Closing gaps in the human genome using sequencing by synthesis

Abstract

The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural' in nature. Another class of gaps is likely to be refractory to clone-based approaches, and cannot be approached in ways previously described. We present an approach for closing these gaps using 454 sequencing. As a proof of principle, we closed all three remaining non-structural gaps in chromosome 15.

Figure 1

Coverage of gap regions. Sequence coverage of the gap regions on human chromosome 15 is shown for gaps at (a) 24 Mb, (b) 25 Mb and (c) 96 Mb. The x-axis indicates base position in the local region containing each gap. The y-axis shows sequence coverage obtained in 454 reads (red line) and small insert library reads (blue line). Coverage was computed as the average in 10-base non-overlapping windows. Arrows indicate primers used to amplify the amplicons sequenced, color coded in pairs. Bars at top indicate bases present in the Celera (dark gray) and NCBI build 36 (light gray) assemblies.