two papers on analyzing whole genome resequencing with objective of detecting selections

This group output some good case of analyzing whole genome resequencing with objective of detecting selections.

2011

Matteo Fumagalli, Manuela Sironi, Uberto Pozzoli, Anna Ferrer-Admettla, Linda Pattini, Rasmus NielsenSignatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure throughhuman evolution. PLoS Genetics in Press Supplementary material, 给出了数据和 Rcode。

Cagliani R, Riva S, Pozzoli U, Fumagalli M, Comi GP, Bresolin N, Clerici M, Sironi M. Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving. BMC Evolutionary Biology 11:171

Common population genetic tests based on the site frequency spectrum (SFS) include Tajima's D (D_T) [14] and Fu and Li's D* and F* [15]. D_T tests the departure from neutrality by comparing two nucleotide diversity indexes: θ_W [16], an estimate of the expected per site heterozigosity, and π[17], the average number of pairwise sequence nucleotide differences. Positive values of D_Tindicate an excess of intermediate frequency variants and are a signature of balancing selection.Fu and Li's F* and D* are also based on SNP frequency spectra and differ from D_T in that they also take into account whether mutations occur in external or internal branches of a genealogy[15]. As an empirical comparison, θ_W, π, as well as D_T, F* and D* were calculated for 5 kbwindows (thereafter referred to as reference windows) deriving from 238 genes resequenced bythe NIEHS program in CEU. Additionally, the statistical significance of neutrality tests wasevaluated by performing coalescent simulations with a population genetic model that incorporatesdemographic scenarios [18].

Rachele Cagliani, Matteo Fumagalli, Franca R. Guerini, Stefania Riva, Daniela Galimberti, Giacomo P. Comi, Cristina Agliardi, Elio Scarpini, Uberto Pozzoli and Diego Forni, et al. Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis. Human Genetics Jul 7

Cereda M, Sironi M, Cavalleri M, Pozzoli U. GeCo++: a C++ library for genomic features computation and annotation in the presence of variants. Bioinformatics 2011 Mar 12. [Epub ahead of print]

Magri F, Del Bo R, D'Angelo MG, Govoni A, Ghezzi S, Gandossini S, Sciacco M, Ciscato P, Bordoni A, Tedeschi S, Fortunato F, Lucchini V, Cereda M, Corti S, Moggio M, Bresolin N, Comi GP. Clinical and molecular characterization of a cohort of patients with novel nucleotide alterations of the Dystrophin gene detected by direct sequencing. BMC Med Genet. 2011 Mar 11;12:37.

Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, Konig J, Hortobágyi T, Nishimura AL, Zupunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE, Ule J. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci. 2011 Apr;14(4):452-8.

Cagliani R, Fruguglietti ME, Berardinelli A, D'Angelo MG, Prelle A, Riva S, Napoli L, Gorni K, Orcesi S, Lamperti C, Pichiecchio A, Signaroldi E, Tupler R, Magri F, Govoni A, Corti S, Bresolin N, Moggio M, Comi GP. New molecular findings in congenital myopathies due to selenoprotein N gene mutations. J Neurol Sci.