An evaluation of allele frequency estimation accuracy using pooled sequencing data
نویسندگان
چکیده
منابع مشابه
Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation
Next-generation sequencing (NGS) technology has provided researchers with opportunities to study the genome in unprecedented detail. In particular, NGS is applied to disease association studies. Unlike genotyping chips, NGS is not limited to a fixed set of SNPs. Prices for NGS are now comparable to the SNP chip, although for large studies the cost can be substantial. Pooling techniques are ofte...
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Quantitative determination of the allele frequency of single-nucleotide polymorphism (SNP) in pooled DNA samples is a promising approach to clarify the relationships between SNPs and diseases. Here, we present such a simple, accurate, and inexpensive method for quantitative determining the allele frequency in pooled DNA samples. Three steps of DNA pooling, PCR amplification and sequencing are i...
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Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a br...
متن کاملEstimating Allele Frequency from Next-Generation Sequencing of Pooled Mitochondrial DNA Samples
BACKGROUND Both common and rare mitochondrial DNA (mtDNA) variants may contribute to genetic susceptibility to some complex human diseases. Understanding of the role of mtDNA variants will provide valuable insights into the etiology of these diseases. However, to date, there have not been any large-scale, genome-wide association studies of complete mtDNA variants and disease risk. One reason fo...
متن کاملSNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
We present a statistical framework for estimation and application of sample allele frequency spectra from New-Generation Sequencing (NGS) data. In this method, we first estimate the allele frequency spectrum using maximum likelihood. In contrast to previous methods, the likelihood function is calculated using a dynamic programming algorithm and numerically optimized using analytical derivatives...
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ژورنال
عنوان ژورنال: International Journal of Computational Biology and Drug Design
سال: 2013
ISSN: 1756-0756,1756-0764
DOI: 10.1504/ijcbdd.2013.056709