Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samplesReportar como inadecuado




Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

BMC Genetics

, 16:62

First Online: 13 June 2015Received: 25 January 2015Accepted: 27 May 2015DOI: 10.1186-s12863-015-0222-z

Cite this article as: Capper, R.L., Jin, Y.K., Lundgren, P.B. et al. BMC Genet 2015 16: 62. doi:10.1186-s12863-015-0222-z

Abstract

BackgroundThe advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism SNP data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources.

ResultsHere, we introduce two cost-efficient quantitative High Resolution Melting qHRM methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the -peaks- method, which can be applied to large numbers of SNPs, and the -curves- method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the -peaks- method can be rapidly scaled to screen several hundred SNPs at once, whereas the -curves- method is better suited for smaller numbers of SNPs.

ConclusionsCompared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies.

KeywordsPooled genotyping Allele frequency High resolution melting SNP Population AbbreviationsHRMHigh resolution melting

qHRMQuantitative high resolution melting

qPCRQuantitative PCR

SNPSingle nucleotide polymorphism

Roxana L. Capper and Young K. Jin contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1186-s12863-015-0222-z contains supplementary material, which is available to authorized users.

Download fulltext PDF



Autor: Roxana L. Capper - Young K. Jin - Petra B. Lundgren - Lesa M. Peplow - Mikhail V. Matz - Madeleine J. H. van Oppen

Fuente: https://link.springer.com/



DESCARGAR PDF




Documentos relacionados