title: Long Fragment Read (LFR) Technology: Cost-Effective, High-Quality Genome-Wide Molecular Haplotyping.
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.
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA, 94043, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: McElwain
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA, 94043, USA.
authors.forename: Rebecca Yu
authors.initials: RY
authors.lastname: Zhang
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA, 94043, USA.|BGI-Shenzhen, Shenzhen, 51803, China.
authors.forename: Radoje
authors.initials: R
authors.lastname: Drmanac
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA, 94043, USA. bpeters@completegenomics.com.|BGI-Shenzhen, Shenzhen, 51803, China. bpeters@completegenomics.com.
authors.forename: Brock A
authors.initials: BA
authors.lastname: Peters
mesh_terms: D015894:Genome, Human / Q000235:genetics; D023281:Genomics; D006239:Haplotypes / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA; D000073336:Whole Genome Sequencing
keywords: Haplotype; Long fragment; Molecular barcode; Next-generation sequencing (NGS); Phasing; Whole-genome amplification (WGA)