Journal ArticleDOI
Pyrosequencing™‐based SNP allele frequency estimation in DNA pools
TLDR
Pyrosequencing™ can be used for allele frequency estimation in DNA pools of SNPs with complex sequencing scenarios with accuracy and precision values in ranges comparable with those of other SNP typing techniques.Abstract:
Association screening involving numerous genetic markers is facilitated by the analysis of pooled DNA samples rather than individual samples. Several genotyping methods have shown high accuracy and precision of allele frequency estimation in pools. Here, we expand the validation of SNP allele frequency estimation in DNA pools using Pyrosequencing by analyzing 186 pools for three SNPs representing complex sequencing cases. The correlation coefficient between estimated and true allele frequencies ranged between 0.979 and 0.996 and tended to increase with pool size, whereas the difference between estimated and true allele frequencies was 2.37+/-0.11%, in post-PCR pools. The precision was 1.73%. Pool size had no significant effect on accuracy and precision. A comparison between post-PCR and pre-PCR pools showed that for pre-PCR pooling efforts to accurately quantify the genomic DNA samples to be pooled and subsequently amplified are critical. To conclude, Pyrosequencing can be used for allele frequency estimation in DNA pools of SNPs with complex sequencing scenarios with accuracy and precision values in ranges comparable with those of other SNP typing techniques. Considering the ease of use, short run and analysis times, and little instrument maintenance requirements, Pyrosequencing may even be a preferred option.read more
Citations
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Journal ArticleDOI
Genetic variation analyses by Pyrosequencing
TL;DR: Recent advances and new applications of Pyrosequencing are reviewed and the cost reduction efforts and future potentials of this technique for large-scale genotyping applications are discussed.
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Inferring relative proportions of DNA variants from sequencing electropherograms
Ian M. Carr,James I. Robinson,Rozalia Dimitriou,Alex F. Markham,Ann W. Morgan,David T. Bonthron +5 more
TL;DR: By analyzing a large panel of genomic DNA samples, the ability of the software to analyze not only common biallelic SNVs, but also SNVs within a locus at which gene conversion between four genomic paralogs operates, and within another that is subject to CNV is demonstrated.
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Insights Into Species Divergence and the Evolution of Hermaphroditism From Fertile Interspecies Hybrids of Caenorhabditis Nematodes
TL;DR: The hybrid genetics of the first Caenorhabditis species pair capable of producing fertile hybrid progeny are described, and the use of backcrosses to render the hybrid genome partial homozygous for C. briggsae alleles did not increase the incidence of selfing or spermatogenesis relative to the F1 generation.
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Targeted screening of cis-regulatory variation in human haplotypes
Dominique J. Verlaan,Bing Ge,Elin Grundberg,Rose Hoberman,Kevin C. L. Lam,Vonda Koka,Joana Dias,Scott Gurd,Nicolas W. Martin,Hans Mallmin,Olof Nilsson,Eef Harmsen,Ken Dewar,Tony Kwan,Tomi Pastinen +14 more
TL;DR: The results indicate that RNA pooling coupled with AE read-out by second generation sequencing or by other methods provides a high-throughput tool for cataloging the impact of common noncoding variants in the human genome.
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Determination of CYP2D6 Gene Copy Number by Pyrosequencing
TL;DR: Analysis of 200 pregenotyped samples showed that this approach reliably resolved 0-4 genome copies of the CYP2D6 gene and was verified on 270 other samples, which gave results that corresponded to the expected genotype.
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