Solexa Announces Sequencing of a Human X-Chromosome
Solexa, Inc. has announced that its scientists, in collaboration with researchers at the Wellcome Trust Sanger Institute, have sequenced a human X-chromosome.
The initial results from this project, which were presented at the Genomes, Medicine and the Environment Conference in Hilton Head, South Carolina, demonstrate that the Solexa Genome Analysis System is achieving the data quality, read length and coverage uniformity required for discovering and characterizing human sequence variation at the genome-wide level.
"In sequencing a human X-chromosome to an average 16-fold depth, we are displaying for the first time the performance of our technology in sequencing at whole genome scale," said Tony Smith, Ph.D., Solexa’s vice president and chief scientific officer.
"We believe these results signify that researchers worldwide will be able to apply our technology to resequence whole human genomes at a fraction of the cost and time required by other platforms."
Scientists at Solexa and the Sanger Institute sequenced purified human X-chromosome DNA from an anonymous female individual and aligned 2.6 gigabases (billion bases) of high quality data to the 155-megabase (million base) reference sequence.
While the scientists intend to add more coverage to this draft sequence in preparation for data release, they were able in their analysis to date to:
- Achieve 16-fold average coverage, with at least 2-fold coverage across >99% of sequenceable bases;
- Achieve >99.99% coverage of all sequenceable exonic bases;
- Confirm 96% of a test set of previously ascertained dbSNP genotypes in this sample and obtain preliminary evidence for the remaining 4%;
- By full genome re-alignment, identify fragments from other chromosomes remaining in the sample as a result of the flow-sorting method used to purify the X-chromosome; these fragments were present at a frequency in line with expectations for this experimental technique (~10%);
- Demonstrate uniform sequencing coverage; and
- Demonstrate the absence of systematic sequence context-related artifacts.
In addition to announcing its draft sequence of a human X-chromosome, Solexa also presented data from digital gene expression, small RNA analysis, microbial resequencing and candidate region resequencing applications.
"We are delighted with the landmark results of this collaboration with researchers at the Sanger Institute," said John West, Solexa’s chief executive officer.
"These initial results from sequencing a human X-chromosome using the Solexa Genome Analysis System validate our belief that Solexa’s groundbreaking technology will enable researchers to tackle larger-scale projects and to do so much more rapidly and economically than ever before."
"Further, these results serve as an important model for our ongoing internal efforts to sequence a human genome, which we expect to complete to draft level by the end of the year."