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Page 1
BinomiRare: A robust test for association of a rare genetic variant with a binary outcome for mixed models and any case-control proportion.
Sofer T, Lee J, Kurniansyah N, Jain D, Laurie CA, Gogarten SM, Conomos MP, Heavner B, Hu Y, Kooperberg C, Haessler J, Vasan RS, Cupples LA, Coombes BJ, Seyerle A, Gharib SA, Chen H, O'Connell JR, Zhang M, Gottlieb DJ, Psaty BM, Longstreth WT Jr, Rotter JI, Taylor KD, Rich SS, Guo X, Boerwinkle E, Morrison AC, Pankow JS, Johnson AD, Pankratz N; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Reiner AP, Redline S, Smith NL, Rice KM, Schifano ED. Sofer T, et al. HGG Adv. 2021 Jul 8;2(3):100040. doi: 10.1016/j.xhgg.2021.100040. Epub 2021 Jun 12. HGG Adv. 2021. PMID: 34337551 Free PMC article.
Analysis commons, a team approach to discovery in a big-data environment for genetic epidemiology.
Brody JA, Morrison AC, Bis JC, O'Connell JR, Brown MR, Huffman JE, Ames DC, Carroll A, Conomos MP, Gabriel S, Gibbs RA, Gogarten SM, Gupta N, Jaquish CE, Johnson AD, Lewis JP, Liu X, Manning AK, Papanicolaou GJ, Pitsillides AN, Rice KM, Salerno W, Sitlani CM, Smith NL; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium; TOPMed Hematology and Hemostasis Working Group; CHARGE Analysis and Bioinformatics Working Group; Heckbert SR, Laurie CC, Mitchell BD, Vasan RS, Rich SS, Rotter JI, Wilson JG, Boerwinkle E, Psaty BM, Cupples LA. Brody JA, et al. Nat Genet. 2017 Oct 27;49(11):1560-1563. doi: 10.1038/ng.3968. Nat Genet. 2017. PMID: 29074945 Free PMC article.
Efficient Variant Set Mixed Model Association Tests for Continuous and Binary Traits in Large-Scale Whole-Genome Sequencing Studies.
Chen H, Huffman JE, Brody JA, Wang C, Lee S, Li Z, Gogarten SM, Sofer T, Bielak LF, Bis JC, Blangero J, Bowler RP, Cade BE, Cho MH, Correa A, Curran JE, de Vries PS, Glahn DC, Guo X, Johnson AD, Kardia S, Kooperberg C, Lewis JP, Liu X, Mathias RA, Mitchell BD, O'Connell JR, Peyser PA, Post WS, Reiner AP, Rich SS, Rotter JI, Silverman EK, Smith JA, Vasan RS, Wilson JG, Yanek LR; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Hematology and Hemostasis Working Group; Redline S, Smith NL, Boerwinkle E, Borecki IB, Cupples LA, Laurie CC, Morrison AC, Rice KM, Lin X. Chen H, et al. Am J Hum Genet. 2019 Feb 7;104(2):260-274. doi: 10.1016/j.ajhg.2018.12.012. Epub 2019 Jan 10. Am J Hum Genet. 2019. PMID: 30639324 Free PMC article.
A fully adjusted two-stage procedure for rank-normalization in genetic association studies.
Sofer T, Zheng X, Gogarten SM, Laurie CA, Grinde K, Shaffer JR, Shungin D, O'Connell JR, Durazo-Arvizo RA, Raffield L, Lange L, Musani S, Vasan RS, Cupples LA, Reiner AP; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Laurie CC, Rice KM. Sofer T, et al. Genet Epidemiol. 2019 Apr;43(3):263-275. doi: 10.1002/gepi.22188. Epub 2019 Jan 17. Genet Epidemiol. 2019. PMID: 30653739 Free PMC article.
Impact of Rare and Common Genetic Variants on Diabetes Diagnosis by Hemoglobin A1c in Multi-Ancestry Cohorts: The Trans-Omics for Precision Medicine Program.
Sarnowski C, Leong A, Raffield LM, Wu P, de Vries PS, DiCorpo D, Guo X, Xu H, Liu Y, Zheng X, Hu Y, Brody JA, Goodarzi MO, Hidalgo BA, Highland HM, Jain D, Liu CT, Naik RP, O'Connell JR, Perry JA, Porneala BC, Selvin E, Wessel J, Psaty BM, Curran JE, Peralta JM, Blangero J, Kooperberg C, Mathias R, Johnson AD, Reiner AP, Mitchell BD, Cupples LA, Vasan RS, Correa A, Morrison AC, Boerwinkle E, Rotter JI, Rich SS, Manning AK, Dupuis J, Meigs JB; TOPMed Diabetes Working Group; TOPMed Hematology Working Group; TOPMed Hemostasis Working Group; National Heart, Lung, and Blood Institute TOPMed Consortium. Sarnowski C, et al. Am J Hum Genet. 2019 Oct 3;105(4):706-718. doi: 10.1016/j.ajhg.2019.08.010. Epub 2019 Sep 26. Am J Hum Genet. 2019. PMID: 31564435 Free PMC article.
De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population.
Kessler MD, Loesch DP, Perry JA, Heard-Costa NL, Taliun D, Cade BE, Wang H, Daya M, Ziniti J, Datta S, Celedón JC, Soto-Quiros ME, Avila L, Weiss ST, Barnes K, Redline SS, Vasan RS, Johnson AD, Mathias RA, Hernandez R, Wilson JG, Nickerson DA, Abecasis G, Browning SR, Zöllner S, O'Connell JR, Mitchell BD; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Population Genetics Working Group; O'Connor TD. Kessler MD, et al. Proc Natl Acad Sci U S A. 2020 Feb 4;117(5):2560-2569. doi: 10.1073/pnas.1902766117. Epub 2020 Jan 21. Proc Natl Acad Sci U S A. 2020. PMID: 31964835 Free PMC article.
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale.
Li X, Li Z, Zhou H, Gaynor SM, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, Broome JG, Conomos MP, Correa A, Cupples LA, Curran JE, Freedman BI, Guo X, Hindy G, Irvin MR, Kardia SLR, Kathiresan S, Khan AT, Kooperberg CL, Laurie CC, Liu XS, Mahaney MC, Manichaikul AW, Martin LW, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Moore JE, Morrison AC, O'Connell JR, Palmer ND, Pampana A, Peralta JM, Peyser PA, Psaty BM, Redline S, Rice KM, Rich SS, Smith JA, Tiwari HK, Tsai MY, Vasan RS, Wang FF, Weeks DE, Weng Z, Wilson JG, Yanek LR; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Neale BM, Sunyaev SR, Abecasis GR, Rotter JI, Willer CJ, Peloso GM, Natarajan P, Lin X. Li X, et al. Nat Genet. 2020 Sep;52(9):969-983. doi: 10.1038/s41588-020-0676-4. Epub 2020 Aug 24. Nat Genet. 2020. PMID: 32839606 Free PMC article.
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.
Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, Das S, Emde AK, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin KH, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers D… See abstract for full author list ➔ Taliun D, et al. Nature. 2021 Feb;590(7845):290-299. doi: 10.1038/s41586-021-03205-y. Epub 2021 Feb 10. Nature. 2021. PMID: 33568819 Free PMC article.
Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program.
Hu Y, Stilp AM, McHugh CP, Rao S, Jain D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH, Yanek LR, Wheeler M, Yao Y, Ren C, Broome J, Moon JY, de Vries PS, Hobbs BD, Sun Q, Surendran P, Brody JA, Blackwell TW, Choquet H, Ryan K, Duggirala R, Heard-Costa N, Wang Z, Chami N, Preuss MH, Min N, Ekunwe L, Lange LA, Cushman M, Faraday N, Curran JE, Almasy L, Kundu K, Smith AV, Gabriel S, Rotter JI, Fornage M, Lloyd-Jones DM, Vasan RS, Smith NL, North KE, Boerwinkle E, Becker LC, Lewis JP, Abecasis GR, Hou L, O'Connell JR, Morrison AC, Beaty TH, Kaplan R, Correa A, Blangero J, Jorgenson E, Psaty BM, Kooperberg C, Walton RT, Kleinstiver BP, Tang H, Loos RJF, Soranzo N, Butterworth AS, Nickerson D, Rich SS, Mitchell BD, Johnson AD, Auer PL, Li Y, Mathias RA, Lettre G, Pankratz N, Laurie CC, Laurie CA, Bauer DE, Conomos MP, Reiner AP; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium. Hu Y, et al. Am J Hum Genet. 2021 May 6;108(5):874-893. doi: 10.1016/j.ajhg.2021.04.003. Epub 2021 Apr 21. Am J Hum Genet. 2021. PMID: 33887194 Free PMC article.
Variant-specific inflation factors for assessing population stratification at the phenotypic variance level.
Sofer T, Zheng X, Laurie CA, Gogarten SM, Brody JA, Conomos MP, Bis JC, Thornton TA, Szpiro A, O'Connell JR, Lange EM, Gao Y, Cupples LA, Psaty BM; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Rice KM. Sofer T, et al. Nat Commun. 2021 Jun 9;12(1):3506. doi: 10.1038/s41467-021-23655-2. Nat Commun. 2021. PMID: 34108454 Free PMC article.
266 results