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Department of Genetics faculty, postdocs, students and collaborators published seventeen papers during March 25-April 7, 2018.

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The journals Cell and Cell Reports published multiple papers in the April issues that included hundreds of authors in the Cancer Genome Atlas Research Network, including Genetics faculty/staff members Katie Hoadley, Joel Parker, Corbin Jones, Shaowu Meng, Piotr Mieczkowski, Amy Perou, Chuck Perou, Tara Skelly, Donghui Tan and Uma Veluvolu.

“Possibly positive or certainly uncertain?”: participants’ responses to uncertain diagnostic results from exome sequencing.

Skinner D, Roche MI, Weck KE, Raspberry KA, Foreman AKM, Strande NT, Berg JS, Evans JP, Henderson GE.

Genet Med. 2018 Mar;20(3):313-319. doi: 10.1038/gim.2017.135. Epub 2017 Oct 2.

PMID: 29593351

Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease.

Raffield LM, Ulirsch JC, Naik RP, Lessard S, Handsaker RE, Jain D, Kang HM, Pankratz N, Auer PL, Bao EL, Smith JD, Lange LA, Lange EM, Li Y, Thornton TA, Young BA, Abecasis GR, Laurie CC, Nickerson DA, McCarroll SA, Correa A, Wilson JG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hematology & Hemostasis, Diabetes, and Structural Variation TOPMed Working Groups, Lettre G, Sankaran VG, Reiner AP.

PLoS Genet. 2018 Mar 28;14(3):e1007293. doi: 10.1371/journal.pgen.1007293. [Epub ahead of print]

PMID: 29590102

Conference Report: Psychiatric Genomics Consortium Meeting: Pathways to Drugs, London, March 2017.

Gaspar HA, Collier DA, Geschwind DH, Lewis CM, Li Q, Roth BL, Sullivan PF, Breen G.

Biol Psychiatry. 2018 Feb 8. pii: S0006-3223(18)30079-9. doi: 10.1016/j.biopsych.2018.01.024. [Epub ahead of print] No abstract available.

PMID: 29576190

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V; Cancer Genome Atlas Research Network, Hu H.

Cell. 2018 Apr 5;173(2):400-416.e11. doi: 10.1016/j.cell.2018.02.052.

PMID: 29625055

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM; Cancer Genome Atlas Network, Stuart JM, Benz CC, Laird PW.

Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022.

PMID: 29625048

A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression.

Kycia I, Wolford BN, Huyghe JR, Fuchsberger C, Vadlamudi S, Kursawe R, Welch RP, Albanus RD, Uyar A, Khetan S, Lawlor N, Bolisetty M, Mathur A, Kuusisto J, Laakso M, Ucar D, Mohlke KL, Boehnke M, Collins FS, Parker SCJ, Stitzel ML.

Am J Hum Genet. 2018 Apr 5;102(4):620-635. doi: 10.1016/j.ajhg.2018.02.020.

PMID: 29625024

Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey.

Spracklen CN, Shi J, Vadlamudi S, Wu Y, Zou M, Raulerson CK, Davis JP, Zeynalzadeh M, Jackson K,Yuan W, Wang H, Shou W, Wang Y, Luo J, Lange LA, Lange EM, Popkin BM, Gordon-Larsen P, Du S, Huang W, Mohlke KL.

PLoS Genet. 2018 Apr 5;14(4):e1007275. doi: 10.1371/journal.pgen.1007275. eCollection 2018 Apr.

PMID: 29621232

Genome-wide association study and meta-analysis identify loci associated with ventricular and supraventricular ectopy.

Napier MD, Franceschini N, Gondalia R, Stewart JD, Méndez-Giráldez R, Sitlani CM, Seyerle AA, Highland HM, Li Y, Wilhelmsen KC, Yan S, Duan Q, Roach J, Yao J, Guo X, Taylor KD, Heckbert SR, Rotter JI, North KE, Reiner AP, Zhang ZM, Tinker LF, Liao D, Laurie CC, Gogarten SM, Lin HJ, Brody JA, Bartz TM, Psaty BM, Sotoodehnia N, Soliman EZ, Avery CL, Whitsel EA.

Sci Rep. 2018 Apr 4;8(1):5675. doi: 10.1038/s41598-018-23843-z.

PMID: 29618737

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK; Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C.

Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063.

PMID: 29617660

Transgenerational Sterility of Piwi Mutants Represents a Dynamic Form of Adult Reproductive Diapause.

Heestand B, Simon M, Frenk S, Titov D, Ahmed S.

Cell Rep. 2018 Apr 3;23(1):156-171. doi: 10.1016/j.celrep.2018.03.015.

PMID: 29617657

pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data.

Sun H, Wang Y, Chen Y, Li Y, Wang S.

Bioinformatics. 2017 Jun 15;33(12):1765-1772. doi: 10.1093/bioinformatics/btx064.

PMID: 28165116

SMAC: Spatial multi-category angle-based classifier for high-dimensional neuroimaging data.

Yu-Feng Liu L, Liu Y, Zhu H; Alzheimer’s Disease Neuroimaging Initiative.

Neuroimage. 2018 Mar 26. pii: S1053-8119(18)30251-9. doi: 10.1016/j.neuroimage.2018.03.040. [Epub ahead of print]

PMID: 29596980

 Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.

Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034.

PMID: 29625051

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G; Cancer Genome Atlas Research Network.

Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033.

PMID: 29625049

Grudging Trust and the Limits of Trustworthy Biorepository Curation.

Meagher KM, Juengst ET, Henderson GE.

Am J Bioeth. 2018 Apr;18(4):23-25. doi: 10.1080/15265161.2018.1431329. No abstract available.

PMID: 29621446

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwaitkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WT, Robertson AG; Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM.

Cell Rep. 2018 Apr 3;23(1):313-326.e5. doi: 10.1016/j.celrep.2018.03.075.

PMID: 29617669

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L.

Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052.

PMID: 29617666