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Building ancestral recombination graphs for whole genomes

Thi Phuong Thao Nguyen and Sy Vinh Le and Bich Hai Ho and Si Quang Le (2016) Building ancestral recombination graphs for whole genomes. In: SW4PHD: the 2016 Scientific Workshop for PhD Students, 26 March 2016, Hanoi.

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Abstract

Ancestral Recombination Graph (ARG) plays an important role in human population genetics. Nevertheless, most of current ARG inference algorithms are only applicable to small data sets due to their computational burden. Margarita by Minichiello and Durbin [1] can handle larger data sets; however, it is still not feasible at genome scale. We hereby propose a heuristic algorithm, called ARG4WG, to construct plausible ARGs from thousands of whole chromosome samples, in which the so-called longest shared end, i.e. the longest match between left or right ends of sequences, is used for recombination in the building process. This strategy not only allows ARG4WG to significantly reduce the computational cost, by hundreds to thousands times faster than Margarita but also leads to ARGs with fewer number of recombination events. The ARGs resulted from our algorithm also perform reasonably well in association study with 5560 haplotypes across whole chromosome 11 of Gambia dataset. These results indicate that ARG4WG is a good candidate for genome-wide association study from large data sets.

Item Type:Conference or Workshop Item (Poster)
Subjects:Information Technology (IT)
Divisions:Faculty of Information Technology (FIT)
ID Code:1537
Deposited By: Dr Ngoc Thang Bui
Deposited On:23 May 2016 03:27
Last Modified:23 May 2016 03:28

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