Localizing and Classifying Adaptive Targets with Trend Filtered Regression.
Localizing and Classifying Adaptive Targets with Trend Filtered Regression.
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DOI：
10.1093/molbev/msy205
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发表时间：
2019-02-01
影响因子：
10.7
通讯作者：
DeGiorgio M
中科院分区：
文献类型：
--
作者：
Mughal MR;DeGiorgio M
Identifying genomic locations of natural selection from sequence data is an ongoing challenge in population genetics. Current methods utilizing information combined from several summary statistics typically assume no correlation of summary statistics regardless of the genomic location from which they are calculated. However, due to linkage disequilibrium, summary statistics calculated at nearby genomic positions are highly correlated. We introduce an approach termed Trendsetter that accounts for the similarity of statistics calculated from adjacent genomic regions through trend filtering, while reducing the effects of multicollinearity through regularization. Our penalized regression framework has high power to detect sweeps, is capable of classifying sweep regions as either hard or soft, and can be applied to other selection scenarios as well. We find that Trendsetter is robust to both extensive missing data and strong background selection, and has comparable power to similar current approaches. Moreover, the model learned by Trendsetter can be viewed as a set of curves modeling the spatial distribution of summary statistics in the genome. Application to human genomic data revealed positively selected regions previously discovered such as LCT in Europeans and EDAR in East Asians. We also identified a number of novel candidates and show that populations with greater relatedness share more sweep signals.
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影响因子：
9.8
作者：
Akey JM;Eberle MA;Rieder MJ;Carlson CS;Shriver MD;Nickerson DA;Kruglyak L
通讯作者：
Kruglyak L
影响因子：
4.5
作者：
Hancock, Angela M.;Witonsky, David B.;Gordon, Adam S.;Eshel, Gidon;Pritchard, Jonathan K.;Coop, Graham;Di Rienzo, Anna
通讯作者：
Di Rienzo, Anna
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7
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Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
7
作者：
Chen, Hua;Patterson, Nick;Reich, David
通讯作者：
Reich, David
影响因子：
5
作者：
GREENLAND, S;LONGNECKER, MP
通讯作者：
LONGNECKER, MP