Sep 21, 2015

Conversion of Genomic DNA to Proxy Constructs Suitable for Accurate Nanopore Sequencing

BioRxiv : the Preprint Server for Biology
Dimitra Tsavachidou

Abstract

Nanopore sequencing at single-base resolution is challenging. There are developing technologies to convert DNA molecules to expanded constructs. Such constructs can be sequenced by nanopores in place of the original DNA molecules. We present a novel method for converting genomic DNA to expanded constructs (proxies) with 99.67% accuracy. Our method reads each base in each DNA fragment and appends an oligonucleotide to the DNA fragment after each base reading. Each appended oligonucleotide represents a specific base type, so that the proxy construct consisting of all the appended oligonucleotides faithfully represents the original DNA sequence. We generated proxies for genomic DNA and confirmed the identities of both the proxies and their corresponding original DNA sequences by performing sequencing using Ion Torrent sequencer. Conversion to proxies had only 0.33% raw error rate. Errors were: 93.96% deletions, 5.29% insertions, and 0.74% substitutions. The longest sequenced proxy was 170 bases, corresponding to a 17-base original DNA sequence. The short length of the detected proxies reflected restrictions imposed by Ion Torrent short reads and was not caused by limitations of our method. The consensus sequence built by using pro...Continue Reading

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Mentioned in this Paper

Base
Genome
Ions
Nucleic Acid Sequencing
Etiology
A 17
Sequencing
Genomic DNA
Oligonucleotides
probe gene fragment

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