SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access

Amigo, Jorge; Salas, Antonio; Phillips, C.; Carracedo, Ángel

doi:10.1186/1471-2105-9-428

Cited by 101 publications

(115 citation statements)

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“…Genotype data from West Africans, European Spaniards, Mesoamerican Amerindians, and Han Chinese from Beijing were used as parental populations. These parental allele frequencies were obtained from three sources: reference publications (Martinez-Marignac et al 2007;Tian et al 2007), Hapmap data extracted from the dbSNP at the NCBI webpage, and the 1000 Genomes project downloaded from SPSmart (Amigo et al 2009;Amigo et al 2008). The triangular plots were generated with the package klaR (Weihs et al 2005) on R (Team 2011).…”

Section: Discussionmentioning

confidence: 99%

Ancestry Informative Markers Clarify the Regional Admixture Variation in the Costa Rican Population

Campos-Sánchez¹,

Raventós²,

Barrantes³

2013

Human Biology

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Section: Discussionmentioning

confidence: 99%

Ancestry Informative Markers Clarify the Regional Admixture Variation in the Costa Rican Population

Campos-Sánchez¹,

Raventós²,

Barrantes³

2013

Human Biology

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“…(Sánchez et al 2006;Phillips et al 2007), all genotyped for a panel of 34 AIMs. The genotyping data were compiled using SPSmart (Amigo et al 2008). (B) Structure bar plot indicating ancestral components of L-European mtDNA carriers based on profiles derived from a set of 34 AIMs.…”

Section: Discussionmentioning

confidence: 99%

Reconstructing ancient mitochondrial DNA links between Africa and Europe

Cerezo¹,

Achilli²,

Olivieri³

et al. 2012

Genome Res.

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Mitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs account for <1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further evaluate this issue, we analyzed 69 mitochondrial genomes belonging to various L sublineages from a wide range of European populations. Phylogeographic analyses showed that~65% of the European L lineages most likely arrived in rather recent historical times, including the Romanization period, the Arab conquest of the Iberian Peninsula and Sicily, and during the period of the Atlantic slave trade. However, the remaining 35% of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago.

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“…Further examination of the extended haplotype blocks in ASN showed that rs2291725 is highly linked with another 43 SNPs Genotypes were analyzed as described using the SPSmart v3 and Haplotter (Voight et al 2006;Amigo et al 2008). The average frequency of two alleles-derived allele GIP 103C and ancestral chimpanzee allele GIP…”

Section: Variants At the Gip Locus Were Partially Selected In Eurasiamentioning

confidence: 99%

Adaptive selection of an incretin gene in Eurasian populations

Chang

Cai

et al. 2010

Genome Res.

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Diversities in human physiology have been partially shaped by adaptation to natural environments and changing cultures. Recent genomic analyses have revealed single nucleotide polymorphisms (SNPs) that are associated with adaptations in immune responses, obvious changes in human body forms, or adaptations to extreme climates in select human populations. Here, we report that the human GIP locus was differentially selected among human populations based on the analysis of a nonsynonymous SNP (rs2291725). Comparative and functional analyses showed that the human GIP gene encodes a cryptic glucose-dependent insulinotropic polypeptide (GIP) isoform (GIP55S or GIP55G) that encompasses the SNP and is resistant to serum degradation relative to the known mature GIP peptide. Importantly, we found that GIP55G, which is encoded by the derived allele, exhibits a higher bioactivity compared with GIP55S, which is derived from the ancestral allele. Haplotype structure analysis suggests that the derived allele at rs2291725 arose to dominance in East Asians ∼8100 yr ago due to positive selection. The combined results suggested that rs2291725 represents a functional mutation and may contribute to the population genetics observation. Given that GIP signaling plays a critical role in homeostasis regulation at both the enteroinsular and enteroadipocyte axes, our study highlights the importance of understanding adaptations in energy-balance regulation in the face of the emerging diabetes and obesity epidemics.

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SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access

Cited by 101 publications

References 9 publications

Ancestry Informative Markers Clarify the Regional Admixture Variation in the Costa Rican Population

Ancestry Informative Markers Clarify the Regional Admixture Variation in the Costa Rican Population

Reconstructing ancient mitochondrial DNA links between Africa and Europe

Adaptive selection of an incretin gene in Eurasian populations

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