scholarly journals DASH-2: Flexible, Low-Cost, and High-Throughput SNP Genotyping by Dynamic Allele-Specific Hybridization on Membrane Arrays

2003 ◽  
Vol 13 (5) ◽  
pp. 916-924 ◽  
Author(s):  
M. Jobs
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Snp Genotyping ◽  
Specific Hybridization ◽  
Allele Specific

High-throughput genotyping with infrared fluorescence allele specific hybridization (iFLASH): A simple, reliable and low-cost alternative

2006 ◽  
Vol 39 (7) ◽  
pp. 739-745 ◽  
Author(s):  
Thomas M. van Himbergen ◽  
Hieronymus A.M. Voorbij ◽  
Arjan D. Barendrecht ◽  
Bas B. van Rijn ◽  
Roberta Brambilla ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Specific Hybridization ◽  
Allele Specific

scholarly journals Modified low cost SNP genotyping technique using cycle threshold (Ct) & melting temperature (Tm) values in allele specific real-time PCR

2015 ◽  
Vol 142 (5) ◽  
pp. 555 ◽  
Author(s):  
BVishnu Bhat ◽  
DBenet Bosco Dhas ◽  
AHiasindh Ashmi ◽  
SubashChandra Parija ◽  
N Banupriya
Keyword(s):  
Real Time ◽  
Melting Temperature ◽  
Real Time Pcr ◽  
Low Cost ◽  
Snp Genotyping ◽  
Cycle Threshold ◽  
Allele Specific

scholarly journals Detecting SARS-CoV-2 variants with SNP genotyping

2020 ◽  
Author(s):  
Helen Harper ◽  
Amanda J. Burridge ◽  
Mark Winfield ◽  
Adam Finn ◽  
Andrew D. Davidson ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Cost Effective ◽  
Snp Genotyping ◽  
Clinical Samples ◽  
Marker Panel ◽  
Qrt Pcr ◽  
Crucial Information ◽  
The Uk ◽  
Genotyping Panel

AbstractTracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARS-CoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020- and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 76% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with our marker panel at a cost of < £1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.

scholarly journals Detecting SARS-CoV-2 variants with SNP genotyping

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0243185 ◽  
Author(s):  
Helen Harper ◽  
Amanda Burridge ◽  
Mark Winfield ◽  
Adam Finn ◽  
Andrew Davidson ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Cost Effective ◽  
Snp Genotyping ◽  
Clinical Samples ◽  
Marker Panel ◽  
Qrt Pcr ◽  
Crucial Information ◽  
The Uk ◽  
Genotyping Panel

Tracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARS-CoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system, we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020 and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 61.9% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with a marker panel at a cost of < £1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.

scholarly journals A high-throughput MS-PCR method on MADGE gels for ANG II type-1 receptor A1166C polymorphism

1999 ◽  
Vol 1 (2) ◽  
pp. 71-73 ◽  
Author(s):  
CLIVE C. J. HUNT ◽  
JODI E. BURLEY ◽  
CAROLINE M. L. CHAPMAN ◽  
JOHN P. BEILBY
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Large Population ◽  
Single Step ◽  
Ang Ii ◽  
A1166c Polymorphism ◽  
Oligonucleotide Hybridization ◽  
Allele Specific ◽  
Pcr Method

Hunt, Clive C. J., Jodi E. Burley, Caroline M. L. Chapman, and John P. Beilby. A high-throughput MS-PCR method on MADGE gels for ANG II type-1 receptor A1166C polymorphism. Physiol. Genomics 1: 71–73, 1999.—We have developed a highly accurate, low-cost, single-step, mutagenically separated polymerase chain reaction (MS-PCR) method for the determination of angiotensin II type-1 receptor (AT1) A1166C gene polymorphism. The genotypes are determined using the microtiter array diagonal gel electrophoresis (MADGE) system. We have compared the MS-PCR method with allele-specific oligonucleotide hybridization and Dde I digestion techniques for determining the AT1 A1166C genotype. The combination of MS-PCR and MADGE serves as a model for high-throughput single-nucleotide polymorphism genotyping in large population studies.

scholarly journals Homogeneous Assays for Single-Nucleotide Polymorphism Typing Using AlphaScreen

2001 ◽  
Vol 11 (4) ◽  
pp. 600-608
Author(s):  
Lucille Beaudet ◽  
Julie Bédard ◽  
Billy Breton ◽  
Roberto J. Mercuri ◽  
Marcia L. Budarf
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Throughput ◽  
Genomic Dna ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Hybridization ◽  
Donor And Acceptor ◽  
Close Proximity ◽  
Allele Specific ◽  
Specific Amplification

AlphaScreen technology allows the development of high-throughput homogeneous proximity assays. In these assays, signal is generated when 680 nm laser light irradiates a donor bead in close proximity to an acceptor bead. For the detection of nucleic acids, donor and acceptor beads are brought into proximity by two bridging probes that hybridize simultaneously to a common target and to the generic oligonucleotides attached covalently to the beads. This method allows the detection of as little as 10 amole of a single-stranded DNA target. The combination of AlphaScreen with allele-specific amplification (ASA) and allele-specific hybridization (ASH) has allowed the development of two homogenous single-nucleotide polymorphism (SNP) genotyping platforms. Both types of assay are very robust, routinely giving accurate genotyping results with < 2 ng of genomic DNA per genotype. An AlphaScreen validation study was performed for 12 SNPs by using ASA assays and seven SNPs by using ASH assays. More than 580 samples were genotyped with accuracy >99%. The two assays are remarkably simple, requiring no post-PCR manipulations. Genotyping has been performed successfully in 96- and 384-well formats with volumes as small as 2 μL, allowing a considerable reduction in the amount of reagents and genomic DNA necessary for genotyping. These results show that the AlphaScreen technology can be successfully adapted to high-throughput genotyping.

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