scholarly journals A comparative analysis of proximity measures to determine the Lithuanian population structure

2021 ◽  
Vol 62 ◽  
pp. 86-93
Author(s):  
Alma Molytė ◽  
Alina Urnikytė
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Comparative Analysis ◽  
Multidimensional Scaling ◽  
Principal Component ◽  
Genetic Data ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Proximity Measures

In this paper the multidimensional scaling, the principal coordinate and principal component methods for the Lithuanian population structure have investigated, taken that the proximity measures are Euclid, Gower, Bray-Curtis, Kulczynski, Jaccard and Morisita. The genome-wide single nucleotide polymorphism genetic data analyzed. A comparative analysis of proximity measures performed. The results of visualization are also presented.

scholarly journals Simulasi Metode Statistik untuk Seleksi Single Nucleotide Polymorphism pada Populasi Plasmodium

Life Science ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 54-64
Author(s):  
Mohamad Ikhsan Nurulloh ◽  
Yustinus Ulung Anggraito ◽  
Hidayat Trimarsanto ◽  
Endah Peniati ◽  
R. Susanti
Keyword(s):  
Principal Component Analysis ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Principal Component ◽  
Selection Method ◽  
Principal Coordinate Analysis ◽  
Neighbor Joining ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Informative Snps

Plasmodium is a pathogen that causes malaria which has high genetic diversity and resistance to antimalarial drugs. Information on the population structure of Plasmodium can be used as molecular markers, one of which is Single Nucleotide Polymorphism (SNP). SNP markers are in large numbers and not entirely informative. The existing method has not been effective in producing informative SNPs, therefore it is necessary to develop an effective SNP selection method. The SNP selection method is developed using FST as the main filter (filter) and combines Linkage Disequilibrium (LD). The population structure of the SNP is known to use Principal Component Analysis (PCA), Principal Coordinate Analysis (PCoA), pairwise FST, and neighbor-joining population trees. Informative SNP criteria known by calculating FST and Minor Allele Frequency (MAF). Statistical methods were tested to determine their effectiveness in producing informative SNPs. The method testing was carried out using genetic data simulation of the Plasmodium population. The results of the study show that the statistical method is effective in producing informative SNPs. The informative SNP criteria are SNPs with MAF 0.2-0.4 and FST 0.1-0.4 and 0.8-1.0.   Plasmodium merupakan patogen penyebab malaria dengan keanekaragaman genetik tinggi dan memiliki resistensi terhadap obat antimalaria. Informasi sturuktur populasi Plasmodium dapat dimanfaatkan sebagai marka molekuler seperti Single Nucleotide Polymorphism (SNP). Marka SNP terdapat dalam jumlah yang banyak dan tidak seluruhnya informatif. Metode yang telah ada belum efektif dalam menghasilkan SNP informatif sehingga perlu dilakukan pengembangan metode seleksi SNP yang efektif. Metode seleksi SNP dikembangkan menggunakan FST sebagai filter (penyaring) utamanya dan gabungkan Linkage Disequilibrium (LD). Struktur populasi dari SNP diketahui menggunakan Principal Component Analysis (PCA), Principal Coordinate Analysis (PCoA), pairwise FST, dan neighbor-joining population tree. Kriteria SNP informatif yang diketahui dengan menghitung FST dan Minor Allele Frequency (MAF). Metode statistika diuji untuk mengetahui keefektifannya dalam menghasilkan SNP informatif. Pengujian metode dilakukan menggunakan simulasi data genetik populasi Plasmodium. Hasil penelitian menunjukkan metode statistika efektif dalam menghasilkan SNP informatif. Kriteria SNP informatif adalah SNP dengan MAF 0.2-0.4 serta FST 0.1-0.4 dan 0.8-1.0.

Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

2006 ◽  
Vol 112 (6) ◽  
pp. 1104-1114 ◽  
Author(s):  
Karl J. Schmid ◽  
Ottó Törjék ◽  
Rhonda Meyer ◽  
Heike Schmuths ◽  
Matthias H. Hoffmann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Large Scale ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Scale Population

scholarly journals Population structure and breed composition prediction in a multi-breed sheep population using genome-wide single nucleotide polymorphism genotypes

animal ◽  
2020 ◽  
Vol 14 (3) ◽  
pp. 464-474
Author(s):  
A.C. O’Brien ◽  
D.C. Purfield ◽  
M.M. Judge ◽  
C. Long ◽  
S. Fair ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Sheep Population ◽  
Genome Wide ◽  
Breed Sheep
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