scholarly journals POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations

2018 ◽  
Vol 25 (4) ◽  
pp. 417-429
Author(s):  
Jaeil Ahn ◽  
Brian Conkright ◽  
Simina M. Boca ◽  
Subha Madhavan
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Copy Number ◽  
Copy Number Variations ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Admixed Population

scholarly journals Single-nucleotide polymorphisms and copy number variations of the FCGR2A and FCGR3A genes in healthy Japanese subjects

2013 ◽  
Vol 2 (2) ◽  
pp. 265-269 ◽  
Author(s):  
HIROYUKI MORIYA ◽  
KATSUHIKO SAITO ◽  
NUALA HELSBY ◽  
NAOMI HAYASHI ◽  
SHIGEKAZU SUGINO ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Copy Number ◽  
Copy Number Variations ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Japanese Subjects

scholarly journals Single nucleotide polymorphisms and copy-number variations in the Trypanosoma brucei repeat (TBR) sequence can be used to enhance amplification and genotyping of Trypanozoon strains

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258711
Author(s):  
Nick Van Reet ◽  
Pati Patient Pyana ◽  
Sara Dehou ◽  
Nicolas Bebronne ◽  
Stijn Deborggraeve ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Trypanosoma Brucei ◽  
Copy Number ◽  
Internal Standard ◽  
Copy Number Variations ◽  
Target Sequence ◽  
Analytical Sensitivity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Relative Copy Number

The Trypanosoma brucei repeat (TBR) is a tandem repeat sequence present on the Trypanozoon minichromosomes. Here, we report that the TBR sequence is not as homogenous as previously believed. BLAST analysis of the available T. brucei genomes reveals various TBR sequences of 177 bp and 176 bp in length, which can be sorted into two TBR groups based on a few key single nucleotide polymorphisms. Conventional and quantitative PCR with primers matched to consensus sequences that target either TBR group show substantial copy-number variations in the TBR repertoire within a collection of 77 Trypanozoon strains. We developed the qTBR, a novel PCR consisting of three primers and two probes, to simultaneously amplify target sequences from each of the two TBR groups into one single qPCR reaction. This dual probe setup offers increased analytical sensitivity for the molecular detection of all Trypanozoon taxa, in particular for T.b. gambiense and T. evansi, when compared to existing TBR PCRs. By combining the qTBR with 18S rDNA amplification as an internal standard, the relative copy-number of each TBR target sequence can be calculated and plotted, allowing for further classification of strains into TBR genotypes associated with East, West or Central Africa. Thus, the qTBR takes advantage of the single-nucleotide polymorphisms and copy number variations in the TBR sequences to enhance amplification and genotyping of all Trypanozoon strains, making it a promising tool for prevalence studies of African trypanosomiasis in both humans and animals.

scholarly journals The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S84 ◽  
Author(s):  
John SK Kauwe ◽  
Sarah Bertelsen ◽  
Laura Bierut ◽  
Gerald Dunn ◽  
Anthony L Hinrichs ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Short Tandem

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags

2011 ◽  
Vol 83 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Toshimi MATSUMOTO ◽  
Naohiko OKUMURA ◽  
Hirohide UENISHI ◽  
Takeshi HAYASHI ◽  
Noriyuki HAMASIMA ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tags ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

scholarly journals Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse Horses

2019 ◽  
Author(s):  
Mohammed Ali Al Abri ◽  
Heather Marie Holl ◽  
Sara E Kalla ◽  
Nate Sutter ◽  
Samantha Brooks
Keyword(s):  
Copy Number ◽  
Copy Number Gain ◽  
Copy Number Variations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Long Distance ◽  
Single Nucleotide ◽  
Evolutionary Selection ◽  
Climatic Environment ◽  
Physiological Adaptations

AbstractThe domesticated horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of horse. To enrich the current collection of genetic variants in the horse, we sequenced whole genomes from six horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six horses with coverage between 15x to 24x per horse. After applying rigorous filtration, we identified and functionally annotated 8,128,658 Single Nucleotide Polymorphisms (SNPs), and 830,370 Insertions/Deletions (INDELs), as well as novel Copy Number Variations (CNVs) and Structural Variations (SVs). Our results revealed putatively functional variants including genes associated with size variation like ANKRD1 and HMGA1 in the very large Percheron and the ZFAT gene in the American Miniature horse. We detected a copy number gain in the Latherin gene that may be the result of evolutionary selection for thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the horse.Author SummaryThe domesticated horse played a unique role in human history, serving not just as a source of dietary animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Although the completion of the horse reference genome yielded the discovery of many genetic variants, the remarkable diversity across breeds of horse calls for additional effort in quantification of the breadth of genetic polymorphism within this unique species. Here, we present genome re-sequencing and variant detection analysis for six horses belonging to geographically and physiologically diverse breeds. We identified and annotated not just single nucleotide polymorphisms (SNPs), but also large insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). Our results illustrate novel sources of polymorphism and highlight potentially impactful variations for phenotypes of body size and conformation. We also detected a copy number gain in the Latherin gene that could be the result of an evolutionary selection for thermoregulation through sweating. Our newly discovered variants were formatted into easy-to-use tracks that can be easily accessed by researchers around the globe.

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