scholarly journals Analysis of a Larger SNP Dataset from the HapMap Project Confirmed That the Modern Human A Allele of the ABO Blood Group Genes Is a Descendant of a Recombinant between B and O Alleles

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Masaya Itou ◽  
Mitsuharu Sato ◽  
Takashi Kitano
Keyword(s):  
Blood Group ◽  
Phylogenetic Network ◽  
Modern Human ◽  
Abo Blood Group ◽  
Hapmap Project ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Critical Amino Acid ◽  
Recombination Point ◽  
Two Populations

The human ABO blood group gene consists of three main alleles (A, B, and O) that encode a glycosyltransferase. The A and B alleles differ by two critical amino acids in exon 7, and the major O allele has a single nucleotide deletion (Δ261) in exon 6. Previous evolutionary studies have revealed that the A allele is the most ancient, B allele diverged from the A allele with two critical amino acid substitutions in exon 7, and the major O allele diverged from the A allele with Δ261 in exon 6. However, a recent phylogenetic network analysis study showed that the A allele of humans emerged through a recombination between the B and O alleles. In the previous study, a restricted dataset from only two populations was used. In this study, therefore, we used a large single nucleotide polymorphism (SNP) dataset from the HapMap Project. The results indicated that the A101-A201-O09 haplogroup was a recombinant lineage between the B and O haplotypes, containing the intact exon 6 from the B allele and the two critical A type sites in exon 7 from the major O allele. Its recombination point was assumed to be located just behind Δ261 in exon 6.

scholarly journals Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

2020 ◽  
Vol 69 (5) ◽  
pp. 848-862 ◽  
Author(s):  
Melisa Olave ◽  
Axel Meyer
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gene Flow ◽  
Genetic Material ◽  
Cichlid Fish ◽  
Phylogenetic Network ◽  
Phylogenetic Networks ◽  
Nucleotide Polymorphism ◽  
Rapid Radiation ◽  
Data Set ◽  
Single Nucleotide

Abstract The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.]

SCANNING AND ANALYSIS OF MISMATCH DISTRIBUTION ON HUMAN GENOME

2012 ◽  
Vol 05 (03) ◽  
pp. 1260010
Author(s):  
QINGYUN WANG ◽  
YAYUAN XIAO ◽  
HAILU CHEN ◽  
QIN ZOU
Keyword(s):  
Human Genome ◽  
Mismatch Distribution ◽  
Chromosome 8 ◽  
International Hapmap Project ◽  
Hapmap Project ◽  
Summary Statistic ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Data ◽  
Descriptive Summary Statistic

The mismatch distribution is a good descriptive summary statistic that describes the phenomena of population genetics. This article scanned mismatch distribution on human genome with single nucleotide polymorphism (SNP) data from the International HapMap Project. It is found that the abnormal mismatch distribution could imply some special segments on some chromosomes. One of the segments, on chromosome 8, was proved as an inversion. Other special segments may also imply some special structure on chromosomes, such as duplication. The conjectures of other segments still need further research.

Predictions of single-nucleotide polymorphism differentiation between two populations in terms of mutual information

2011 ◽  
Vol 20 (15) ◽  
pp. 3156-3166 ◽  
Author(s):  
RODERICK C. DEWAR ◽  
WILLIAM B. SHERWIN ◽  
EMMA THOMAS ◽  
CLARE E. HOLLELEY ◽  
RICHARD A. NICHOLS
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Mutual Information ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Two Populations

scholarly journals The Ser19Stop single nucleotide polymorphism (SNP) of human PHYHIPL affects the cerebellum in mice

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Hisako Sugimoto ◽  
Takuro Horii ◽  
Jun-Na Hirota ◽  
Yoshitake Sano ◽  
Yo Shinoda ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Research Effort ◽  
Molecular Layer ◽  
Learning Ability ◽  
Hapmap Project ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Interacting Protein ◽  
Health And Disease ◽  
Cerebellar Purkinje Cells

AbstractThe HapMap Project is a major international research effort to construct a resource to facilitate the discovery of relationships between human genetic variations and health and disease. The Ser19Stop single nucleotide polymorphism (SNP) of human phytanoyl-CoA hydroxylase-interacting protein-like (PHYHIPL) gene was detected in HapMap project and registered in the dbSNP. PHYHIPL gene expression is altered in global ischemia and glioblastoma multiforme. However, the function of PHYHIPL is unknown. We generated PHYHIPL Ser19Stop knock-in mice and found that PHYHIPL impacts the morphology of cerebellar Purkinje cells (PCs), the innervation of climbing fibers to PCs, the inhibitory inputs to PCs from molecular layer interneurons, and motor learning ability. Thus, the Ser19Stop SNP of the PHYHIPL gene may be associated with cerebellum-related diseases.

Abstract 16411: Abo Blood Group and Risk of Myocardial Infarction in Hispanics

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Tao Huang ◽  
Yanping Li ◽  
Min Xu ◽  
Ana Baylin ◽  
Hannia Campos ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Blood Group ◽  
Population Based ◽  
Abo Blood Group ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Lifestyle Risk Factors ◽  
History Of ◽  
Group A ◽  
Lifestyle Risk

Hypothesis: ABO blood group has been associated with myocardial infarction (MI) in Caucasians. This study evaluated whether genotype-derived ABO blood group associated with MI in Hispanics, and whether lifestyle risk factors modified the associations. Methods: Cases (n=2273) with a first acute nonfatal MI and population-based controls (n=2274) living in Costa Rica were studied. Five ABO single-nucleotide polymorphisms (SNPs) were genotyped. RESULTS: Three SNPs (rs687289, rs507666, and rs579459) at ABO locus showed significant associations with MI risk, with odds ratios (ORs, 95% confidence interval) of 1.17(1.05-1.30), 1.18(1.05-1.32), and 1.14(1.02-1.28), respectively. Compared to subjects with blood group O, the ORs for blood group A, AB and B were 1.24 (95% CI, 1.08-1.43), 1.15 (95% CI, 0.95-1.39), and 1.10 (95% CI, 0.77-1.57), respectively. Subjects with non-O blood group had an adjusted OR for MI of 1.20 (95% CI, 1.05-1.37) when compared to subjects with O blood group after adjustment for age, sex, area of residence, smoking, alcohol consumption, physical activity, total calories, and family history of MI. CONCLUSIONS: Our results indicate both the consistency and disparity of ABO genetic effects on MI risk between Hispanics and Caucasians.

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