Chapter title |
Long Fragment Read (LFR) Technology: Cost-Effective, High-Quality Genome-Wide Molecular Haplotyping
|
---|---|
Chapter number | 11 |
Book title |
Haplotyping
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-6750-6_11 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6748-3, 978-1-4939-6750-6
|
Authors |
Mark A. McElwain, Rebecca Yu Zhang, Radoje Drmanac, Brock A. Peters, McElwain, Mark A., Zhang, Rebecca Yu, Drmanac, Radoje, Peters, Brock A. |
Editors |
Irene Tiemann-Boege, Andrea Betancourt |
Abstract |
In this chapter, we describe Long Fragment Read (LFR) technology, a DNA preprocessing method for genome-wide haplotyping by whole genome sequencing (WGS). The addition of LFR prior to WGS on any high-throughput DNA sequencer (e.g., Complete Genomics Revolocity™, BGISEQ-500, Illumina HiSeq, etc.) enables the assignment of single-nucleotide polymorphisms (SNPs) and other genomic variants onto contigs representing contiguous DNA from a single parent (haplotypes) with N50 lengths of up to ~1 Mb. Importantly, this is achieved independent of any parental sequencing data or knowledge of parental haplotypes. Further, the nature of this method allows for the correction of most amplification, sequencing, and mapping errors, resulting in false-positive error rates as low as 10(-9). This method can be employed either manually using hand-held micropipettors or in the preferred, automated manner described below, utilizing liquid-handling robots capable of pipetting in the nanoliter range. Automating the method limits the amount of hands-on time and allows significant reduction in reaction volumes. Further, the cost of LFR, as described in this chapter, is moderate, while it adds invaluable whole genome haplotype data to almost any WGS process. |
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