Application of the iPLEXTM Gold SNP genotyping method for the analysis of Amerindian ancient DNA samples: Benefits for ancient population studies

2011 ◽  
Vol 32 (3-4) ◽  
pp. 386-393 ◽  
Author(s):  
Fanny Mendisco ◽  
Christine Keyser ◽  
Clémence Hollard ◽  
Veronica Seldes ◽  
Axel E. Nielsen ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Population Studies ◽  
Snp Genotyping ◽  
Ancient Population ◽  
Genotyping Method

scholarly journals Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

2018 ◽  
Author(s):  
Umberto Esposito ◽  
Ranajit Das ◽  
Mehdi Pirooznia ◽  
Eran Elhaik
Keyword(s):  
Population Structure ◽  
Ancient Dna ◽  
Principal Component ◽  
Population History ◽  
Fine Scale ◽  
Ancestry Informative Markers ◽  
Ancient Population ◽  
Human Genomes ◽  
Rapid Accumulation ◽  
Time Periods

AbstractThe rapid accumulation of ancient human genomes from various areas and time periods potentially allows the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations known to misrepresent the population structure. Past studies addressed these problems using ancestry informative markers (AIMs). However, it is unclear whether AIMs derived from contemporary human genomes can capture ancient population structure and whether AIM finding methods are applicable to ancient DNA (aDNA) provided that the high missingness rates in ancient, oftentimes haploid, DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperforms all competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of population microarrays and the interpretation of aDNA results.

An innovative SNP genotyping method adapting to multiple platforms and throughputs

2016 ◽  
Vol 130 (3) ◽  
pp. 597-607 ◽  
Author(s):  
Y. M. Long ◽  
W. S. Chao ◽  
G. J. Ma ◽  
S. S. Xu ◽  
L. L. Qi
Keyword(s):  
Snp Genotyping ◽  
Genotyping Method

A gel-free SNP genotyping method: bioluminometric assay coupled with modified primer extension reactions (BAMPER) directly from double-stranded PCR products

2004 ◽  
Vol 24 (2) ◽  
pp. 155-163 ◽  
Author(s):  
Guo-Hua Zhou ◽  
Hiromi Shirakura ◽  
Masao Kamahori ◽  
Kazunori Okano ◽  
Keiichi Nagai ◽  
...  
Keyword(s):  
Snp Genotyping ◽  
Primer Extension ◽  
Genotyping Method ◽  
Pcr Products

Tetra-primer ARMS-PCR is an efficient SNP genotyping method: An example from SIRT2

2014 ◽  
Vol 6 (6) ◽  
pp. 1835-1840 ◽  
Author(s):  
Mingxun Li ◽  
Xiaomei Sun ◽  
Jing Jiang ◽  
Yujia Sun ◽  
Xianyong Lan ◽  
...  
Keyword(s):  
Snp Genotyping ◽  
Genotyping Method ◽  
Arms Pcr ◽  
Pcr Rflp ◽  
Pcr Method ◽  
Rflp Assay

We have successfully genotyped a new identified bovine SIRT2 SNP g.4140A > G by T-ARMS-PCR method and validated the accuracy by PCR-RFLP assay using 1255 animals representing the five main Chinese breeds.

Neolithic cattle domestication as seen from ancient DNA

2007 ◽  
Author(s):  
Ruth Bollongino ◽  
Joachim Burger
Keyword(s):  
Genetic Diversity ◽  
Middle East ◽  
Bronze Age ◽  
Ancient Dna ◽  
Population Studies ◽  
Centre Of Origin ◽  
Mitochondrial Data ◽  
Geographical Regions ◽  
Taurine Cattle ◽  
Cattle Domestication

Studies on modern cattle populations demonstrate the relations of the two major cattle breeds, the humpless taurine cattle (B. Taurus) and the Asian humped zebu (B. indicus). Studies by Loftus et al. (1994), Bradley et al. (1996), and MacHugh et al. (1997) showed that these two groups stem from independent domestication events in different geographical regions. Concerning the taurine cattle, recent population studies show that today the genetic diversity is highest in the Near and Middle East. This is an indication of the centre of origin in this region. But modern data can be biased by recent breeding practices and introgression. Only the analysis of ancient samples can help to get at detailed information about prehistoric situations. This chapter presents ancient mitochondrial data from 40 domestic cattle and 17 aurochs samples (plus ancient bison for comparison) that date mainly to the Neolithic, but which also include some of Mesolithic and Bronze Age date.

A Microfluidic-Based SNP Genotyping Method for Hereditary Hearing-Loss Detection

2019 ◽  
Vol 91 (9) ◽  
pp. 6111-6117
Author(s):  
Ying Lu ◽  
Shan Chen ◽  
Li Wei ◽  
Lanhua Sun ◽  
Houming Liu ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Snp Genotyping ◽  
Hereditary Hearing Loss ◽  
Genotyping Method
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