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Services utilizing Capillary Electorphoresis (CE)
| ||Sanger Sequencing|
| ||GPCL utilizes 3730xl and 3130 DNA Analyzers from Applied Biosystems for standard Sanger sequencing. Samples may be submitted for sequencing reaction and capillary run or more experienced laboratories may submit full plates of samples for capillary run only.|
| ||Genotyping Services|
| ||GPCL provides support for fragment analysis technologies (AFLP and STRP genotyping) via instrument data generation only. GPCL does not perform PCR processing for these applications. PCR products can be submitted for capillary run. Instrument output data will be provided. Investigator laboratories are responsible for data analysis yielding final genotyping calls.|
CE Service Overview
Sample Preparation and Submission
Scheduling and Turn Around
Methods and Data Delivery
High Throughput "Next Generation" sequencing
GPCL offers next generation DNA sequencing services using the Life Technologies Ion Torrent.AN. semiconductor sequencing instruments. The Ion PGM Sequencer is the instrument of choice for small to medium sequencing projects including small genomes and Chip-Seq while the Ion Proton provides more capacity for in depth studies needing greater data output such as whole transcriptome, human exome resequencing or large genomes. For the most recent information on instrument capabilities, please see the Life Technologies Ion Torrent web page.
If you would like to access the Ion instruments at GPCL, please contact us to schedule a consultation.
| ||Ion PGM|
Average read lengths for the PGM can be set anywhere from 35 to 400 bp by adjusting run time parameters. Varying chip sizes provide flexibility of throughput between 300K and 6M reads per run. Barcodes are supported to allow multiple samples to be run together.
The Proton is a higher capacity instrument, which uses the same chemistry as the PGM. At this time read lengths of up to 200 bp are supported and the only available chip returns 60M reads. Longer read lengths and higher density chips are expected to be available in the near future.
Targeted Resequencing Options
| ||Amplification Enrichment|
There are several approaches to PCR amplification of regions of interest that are compatible with Ion technology. Amplicons of several kb in length can be treated similarly to gDNA with fragmentation to appropriate size. Fusion primers that include both the sequencing adapters and the target specific primer provide a way to specify read direction. AmpliSeq™ technology utilizes multiplex PCR of up to 4,000 targets from as little as 10 ng of DNA. Pre-designed and custom panels are available. For more information see the AmpliSeq web site.
Capture Based Enrichment
There are several vendors offering methods to enrich for regions via hybridization with capture probes. Not all of them are marketed in configurations fully compatible with Ion technology, but modifications may be available. Ion TargetSeq by Life Technologies is fully compatible as is Agilent.FN"s Haloplex. Both have human whole exome products as well as custom options. AgilentN"s SureSelect and RocheN"s SeqCapEZ require modifications to the standard library preparation methods and may not be compatible. Please contact us to schedule a consultation.