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Items: 1 to 50 of 104

1.

Dynamics of tumor and immune responses during immune checkpoint blockade in non-small cell lung cancer.

Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone KA, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE.

Cancer Res. 2018 Dec 12. pii: canres.1127.2018. doi: 10.1158/0008-5472.CAN-18-1127. [Epub ahead of print]

PMID:
30541742
2.

Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions.

Kuboki Y, Fischer CG, Beleva Guthrie V, Huang W, Yu J, Chianchiano P, Hosoda W, Zhang H, Zheng L, Shao X, Thompson ED, Waters K, Poling J, He J, Weiss MJ, Wolfgang CL, Goggins MG, Hruban RH, Roberts NJ, Karchin R, Wood LD.

J Pathol. 2019 Mar;247(3):347-356. doi: 10.1002/path.5194. Epub 2019 Jan 16.

PMID:
30430578
3.

Correction: Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy.

Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang CY, Shun CT, Turesky RJ, Yun BH, Rosenquist TA, Pu YS, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ.

Elife. 2018 Nov 12;7. pii: e43237. doi: 10.7554/eLife.43237.

4.

Minimal functional driver gene heterogeneity among untreated metastases.

Reiter JG, Makohon-Moore AP, Gerold JM, Heyde A, Attiyeh MA, Kohutek ZA, Tokheim CJ, Brown A, DeBlasio RM, Niyazov J, Zucker A, Karchin R, Kinzler KW, Iacobuzio-Donahue CA, Vogelstein B, Nowak MA.

Science. 2018 Sep 7;361(6406):1033-1037. doi: 10.1126/science.aat7171.

PMID:
30190408
5.

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.

PMID:
30185652
6.

Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.

Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin R, Jagtap PD, Griffin TJ.

J Proteome Res. 2018 Sep 5. doi: 10.1021/acs.jproteome.8b00404. [Epub ahead of print]

PMID:
30130115
7.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Aug 9;174(4):1034-1035. doi: 10.1016/j.cell.2018.07.034. No abstract available.

8.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Erratum in: Cell. 2018 Aug 9;174(4):1034-1035.

9.

Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers.

Wang Y, Li L, Douville C, Cohen JD, Yen TT, Kinde I, Sundfelt K, Kjær SK, Hruban RH, Shih IM, Wang TL, Kurman RJ, Springer S, Ptak J, Popoli M, Schaefer J, Silliman N, Dobbyn L, Tanner EJ, Angarita A, Lycke M, Jochumsen K, Afsari B, Danilova L, Levine DA, Jardon K, Zeng X, Arseneau J, Fu L, Diaz LA Jr, Karchin R, Tomasetti C, Kinzler KW, Vogelstein B, Fader AN, Gilbert L, Papadopoulos N.

Sci Transl Med. 2018 Mar 21;10(433). pii: eaap8793. doi: 10.1126/scitranslmed.aap8793.

10.

Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy.

Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang CY, Shun CT, Turesky RJ, Yun BH, Rosenquist TA, Pu YS, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ.

Elife. 2018 Mar 20;7. pii: e32143. doi: 10.7554/eLife.32143. Erratum in: Elife. 2018 Nov 12;7:.

11.

Systematic Functional Annotation of Somatic Mutations in Cancer.

Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB.

Cancer Cell. 2018 Mar 12;33(3):450-462.e10. doi: 10.1016/j.ccell.2018.01.021.

PMID:
29533785
12.

Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations.

Beleva Guthrie V, Masica DL, Fraser A, Federico J, Fan Y, Camps M, Karchin R.

Mol Biol Evol. 2018 Jun 1;35(6):1507-1519. doi: 10.1093/molbev/msy036.

13.

IPMNs with co-occurring invasive cancers: neighbours but not always relatives.

Felsenstein M, Noë M, Masica DL, Hosoda W, Chianchiano P, Fischer CG, Lionheart G, Brosens LAA, Pea A, Yu J, Gemenetzis G, Groot VP, Makary MA, He J, Weiss MJ, Cameron JL, Wolfgang CL, Hruban RH, Roberts NJ, Karchin R, Goggins MG, Wood LD.

Gut. 2018 Sep;67(9):1652-1662. doi: 10.1136/gutjnl-2017-315062. Epub 2018 Mar 2.

PMID:
29500184
14.

Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs).

Douville C, Springer S, Kinde I, Cohen JD, Hruban RH, Lennon AM, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1871-1876. doi: 10.1073/pnas.1717846115. Epub 2018 Feb 5.

15.

Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.

Guidugli L, Shimelis H, Masica DL, Pankratz VS, Lipton GB, Singh N, Hu C, Monteiro ANA, Lindor NM, Goldgar DE, Karchin R, Iversen ES, Couch FJ.

Am J Hum Genet. 2018 Feb 1;102(2):233-248. doi: 10.1016/j.ajhg.2017.12.013. Epub 2018 Jan 25.

16.

Methods and tools for assessing the impact of genetic variations: The 2017 Annual Scientific Meeting of the Human Genome Variation Society.

Oetting WS, Béroud C, Brenner SE, Greenblatt MS, Karchin R, Mooney SD.

Hum Mutat. 2018 Mar;39(3):454-458. doi: 10.1002/humu.23393. Epub 2018 Jan 15. No abstract available.

17.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y. Review.

18.

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit.

Masica DL, Douville C, Tokheim C, Bhattacharya R, Kim R, Moad K, Ryan MC, Karchin R.

Cancer Res. 2017 Nov 1;77(21):e35-e38. doi: 10.1158/0008-5472.CAN-17-0338.

19.

High grade serous ovarian carcinomas originate in the fallopian tube.

Labidi-Galy SI, Papp E, Hallberg D, Niknafs N, Adleff V, Noe M, Bhattacharya R, Novak M, Jones S, Phallen J, Hruban CA, Hirsch MS, Lin DI, Schwartz L, Maire CL, Tille JC, Bowden M, Ayhan A, Wood LD, Scharpf RB, Kurman R, Wang TL, Shih IM, Karchin R, Drapkin R, Velculescu VE.

Nat Commun. 2017 Oct 23;8(1):1093. doi: 10.1038/s41467-017-00962-1.

20.

Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort.

Monson ET, Pirooznia M, Parla J, Kramer M, Goes FS, Gaine ME, Gaynor SC, de Klerk K, Jancic D, Karchin R, McCombie WR, Zandi PP, Potash JB, Willour VL.

Mol Neuropsychiatry. 2017 Jul;3(1):1-11. doi: 10.1159/000454773. Epub 2017 Jan 18.

21.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD.

Hum Mutat. 2017 Sep;38(9):1266-1276. doi: 10.1002/humu.23265. Epub 2017 Jun 19.

22.

Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society.

Oetting WS, Béroud C, Brenner SE, Greenblatt M, Karchin R, Mooney SD, Sunyaev S.

Hum Mutat. 2017 Apr;38(4):460-463. doi: 10.1002/humu.23169. Epub 2017 Feb 14. No abstract available.

PMID:
28054414
23.

Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE.

Cancer Discov. 2017 Mar;7(3):264-276. doi: 10.1158/2159-8290.CD-16-0828. Epub 2016 Dec 28.

24.

Autologous reconstitution of human cancer and immune system in vivo.

Fu J, Sen R, Masica DL, Karchin R, Pardoll D, Walter V, Hayes DN, Chung CH, Kim YJ.

Oncotarget. 2017 Jan 10;8(2):2053-2068. doi: 10.18632/oncotarget.14026.

25.

Evaluating the evaluation of cancer driver genes.

Tokheim CJ, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R.

Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):14330-14335. Epub 2016 Nov 22.

26.

Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation.

Karchin R, Nussinov R.

PLoS Comput Biol. 2016 Aug 18;12(8):e1005043. doi: 10.1371/journal.pcbi.1005043. eCollection 2016 Aug. No abstract available.

27.

A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts.

Masica DL, Dal Molin M, Wolfgang CL, Tomita T, Ostovaneh MR, Blackford A, Moran RA, Law JK, Barkley T, Goggins M, Irene Canto M, Pittman M, Eshleman JR, Ali SZ, Fishman EK, Kamel IR, Raman SP, Zaheer A, Ahuja N, Makary MA, Weiss MJ, Hirose K, Cameron JL, Rezaee N, He J, Joon Ahn Y, Wu W, Wang Y, Springer S, Diaz LL Jr, Papadopoulos N, Hruban RH, Kinzler KW, Vogelstein B, Karchin R, Lennon AM.

J Am Med Inform Assoc. 2017 Jan;24(1):145-152. doi: 10.1093/jamia/ocw069. Epub 2016 Jun 21.

28.

Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R.

Cancer Res. 2016 Jul 1;76(13):3719-31. doi: 10.1158/0008-5472.CAN-15-3190. Epub 2016 Apr 28.

29.

Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants.

Masica DL, Karchin R.

PLoS Comput Biol. 2016 May 12;12(5):e1004725. doi: 10.1371/journal.pcbi.1004725. eCollection 2016 May. Review. No abstract available.

30.

Exome Sequencing of Familial Bipolar Disorder.

Goes FS, Pirooznia M, Parla JS, Kramer M, Ghiban E, Mavruk S, Chen YC, Monson ET, Willour VL, Karchin R, Flickinger M, Locke AE, Levy SE, Scott LJ, Boehnke M, Stahl E, Moran JL, Hultman CM, Landén M, Purcell SM, Sklar P, Zandi PP, McCombie WR, Potash JB.

JAMA Psychiatry. 2016 Jun 1;73(6):590-7. doi: 10.1001/jamapsychiatry.2016.0251.

31.

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.

32.

Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society.

Oetting WS, Brenner SE, Brookes AJ, Greenblatt MS, Hart RK, Karchin R, Sunyaev SR, Taschner PE.

Hum Mutat. 2016 Apr;37(4):406-11. doi: 10.1002/humu.22958. Epub 2016 Feb 12. No abstract available.

33.

Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer.

Roberts NJ, Norris AL, Petersen GM, Bondy ML, Brand R, Gallinger S, Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stoffel E, Syngal S, Zogopoulos G, Ali SZ, Axilbund J, Chaffee KG, Chen YC, Cote ML, Childs EJ, Douville C, Goes FS, Herman JM, Iacobuzio-Donahue C, Kramer M, Makohon-Moore A, McCombie RW, McMahon KW, Niknafs N, Parla J, Pirooznia M, Potash JB, Rhim AD, Smith AL, Wang Y, Wolfgang CL, Wood LD, Zandi PP, Goggins M, Karchin R, Eshleman JR, Papadopoulos N, Kinzler KW, Vogelstein B, Hruban RH, Klein AP.

Cancer Discov. 2016 Feb;6(2):166-75. doi: 10.1158/2159-8290.CD-15-0402. Epub 2015 Dec 9.

34.

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).

Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R.

Hum Mutat. 2016 Jan;37(1):28-35. doi: 10.1002/humu.22911. Epub 2015 Oct 26.

35.

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.

Niknafs N, Beleva-Guthrie V, Naiman DQ, Karchin R.

PLoS Comput Biol. 2015 Oct 5;11(10):e1004416. doi: 10.1371/journal.pcbi.1004416. eCollection 2015 Oct.

36.

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.

37.

A combination of molecular markers and clinical features improve the classification of pancreatic cysts.

Springer S, Wang Y, Dal Molin M, Masica DL, Jiao Y, Kinde I, Blackford A, Raman SP, Wolfgang CL, Tomita T, Niknafs N, Douville C, Ptak J, Dobbyn L, Allen PJ, Klimstra DS, Schattner MA, Schmidt CM, Yip-Schneider M, Cummings OW, Brand RE, Zeh HJ, Singhi AD, Scarpa A, Salvia R, Malleo G, Zamboni G, Falconi M, Jang JY, Kim SW, Kwon W, Hong SM, Song KB, Kim SC, Swan N, Murphy J, Geoghegan J, Brugge W, Fernandez-Del Castillo C, Mino-Kenudson M, Schulick R, Edil BH, Adsay V, Paulino J, van Hooft J, Yachida S, Nara S, Hiraoka N, Yamao K, Hijioka S, van der Merwe S, Goggins M, Canto MI, Ahuja N, Hirose K, Makary M, Weiss MJ, Cameron J, Pittman M, Eshleman JR, Diaz LA Jr, Papadopoulos N, Kinzler KW, Karchin R, Hruban RH, Vogelstein B, Lennon AM.

Gastroenterology. 2015 Nov;149(6):1501-10. doi: 10.1053/j.gastro.2015.07.041. Epub 2015 Aug 4.

38.

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns.

Turner TN, Douville C, Kim D, Stenson PD, Cooper DN, Chakravarti A, Karchin R.

Hum Mol Genet. 2015 Nov 1;24(21):5995-6002. doi: 10.1093/hmg/ddv309. Epub 2015 Aug 5.

39.

Human genetics special issue on computational molecular medicine.

Karchin R, Cline MS.

Hum Genet. 2015 May;134(5):455-7. doi: 10.1007/s00439-015-1545-6. No abstract available. Erratum in: Hum Genet. 2015 May;134(5):509.

40.

Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing.

Chung CH, Guthrie VB, Masica DL, Tokheim C, Kang H, Richmon J, Agrawal N, Fakhry C, Quon H, Subramaniam RM, Zuo Z, Seiwert T, Chalmers ZR, Frampton GM, Ali SM, Yelensky R, Stephens PJ, Miller VA, Karchin R, Bishop JA.

Ann Oncol. 2015 Jun;26(6):1216-23. doi: 10.1093/annonc/mdv109. Epub 2015 Feb 23.

41.

Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features.

Rettig EM, Chung CH, Bishop JA, Howard JD, Sharma R, Li RJ, Douville C, Karchin R, Izumchenko E, Sidransky D, Koch W, Califano J, Agrawal N, Fakhry C.

Cancer Prev Res (Phila). 2015 Apr;8(4):287-95. doi: 10.1158/1940-6207.CAPR-14-0366. Epub 2015 Jan 29.

42.

Germline & somatic mosaicism: the 2014 annual scientific meeting of the Human Genome Variation Society.

Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD.

Hum Mutat. 2015 Mar;36(3):390-3. doi: 10.1002/humu.22757. No abstract available.

PMID:
25597405
43.

Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity.

Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R.

Hum Mol Genet. 2015 Apr 1;24(7):1908-17. doi: 10.1093/hmg/ddu607. Epub 2014 Dec 8.

44.

A probabilistic model to predict clinical phenotypic traits from genome sequencing.

Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R.

PLoS Comput Biol. 2014 Sep 4;10(9):e1003825. doi: 10.1371/journal.pcbi.1003825. eCollection 2014 Sep.

45.

Predicting survival in head and neck squamous cell carcinoma from TP53 mutation.

Masica DL, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch WM, Chung CH, Karchin R.

Hum Genet. 2015 May;134(5):497-507. doi: 10.1007/s00439-014-1470-0. Epub 2014 Aug 10.

46.

Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions.

Sharma N, Sosnay PR, Ramalho AS, Douville C, Franca A, Gottschalk LB, Park J, Lee M, Vecchio-Pagan B, Raraigh KS, Amaral MD, Karchin R, Cutting GR.

Hum Mutat. 2014 Oct;35(10):1249-59. doi: 10.1002/humu.22624. Epub 2014 Sep 10.

47.

Human bile contains microRNA-laden extracellular vesicles that can be used for cholangiocarcinoma diagnosis.

Li L, Masica D, Ishida M, Tomuleasa C, Umegaki S, Kalloo AN, Georgiades C, Singh VK, Khashab M, Amateau S, Li Z, Okolo P, Lennon AM, Saxena P, Geschwind JF, Schlachter T, Hong K, Pawlik TM, Canto M, Law J, Sharaiha R, Weiss CR, Thuluvath P, Goggins M, Shin EJ, Peng H, Kumbhari V, Hutfless S, Zhou L, Mezey E, Meltzer SJ, Karchin R, Selaru FM.

Hepatology. 2014 Sep;60(3):896-907. doi: 10.1002/hep.27050. Epub 2014 Jul 25. Erratum in: Hepatology. 2014 Dec;60(6):2135.

48.

Predicting the functional consequences of somatic missense mutations found in tumors.

Carter H, Karchin R.

Methods Mol Biol. 2014;1101:135-59. doi: 10.1007/978-1-62703-721-1_8.

PMID:
24233781
49.

Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas.

Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, Niknafs N, Guthrie VB, Maitra A, Argani P, Offerhaus GJA, Roa JC, Roberts LR, Gores GJ, Popescu I, Alexandrescu ST, Dima S, Fassan M, Simbolo M, Mafficini A, Capelli P, Lawlor RT, Ruzzenente A, Guglielmi A, Tortora G, de Braud F, Scarpa A, Jarnagin W, Klimstra D, Karchin R, Velculescu VE, Hruban RH, Vogelstein B, Kinzler KW, Papadopoulos N, Wood LD.

Nat Genet. 2013 Dec;45(12):1470-1473. doi: 10.1038/ng.2813. Epub 2013 Nov 3.

50.

Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene.

Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, Ramalho AS, Amaral MD, Dorfman R, Zielenski J, Masica DL, Karchin R, Millen L, Thomas PJ, Patrinos GP, Corey M, Lewis MH, Rommens JM, Castellani C, Penland CM, Cutting GR.

Nat Genet. 2013 Oct;45(10):1160-7. doi: 10.1038/ng.2745. Epub 2013 Aug 25.

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