Recombinations

Meiotic recombination is the process through which nucleotide sequences are exchanged between DNA molecules. It plays a key evolutionary role in shaping the genetic diversity of a species by allowing the offspring to have different allele combinations compared to the parents. Many statistical algorithms have been proposed in literature which compute their relative frequency across the genome. We take an orthogonal approach in identifying individual recombination events which can be detected with high confidence. The information gleaned from these detected events is integrated in an ancestral recombination graph. The ARG is not fully resolved since it contains high confidence nodes only; hence we call it a subARG. The methodology has been validated in coalescent simulations mimicking accepted human demography. Population structure inferred from the subARG, in real world population data, shows concordance with the more traditional SNP and haplotype based analysis; and adds a new dimension to population genomic analysis.

The right figure shows the subARG in a coalescent simulation. African, European and Asian extant samples are colored in blue, green and yellow respectively. The reconstructed ARG nodes and edges are indicated in red and the rest in gray. (Click on the image for a high resolution version)

 

Publications

A. Javed, M. Melé, M. Pybus, P. Zalloua, M. Haber, D. Comas, M. Netea, O. Balanovsky, E. Balanovska, L. Jin, Y. Yang, G. Arunkumar , R.M. Pitchappan, J. Bertranpetit, F. Calafell, L. Parida, and The Genographic Consortium, Recombination networks as genetic markers: a human variation study of the Old World, Human Genetics (accepted)

M. Melé, A. Javed, M. Pybus, P. Zalloua, M. Haber, D. Comas, M. Netea, O. Balanovsky, E. Balanovska, L. Jin, Y. Yang, R.M. Pitchappan, G. Arunkumar , L. Parida, F. Calafell, J. Bertranpetit, and The Genographic Consortium, Recombination gives a new insight in the effective population size and the history of the old world human populations., Molecular Biology and Evolution, October 2011 [pubmed]

A. Javed, M. Pybus, M. Melé, F. Utro, J. Bertranpetit, F. Calafell, and L. Parida, IRiS: Construction of ARG network at genomic scales, Bioinformatics, July 2011 [pubmed]

L. Parida, P.F. Palamara, and A. Javed, A Minimal Descriptor of an Ancestral Recombinations Graph, BMC Bioinformatics, APBC, February 2011 [pubmed]

M. Melé, A. Javed, M. Pybus, F. Calafell, L. Parida, J. Bertranpetit, and The Genographic Consortium, A New Method to Reconstruct Recombination Events at a Genomic Scale, PLoS Computational Biology, November 2010 [pubmed]

A. Javed, and L. Parida,Recombinomics: Population Genomics from a Recombination Perspective, Proceedings of C3S2E, May 2010 [ACM DL]

L. Parida, A. Javed, M. Melé, F. Calafell, J. Bertranpetit, and The Genographic Consortium, Minimizing recombinations in consensus networks for phylogeographic studies, BMC Bioinformatics, APBC, January 2009 [pubmed]

L. Parida, A. Javed, M. Melé, and J. Bertranpetit, A case for Recombinomics, IBM Technical Report RC24677, August 2008