Next Generation Sequencing and Genotyping
William Marzluff, PhD, Faculty Advisor
Corbin Jones, PhD (NextGen); William Marzluff, PhD (DNASeq), Michael Topal, PhD (Genotype), Faculty Directors
Piotr Mieczkowski, PhD (NextGen); Laura Livingstone, PhD (DNASeq), Jingchun Luo, MD,MS (Genotype), Facility Directors
Next Generation Sequencing
Provides comprehensive Next-Generation high-throughput sequencing services via eight (8) Illumina Genome Analyzers and a Roche/454 Titanium. Four of these have been upgraded to the HiSeq 2000. Four HiSeq 2000 will be added in August 2010 and a Pacific Biosciences SMRT DNA sequencing system in Fall 2010.
- Whole Genome Shotgun Sequencing
- Microbiome surveys
- Post-capture exon-surveys
The DNA Sequencing component continues to operate two 3730xl 96-capillary DNA Analyzers. The following services are offered:
- Sequencing of DNA samples on the ABI 3730xl DNA Analyzer, including a long read (1000 bases) sequencing options
- Low cost high throughput DNA sequencing in sets of 95 samples (96 well plate format) using the ABI 3730xl DNA Analyzer.
- Provision of standard vector primers known to work well in DNA sequencing.
- Custom sequencing for reading through difficult regions of sequence using alternative sequencing chemistries and protocols.
High Throughput Genotyping
The component offers an array of SNP Genotyping services including:
- TaqMan standard and custom SNP genotyping: 1 SNP on each sample at a time.
- GoldenGate custom SNP genotyping: from 96 to 1,536 SNPs on each sample at a time.
- Select Infinium custom panels: From 3,000 to 200,000 SNPs.
- Whole Genome Genotyping from 300,000 to 1,200,000 SNPs.
- Human copy number analysis: DNA copy number variations (CNVs) and loss of heterozygosity (LOH) analysis using the Illumina Infinium Genotyping BeadChips.