Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate

Buschmann, Tilo; Zhang, Rong; Brash, Douglas E.; Bystrykh, Leonid

doi:10.1186/1471-2105-15-264

Cited by 13 publications

(12 citation statements)

References 31 publications

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“…It may be argued that LDPC barcodes are two or three times larger than commercial random barcodes currently in use and systematic barcoding designs based on Hamming or Golay codes, which at most require a handy number of bases. In agreement with [ 57 ], our results suggest that there could be a high price to paid for using such small barcoding systems, either high rates of critical undetected multiplexation errors or high rates of read losses must be tolerated.…”

Section: Discussionsupporting

confidence: 90%

DNA Barcoding through Quaternary LDPC Codes

et al. 2015

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For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10−2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10−9 at the expense of a rate of read losses just in the order of 10−6.

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Section: Discussionsupporting

confidence: 90%

DNA Barcoding through Quaternary LDPC Codes

et al. 2015

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“…Resent research shows that even for sequencing approaches the detection of barcodes is quite challenging. In [ 24 ] they focus on a specific problem with certain setups on the PacBio SMRT platform. Caused by technical reasons, sporadically barcodes are not present in the sequence data.…”

Section: Resultsmentioning

confidence: 99%

“…On codes based on sequence edit distance this extended problem is addressed for, e.g. the PacBio SMRT platform in [ 24 ]. We conjecture that the detection problem of barcodes based on watermarks can be solved in future investigations.…”

Section: Methodsmentioning

confidence: 99%

“…The relative frequency of a subset of two symbols should not be below 40% and above 60% in each barcode, otherwise we excluded the barcode. We furthermore exclude barcodes with prefect self-complementation and more than two sequential repetitions of the same base (homopolymer length), similar to the restrictions stated in [ 24 ]. We consider this settings as sufficient and strict enough to avoid experimental problems during the preparation in real sequencing tasks.…”

Section: Methodsmentioning

confidence: 99%

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Insertion and deletion correcting DNA barcodes based on watermarks

Kracht

Schober

2015

BMC Bioinformatics

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BackgroundBarcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequencing procedure. A post-processing step is needed to sort the sequencing data according to their origin, utilizing these DNA labels. The final separation step is called demultiplexing and is mainly determined by the characteristics of the DNA code words used as labels.Currently, we are facing two different strategies for barcoding: One is based on the Hamming distance, the other uses the edit metric to measure distances of code words. The theory of channel coding provides well-known code constructions for Hamming metric. They provide a large number of code words with variable lengths and maximal correction capability regarding substitution errors. However, some sequencing platforms are known to have exceptional high numbers of insertion or deletion errors. Barcodes based on the edit distance can take insertion and deletion errors into account in the decoding process. Unfortunately, there is no explicit code-construction known that gives optimal codes for edit metric.ResultsIn the present work we focus on an entirely different perspective to obtain DNA barcodes. We consider a concatenated code construction, producing so-called watermark codes, which were first proposed by Davey and Mackay, to communicate via binary channels with synchronization errors. We adapt and extend the concepts of watermark codes to use them for DNA sequencing. Moreover, we provide an exemplary set of barcodes that are experimentally compatible with common next-generation sequencing platforms. Finally, a realistic simulation scenario is use to evaluate the proposed codes to show that the watermark concept is suitable for DNA sequencing applications.ConclusionOur adaption of watermark codes enables the construction of barcodes that are capable of correcting substitutions, insertion and deletion errors. The presented approach has the advantage of not needing any markers or technical sequences to recover the position of the barcode in the sequencing reads, which poses a significant restriction with other approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0482-7) contains supplementary material, which is available to authorized users.

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“…It is therefore important to adopt proper quality control measures that include the use of control samples. Sequencing laboratories sporadically report carry-over contamination between successive sequencing experiments (49), or crosstalk between sequencing libraries in the case of multiplexed runs (50).…”

Section: Carry-overmentioning

confidence: 99%

Next-generation sequencing workflows in veterinary infection biology: towards validation and quality assurance

Borm

Wang

Granberg

et al. 2016

Rev. Sci. Tech. OIE

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Recent advancements in DNA sequencing methodologies and sequence data analysis have revolutionised research in many areas of biology and medicine, including veterinary infection biology. New technology is poised to bridge the gap between the research and diagnostic laboratory. This paper defines the potential diagnostic value and purposes of next-generation sequencing (NGS) applications in veterinary infection biology and explores their compatibility with the existing validation principles and methods of the World Organisation for Animal Health. Critical parameters for validation and quality control (quality metrics) are suggested, with reference to established validation and quality assurance guidelines for NGS-based methods of diagnosing human heritable diseases. Although most currently described NGS applications in veterinary infection biology are not primary diagnostic tests that directly result in control measures, this critical reflection on the advantages and remaining challenges of NGS technology should stimulate discussion on its diagnostic value and on the potential to validate NGS methods and monitor their diagnostic performance.

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Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate

Cited by 13 publications

References 31 publications

DNA Barcoding through Quaternary LDPC Codes

DNA Barcoding through Quaternary LDPC Codes

Insertion and deletion correcting DNA barcodes based on watermarks

Next-generation sequencing workflows in veterinary infection biology: towards validation and quality assurance

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