Barrett MT, Anagnostou V, Parpart-Li S, Murphy D, Kay Li Q, Hruban CA, Scharpf R, White JR, O'Dwyer PJ, Allen PJ, Eshleman JR, Thompson CB, Klimstra DS, Linehan DC, Maitra A, Hruban RH, Diaz LA Jr, Von Hoff DD, Johansen JS, Drebin JA, Velculescu VE.

Nat Commun. 2015 Jul 7;6:7686. doi: 10.1038/ncomms8686.

10.

Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas.

Wang Y, Springer S, Mulvey CL, Silliman N, Schaefer J, Sausen M, James N, Rettig EM, Guo T, Pickering CR, Bishop JA, Chung CH, Califano JA, Eisele DW, Fakhry C, Gourin CG, Ha PK, Kang H, Kiess A, Koch WM, Myers JN, Quon H, Richmon JD, Sidransky D, Tufano RP, Westra WH, Bettegowda C, Diaz LA Jr, Papadopoulos N, Kinzler KW, Vogelstein B, Agrawal N.

Sci Transl Med. 2015 Jun 24;7(293):293ra104. doi: 10.1126/scitranslmed.aaa8507.

11.

Personalized genomic analyses for cancer mutation discovery and interpretation.

Jones S, Anagnostou V, Lytle K, Parpart-Li S, Nesselbush M, Riley DR, Shukla M, Chesnick B, Kadan M, Papp E, Galens KG, Murphy D, Zhang T, Kann L, Sausen M, Angiuoli SV, Diaz LA Jr, Velculescu VE.

Sci Transl Med. 2015 Apr 15;7(283):283ra53. doi: 10.1126/scitranslmed.aaa7161.

12.

Circulating tumor DNA analysis as a real-time method for monitoring tumor burden in melanoma patients undergoing treatment with immune checkpoint blockade.

Lipson EJ, Velculescu VE, Pritchard TS, Sausen M, Pardoll DM, Topalian SL, Diaz LA Jr.

J Immunother Cancer. 2014 Dec 16;2(1):42. doi: 10.1186/s40425-014-0042-0. eCollection 2014.

13.

Somatic mutations of SUZ12 in malignant peripheral nerve sheath tumors.

Zhang M, Wang Y, Jones S, Sausen M, McMahon K, Sharma R, Wang Q, Belzberg AJ, Chaichana K, Gallia GL, Gokaslan ZL, Riggins GJ, Wolinksy JP, Wood LD, Montgomery EA, Hruban RH, Kinzler KW, Papadopoulos N, Vogelstein B, Bettegowda C.

Nat Genet. 2014 Nov;46(11):1170-2. doi: 10.1038/ng.3116. Epub 2014 Oct 12.

14.

Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes.

Jones S, Stransky N, McCord CL, Cerami E, Lagowski J, Kelly D, Angiuoli SV, Sausen M, Kann L, Shukla M, Makar R, Wood LD, Diaz LA Jr, Lengauer C, Velculescu VE.

Nat Commun. 2014 Sep 19;5:5006. doi: 10.1038/ncomms6006.

15.

Circulating tumor DNA moves further into the spotlight.

Sausen M, Parpart S, Diaz LA Jr.

Genome Med. 2014 May 28;6(5):35. doi: 10.1186/gm552. eCollection 2014.

16.

Detection of circulating tumor DNA in early- and late-stage human malignancies.

Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, Antonarakis ES, Azad NS, Bardelli A, Brem H, Cameron JL, Lee CC, Fecher LA, Gallia GL, Gibbs P, Le D, Giuntoli RL, Goggins M, Hogarty MD, Holdhoff M, Hong SM, Jiao Y, Juhl HH, Kim JJ, Siravegna G, Laheru DA, Lauricella C, Lim M, Lipson EJ, Marie SK, Netto GJ, Oliner KS, Olivi A, Olsson L, Riggins GJ, Sartore-Bianchi A, Schmidt K, Shih lM, Oba-Shinjo SM, Siena S, Theodorescu D, Tie J, Harkins TT, Veronese S, Wang TL, Weingart JD, Wolfgang CL, Wood LD, Xing D, Hruban RH, Wu J, Allen PJ, Schmidt CM, Choti MA, Velculescu VE, Kinzler KW, Vogelstein B, Papadopoulos N, Diaz LA Jr.

Sci Transl Med. 2014 Feb 19;6(224):224ra24. doi: 10.1126/scitranslmed.3007094.

17.

Insights into therapeutic resistance from whole-genome analyses of circulating tumor DNA.

Diaz LA Jr, Sausen M, Fisher GA, Velculescu VE.

Oncotarget. 2013 Oct;4(10):1856-7. No abstract available.

18.

Cancer detection using whole-genome sequencing of cell free DNA.

Leary RJ, Sausen M, Diaz LA Jr, Velculescu VE.

Oncotarget. 2013 Aug;4(8):1119-20. No abstract available.

19.

Amplification of the MET receptor drives resistance to anti-EGFR therapies in colorectal cancer.

Bardelli A, Corso S, Bertotti A, Hobor S, Valtorta E, Siravegna G, Sartore-Bianchi A, Scala E, Cassingena A, Zecchin D, Apicella M, Migliardi G, Galimi F, Lauricella C, Zanon C, Perera T, Veronese S, Corti G, Amatu A, Gambacorta M, Diaz LA Jr, Sausen M, Velculescu VE, Comoglio P, Trusolino L, Di Nicolantonio F, Giordano S, Siena S.

Cancer Discov. 2013 Jun;3(6):658-73. doi: 10.1158/2159-8290.CD-12-0558. Epub 2013 Jun 2.

20.

Exomic sequencing of medullary thyroid cancer reveals dominant and mutually exclusive oncogenic mutations in RET and RAS.

Agrawal N, Jiao Y, Sausen M, Leary R, Bettegowda C, Roberts NJ, Bhan S, Ho AS, Khan Z, Bishop J, Westra WH, Wood LD, Hruban RH, Tufano RP, Robinson B, Dralle H, Toledo SP, Toledo RA, Morris LG, Ghossein RA, Fagin JA, Chan TA, Velculescu VE, Vogelstein B, Kinzler KW, Papadopoulos N, Nelkin BD, Ball DW.

J Clin Endocrinol Metab. 2013 Feb;98(2):E364-9. doi: 10.1210/jc.2012-2703. Epub 2012 Dec 21.

21.

Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma.

Sausen M, Leary RJ, Jones S, Wu J, Reynolds CP, Liu X, Blackford A, Parmigiani G, Diaz LA Jr, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE, Hogarty MD.

Nat Genet. 2013 Jan;45(1):12-7. doi: 10.1038/ng.2493. Epub 2012 Dec 2.

22.

Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing.

Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O'Shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, Diaz LA Jr, Velculescu VE.

Sci Transl Med. 2012 Nov 28;4(162):162ra154. doi: 10.1126/scitranslmed.3004742.

23.

Identification of a HMGA2-EFCAB6 gene rearrangement following next-generation sequencing in a patient with a t(12;22)(q14.3;q13.2) and JAK2V617F-positive myeloproliferative neoplasm.

Martin SE, Sausen M, Joseph A, Kingham BF, Martin ES.

Cancer Genet. 2012 Jun;205(6):295-303. doi: 10.1016/j.cancergen.2012.03.006.

PMID:
22749035
24.

Mutations in CIC and FUBP1 contribute to human oligodendroglioma.

Bettegowda C, Agrawal N, Jiao Y, Sausen M, Wood LD, Hruban RH, Rodriguez FJ, Cahill DP, McLendon R, Riggins G, Velculescu VE, Oba-Shinjo SM, Marie SK, Vogelstein B, Bigner D, Yan H, Papadopoulos N, Kinzler KW.

Science. 2011 Sep 9;333(6048):1453-5. doi: 10.1126/science.1210557. Epub 2011 Aug 4.

25.

Chronic myeloid leukemia with e19a2 atypical transcript: early imatinib resistance and complete response to dasatinib.

Martin SE, Sausen M, Joseph A, Kingham BF.

Cancer Genet Cytogenet. 2010 Sep;201(2):133-4. doi: 10.1016/j.cancergencyto.2010.05.012. No abstract available.

PMID:
20682399
26.

Enhanced metaboreflex sensitivity in hypertensive humans.

Sausen MT, Delaney EP, Stillabower ME, Farquhar WB.

Eur J Appl Physiol. 2009 Feb;105(3):351-6. doi: 10.1007/s00421-008-0910-8. Epub 2008 Nov 7.

PMID:
18989694
27.

BRCA1 E1644X: a deleterious mutation in an African American individual with early onset breast cancer.

Martin SE, Sausen M, Joseph A, Biggs DD, Kingham BF, Martin ES.

Breast Cancer Res Treat. 2009 Jan;113(2):393-5. doi: 10.1007/s10549-008-9928-1. Epub 2008 Mar 2.

PMID:
18311584

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