NetView: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation.

ABSTRACT: High-throughput sequencing and single nucleotide polymorphism (SNP) genotyping can be used to infer complex population structures. Fine-scale population structure analysis tracing individual ancestry remains one of the major challenges. Based on network theory and recent advances in SNP chip technology, we investigated an unsupervised network clustering method called Super Paramagnetic Clustering (Spc). When applied to whole-genome marker data it identifies the natural divisions of groups of individuals into population clusters without use of prior ancestry information. Furthermore, we optimised an analysis pipeline called NetView, a high-definition network visualization, starting with computation of genetic distance, followed clustering using Spc and finally visualization of clusters with

SUBMITTER: Neuditschko M 

PROVIDER: S-EPMC3485224 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature