Department of Genetics Publications for May 28 – June 9, 2017

Department of Genetics faculty and collaborators published twenty-nine papers during the past two weeks.

Genetic risk scores in the prediction of plasma glucose, impaired insulin secretion, insulin resistance and incident type 2 diabetes in the METSIM study.

Stančáková A, Kuulasmaa T, Kuusisto J, Mohlke KL, Collins FS, Boehnke M, Laakso M.

Diabetologia. 2017 Jun 1. doi: 10.1007/s00125-017-4313-4. [Epub ahead of print]

PMID: 28573393

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans.

Scott RA, Scott LJ, Mägi R, Marullo L, Gaulton KJ, Kaakinen M, Pervjakova N, Pers TH, Johnson AD, Eicher JD, Jackson AU, Ferreira T, Lee Y, Ma C, Steinthorsdottir V, Thorleifsson G, Qi L, Van Zuydam NR, Mahajan A, Chen H, Almgren P, Voight BF, Grallert H, Müller-Nurasyid M, Ried JS, Rayner WN, Robertson N, Karssen LC, van Leeuwen EM, Willems SM, Fuchsberger C, Kwan P, Teslovich TM, Chanda P, Li M, Lu Y, Dina C, Thuillier D, Yengo L, Jiang L, Sparso T, Kestler HA, Chheda H, Eisele L, Gustafsson S, Frånberg M, Strawbridge RJ, Benediktsson R, Hreidarsson AB, Kong A, Sigurðsson G, Kerrison ND, Luan J, Liang L, Meitinger T, Roden M, Thorand B, Esko T, Mihailov E, Fox C, Liu CT, Rybin D, Isomaa B, Lyssenko V, Tuomi T, Couper DJ, Pankow JS, Grarup N, Have CT, Jørgensen ME, Jørgensen T, Linneberg A, Cornelis MC, van Dam RM, Hunter DJ, Kraft P, Sun Q, Edkins S, Owen KR, Perry JR, Wood AR, Zeggini E, Tajes-Fernandes J, Abecasis GR, Bonnycastle LL, Chines PS, Stringham HM, Koistinen HA, Kinnunen L, Sennblad B, Mühleisen TW, Nöthen MM, Pechlivanis S, Baldassarre D, Gertow K, Humphries SE, Tremoli E, Klopp N, Meyer J, Steinbach G, Wennauer R, Eriksson JG, Mӓnnistö S, Peltonen L, Tikkanen E, Charpentier G, Eury E, Lobbens S, Gigante B, Leander K, McLeod O, Bottinger EP, Gottesman O, Ruderfer D, Blüher M, Kovacs P, Tonjes A, Maruthur NM, Scapoli C, Erbel R, Jöckel KH, Moebus S, de Faire U, Hamsten A, Stumvoll M, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, Ripatti S, Salomaa V, Pedersen NL, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Tuomilehto J, Hansen T, Pedersen O, Barroso I, Lannfelt L, Ingelsson E, Lind L, Lindgren CM, Cauchi S, Froguel P, Loos RJ, Balkau B, Boeing H, Franks PW, Gurrea AB, Palli D, van der Schouw YT, Altshuler D, Groop LC, Langenberg C, Wareham NJ, Sijbrands E, van Duijn CM, Florez JC, Meigs JB, Boerwinkle E, Gieger C, Strauch K, Metspalu A, Morris AD, Palmer CN, Hu FB, Thorsteinsdottir U, Stefansson K, Dupuis J, Morris AP, Boehnke M, McCarthy MI, Prokopenko I; DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium..

Diabetes. 2017 May 31. pii: db161253. doi: 10.2337/db16-1253. [Epub ahead of print]

PMID: 28566273

Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion.

Tse LV, Klinc KA, Madigan VJ, Castellanos Rivera RM, Wells LF, Havlik LP, Smith JK, Agbandje-McKenna M, Asokan A.

Proc Natl Acad Sci U S A. 2017 May 30. pii: 201704766. doi: 10.1073/pnas.1704766114. [Epub ahead of print]

PMID: 28559317

Comparative genomic evidence for the involvement of schizophrenia risk genes in antipsychotic effects.

Kim Y, Giusti-Rodriguez P, Crowley JJ, Bryois J, Nonneman RJ, Ryan AK, Quackenbush CR, Iglesias-Ussel MD, Lee PH, Sun W, de Villena FP, Sullivan PF.

Mol Psychiatry. 2017 May 30. doi: 10.1038/mp.2017.111. [Epub ahead of print]

PMID: 28555076

Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource.

Strande NT, Riggs ER, Buchanan AH, Ceyhan-Birsoy O, DiStefano M, Dwight SS, Goldstein J, Ghosh R, Seifert BA, Sneddon TP, Wright MW, Milko LV, Cherry JM, Giovanni MA, Murray MF, O’Daniel JM, Ramos EM, Santani AB, Scott AF, Plon SE, Rehm HL, Martin CL, Berg JS.

Am J Hum Genet. 2017 Jun 1;100(6):895-906. doi: 10.1016/j.ajhg.2017.04.015. Epub 2017 May 25.

PMID: 28552198

Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos.

Hodonsky CJ, Jain D, Schick UM, Morrison JV, Brown L, McHugh CP, Schurmann C, Chen DD, Liu YM, Auer PL, Laurie CA, Taylor KD, Browning BL, Li Y, Papanicolaou G, Rotter JI, Kurita R, Nakamura Y, Browning SR, Loos RJF, North KE, Laurie CC, Thornton TA, Pankratz N, Bauer DE, Sofer T, Reiner AP.

PLoS Genet. 2017 Apr 28;13(4):e1006760. doi: 10.1371/journal.pgen.1006760. eCollection 2017 Apr.

PMID: 28453575

Genome-wide physical activity interactions in adiposity – A meta-analysis of 200,452 adults.

Graff M, Scott RA, Justice AE, Young KL, Feitosa MF, Barata L, Winkler TW, Chu AY, Mahajan A, Hadley D, Xue L, Workalemahu T, Heard-Costa NL, den Hoed M, Ahluwalia TS, Qi Q, Ngwa JS, Renström F, Quaye L, Eicher JD, Hayes JE, Cornelis M, Kutalik Z, Lim E, Luan J, Huffman JE, Zhang W, Zhao W, Griffin PJ, Haller T, Ahmad S, Marques-Vidal PM, Bien S, Yengo L, Teumer A, Smith AV, Kumari M, Harder MN, Justesen JM, Kleber ME, Hollensted M, Lohman K, Rivera NV, Whitfield JB, Zhao JH, Stringham HM, Lyytikäinen LP, Huppertz C, Willemsen G, Peyrot WJ, Wu Y, Kristiansson K, Demirkan A, Fornage M, Hassinen M, Bielak LF, Cadby G, Tanaka T, Mägi R, van der Most PJ, Jackson AU, Bragg-Gresham JL, Vitart V, Marten J, Navarro P, Bellis C, Pasko D, Johansson Å, Snitker S, Cheng YC, Eriksson J, Lim U, Aadahl M, Adair LS, Amin N, Balkau B, Auvinen J, Beilby J, Bergman RN, Bergmann S, Bertoni AG, Blangero J, Bonnefond A, Bonnycastle LL, Borja JB, Brage S, Busonero F, Buyske S, Campbell H, Chines PS, Collins FS, Corre T, Smith GD, Delgado GE, Dueker N, Dörr M, Ebeling T, Eiriksdottir G, Esko T, Faul JD, Fu M, Færch K, Gieger C, Gläser S, Gong J, Gordon-Larsen P, Grallert H, Grammer TB, Grarup N, van Grootheest G, Harald K, Hastie ND, Havulinna AS, Hernandez D, Hindorff L, Hocking LJ, Holmens OL, Holzapfel C, Hottenga JJ, Huang J, Huang T, Hui J, Huth C, Hutri-Kähönen N, James AL, Jansson JO, Jhun MA, Juonala M, Kinnunen L, Koistinen HA, Kolcic I, Komulainen P, Kuusisto J, Kvaløy K, Kähönen M, Lakka TA, Launer LJ, Lehne B, Lindgren CM, Lorentzon M, Luben R, Marre M, Milaneschi Y, Monda KL, Montgomery GW, De Moor MHM, Mulas A, Müller-Nurasyid M, Musk AW, Männikkö R, Männistö S, Narisu N, Nauck M, Nettleton JA, Nolte IM, Oldehinkel AJ, Olden M, Ong KK, Padmanabhan S, Paternoster L, Perez J, Perola M, Peters A, Peters U, Peyser PA, Prokopenko I, Puolijoki H, Raitakari OT, Rankinen T, Rasmussen-Torvik LJ, Rawal R, Ridker PM, Rose LM, Rudan I, Sarti C, Sarzynski MA, Savonen K, Scott WR, Sanna S, Shuldiner AR, Sidney S, Silbernagel G, Smith BH, Smith JA, Snieder H, Stančáková A, Sternfeld B, Swift AJ, Tammelin T, Tan ST, Thorand B, Thuillier D, Vandenput L, Vestergaard H, van Vliet-Ostaptchouk JV, Vohl MC, Völker U, Waeber G, Walker M, Wild S, Wong A, Wright AF, Zillikens MC, Zubair N, Haiman CA, Lemarchand L, Gyllensten U, Ohlsson C, Hofman A, Rivadeneira F, Uitterlinden AG, Pérusse L, Wilson JF, Hayward C, Polasek O, Cucca F, Hveem K, Hartman CA, Tönjes A, Bandinelli S, Palmer LJ, Kardia SLR, Rauramaa R, Sørensen TIA, Tuomilehto J, Salomaa V, Penninx BWJH, de Geus EJC, Boomsma DI, Lehtimäki T, Mangino M, Laakso M, Bouchard C, Martin NG, Kuh D, Liu Y, Linneberg A, März W, Strauch K, Kivimäki M, Harris TB, Gudnason V, Völzke H, Qi L, Järvelin MR, Chambers JC, Kooner JS, Froguel P, Kooperberg C, Vollenweider P, Hallmans G, Hansen T, Pedersen O, Metspalu A, Wareham NJ, Langenberg C, Weir DR, Porteous DJ, Boerwinkle E, Chasman DI; CHARGE Consortium.; EPIC-InterAct Consortium.; PAGE Consortium., Abecasis GR, Barroso I, McCarthy MI, Frayling TM, O’Connell JR, van Duijn CM, Boehnke M, Heid IM, Mohlke KL, Strachan DP, Fox CS, Liu CT, Hirschhorn JN, Klein RJ, Johnson AD, Borecki IB, Franks PW, North KE, Cupples LA, Loos RJF, Kilpeläinen TO.

PLoS Genet. 2017 Apr 27;13(4):e1006528. doi: 10.1371/journal.pgen.1006528. eCollection 2017 Apr.

PMID: 28448500

Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium.

Ng MCY, Graff M, Lu Y, Justice AE, Mudgal P, Liu CT, Young K, Yanek LR, Feitosa MF, Wojczynski MK, Rand K, Brody JA, Cade BE, Dimitrov L, Duan Q, Guo X, Lange LA, Nalls MA, Okut H, Tajuddin SM, Tayo BO, Vedantam S, Bradfield JP, Chen G, Chen WM, Chesi A, Irvin MR, Padhukasahasram B, Smith JA, Zheng W, Allison MA, Ambrosone CB, Bandera EV, Bartz TM, Berndt SI, Bernstein L, Blot WJ, Bottinger EP, Carpten J, Chanock SJ, Chen YI, Conti DV, Cooper RS, Fornage M, Freedman BI, Garcia M, Goodman PJ, Hsu YH, Hu J, Huff CD, Ingles SA, John EM, Kittles R, Klein E, Li J, McKnight B, Nayak U, Nemesure B, Ogunniyi A, Olshan A, Press MF, Rohde R, Rybicki BA, Salako B, Sanderson M, Shao Y, Siscovick DS, Stanford JL, Stevens VL, Stram A, Strom SS, Vaidya D, Witte JS, Yao J, Zhu X, Ziegler RG, Zonderman AB, Adeyemo A, Ambs S, Cushman M, Faul JD, Hakonarson H, Levin AM, Nathanson KL, Ware EB, Weir DR, Zhao W, Zhi D; Bone Mineral Density in Childhood Study (BMDCS) Group., Arnett DK, Grant SFA, Kardia SLR, Oloapde OI, Rao DC, Rotimi CN, Sale MM, Williams LK, Zemel BS, Becker DM, Borecki IB, Evans MK, Harris TB, Hirschhorn JN, Li Y, Patel SR, Psaty BM, Rotter JI, Wilson JG, Bowden DW, Cupples LA, Haiman CA, Loos RJF, North KE.

PLoS Genet. 2017 Apr 21;13(4):e1006719. doi: 10.1371/journal.pgen.1006719. eCollection 2017 Apr.

PMID: 28430825

BRG1 and BRM function antagonistically with c-MYC in adult cardiomyocytes to regulate conduction and contractility.

Willis MS, Holley DW, Wang Z, Chen X, Quintana M, Jensen BC, Tannu M, Parker J, Jeyaraj D, Jain MK, Wolfram JA, Lee HG, Bultman SJ.

J Mol Cell Cardiol. 2017 Apr;105:99-109. doi: 10.1016/j.yjmcc.2017.02.003. Epub 2017 Feb 21.

PMID: 28232072

DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.

Quach B, Furey TS.

Bioinformatics. 2017 Apr 1;33(7):956-963. doi: 10.1093/bioinformatics/btw740.

PMID: 27993786

Evidence for Association between SH2B1 Gene Variants and Glycated Hemoglobin in Nondiabetic European American Young Adults: The Add Health Study.

Lange LA, Graff M, Lange EM, Young KL, Richardson AS, Mohlke KL, North KE, Harris KM, Gordon-Larsen P.

Ann Hum Genet. 2016 Sep;80(5):294-305. doi: 10.1111/ahg.12165.

PMID: 27530450

Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice.

Gralinski LE, Menachery VD, Morgan AP, Totura AL, Beall A, Kocher J, Plante J, Harrison-Shostak DC, Schäfer A, Pardo-Manuel de Villena F, Ferris MT, Baric RS.

G3 (Bethesda). 2017 Jun 7;7(6):1653-1663. doi: 10.1534/g3.117.041434.

PMID: 28592648

Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders.

Oreper D, Cai Y, Tarantino LM, de Villena FP, Valdar W.

G3 (Bethesda). 2017 Jun 7;7(6):1623-1630. doi: 10.1534/g3.117.041491.

PMID: 28592645

Combined immune checkpoint blockade as a therapeutic strategy for BRCA1-mutated breast cancer.

Nolan E, Savas P, Policheni AN, Darcy PK, Vaillant F, Mintoff CP, Dushyanthen S, Mansour M, Pang JB, Fox SB; Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Perou CM, Visvader JE, Gray DHD, Loi S, Lindeman GJ.

Sci Transl Med. 2017 Jun 7;9(393). pii: eaal4922. doi: 10.1126/scitranslmed.aal4922.

PMID: 28592566

Genomes of the Mouse Collaborative Cross.

Srivastava A, Morgan AP, Najarian ML, Sarsani VK, Sigmon JS, Shorter JR, Kashfeen A, McMullan RC, Williams LH, Giusti-Rodríguez P, Ferris MT, Sullivan P, Hock P, Miller DR, Bell TA, McMillan L, Churchill GA, de Villena FP.

Genetics. 2017 Jun;206(2):537-556. doi: 10.1534/genetics.116.198838.

PMID: 28592495

Hepatocyte ABCA1 Deletion Impairs Liver Insulin Signaling and Lipogenesis.

Key CC, Liu M, Kurtz CL, Chung S, Boudyguina E, Dinh TA, Bashore A, Phelan PE, Freedman BI, Osborne TF, Zhu X, Ma L,Sethupathy P, Biddinger SB, Parks JS.

Cell Rep. 2017 Jun 6;19(10):2116-2129. doi: 10.1016/j.celrep.2017.05.032.

PMID: 28591582

HUGIn: Hi-C Unifying Genomic Interrogator.

Martin JS, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, Hu M, Li Y.

Bioinformatics. 2017 Jun 5. doi: 10.1093/bioinformatics/btx359. [Epub ahead of print]

PMID: 28582503

Long Noncoding RNA Moderates MicroRNA Activity to Maintain Self-Renewal in Embryonic Stem Cells.

Smith KN, Starmer J, Miller SC, Sethupathy P, Magnuson T.

Stem Cell Reports. 2017 May 31. pii: S2213-6711(17)30212-6. doi: 10.1016/j.stemcr.2017.05.005. [Epub ahead of print]

PMID: 28579393

EZH1 in germ cells safeguards the function of PRC2 during spermatogenesis.

Mu W, Starmer J, Shibata Y, Yee D, Magnuson T.

Dev Biol. 2017 Apr 15;424(2):198-207. doi: 10.1016/j.ydbio.2017.02.017. Epub 2017 Feb 28.

PMID: 28254491

Inducing circular RNA formation using the CRISPR endoribonuclease Csy4.

Borchardt EK, Meganck RM, Vincent HA, Ball CB, Ramos SBV, Moorman NJ, Marzluff WF, Asokan A.

RNA. 2017 May;23(5):619-627. doi: 10.1261/rna.056838.116. Epub 2017 Feb 21.

PMID: 28223408

Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses.

Simon JM, Davis JP, Lee SE, Schaner MR, Gipson GR, Weiser M, Sartor RB, Herfarth HH, Rahbar R, Sadiq TS, Koruda MJ, McGovern DP, Lieb JD, Mohlke KL, Furey TS, Sheikh SZ.

Eur J Immunol. 2016 Aug;46(8):1912-25. doi: 10.1002/eji.201546237. Epub 2016 Jun 1.

PMID: 27159132

Butyrate, neuroepigenetics and the gut microbiome: Can a high fiber diet improve brain health?

Bourassa MW, Alim I, Bultman SJ, Ratan RR.

Neurosci Lett. 2016 Jun 20;625:56-63. doi: 10.1016/j.neulet.2016.02.009. Epub 2016 Feb 8. Review.

PMID: 26868600

MYC activation cooperates with Vhl and Ink4a/Arf loss to induce clear cell renal cell carcinoma.

Bailey ST, Smith AM, Kardos J, Wobker SE, Wilson HL, Krishnan B, Saito R, Lee HJ, Zhang J, Eaton SC, Williams LA, Manocha U, Peters DJ, Pan X, Carroll TJ, Felsher DW, Walter V, Zhang Q, Parker JS, Yeh JJ, Moffitt RA, Leung JY, Kim WY.

Nat Commun. 2017 Jun 8;8:15770. doi: 10.1038/ncomms15770.

PMID: 28593993

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross.

Green R, Wilkins C, Thomas S, Sekine A, Hendrick DM, Voss K, Ireton RC, Mooney M, Go JT, Choonoo G, Jeng S, de Villena FP, Ferris MT, McWeeney S, Gale M Jr.

G3 (Bethesda). 2017 Jun 7;7(6):1665-1682. doi: 10.1534/g3.117.041624.

PMID: 28592649

Analysis of Natural Product Regulation of Cannabinoid Receptors in the treatment of Human Disease.

Badal S, Smith KN, Rajnarayanan R.

Pharmacol Ther. 2017 Jun 2. pii: S0163-7258(17)30151-1. doi: 10.1016/j.pharmthera.2017.06.003. [Epub ahead of print] Review.

PMID: 28583800

Age at diagnosis, obesity, smoking, and molecular subtypes in muscle-invasive bladder cancer.

Sun X, Hoadley KA, Kim WY, Furberg H, Olshan AF, Troester MA.

Cancer Causes Control. 2017 Jun;28(6):539-544. doi: 10.1007/s10552-017-0885-z. Epub 2017 Mar 20.

PMID: 28321693

Senescence in Health and Disease.

He S, Sharpless NE.