Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA

2004 ◽  
Vol 333 (1) ◽  
pp. 72-78 ◽  
Author(s):  
Ye Bang-Ce ◽  
Zuo Peng ◽  
Yi Bincheng ◽  
Li Songyang
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Microarray Hybridization ◽  
Single Nucleotide ◽  
Pooled Dna ◽  
Different Populations

scholarly journals Precise Estimation of Allele Frequencies of Single-Nucleotide Polymorphisms by a Quantitative SSCP Analysis of Pooled DNA

2001 ◽  
Vol 68 (1) ◽  
pp. 214-218 ◽  
Author(s):  
Tomonari Sasaki ◽  
Tomoko Tahira ◽  
Akari Suzuki ◽  
Koichiro Higasa ◽  
Yoji Kukita ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequencies ◽  
Sscp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Precise Estimation ◽  
Pooled Dna

scholarly journals Population Screening of Single-Nucleotide Polymorphisms Exemplified by Analysis of 8000 Alleles

2002 ◽  
Vol 7 (6) ◽  
pp. 501-506 ◽  
Author(s):  
Per Olaf Ekstrøm ◽  
Jens Bjørheim ◽  
Gustav Gaudernack ◽  
Karl-Erik Giercksky
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequencies ◽  
Sample Treatment ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pooled Data ◽  
Pooled Dna ◽  
Hardy Weinberg Equilibrium ◽  
Melting Properties ◽  
Pooled Samples

The authors describe a method in which the population frequency of single-nucleotide polymorphisms (SNPs) can be efficiently detected and their allele frequencies accurately measured. Selected SNPs in TNF, IL-4, and CTLA-4 were used to demonstrate the method. Blood from 4000 individuals was pooled, DNA was extracted, and target sequences were PCR amplified and analyzed by denaturant capillary electrophoresis. Alleles were separated into peaks based on melting properties of the double DNA helix. Frequencies of the different alleles were determined by calculating the area under the peaks. Allele frequencies and Hardy-Weinberg equilibrium estimated from the pooled data were verified by analyzing 7.5% of the samples randomly selected from the blood donor series. The method herein is equally suitable for single-samples and/or pooled-samples analysis of SNPs, in which sample treatment is kept to a minimum. The potential throughput of the method is beyond obtainable numbers of samples.

scholarly journals Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds

2006 ◽  
Vol 6 (4) ◽  
pp. 992-997 ◽  
Author(s):  
I. CAPPUCCIO ◽  
L. PARISET ◽  
P. AJMONE-MARSAN ◽  
S. DUNNER ◽  
O. CORTES ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
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

Prognostic Assessment of Three Single Nucleotide Polymorphisms (BCL2–938C>A, MTHFR 677C>T, GNAS1 T393C) in Chronic Lymphocytic Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2080-2080
Author(s):  
Thorsten Zenz ◽  
Ulrich Duehrsen ◽  
Harald Dohner ◽  
Winfried Siffert ◽  
Stephan Stilgenbauer ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Single Nucleotide Polymorphisms ◽  
Molecular Genetics ◽  
Association Studies ◽  
Lymphocytic Leukemia ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Gnas1 T393c

Abstract A number of single nucleotide polymorphisms (SNP) have been implicated to impact on the disease course in chronic lymphocytic leukemia (CLL). Nonetheless, there have been few polymorphisms for which replications of association were done in different studies. We genotyped three recently described SNPs (BCL2 –938C>A, MTHFR 677C>T, GNAS1 T393C) in a large group of CLL patients (n=273) with mature follow up and detailed analysis of molecular genetics. The cohort had a median follow-up of over 150 months and the known poor risk molecular genetics (17p–, 11q– and unmutated VH-status) were associated with poor prognosis. The allele frequencies for all three SNPs were in Hardy Weinberg equilibrium and we could not identify imbalances when we stratified for subgroups (genomic aberrations, VH status, stage according to Binet). Moreover, the polymorphisms did not affect clinical outcome (time to first treatment and overall survival) in univariate or multivariate analysis in the current cohort. Comparing CLL patients with over 100 healthy controls we found no significant differences in allele frequencies or genotype distributions for all three polymorphisms. While there have been reports showing the molecular effects and clinical consequences of the polymorphisms we studied, we did not find SNP genotype-dependent effects in a large cohort of CLL patients. Potential reasons for the discrepancy of the results are numerous. Because of the advancement of genotyping technologies, a large number of SNPs can be evaluated (multiple testing). The sample sizes of the reported association studies are often too small and frequently only one patient cohort is investigated. Moreover, negative results are often not published (publication bias). One major reason for the different results is the different genetic background of the populations due to ethnicity (selection bias). Summarized, this study supports the importance of confirmation of initial findings in an independent data set. However, results of genome-wide association studies will soon be reported with additional novel genes identified and will help making great strides in identifying the genetic determinants of CLL risk.

scholarly journals A Whole-Genome Scan for Association with Invasion Success in the Fruit Fly Drosophila suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure

2020 ◽  
Vol 37 (8) ◽  
pp. 2369-2385 ◽  
Author(s):  
Laure Olazcuaga ◽  
Anne Loiseau ◽  
Hugues Parrinello ◽  
Mathilde Paris ◽  
Antoine Fraimout ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Genome Wide Association Study ◽  
Allele Frequencies ◽  
Invasion Success ◽  
Nucleotide Polymorphisms ◽  
Drosophila Suzukii ◽  
Single Nucleotide ◽  
A Genome ◽  
Invasive Status

Abstract Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. We evaluated this new statistical framework using simulated data sets and implemented it in an upgraded version of the program BayPass. We identified a relatively small set of single-nucleotide polymorphisms that show a highly significant association with the invasive status of D. suzukii populations. In particular, two genes, RhoGEF64C and cpo, contained single-nucleotide polymorphisms significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by nonequilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

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