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Items: 7

1.

A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data.

Ainscough BJ, Barnell EK, Ronning P, Campbell KM, Wagner AH, Fehniger TA, Dunn GP, Uppaluri R, Govindan R, Rohan TE, Griffith M, Mardis ER, Swamidass SJ, Griffith OL.

Nat Genet. 2018 Dec;50(12):1735-1743. doi: 10.1038/s41588-018-0257-y. Epub 2018 Nov 5.

PMID:
30397337
2.

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.

Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL; Clinical Genome Resource Somatic Working Group and Clinical Interpretation of Variants in Cancer team members.

Hum Mutat. 2018 Nov;39(11):1721-1732. doi: 10.1002/humu.23651.

PMID:
30311370
3.

Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples.

Barnell EK, Ronning P, Campbell KM, Krysiak K, Ainscough BJ, Sheta LM, Pema SP, Schmidt AD, Richters M, Cotto KC, Danos AM, Ramirez C, Skidmore ZL, Spies NC, Hundal J, Sediqzad MS, Kunisaki J, Gomez F, Trani L, Matlock M, Wagner AH, Swamidass SJ, Griffith M, Griffith OL.

Genet Med. 2018 Oct 5. doi: 10.1038/s41436-018-0278-z. [Epub ahead of print]

PMID:
30287923
4.

Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity.

Campbell KM, Lin T, Zolkind P, Barnell EK, Skidmore ZL, Winkler AE, Law JH, Mardis ER, Wartman LD, Adkins DR, Chernock RD, Griffith M, Uppaluri R, Griffith OL.

Cell Rep. 2018 Aug 21;24(8):2167-2178. doi: 10.1016/j.celrep.2018.07.058.

5.

A Phase II Trial of Neoadjuvant MK-2206, an AKT Inhibitor, with Anastrozole in Clinical Stage II or III PIK3CA-Mutant ER-Positive and HER2-Negative Breast Cancer.

Ma CX, Suman V, Goetz MP, Northfelt D, Burkard ME, Ademuyiwa F, Naughton M, Margenthaler J, Aft R, Gray R, Tevaarwerk A, Wilke L, Haddad T, Moynihan T, Loprinzi C, Hieken T, Barnell EK, Skidmore ZL, Feng YY, Krysiak K, Hoog J, Guo Z, Nehring L, Wisinski KB, Mardis E, Hagemann IS, Vij K, Sanati S, Al-Kateb H, Griffith OL, Griffith M, Doyle L, Erlichman C, Ellis MJ.

Clin Cancer Res. 2017 Nov 15;23(22):6823-6832. doi: 10.1158/1078-0432.CCR-17-1260. Epub 2017 Sep 5.

6.

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL.

Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. No abstract available.

7.

Growth and HIV-free survival of HIV-exposed infants in Malawi: a randomized trial of two complementary feeding interventions in the context of maternal antiretroviral therapy.

Thakwalakwa C, Phiri A, Rollins N, Heikens GT, Barnell EK, Manary M.

J Acquir Immune Defic Syndr. 2014 Jun 1;66(2):181-7. doi: 10.1097/QAI.0000000000000150.

PMID:
24662296

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