國家衛生研究院 NHRI:Item 3990099045/12950
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    Please use this identifier to cite or link to this item: http://ir.nhri.org.tw/handle/3990099045/12950


    Title: Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale
    Authors: Li, XH;Li, ZL;Zhou, HF;Gaynor, SM;Liu, YW;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, XQ;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, MCY;Vasan, RS;Wang, FF;Weeks, DE;Weng, ZP;Wilson, JG;Yanek, LR;Abe, N;Abe, N;Abecasis, GR;Aguet, F;Albert, C;Almasy, L;Alonso, A;Ament, S;Anderson, P;Anugu, P;Applebaum-Bowden, D;Ardlie, K;Arking, D;Arnett, DK;Ashley-Koch, A;Aslibekyan, S;Assimes, T;Auer, P;Avramopoulos, D;Barnard, J;Barnes, K;Barr, RG;Barron-Casella, E;Barwick, L;Beaty, T;Beck, G;Becker, D;Becker, L;Beer, R;Beitelshees, A;Benjamin, E;Benos, T;Bezerra, M;Bielak, LF;Bis, J;Blackwell, T;Blangero, J;Boerwinkle, E;Bowden, DW;Bowler, R;Brody, J;Broeckel, U;Broome, JG, et al.
    Contributors: Institute of Population Health Sciences;National Institute of Cancer Research
    Abstract: Large-scale whole-genome sequencing studies have enabled the analysis of rare variants (RVs) associated with complex phenotypes. Commonly used RV association tests have limited scope to leverage variant functions. We propose STAAR (variant-set test for association using annotation information), a scalable and powerful RV association test method that effectively incorporates both variant categories and multiple complementary annotations using a dynamic weighting scheme. For the latter, we introduce 'annotation principal components', multidimensional summaries of in silico variant annotations. STAAR accounts for population structure and relatedness and is scalable for analyzing very large cohort and biobank whole-genome sequencing studies of continuous and dichotomous traits. We applied STAAR to identify RVs associated with four lipid traits in 12,316 discovery and 17,822 replication samples from the Trans-Omics for Precision Medicine Program. We discovered and replicated new RV associations, including disruptive missense RVs ofNPC1L1and an intergenic region nearAPOC1P1associated with low-density lipoprotein cholesterol. STAAR is a powerful rare variant association test that incorporates variant functional categories and complementary functional annotations using a dynamic weighting scheme based on annotation principal components. STAAR accounts for population structure and relatedness and is scalable for analyzing large whole-genome sequencing studies.
    Date: 2020-09
    Relation: Nature Genetics. 2020 Sep;52(9):969-983.
    Link to: http://dx.doi.org/10.1038/s41588-020-0676-4
    JIF/Ranking 2023: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=1061-4036&DestApp=IC2JCR
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000562341800001
    Cited Times(Scopus): https://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85089736482
    Appears in Collections:[Ren-Hua Chung] Periodical Articles
    [Chao A. Hsiung] Periodical Articles
    [I-Shou Chang] Periodical Articles

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