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Massive Parallel Sequencing

Engineering Plans

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Massive Parallel Sequencing (MPS), also known as Next Generation Sequencing (NGS) is the collection of technologies that are able to genotype (determine the sequence) of DNA or RNA fragments in a massive and parallel fashion.

The second generation MPS technologies rely on clonal amplification of the DNA/RNA fragments to be genotyped, whilst third generation MPS technologies can directly sequence single DNA/RNA fragments without prior clonal amplification.

The second generation technologies generate short sequences of the clonally amplified fragments and are referred to as short-read sequencers. They rely on sequencing-by-synthesis (SBS), where the stepwise incorporation of nucleotides - starting from a sequencing primer - is detected through changes in either fluorescence, pH or impedance. These technologies generally have a low error rate.

The third generation technologies generate long sequences and are referred to as long-read sequencers. The sequence of the DNA (or RNA) fragment to be inferred, is established by measuring either (1) the potential difference over a membrane when this fragment migrates through an nanopore embedded in this membrane or (2) the real-time incorporation of fluorescently labelled nucleic acids by a polymerase. Generally, these technologies have a higher error rate than the 2nd generation sequencing technologies.

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Specifications & applications

Sequencing long reads is no hassle on this device. It can sequence 5 MinION flowcells simultaneously and perform the data analysis on board.
NanoPore GridION x5
Our lowest capacity short reads sequencer, able to generate reads up to 300 bp in length and this at a throughput of 1M to 30M reads per run.
Illumina MiSeq
Our highest capacity short read sequencer. This device can generate reads up to 250 bp in length (on the SP flowcell) and generate up to 10B reads per flowcell (S4).
Illumina NovaSeq 6000
Flow cell types

R9.4.1
R10.4

Standard v2
Standard v3
Nano v2
Micro v2

SP
S1
S2
S4

Max. read length

> 4 Mb

250 bp
300 bp
250 bp
150 bp

250 bp
150 bp
150 bp
150 bp

Max. run time

72h (interruptible at all time)

39h
56h
28h
19h

38h
25h
36h
44h

Max. capacity (bases)

< 50 Gb

8,5 Gb
15 Gb
0,5 Gb
1,2 Gb

400 Gb
500 Gb
1250 Gb
3000 Gb

Max. capacity (reads)*

< 5M (for avg. 10K bp reads)

15M SE - 30M PE
25M SE - 50M PE
1M SE - 2M PE
4M SE - 8M PE

0,8B SE - 1,6B PE
1,6B SE - 3,2B PE
4,1B SE - 8,2B PE
10B SE - 20B PE

* Abbreviations used : SR = Single Read ; PE = Paired End ; M = million ; B = Billion ; Gb = Gigabases

** To know more about the Q score metric, see below


Image by Lukas Tennie
Specifications
Image by Mezidi Zineb

Sample types

PCR products (amplicons) > DNA

Microtube* or 96 well plate

See test details/specifications

Room temperature

Blood > DNA

EDTA tube

10 ml (min. 3 ml)

Room temperature

Blood > RNA

PAXgene Blood RNA tube

10 ml (2,5 ml blood)

Ice pack

Blood > cfDNA/ctDNA

Streck Cell-Free DNA BCT

9 ml

Room temperature

Blood > cfRNA/exoRNA

Streck RNA Complete BCT

10 ml

Room temperature

Cells of various tissue origins > DNA

Microtube* with cell pellet or on lysis buffer

> 5 million cells

Dry ice

Cells of various tissue origins > RNA

Microtube* with cells on lysis buffer

> 5 million cells

Dry ice

DNA from various tissues > DNA

Microtube* or 96 well plate

See test details/specifications

Room temperature

Blood > DNA

DBS / Guthrie card / Punch in microtube*

Min. 1 punch

Room temperature

FFPE block of various tissues > DNA

Paraffin block (in cassette)

Representative block ; Tumor load preferentially >10% ; To be processed by our pathology department (microtome section needed)

Room temperature

FFPE block of various tissues > RNA

Paraffin block (in cassette)

Representative block ; Tumor load preferentially >10% ; To be processed by our pathology department (microtome section needed)

Room temperature

FFPE section of various tissues > DNA

Microtube*

Min. 1x 10 µm section (up to 2 mm³ tissue) ; Tumor load preferentially >10%

Room temperature

FFPE section of various tissues > RNA

Microtube*

Min. 1x 10 µm section (up to 2 mm³ tissue) ; Tumor load preferentially >10%

Room temperature

NGS library (non-PCR free) > DNA

Microtube* or 96 well plate

See test details/specifications

Room temperature or ice pack

NGS library (PCR free) > DNA

Microtube* or 96 well plate

See test details/specifications

Ice (max. 1 day) or dry ice

Plasma > cfDNA/ctDNA

DNA LoBind 5 ml tube

> 2ml

Dry ice

Plasma > cfRNA/exoRNA

DNA LoBind 5 ml tube

> 2ml

Dry ice

RNA from various tissues > RNA

Microtube*

See test details/specifications

Ice (max. 20 min) or dry ice

RNA from various tissues > RNA

Microtube* or 96 well plate

See test details/specifications

Ice (max. 20 min) or dry ice

Sars-Cov2 RNA (naso/oropharyngeal) > RNA

Microtube* or 96 wel plate (plate is preferred)

Log(copies/ml) > 3 (min. 10 µl)

Ice (max. 20 min) or dry ice

Extra requirements

See test/application specific recommendations

Optimum : [Acceptable range (-)]

More information can be found on the subpages (related tests)

Sample types

Deliverables