High-Throughput Multi-Capillary Fragment Analyzer

What is the High-Throughput Multi-Capillary Fragment Analyzer?

A high-throughput multi-capillary analyzer runs 96 to 384 samples per batch across parallel capillaries for sequencing cores and service laboratories that quality-check libraries in large numbers. It prioritises throughput and reproducibility over the widest sizing range.

Overview

The instrument arranges 8 to 48 capillaries in parallel and processes a standard 96-well or 384-well plate in a single batch, with run times of about 1.5 to 4 hours. Each capillary has its own injection and detection path, so samples are separated simultaneously rather than sequentially, and throughput reaches several hundred samples per shift. Barcode-driven plate loading, automatic capillary conditioning and lot tracking of polymer and ladders reduce operator effort in a busy service laboratory. Software aggregates results into batch reports, flags failed wells so they can be repeated, and can push results to a laboratory information system. Sizing resolution and accuracy are comparable to single-channel systems when the same kit chemistry is used, and many models accept long-read library kits alongside standard amplicon and RNA kits.

How does it work?

Fragment analysis separates charged nucleic acid fragments in a sieving matrix and detects them by fluorescence. In capillary systems, samples are injected electrokinetically into a polymer-filled capillary, where smaller fragments migrate faster and reach the detector earlier. A laser excites intercalating dye bound to the DNA or RNA, and the software converts migration times into fragment sizes using an internal ladder and into concentrations using a quantitative marker. Microfluidic chips work on the same principle with shorter separation channels and smaller volumes. Automated agarose gel instruments draw samples through a gel by voltage and image the bands after staining. Because the sizing algorithm depends on the ladder and the polymer lot, run quality flags such as marker height and baseline noise should be reviewed before results are accepted.

What are the key features?

• 8 to 48 parallel capillaries with independent detection
• Processes 96-well and 384-well plates in one batch
• Automatic capillary conditioning and polymer exchange
• Barcode plate tracking with batch result aggregation
• Failed-well flagging so only affected samples are repeated
• Polymer and ladder lot tracking for traceable sizing

What are the technical specifications?

A typical high-throughput multi-capillary fragment analyzer configuration offers capillaries of 8–48 parallel channels, plate formats of 96-well and 384-well, samples per batch of 96–384, batch time of approx. 1.5–4 h, sizing range of 10 bp–50 kb (kit dependent) and sizing accuracy of within ±5% (typical). Values are indicative of the product class; the exact figures for each configuration are confirmed on the quotation and the calibration documents supplied with the instrument.

Which applications is it used for?

The High-Throughput Multi-Capillary Fragment Analyzer is used in high-volume sequencing library quality control, service core facility sample screening, large RNA quality control programmes and genotyping fragment analysis at scale. Across the wider Fragment Analyzers class, laboratories also deploy it for next-generation sequencing library quality control, RNA integrity assessment before expression studies and PCR amplicon and restriction digest checks.

Which standards and certifications apply?

Relevant standards and methods include ISO 20395, ISO 22174, CLSI MM09, IEC 61010-1 and ISO 15189. Certification candidates for this model are CE, ISO 9001 manufacturing and IEC 61010-1 safety; each is to be confirmed for the specific configuration before shipment, and certificates are supplied only where they have been issued.

Install the analyzer on a level bench away from vibration and direct sunlight, because optical alignment and polymer flow are sensitive to movement. Store polymer, ladders and dye kits within their stated temperature range and note lot numbers, since a ladder or polymer change can shift sizing by several percent. Run a ladder and a known control with each batch, and review quality flags before releasing data. Replace polymer and clean electrodes as instructed to prevent carry-over between samples. Keep the instrument in a room with stable temperature to limit baseline drift, and include the analyzer in the laboratory's pipette and instrument calibration schedule. Verify performance after any service or software upgrade.

How do I select the right High-Throughput Multi-Capillary Fragment Analyzer?

Select a multi-capillary analyzer when you routinely fill 96-well plates with libraries or RNA and turnaround per plate matters. Specify capillary count, supported plate formats, batch time, consumable cost per plate, quality-flag policy and the depth of lot tracking required for your quality system.

How does it compare with other Fragment Analyzers variants?

Choose by the sample type, resolution and throughput you need. Capillary systems give the best sizing accuracy and reproducibility, which matters for sequencing libraries and RNA integrity scoring. Microfluidic chip systems run more samples in less time with microlitre volumes but give approximate sizing. Automated gel systems handle many samples at low consumable cost with lower resolution. Check the sizing range against your fragments: amplicons of 100–1,000 bp behave differently from long-read libraries above 20 kb, and high-sensitivity kits are needed below 1 ng/µL. Confirm sample volume, consumable cost, run time, and whether the software exports results to a laboratory information system. Where quantification must be exact, pair the analyzer with a fluorometric or digital PCR method.