DCA for genome-wide epistasis analysis: the statistical genetics perspective

Gao, Chen-YiChinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.;Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China. (författare)

DCA for genome-wide epistasis analysis : the statistical genetics perspective

QC 20190219
Direct coupling analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to sequences of homologous proteins, and also more recently to whole-genome population-wide sequencing data. We here argue that the use of DCA on the genome scale is contingent on fundamental issues of population genetics. DCA can be expected to yield meaningful results when a population is in the quasi-linkage equilibrium (QLE) phase studied by Kimura and others, but not, for instance, in a phase of clonal competition. We discuss how the exponential (Potts model) distributions emerge in QLE, and compare couplings to correlations obtained in a study of about 3000 genomes of the human pathogen Streptococcus pneumoniae.

Cecconi, FabioSapienza Univ Roma, CNR ISC, Ple Moro 2, I-00185 Rome, Italy.;Sapienza Univ Roma, Dipartimento Fis, Ple Moro 2, I-00185 Rome, Italy. (författare)
Vulpiani, AngeloSapienza Univ Roma, CNR ISC, Ple Moro 2, I-00185 Rome, Italy.;Sapienza Univ Roma, Dipartimento Fis, Ple Moro 2, I-00185 Rome, Italy.;Accademia Lincei, Ctr Interdisciplinare B Segre, Rome, Italy. (författare)
Zhou, Hai-JunChinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.;Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China. (författare)
Aurell, ErikKTH,Beräkningsvetenskap och beräkningsteknik (CST),Aalto Univ, Dept Appl Phys, FIN-00076 Aalto, Finland.;Aalto Univ, Dept Comp Sci, FIN-00076 Aalto, Finland.;PSL Res Univ, Lab Phys Chim Theor, UMR CNRS Gulliver 7083, ESPCI, 10 Rue Vauquelin, F-75231 Paris, France.(Swepub:kth)u1uc9cqo (författare)
Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.;Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.Sapienza Univ Roma, CNR ISC, Ple Moro 2, I-00185 Rome, Italy.;Sapienza Univ Roma, Dipartimento Fis, Ple Moro 2, I-00185 Rome, Italy. (creator_code:org_t)

Av författaren/redakt...: Gao, Chen-Yi; Cecconi, Fabio; Vulpiani, Angelo; Zhou, Hai-Jun; Aurell, Erik

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