We genotyped 196,710 genetic variants prioritized on the basis of prior GWAS for cardiovascular and metabolic phenotypes using the Illumina iSelect Metabochip
8 genotyping array. To design the Metabochip, we used our previous GWAS of ~100,000 individuals
4 (link) to prioritize 5,023 SNPs for HDL cholesterol, 5,055 for LDL cholesterol, 5,056 for triglycerides, and 938 for total cholesterol. These independent SNPs represent most loci with
P < .005 in our original GWAS for HDL cholesterol, LDL cholesterol and triglycerides and with
P < .0005 for total cholesterol. An additional 28,923 SNPs were selected for fine-mapping of 65 previously identified lipid loci. The Metabochip also included 50,459 SNPs prioritized based on GWAS of non-lipid traits and 93,308 SNPs selected for fine-mapping of loci associated with non-lipid traits (5 of these loci were associated with blood lipids by the analyses described here).
Partial Protocol Preview
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Willer C.J., Schmidt E.M., Sengupta S., Peloso G.M., Gustafsson S., Kanoni S., Ganna A., Chen J., Buchkovich M.L., Mora S., Beckmann J.S., Bragg-Gresham J.L., Chang H.Y., Demirkan A., Den Hertog H.M., Do R., Donnelly L.A., Ehret G.B., Esko T., Feitosa M.F., Ferreira T., Fischer K., Fontanillas P., Fraser R.M., Freitag D.F., Gurdasani D., Heikkilä K., Hyppönen E., Isaacs A., Jackson A.U., Johansson Å., Johnson T., Kaakinen M., Kettunen J., Kleber M.E., Li X., Luan J., Lyytikäinen L.P., Magnusson P.K., Mangino M., Mihailov E., Montasser M.E., Müller-Nurasyid M., Nolte I.M., O’Connell J.R., Palmer C.D., Perola M., Petersen A.K., Sanna S., Saxena R., Service S.K., Shah S., Shungin D., Sidore C., Song C., Strawbridge R.J., Surakka I., Tanaka T., Teslovich T.M., Thorleifsson G., Van den Herik E.G., Voight B.F., Volcik K.A., Waite L.L., Wong A., Wu Y., Zhang W., Absher D., Asiki G., Barroso I., Been L.F., Bolton J.L., Bonnycastle L.L., Brambilla P., Burnett M.S., Cesana G., Dimitriou M., Doney A.S., Döring A., Elliott P., Epstein S.E., Ingi Eyjolfsson G., Gigante B., Goodarzi M.O., Grallert H., Gravito M.L., Groves C.J., Hallmans G., Hartikainen A.L., Hayward C., Hernandez D., Hicks A.A., Holm H., Hung Y.J., Illig T., Jones M.R., Kaleebu P., Kastelein J.J., Khaw K.T., Kim E., Klopp N., Komulainen P., Kumari M., Langenberg C., Lehtimäki T., Lin S.Y., Lindström J., Loos R.J., Mach F., McArdle W.L., Meisinger C., Mitchell B.D., Müller G., Nagaraja R., Narisu N., Nieminen T.V., Nsubuga R.N., Olafsson I., Ong K.K., Palotie A., Papamarkou T., Pomilla C., Pouta A., Rader D.J., Reilly M.P., Ridker P.M., Rivadeneira F., Rudan I., Ruokonen A., Samani N., Scharnagl H., Seeley J., Silander K., Stančáková A., Stirrups K., Swift A.J., Tiret L., Uitterlinden A.G., van Pelt L.J., Vedantam S., Wainwright N., Wijmenga C., Wild S.H., Willemsen G., Wilsgaard T., Wilson J.F., Young E.H., Zhao J.H., Adair L.S., Arveiler D., Assimes T.L., Bandinelli S., Bennett F., Bochud M., Boehm B.O., Boomsma D.I., Borecki I.B., Bornstein S.R., Bovet P., Burnier M., Campbell H., Chakravarti A., Chambers J.C., Chen Y.D., Collins F.S., Cooper R.S., Danesh J., Dedoussis G., de Faire U., Feranil A.B., Ferrières J., Ferrucci L., Freimer N.B., Gieger C., Groop L.C., Gudnason V., Gyllensten U., Hamsten A., Harris T.B., Hingorani A., Hirschhorn J.N., Hofman A., Hovingh G.K., Hsiung C.A., Humphries S.E., Hunt S.C., Hveem K., Iribarren C., Järvelin M.R., Jula A., Kähönen M., Kaprio J., Kesäniemi A., Kivimaki M., Kooner J.S., Koudstaal P.J., Krauss R.M., Kuh D., Kuusisto J., Kyvik K.O., Laakso M., Lakka T.A., Lind L., Lindgren C.M., Martin N.G., März W., McCarthy M.I., McKenzie C.A., Meneton P., Metspalu A., Moilanen L., Morris A.D., Munroe P.B., Njølstad I., Pedersen N.L., Power C., Pramstaller P.P., Price J.F., Psaty B.M., Quertermous T., Rauramaa R., Saleheen D., Salomaa V., Sanghera D.K., Saramies J., Schwarz P.E., Sheu W.H., Shuldiner A.R., Siegbahn A., Spector T.D., Stefansson K., Strachan D.P., Tayo B.O., Tremoli E., Tuomilehto J., Uusitupa M., van Duijn C.M., Vollenweider P., Wallentin L., Wareham N.J., Whitfield J.B., Wolffenbuttel B.H., Ordovas J.M., Boerwinkle E., Palmer C.N., Thorsteinsdottir U., Chasman D.I., Rotter J.I., Franks P.W., Ripatti S., Cupples L.A., Sandhu M.S., Rich S.S., Boehnke M., Deloukas P., Kathiresan S., Mohlke K.L., Ingelsson E, & Abecasis G.R. (2013). Discovery and Refinement of Loci Associated with Lipid Levels. Nature genetics, 45(11), 1274-1283.