CAP TODAY magazine features advances in tests and laboratory equipment, trends in management and clinical operation, regulatory changes and finance, plus news about the laboratory improvement programs of the College of American Pathologists.
Issue link: https://captoday.epubxp.com/i/414768
Next-generation sequencing instruments november 2014 | cap today 67 Tabulation does not represent an endorsement by the College of American Pathologists. Part 1 of 4 Illumina Illumina info@illumina.com info@illumina.com See captodayonline.com/productguides for an interactive version of guide 5200 Research Place, San Diego, CA 92122 5200 Research Place, San Diego, CA 92122 858-202-4500 www.illumina.com 858-202-4500 www.illumina.com Name of instrument MiSeq NextSeq 500 Sequencing System Name of model/Model has been upgraded —/no —/no Country where designed/Manufactured/FDA cleared or approved U.S./U.S./yes U.S./Singapore/— First year sold in U.S./Outside U.S./First year installed 2011/2011/2011 2014/2014/2014 Dimensions in inches (H × W × D)/Footprint of all instrumentation and computing hardware 20.6 × 27 × 22.2/~4.2 square feet 25 × 23 × 21/4 square feet Equipment supplied with system/Automation for library preparation system is a single unit inclusive of amplifcation, sequencing, paired-end, and analysis/yes system is inclusive for fowcell clustering and sequencing; library preparation and data analysis are done off board/yes Necessary equipment not included with system and additional cost — BaseSpace (no charge), BaseSpace Onsite ($60,000), or custom informatics pipeline (variable) Bioinformatics tools provided/For use by biologist or bioinformatician MiSeq Reporter/biologist; BaseSpace/biologist BaseSpace/biologist Supplied with UPS/Entire workfow can occur in same lab no/yes no/yes Clean room requirements/Electrical connection —/100–240 VAC at 50–60 Hz, 400 W —/100–120 VAC 15 A or 220–240 VAC 10A List price/Total list price for equipment needed to perform simplest and fastest workfow from amplifcation through variant calling (not typically found in lab) $99,000/— $250,000/$250,000 Purchase options purchase, reagent rental, or lease (fnancing available) purchase, reagent rental, lease Warranties offered frst year included with instrument purchase, extended options available frst year included, extended options available Training included/Total time for standard install and basic training yes/<1 day yes/1 day install, 2 days training Training location/Follow-up training available on site/yes, extra charge on site/yes, extra charge Instrument core performance: Maximum No. of libraries amplifed in single amplifcation event 384 for some applications 384 for some applications Read length/Percent bases >Q30 up to 2 × 300 bp/70 (for 2 × 300 bp) up to 150 bp/75 Paired-end capability/Tag lengths/Spans yes/up to 2 × 300 bp/200–550 bp yes/up to 350 bp/up to 2 × 150 bp Fragment/Tag lengths/Spans yes/up to 2 × 300 bp/200–550 bp yes/up to 350 bp/up to 2 × 150 bp Mate-pair/Tag lengths/Spans yes/up to 2 × 150 bp/3–15 kb yes/2–12 kb/up to 2 × 150 bp Single-end/Tag lengths/Spans yes/up to 1 × 600 bp/550 bp yes/up to 350 bp/up to 1 × 150 bp RNA sequencing/Tag lengths/Spans yes/up to 2 × 300 bp/100–300 bp yes/150–350 bp/up to 2 × 150 bp ChIP sequencing/Tag lengths/Spans yes/up to 2 × 300 bp/100–300 bp yes/200–350 bp/up to 2 × 150 bp Bisulfte sequencing/Tag lengths/Spans yes/2 × 300 bp/100–300 bp yes/up to 350 bp/up to 2 × 150 bp Output per run up to 15 Gb up to 120 Gb Total time from library construction to variant calling to achieve output per run/Technical bench time/Bioinformatics time 4–55 hours depending on read length/2 hours/2 hours 22–45 hours depending on application/90 minutes–12 hours/ 30 minutes–12 hours Sample preparation: Total time for generating standard gDNA library <2 hours <2 hours • Paired-end <2 hours <2 hours • Fragment <2 hours <8 hours • Mate-pair <2 days 2 days • Single-end <2 hours <2 hours • RNA sequencing <2 hours <9 hours • ChIP sequencing <2 hours <9 hours • Bisulfte sequencing ~9 hours 5 hours Hands-on time each: • Paired-end <30 minutes 15 minutes • Fragment <30 minutes <3 hours • Mate-pair ~3 hours <2 hours • Single-end <30 minutes 15 minutes • RNA sequencing <4 hours <5.5 hours • ChIP sequencing ~5 hours <5.5 hours • Bisulfte sequencing — 3 hours Equipment required for library construction standard lab equipment standard lab equipment Reagents and controls: Cost per run $725–$1,400 $975–$4,000 Cost per sample* MiSeq V3 kits: $41–$47; MiSeq V2 kits**: $42–$43 NextSeq 2 × 75 mid-output: $42.84 for 96 samples (1 Mb, 200x); $34.96 for 384 samples (1 Mb, 50x) Reagent tracking method on instrument RFID RFID Information contained in tracking method serial No., expiration date, lot and part numbers, number of cycles, PE-SR part number, lot number, serial number, expiration date, and number of cycles Reagent shipping conditions/Storage conditions box 1: dry ice; box 2: gel pack/box 1: -15°– - 20°C; box 2: 2°–8°C dry ice, gel pack, or ambient/-20°C, 4°C, 25°C Shelf life of amplifcation and sequencing reagents guaranteed 3 months guaranteed 3 months Controls introduced during creation of library/Sequencing control avail. yes/yes yes/yes Capable of complete walkaway automation for amp., seq., var. calling yes no Remote system monitoring yes yes Instrument control software and devices to start run/for data analysis 10 minutes/2 hours 10 minutes/5 minutes (performed off board in BaseSpace) Total time required for setup of amplifcation, sequencing, and variant calling steps 10 minutes 10 minutes Maximum No. of libraries sequenced in a single run up to 96 (384 for targeted RNA) 384 Types of maintenance plans available parts only, basic, comprehensive, advantage, dedicated on site parts only, basic, comprehensive, advantage, dedicated on site No. of feld apps scientists and engineers based in U.S. — — Weekly maintenance required/Monthly/Pre-run water wash/water wash/water wash none/manual wash if instrument is idle for 2 weeks/none, automatic wash is completed after every run System offers secondary analysis software developed by instrument vendor yes yes Variant report generated directly on instrument yes no Third-party analysis software available yes, BaseSpace apps store or Avadis NGS yes Ability of software to detect mutations substitutions, indels, copy number changes substitutions, indels, copy number changes Total No. of peer-reviewed publications for this platform >5,300 publications — Published applications in pathology-related research — — Fastest published turnaround time from sample to analyzed result 1.5 days (Koser, et al.) — Lowest published variant sensitivity level <5 percent (Harismendy, et al.) — Distinguishing features of sequencer (supplied by company) *inclusive of sample prep, for multiple confgurations, using 1 Mb and 30x average coverage per sample Note: a dash in lieu of an answer means company did not answer question or question is not applicable quality scores with >70% of bases higher than Q30 at 2 × 300 bp and >85% bases higher than Q30 at 2 × 75 bp and benchtop sequencer (per Loman, et al.) based on industry's most-adopted sequencing technology (>5,300 publications); single instrument takes samples from library prep through secondary analysis with no ancillary equipment needed; simple, streamlined workfow with as little as 30 minutes hands-on time from sample to answer **actual coverage is much higher than 30x due to only 96 barcodes available fast and simple workfow, powerful desktop sequencer capable of whole-human genome sequencing in 29 hours; mid- and high-output kits allow for fexibility in sample multiplexing based on coverage needs, which permits a wide variety of applications such as RNA sequencing, WGS, exomes, and targeted resequencing; leverages the industry's most-adopted sequencing technology and generates high- quality data with >75% bases higher than Q30 at 2 × 150 bp