UCL Cancer Institute

Next Generation Sequencing - Solexa Technology

We now have 2 Illumina Genome Analyser II's in the Scientific Support Services Laboratory within the Paul O'Gorman Building. The high-throughput systems are based on a new SOLEXA® Technology which uses a massively parallel sequencing-by-synthesis approach to generate billions of bases of high-quality DNA sequence per run. The Genome Analyser system can generate highly accurate results in under a week for discoveries in genomics, epigenomics, gene expression analysis and protein-nucleic acid inteactions.

Whole-genome sequencing and resequencing

single or paired-end reads enable sequencing of an entire genome or candidate regions

• de novo sequencing,
• discovery of SNP's,
• discovery of Copy Number Variations (CNV's),
• discovery of chromasomal rearrangements including deletions, insertions and translocations.

Transcriptome Analysis Applications (Digital Gene Expression)

• mRNA profiling,
• mRNA Tag profiling (sequencing),
• dsmall RNA discovery and analysis.

Protein-nucleic acid interactions analysis

• quantify in vivo protein-DNA interactions using the combination of chromatin immunoprecipitation with sequencing on a genome-wide scale.(ChIP-Seq),
• sequencing millions of ChIP-enriched DNA fragments enables cost-effective and precise analysis of the binding sites of transcription factors, replication and transcriptional machinery, structural proteins such as histones, as well as the impact of protein modifications on genome occupancy.

DNA Methylation Analysis

• discovery of methylation variable positions (MVP's) across the entire genome at single site resolution,
• map methylation patterns by sequencing bisulphite-converted DNA,
• methylation-sensitive restriction digest enriched fragments,
• anti-methyl-C precipitated fragments,
• chromatin immunoprecipitates of methyltranferases trapped to aza-labelled DNA.

Expanded Sequencing Applications

• multiplex sequencing allows to pool up to 12 samples per lane of a flow cell by introducing index sequences onto DNA fragments, thus decreasing the cost of experiment and time. Ideal for targeting genomic sub-regions or studying small genomes. Can be applied to whole-transcriptome sequencing and to DNA recovered by chromatin immunoprecipitation (ChIP-Seq) experiments,
• improved chemistry allows extending the length of the read up to 75bp per run.