RT Journal Article
SR Electronic
T1 Cost-effective, high-throughput, single-haplotype iterative mapping and sequencing for complex genomic structures
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 157206
DO 10.1101/157206
A1 Daniel W. Bellott
A1 Ting-Jan Cho
A1 Jennifer F. Hughes
A1 Helen Skaletsky
A1 David C. Page
YR 2017
UL http://biorxiv.org/content/early/2017/06/29/157206.abstract
AB Reference sequence of structurally complex regions can only be obtained through highly accurate clone-based approaches. We and others have successfully employed Single-Haplotype Iterative Mapping and Sequencing (SHIMS 1.0) to assemble structurally complex regions across the sex chromosomes of several vertebrate species and in targeted improvements to the reference sequences of human autosomes. However, SHIMS 1.0 was expensive and time consuming, requiring the resources that only a genome center could command. Here we introduce SHIMS 2.0, an improved SHIMS protocol to allow even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library preparation protocol, and taking advantage of high-throughput, inexpensive, short-read sequencing technologies, a small group can sequence and assemble hundreds of clones in a week. Relative to SHIMS 1.0, SHIMS 2.0 reduces the cost and time required by two orders of magnitude, while preserving high sequencing accuracy.