What sequencing platforms do you use?
PerkinElmer continually evaluates sequencing platforms and technologies to ensure we are providing the best-available systems and processes to our customers. Currently we are utilizing GAIIx and HiSeq 2000 instruments from Illumina. These instruments can generate a variety of read lengths, are capable of single direction or paired end sequencing, and allow for sample multiplexing in individual lanes.
How is PerkinElmer DNA Sequencing and Analysis different than other sequencing service providers?
PerkinElmer’s state-of-the-art center in Branford, Connecticut provides both DNA sequencing AND analysis. The laboratory is equipped with the best and most-proven technologies available for Next Generation Sequencing. This includes a fully implemented Geospiza™ GeneSifter Lab Edition software for process and sample tracking, automated sample processing on PerkinElmer JANUS workstations to ensure uniformity and integrity of results, and an RSS feed to let you know how your project is progressing. After sequencing, your data never have to leave PerkinElmer unless you want it; your data are immediately available through a simple web interface to our private cloud environment powered by Geospiza’s GeneSifter Analysis Edition software.
What kind of sequencing projects do you accept?
Most of our customers are in need of large scale targeted or exome capture re-sequencing projects. We accept other types of projects, such as whole genome, microbial and plant re-sequencing, or smaller re-sequencing projects requiring high quality data and fast turnaround times. Please contact us to discuss your specific project requirements.
What sequence capture platform do you use?
We currently offer Agilent’s SureSelect, Illumina TruSeq Exome Enrichment and Roche Nimblegen On-Array and SeqCap EZ Exome products. This includes standard and custom product offerings.
Do you provide services to researchers outside of the USA?
Yes, we have a global customer base.
How much do you charge for your services?
We offer competitive prices, but actual pricing is dependent on specific project requirements. To find out more or request a quote, please contact us at SeqSales@perkinelmer.com or call +1-877-737-5468.
Will PerkinElmer provide a service quote for my grant application?
Yes. Academic researchers are an important part of our business and we can provide documentation to support your grant applications. We are also very interested in speaking with you as you consider certain grant opportunities, especially as part of a consortium. Please contact us to discuss your specific grant requirements.
Can I make my own libraries and have you sequence them?
Yes. Although we have library construction and exome capture as part of our standard service offerings, we do accept customer-made libraries or customer-provided exome capture samples. However, with these samples we cannot make any specific guarantees about data quality.
What type of samples do you accept?
We are currently accepting only purified DNA or customer-supplied materials that are suitable for standard Illumina sequencing protocols.
How much DNA do I need to send you?
Generally, incoming genomic DNA samples should contain at least 3 μg of DNA per sample at a concentration of ≥ 100 ng/μL. PerkinElmer recommends the use of PicoGreen fluorometry when determining the quantity of each sample. Samples must be provided in 50 μL – 100 μL of molecular biology grade water or TE buffer. Any unused sample can be returned. We ask that you include a completed Sample Description Form with all samples shipped.
This form is available from your Sales Representative or can be obtained electronically at: http://perkinelmer.com/PDFs/downloads/sampledescriptionform.pdf
Additional details on sample preparation and requirements are available at: http://www.perkinelmer.com/PDFs/downloads/sampleprepguidelines.pdf
Where do I send my samples?
Ship samples by a next day shipping carrier to:
PerkinElmer, Inc.
DNA Sequencing and Analysis Services
29 Business Park Drive
Branford, CT 06405 USA
Phone: +1-877-737-5468
Please email shipment tracking information to SeqProject@perkinelmer.com
How do I order services?
Simply email (preferred), or fax your quotation, with your Purchase Order to the attention of:
Customer Care
Perkin Elmer Life and Analytical Sciences
710 Bridgeport Ave.
Shelton, CT 06484 USA
SeqSales@perkinelmer.com
FAX: 203-944-4904
Please copy your PerkinElmer sales representative on all Purchase Order communications
What do I typically receive as a deliverable for my project?
All projects provide you final base called sequences as standard FASTQ formatted files. For single ended sequencing there will be one file per sample, while for paired end sequencing you will receive two files labeled for direction. FASTQ files are text format files that are compressed using the common Linux GZip compression format for ease of handling. If your project includes basic analysis, you will also receive an alignment of reads against the suitable reference sequence in industry standard BAM format, along with a text listing of all detected variants. These files will be delivered on hard disk. In addition, with the inclusion of bioinformatics analysis, you will receive four months of free access to the PerkinElmer Web based analysis platform, which leverages the tools and visualization of the Geospiza analysis software.
What software is used in the default analysis process?
Alignments to a reference sequence are performed using BWA. This aligner offers a widely accepted balance between performance and accuracy and allows detection of smaller indels. The default variant detection is performed with Samtools or optionally, GATK. Annotation, visualization and result filtering tools are provided in the framework of the Geospiza analysis software. In addition, with consultation with PerkinElmer’s bioinformatics team, we can create custom analysis solutions to meet your specific needs.