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Page 1
The GA4GH Phenopacket schema defines a computable representation of clinical data.
Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C; GAGH Phenopacket Modeling Consortium; Haendel MA, Robinson PN. Jacobsen JOB, et al. Among authors: beckmann js. Nat Biotechnol. 2022 Jun;40(6):817-820. doi: 10.1038/s41587-022-01357-4. Nat Biotechnol. 2022. PMID: 35705716 Free PMC article. No abstract available.
GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen … See abstract for full author list ➔ Rehm HL, et al. Among authors: beckmann js. Cell Genom. 2021 Nov 10;1(2):100029. doi: 10.1016/j.xgen.2021.100029. Cell Genom. 2021. PMID: 35072136 Free PMC article.
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.
Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA; Variant Interpretation for Cancer Consortium. Wagner AH, et al. Among authors: beckmann js. Nat Genet. 2020 Apr;52(4):448-457. doi: 10.1038/s41588-020-0603-8. Epub 2020 Apr 3. Nat Genet. 2020. PMID: 32246132 Free PMC article.
New genetic loci link adipose and insulin biology to body fat distribution.
Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE, Mägi R, Strawbridge RJ, Pers TH, Fischer K, Justice AE, Workalemahu T, Wu JMW, Buchkovich ML, Heard-Costa NL, Roman TS, Drong AW, Song C, Gustafsson S, Day FR, Esko T, Fall T, Kutalik Z, Luan J, Randall JC, Scherag A, Vedantam S, Wood AR, Chen J, Fehrmann R, Karjalainen J, Kahali B, Liu CT, Schmidt EM, Absher D, Amin N, Anderson D, Beekman M, Bragg-Gresham JL, Buyske S, Demirkan A, Ehret GB, Feitosa MF, Goel A, Jackson AU, Johnson T, Kleber ME, Kristiansson K, Mangino M, Leach IM, Medina-Gomez C, Palmer CD, Pasko D, Pechlivanis S, Peters MJ, Prokopenko I, Stančáková A, Sung YJ, Tanaka T, Teumer A, Van Vliet-Ostaptchouk JV, Yengo L, Zhang W, Albrecht E, Ärnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Böhringer S, Bonnet F, Böttcher Y, Bruinenberg M, Carba DB, Caspersen IH, Clarke R, Daw EW, Deelen J, Deelman E, Delgado G, Doney AS, Eklund N, Erdos MR, Estrada K, Eury E, Friedrich N, Garcia ME, Giedraitis V, Gigante B, Go AS, Golay A, Grallert H, Grammer TB, Gräßler J, Grewal J, Groves CJ, Haller T, Hallmans G, Hartman CA, Hassinen M, Hayward C, Heikkilä K, Herzig KH, Helmer Q, Hi… See abstract for full author list ➔ Shungin D, et al. Nature. 2015 Feb 12;518(7538):187-196. doi: 10.1038/nature14132. Nature. 2015. PMID: 25673412 Free PMC article.
Genetic studies of body mass index yield new insights for obesity biology.
Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR, Powell C, Vedantam S, Buchkovich ML, Yang J, Croteau-Chonka DC, Esko T, Fall T, Ferreira T, Gustafsson S, Kutalik Z, Luan J, Mägi R, Randall JC, Winkler TW, Wood AR, Workalemahu T, Faul JD, Smith JA, Zhao JH, Zhao W, Chen J, Fehrmann R, Hedman ÅK, Karjalainen J, Schmidt EM, Absher D, Amin N, Anderson D, Beekman M, Bolton JL, Bragg-Gresham JL, Buyske S, Demirkan A, Deng G, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Goel A, Gong J, Jackson AU, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Mangino M, Leach IM, Medina-Gomez C, Medland SE, Nalls MA, Palmer CD, Pasko D, Pechlivanis S, Peters MJ, Prokopenko I, Shungin D, Stančáková A, Strawbridge RJ, Sung YJ, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Isaacs A, Albrecht E, Ärnlöv J, Arscott GM, Attwood AP, Bandinelli S, Barrett A, Bas IN, Bellis C, Bennett AJ, Berne C, Blagieva R, Blüher M, Böhringer S, Bonnycastle LL, Böttcher Y, Boyd HA, Bruinenberg M, Caspersen IH, Chen YI, Clarke R, Daw EW, de Craen AJM, Delgado G, Dimitriou M, Doney ASF, Eklund N, Estrada K, Eury E, Folkersen L, Fraser RM, Garci… See abstract for full author list ➔ Locke AE, et al. Among authors: beckmann js. Nature. 2015 Feb 12;518(7538):197-206. doi: 10.1038/nature14177. Nature. 2015. PMID: 25673413 Free PMC article.
Common variants associated with plasma triglycerides and risk for coronary artery disease.
Do R, Willer CJ, Schmidt EM, Sengupta S, Gao C, Peloso GM, Gustafsson S, Kanoni S, Ganna A, Chen J, Buchkovich ML, Mora S, Beckmann JS, Bragg-Gresham JL, Chang HY, Demirkan A, Den Hertog HM, Donnelly LA, Ehret GB, Esko T, Feitosa MF, Ferreira T, Fischer K, Fontanillas P, Fraser RM, Freitag DF, Gurdasani D, Heikkilä K, Hyppönen E, Isaacs A, Jackson AU, Johansson A, Johnson T, Kaakinen M, Kettunen J, Kleber ME, Li X, Luan J, Lyytikäinen LP, Magnusson PK, Mangino M, Mihailov E, Montasser ME, Müller-Nurasyid M, Nolte IM, O'Connell JR, Palmer CD, Perola M, Petersen AK, Sanna S, Saxena R, Service SK, Shah S, Shungin D, Sidore C, Song C, Strawbridge RJ, Surakka I, Tanaka T, Teslovich TM, Thorleifsson G, Van den Herik EG, Voight BF, Volcik KA, Waite LL, Wong A, Wu Y, Zhang W, Absher D, Asiki G, Barroso I, Been LF, Bolton JL, Bonnycastle LL, Brambilla P, Burnett MS, Cesana G, Dimitriou M, Doney AS, Döring A, Elliott P, Epstein SE, Eyjolfsson GI, Gigante B, Goodarzi MO, Grallert H, Gravito ML, Groves CJ, Hallmans G, Hartikainen AL, Hayward C, Hernandez D, Hicks AA, Holm H, Hung YJ, Illig T, Jones MR, Kaleebu P, Kastelein JJ, Khaw KT, Kim E, Klopp N, Komulainen P, Kumari M, Langenberg… See abstract for full author list ➔ Do R, et al. Among authors: beckmann js. Nat Genet. 2013 Nov;45(11):1345-52. doi: 10.1038/ng.2795. Epub 2013 Oct 6. Nat Genet. 2013. PMID: 24097064 Free PMC article.
Defining the role of common variation in the genomic and biological architecture of adult human height.
Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z, Amin N, Buchkovich ML, Croteau-Chonka DC, Day FR, Duan Y, Fall T, Fehrmann R, Ferreira T, Jackson AU, Karjalainen J, Lo KS, Locke AE, Mägi R, Mihailov E, Porcu E, Randall JC, Scherag A, Vinkhuyzen AA, Westra HJ, Winkler TW, Workalemahu T, Zhao JH, Absher D, Albrecht E, Anderson D, Baron J, Beekman M, Demirkan A, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Fraser RM, Goel A, Gong J, Justice AE, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Lui JC, Mangino M, Mateo Leach I, Medina-Gomez C, Nalls MA, Nyholt DR, Palmer CD, Pasko D, Pechlivanis S, Prokopenko I, Ried JS, Ripke S, Shungin D, Stancáková A, Strawbridge RJ, Sung YJ, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Afzal U, Arnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Bolton JL, Böttcher Y, Boyd HA, Bruinenberg M, Buckley BM, Buyske S, Caspersen IH, Chines PS, Clarke R, Claudi-Boehm S, Cooper M, Daw EW, De Jong PA, Deelen J, Delgado G, Denny JC, Dhonukshe-Rutten R, Dimitriou M, Doney AS, Dörr M, Eklund N, Eury E, F… See abstract for full author list ➔ Wood AR, et al. Among authors: beckmann js. Nat Genet. 2014 Nov;46(11):1173-86. doi: 10.1038/ng.3097. Epub 2014 Oct 5. Nat Genet. 2014. PMID: 25282103 Free PMC article.
CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits.
Macé A, Tuke MA, Deelen P, Kristiansson K, Mattsson H, Nõukas M, Sapkota Y, Schick U, Porcu E, Rüeger S, McDaid AF, Porteous D, Winkler TW, Salvi E, Shrine N, Liu X, Ang WQ, Zhang W, Feitosa MF, Venturini C, van der Most PJ, Rosengren A, Wood AR, Beaumont RN, Jones SE, Ruth KS, Yaghootkar H, Tyrrell J, Havulinna AS, Boers H, Mägi R, Kriebel J, Müller-Nurasyid M, Perola M, Nieminen M, Lokki ML, Kähönen M, Viikari JS, Geller F, Lahti J, Palotie A, Koponen P, Lundqvist A, Rissanen H, Bottinger EP, Afaq S, Wojczynski MK, Lenzini P, Nolte IM, Sparsø T, Schupf N, Christensen K, Perls TT, Newman AB, Werge T, Snieder H, Spector TD, Chambers JC, Koskinen S, Melbye M, Raitakari OT, Lehtimäki T, Tobin MD, Wain LV, Sinisalo J, Peters A, Meitinger T, Martin NG, Wray NR, Montgomery GW, Medland SE, Swertz MA, Vartiainen E, Borodulin K, Männistö S, Murray A, Bochud M, Jacquemont S, Rivadeneira F, Hansen TF, Oldehinkel AJ, Mangino M, Province MA, Deloukas P, Kooner JS, Freathy RM, Pennell C, Feenstra B, Strachan DP, Lettre G, Hirschhorn J, Cusi D, Heid IM, Hayward C, Männik K, Beckmann JS, Loos RJF, Nyholt DR, Metspalu A, Eriksson JG, Weedon MN, Salomaa V, Franke L, Reymond A, Frayling TM, … See abstract for full author list ➔ Macé A, et al. Among authors: beckmann js. Nat Commun. 2017 Sep 29;8(1):744. doi: 10.1038/s41467-017-00556-x. Nat Commun. 2017. PMID: 28963451 Free PMC article.
FTO genotype is associated with phenotypic variability of body mass index.
Yang J, Loos RJ, Powell JE, Medland SE, Speliotes EK, Chasman DI, Rose LM, Thorleifsson G, Steinthorsdottir V, Mägi R, Waite L, Smith AV, Yerges-Armstrong LM, Monda KL, Hadley D, Mahajan A, Li G, Kapur K, Vitart V, Huffman JE, Wang SR, Palmer C, Esko T, Fischer K, Zhao JH, Demirkan A, Isaacs A, Feitosa MF, Luan J, Heard-Costa NL, White C, Jackson AU, Preuss M, Ziegler A, Eriksson J, Kutalik Z, Frau F, Nolte IM, Van Vliet-Ostaptchouk JV, Hottenga JJ, Jacobs KB, Verweij N, Goel A, Medina-Gomez C, Estrada K, Bragg-Gresham JL, Sanna S, Sidore C, Tyrer J, Teumer A, Prokopenko I, Mangino M, Lindgren CM, Assimes TL, Shuldiner AR, Hui J, Beilby JP, McArdle WL, Hall P, Haritunians T, Zgaga L, Kolcic I, Polasek O, Zemunik T, Oostra BA, Junttila MJ, Grönberg H, Schreiber S, Peters A, Hicks AA, Stephens J, Foad NS, Laitinen J, Pouta A, Kaakinen M, Willemsen G, Vink JM, Wild SH, Navis G, Asselbergs FW, Homuth G, John U, Iribarren C, Harris T, Launer L, Gudnason V, O'Connell JR, Boerwinkle E, Cadby G, Palmer LJ, James AL, Musk AW, Ingelsson E, Psaty BM, Beckmann JS, Waeber G, Vollenweider P, Hayward C, Wright AF, Rudan I, Groop LC, Metspalu A, Khaw KT, van Duijn CM, Borecki IB, Province … See abstract for full author list ➔ Yang J, et al. Among authors: beckmann js. Nature. 2012 Oct 11;490(7419):267-72. doi: 10.1038/nature11401. Epub 2012 Sep 16. Nature. 2012. PMID: 22982992 Free PMC article.
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