Attachment 1 - Pyrosequencer Specifications.pdf

USDA ARS Grand Forks Human Nutrition Research Center

2420 2nd Ave. North

Grand Forks, ND 58203

Minimum Required Specifications

Pyrosequencer Specifications:

• Automated pyrosequencer

• High degree of automation after loading sample, reagents, template preparation, sequencing as well as cartridge maintenance is fully automated

• Annealing of sequencing primer can be automated for up to 4 different sequencing primers by automated primer dispensation

• Template preparation

• Produces high-resolution quantitative sequence data

• Performs long and reliable sequence runs

• Single reaction producing high accurate read length of 140 or more bases

• Performs allele quantification, methylation analysis, and sequencing analysis

• Uses sequencing-by-synthesis technology for the ability to produce a detectable patter of light signals that reflect the true sequence of the DNA being analyzed

• Simultaneous running of multiple assays and assay types including SNP, AQ, CpG and SQA to produce methylation analysis, de novo sequencing, mutation characterization including In/Dels, speciation quantitative allele sequencing and SNP genotyping

• Quantitative analysis at consecutive CpG and CpN sites

• Ability for sequencing primer to be added in automation or manually to increase number of different assays per run

• Multiple Primer Dispensation to automate sequencing primer dispensation

• Each primer anneals only to its specific target sequence and is elongated during the

Pyrosequencing reaction

• Contains one USB port

• Ethernet connection

• Compatible with PyroMark Q48 Advanced Reagents o Compatible with previously designed Pyrosequencing assays

• Disc design enables magnetic template preparation without cross contamination

• Process 1-48 samples per run

• Operating temperature between 18-30°C

• Sensitive detection technology monitored by sensitive photomultiplier such that data are recorded continuously and simultaneously for all sequencing reactions

• High sequencing fidelity being very precise with no lag between primer placement and the delivered nucleotide making the first base after the sequencing primer is the first data point

• Capable of sequencing and analyzing 48 samples of a 60-base-long target in approximately 1,5 hours

• Internal instrument controls including detection of a discs and correct insertion of the cartridges before the run, and a functional control of the cartridge before and during the run ensuring that the run is not started when a cartridge shows any malfunction

• Detection and quantification of multiple types of genetic variation

• High fidelity of sequencing-by-synthesis coupled with powerful analysis software

• Practically limitless types of sequence variants that can be detected and quantified including complex mutations with more than one variant in the analyzed region, point mutations, insertion/deletions, SNPs, di-, tri-, and tetrapolymorphisms, and STRs

• Sensitive detection routinely capable of detection sequence variants present at frequencies as low as 5%, and potentially lower for some targets

• Broad range of applications that delivers high-resolution data to quantify methylation levels of single and multiple CpG sites as well as CpN sites, to discriminate microbial species, to determine microbial strain and type, and to assess genetic pattern that convey antibiotic resistance

• Flexibility in assay set up within a single run as each reaction well is handled as a separate assay

• Able to perform 48 different assays in a single run

• Built-in quality controls allowing user to check sequences surrounding a target site to ensure that the correct DNA region has been analyzed

• Use of negative sequencing controls can be built into a reaction by including dispensations of nucleotides at sites where they should not be incorporated into the synthesized DNA strands

• For analysis of CpG methylation, sites where cytosine is not followed by guanine serve as internal controls for bisulfite treatment

• Software that compares the sequence and allele quantification data resulting from a

Pyrosequencing run to preset limits

• Data quality assessment that identifies segments of the data that may require review or do not meet quality standards

• Ability to monitor run in real-time on the built-in screen

• Data stored simultaneously on the instrument internal memory and on a USB stick

• Versatile analysis modes, detailed quality assessment, flexibility of electronic and printed data reports

• Operating system runs on Microsoft Windows

• Must include delivery in price

• Delivery within 120 days after award