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

Services

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.

Technologies offered:

    • Whole Genome Shotgun Sequencing
    • ChIP-seq
    • FAIRE-seq
    • RNA-seq
    • SmallRNA-seq
    • Microbiome surveys
    • Post-capture exon-surveys

 

DNA Sequencing

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.

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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.


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