scholarly journals Automated melting curve analysis in droplet microfluidics for single nucleotide polymorphisms (SNP) genotyping

RSC Advances ◽  
2017 ◽  
Vol 7 (8) ◽  
pp. 4646-4655 ◽  
Author(s):  
F.-W. Liu ◽  
S.-T. Ding ◽  
E.-C. Lin ◽  
Y.-W. Lu ◽  
J.-S. R. Jang
Keyword(s):  
Melting Curve ◽  
Automated Analysis ◽  
Curve Analysis ◽  
Snp Genotyping ◽  
Droplet Microfluidics ◽  
Melting Curve Analysis ◽  
Dna Melting ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

An integrated microchip platform with automated analysis capability for DNA melting curves is developed for Single Nucleotide Polymorphism (SNP) genotyping applications.

scholarly journals Sub-7-second genotyping of single-nucleotide polymorphism by high-resolution melting curve analysis on a thermal digital microfluidic device

Lab on a Chip ◽  
2016 ◽  
Vol 16 (4) ◽  
pp. 743-752 ◽  
Author(s):  
Tianlan Chen ◽  
Yanwei Jia ◽  
Cheng Dong ◽  
Jie Gao ◽  
Pui-In Mak ◽  
...  
Keyword(s):  
High Resolution Melting ◽  
Melting Curve ◽  
Curve Analysis ◽  
Melting Curve Analysis ◽  
Dna Melting ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
High Resolution Melting Curve ◽  
Digital Microfluidic ◽  
Multiple Samples

A novel thermal digital microfluidic (T-DMF) device enables precise thermal modulation and pipelined measurement of multiple samples. Ultrafast DNA melting curve analysis is achieved in less than 7 seconds, with the resolution adequate for single-nucleotide discrimination.

scholarly journals High-Resolution Melting Curve Analysis of Genomic and Whole-Genome Amplified DNA

2008 ◽  
Vol 54 (12) ◽  
pp. 2055-2058 ◽  
Author(s):  
Michael H Cho ◽  
Dawn Ciulla ◽  
Barbara J Klanderman ◽  
Benjamin A Raby ◽  
Edwin K Silverman
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Melting Curve ◽  
Curve Analysis ◽  
Melting Curve Analysis ◽  
Dna Melting ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
High Resolution Melting Curve

Abstract Background: High-resolution melting curve analysis is an accurate method for mutation detection in genomic DNA. Few studies have compared the performance of high-resolution DNA melting curve analysis (HRM) in genomic and whole-genome amplified (WGA) DNA. Methods: In 39 paired genomic and WGA samples, 23 amplicons from 9 genes were PCR amplified and analyzed by high-resolution melting curve analysis using the 96-well LightScanner (Idaho Technology). We used genotyping and bidirectional resequencing to verify melting curve results. Results: Melting patterns were concordant between the genomic and WGA samples in 823 of 863 (95%) analyzed sample pairs. Of the discordant patterns, there was an overrepresentation of alternate melting curve patterns in the WGA samples, suggesting the presence of a mutation (false positives). Targeted resequencing in 135 genomic and 136 WGA samples revealed 43 single nucleotide polymorphisms (SNPs). All SNPs detected in genomic samples were also detected in WGA. Additional genotyping and sequencing allowed the classification of 628 genomic and 614 WGA amplicon samples. Heterozygous variants were identified by non–wild-type melting pattern in 98% of genomic and 97% of WGA samples (P = 0.11). Wild types were correctly classified in 99% of genomic and 91% of WGA samples (P < 0.001). Conclusions: In WGA DNA, high-resolution DNA melting curve analysis is a sensitive tool for SNP discovery through detection of heterozygote variants; however, it may misclassify a greater number of wild-type samples.

DNA methylation assay using droplet-based DNA melting curve analysis

Lab on a Chip ◽  
2018 ◽  
Vol 18 (3) ◽  
pp. 514-521 ◽  
Author(s):  
F.-W. Liu ◽  
H.-F. Liao ◽  
S.-P. Lin ◽  
Y.-W. Lu
Keyword(s):  
Dna Methylation ◽  
Methylation Status ◽  
Melting Curve ◽  
Genomic Region ◽  
Curve Analysis ◽  
Droplet Microfluidics ◽  
Melting Curve Analysis ◽  
Dna Melting ◽  
Methylation Assay ◽  
Specific Genomic Region

A novel platform, combining droplet microfluidics and melting curve analysis, was developed to detect and to quantify the methylation status in a specific genomic region.

The mechanism and regularity of quenching the effect of bases on fluorophores: the base-quenched probe method

The Analyst ◽  
2018 ◽  
Vol 143 (14) ◽  
pp. 3292-3301 ◽  
Author(s):  
Huihui Mao ◽  
Guanghua Luo ◽  
Yuxia Zhan ◽  
Jun Zhang ◽  
Shuang Yao ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Real Time ◽  
Real Time Pcr ◽  
Melting Curve ◽  
Curve Analysis ◽  
Probe Method ◽  
Melting Curve Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

The base-quenched probe method for detecting single nucleotide polymorphisms (SNPs) relies on real-time PCR and melting-curve analysis, which might require only one pair of primers and one probe.

scholarly journals Rapid Detection of Aneuploidy (Trisomy 21) by Allele Quantification Combined with Melting Curves Analysis of Single-Nucleotide Polymorphism Loci

2003 ◽  
Vol 49 (7) ◽  
pp. 1087-1094 ◽  
Author(s):  
Genevieve Pont-Kingdon ◽  
Elaine Lyon
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Trisomy 21 ◽  
Tandem Repeats ◽  
Melting Curve ◽  
Curve Analysis ◽  
Chromosome 21 ◽  
Melting Curve Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Melting Curves

Abstract Background: Molecular approaches for the detection of chromosomal abnormalities will allow the development of rapid, cost-effective screening strategies. We present here a molecular alternative for the detection of aneuploidies and, more specifically, trisomy 21. Methods: We used the quantitative value of melting curve analysis of heterozygous genetic loci to establish a relative allelic count. The two alleles of a given single-nucleotide polymorphism (SNP) were differentiated by thermodynamic stability with a fluorescently labeled hybridization probe and were quantified by relative areas of derivative melting curves detected after fluorescence resonance energy transfer. Heterozygous SNPs provided internal controls for the assay. Results: We selected six SNPs, heterozygous in at least 30% of a random population, to form a panel of informative loci in the majority of a random population. After normalization to a heterozygous control, samples segregated into three categories; nontrisomic samples had mean allele ratios of 0.96–1.09, whereas trisomic samples had mean ratios of 1.84–2.09 or 0.46–0.61, depending on which allele was duplicated. Within-run mean CVs of ratios were 6.5–27%, and between-assay mean CVs were 13–24%. Conclusions: The use of melting curve analysis of multiple SNPs is an alternative to the use of small tandem repeats for the detection of trisomies. Because of the high density of SNPs, the approach may be specifically useful for very fine mapping of the regions of chromosome 21 that are critical for Down syndrome; it is also applicable to aneuploidies other than trisomy 21 and to specimens that are not amenable to cytogenetic analysis.

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