DNA Barcoding through Quaternary LDPC Codes

TAPIA, ELIZABETH; SPETALE, FLAVIO; KRSTICEVIC, FLAVIA; ANGELONE, LAURA; BULACIO, PILAR

PLOS ONE

PUBLIC LIBRARY SCIENCE

Lugar: San Francisco; Año: 2015 vol. 10 p. 1 - 17

1932-6203

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