Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools

2000 ◽  
Vol 107 (5) ◽  
pp. 488-493 ◽  
Author(s):  
Bastiaan Hoogendoorn ◽  
Nadine Norton ◽  
George Kirov ◽  
Nigel Williams ◽  
Marian Hamshere ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Frequency Estimation ◽  
Primer Extension ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Allele Frequency Estimation ◽  
Dna Pools

scholarly journals Rapid detection of single nucleotide polymorphisms using the MinION nanopore sequencer: a feasibility study for perioperative precision medicine

2022 ◽  
Author(s):  
Yoshiteru Tabata ◽  
Yoshiyuki Matsuo ◽  
Yosuke Fujii ◽  
Atsufumi Ohta ◽  
Kiichi Hirota
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Precision Medicine ◽  
Allele Frequency ◽  
Frequency Estimation ◽  
Perioperative Complications ◽  
Perioperative Outcomes ◽  
Nanopore Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Dideoxy Sequencing

Introduction: Precision medicine is a phrase used to describe personalized medical care tailored to specific patients based on their clinical presentation and genetic makeup. However, despite the fact that several single nucleotide polymorphisms (SNPs) have been reported to be associated with increased susceptibility to particular anesthetic agents and the occurrence of perioperative complications, genomic profiling and thus precision medicine has not been widely applied in perioperative management. Methods: We validated six SNP loci known to affect perioperative outcomes in Japanese patients using genomic DNA from saliva specimens and nanopore sequencing of each SNP loci to facilitate allele frequency calculations and then compared the nanopore results to those produced using the conventional dideoxy sequencing method. Results: Nanopore sequencing reads clustered into the expected genotypes in both homozygous and heterozygous cases. In addition, the nanopore sequencing results were consistent with those obtained using conventional dideoxy sequencing and the workflow provided reliable allele frequency estimation, with a total analysis time of less than 4 h. Conclusion: Thus, our results suggest that nanopore sequencing may be a promising and versatile tool for SNP genotyping, allowing for rapid and feasible risk prediction of perioperative outcomes.

Genotyping of Single-Nucleotide Polymorphisms by Primer Extension Reaction in a Dry-Reagent Dipstick Format

2007 ◽  
Vol 79 (2) ◽  
pp. 395-402 ◽  
Author(s):  
Ioannis K. Litos ◽  
Penelope C. Ioannou ◽  
Theodore K. Christopoulos ◽  
Joanne Traeger-Synodinos ◽  
Emmanuel Kanavakis
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Primer Extension ◽  
Nucleotide Polymorphisms ◽  
Primer Extension Reaction ◽  
Single Nucleotide

scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

scholarly journals Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Samuele Bovo ◽  
Francesca Bertolini ◽  
Giuseppina Schiavo ◽  
Gianluca Mazzoni ◽  
Stefania Dall’Olio ◽  
...  
Keyword(s):  
Frequency Estimation ◽  
Breeding Value ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Large White ◽  
Single Nucleotide ◽  
Reduced Representation ◽  
Novel Variants ◽  
Dna Pools ◽  
Fat Thickness

The aim of this study was to identify single nucleotide polymorphisms (SNPs) that could be associated with back fat thickness (BFT) in pigs. To achieve this goal, we evaluated the potential and limits of an experimental design that combined several methodologies. DNA samples from two groups of Italian Large White pigs with divergent estimating breeding value (EBV) for BFT were separately pooled and sequenced, after preparation of reduced representation libraries (RRLs), on the Ion Torrent technology. Taking advantage from SNAPE for SNPs calling in sequenced DNA pools, 39,165 SNPs were identified; 1/4 of them were novel variants not reported in dbSNP. Combining sequencing data with Illumina PorcineSNP60 BeadChip genotyping results on the same animals, 661 genomic positions overlapped with a good approximation of minor allele frequency estimation. A total of 54 SNPs showing enriched alleles in one or in the other RRLs might be potential markers associated with BFT. Some of these SNPs were close to genes involved in obesity related phenotypes.

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