Whole Genome Sequencing

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Using Whole Genome Sequencing (WGS), the complete genomic context of an organism (either DNA or RNA bearing) can be established.

WGS has been transformative in diagnostics for the identification of inherited disorders, but also for the identification of genetic traits in plants/livestock/bacteria in research or commercial applications.

Generally, at BRIGHTcore Whole Genome Sequencing (WGS) is performed through 2 main methods : (1) PCR free library preparation for Illumina and (2) PCR free library preparation for NanoPore.

Both methodologies require DNA fragments of a specific size, so fragmentation might be necessary. More on DNA fragmentation can be found here :

DNA fragmentation

Following fragmentation, the 3' and 5' overhangs are blunt ended by respectively a 3' exonuclease and a DNA polymerase. After this "end repair" step, the 5' ends are phosphorylated (polynucleotide kinase) and the 3' ends adenylated (exo-klenow), this in order to generate a substrate for the adapter ligation.

Finally, the resulting libraries are ready to be sequenced according to the requesting scientist's needs. More on sequencing can be found here :

Massive Parallel Sequencing

For Illumina based sequencing, the read length may vary per project (read length is a parameter inputted on the sequencing device). For NanoPore based sequencing, the read length is determined during the fragmentation process.

Occasionally, a non-PCR free library is generated by e.g. the use of a tagmentation based library preparation. This strategy is mainly applied to low complexity genomes (bacterial / viral).

For more information about WGS, please see our information leaflet or contact us.

The instrument(s) listed below are relevant in context of this test :

Illumina MiSeq

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.

MGI DNBSEQ-T7

Our highest capacity short read sequencer. This device can generate up to 5,8B reads per flowcell. We standardly run SE50 bp and PE150 bp runs, but read length can be flexibily adjusted (to >200 bp).

NanoPore P2i

The P2i is our high capacity long read sequencer, which can process 2 PromethION flowcells simultaneously. Data analysis is performed on the on board computer.

Illumina NovaSeq 6000

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).

NanoPore GridION x5

Sequencing long reads is no hassle on this device. It can sequence 5 MinION flowcells simultaneously and perform the data analysis on board.

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Specifications & applications

Our highest capacity short read sequencer. This device can generate up to 5,8B reads per flowcell. We standardly run SE50 bp and PE150 bp runs, but read length can be flexibily adjusted (to >200 bp).

MGI DNBSEQ-T7

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

Flow cell types

v3 (SM1.0)
v5 (SM2.0)

R10.4
R9.4.1 (discontinued)

Standard v2
Standard v3
Nano v2
Micro v2

Max. read length

v3 (SM1.0) : 150 bp
v5 (SM2.0) : 150 bp

> 4 Mb

Standard v2 : 250 bp
Standard v3 : 300 bp
Nano v2 : 250 bp
Micro v2 : 150 bp

Max. run time

v3 (SM1.0) : 24-30h
v5 (SM2.0) : 24-30h

72h (interruptible at all time)

Standard v2 : 39h
Standard v3 : 56h
Nano v2 : 28h
Micro v2 : 19h

Max. capacity (bases)

v3 (SM1.0) : 1500 Gb
v5 (SM2.0) : 1500 Gb

< 50 Gb

Standard v2 : 8,5 Gb
Standard v3 : 15 Gb
Nano v2 : 0,5 Gb
Micro v2 : 1,2 Gb

Max. capacity (reads)*

v3 (SM1.0) : 5,8B SE - 11,6 PE
v5 (SM2.0) : 5,8B SE - 11,6 PE

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

Standard v2 : 15M SE - 30M PE
Standard v3 : 25M SE - 50M PE
Nano v2 : 1M SE - 2M PE
Micro v2 : 4M SE - 8M PE

MGI DNBSEQ-T7

NanoPore GridION x5

Illumina MiSeq

Applications (possible)

Whole Genome Sequencing, Whole Exome Sequencing, Large Gene Panels, RNAseq, Methyl-seq, ChIPseq, Small genomes, Mitochondrial resequencing

Small genomes, Long Range Amplicon sequencing, RNAseq, Methyl-seq, Whole Genome Sequencing

Small genomes, Amplicon resequencing, Mitochondrial resequencing

Applications (in use)

Whole Genome Sequencing, Whole Exome Sequencing, Large Gene Panels, RNAseq, Methyl-seq, ChIPseq, Small genomes, Mitochondrial resequencing

Small genomes, Long Range Amplicon sequencing, RNAseq, Methyl-seq, Whole Genome Sequencing

Small genomes, Amplicon resequencing, Mitochondrial resequencing

Remarks

As the highest capacity short read instrument in our portfolio, it is the cheapest/base. Whole Human Genomes at 30x coverage are possible at prices around 500€. The system is highly flexible in run configuration and can sequence 'dark bases' on demand (eg. to circumvent unwanted polyA tails or tags/primersequences introduced during library prep).
The DNBSEQ-T7 can sequence 4 flow cells simultaneously.

The ability to generate long reads and the flexibility of the run times are highly useful in (small) genome sequencing and metagenomics. This, despite its higher error rate. Single contig small genomes are possible. Also, due to the short run times, the Nanopore technology proved to be essential in Sars-Cov2 typing.

The GridION can sequence 5 flow cells simultaneously.

As the lowest capacity short read instrument, it unfortunately also comes at the highest cost/base. The possibility to generate high quality 'long' reads (up to 300 bp) is the main advantage.

The MiSeq can only sequence 1 flow cell per run.

Specifications

Sample types

Blood > DNA

EDTA tube

10 ml (min. 3 ml)

Room temperature

Blood > cfDNA/ctDNA

Streck Cell-Free DNA BCT

9 ml

Room temperature

Cells of various tissue origins > DNA

Microtube* with cell pellet or 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 section of various tissues > DNA

Microtube*

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

Room temperature

Plasma > cfDNA/ctDNA

DNA LoBind 5 ml tube

> 2ml

Dry ice

Tissue of various origins > DNA

Cryovial containing stabilizer (eg. AllProtect) or tissue homogenized on lysis buffer

Application/tissue specific (contact us)

Dry ice

Extra requirements

See test/application specific recommendations

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

Sample types

Deliverables

Below, you can find the type of data files that can be retrieved for this test.

If you require more information or need a more custom output, please consult our Bioinformatics page.

Bioinformatics

Raw data - fast5 file

Raw data file generated by Oxford NanoPore sequencers

RUO (on request)

Annotated variant file

Text file containing all detected variants + relevant annotation (cross reference to various databases)

Diagnostic / RUO

Called variants - vcf file

Text file containing all detected variants as compared to the relevant reference genome

Diagnostic / RUO

Raw data - bam file

Binary data file containing the aligned reads

RUO (on request)

Raw data - fastq file

Data file containing the raw (unaligned) reads

RUO (on request)

Deliverables

Costs

Below, you can find indicative prices (excl. VAT) for all potential options you'd require to accomplish your project. If you are interested, please contact us to receive a tailored quotation.

Request quote

Update pending

Our prices are being updated. More info soon.

Costs

Documents & certificates

141-TEST (BRIGHTcore)

Documents

Plan Experiment

Plan experiment

For Diagnostics

This test is mainly performed as a diagnostic assay. In this case, please contact your General Practitioner or Clinical Geneticist (Centre for Medical Genetics of choice) to get the diagnosis started.

For Research

This test can also be applied in context of research. For this, please get approval from your local ethical committee and/or make proper arrangements with your Biobank.

Please follow the steps below to start up an experiment with us.

Get in touch (ONLY FOR NEW PROJECTS)

Explain your project, so we can assist you to find the best solution.

Expect questions like :

What type of sample would you like to analyze?
Which elution buffer did you use?
What are the expected concentrations of your samples?
How many samples would you like to process?
How fast do you need the results (TAT) and/or do we need to expedite?
If you deviate from our sample types, are there test samples available?
Are our standard deliverables ok?
...

1

Start here

Request quotation

Once you know which experiment you want to set up, fill out the 'Quote request' form, with the essential details of your project :

Coordinates of the person to whom to address the quotation
Which type of test you'd like to set up
Do you require a specific deliverable?
Do we need to expedite (comes at extra cost)?
...

2

Quotation

Submit your samples

Once you agree with our terms (quote / TAT / terms & conditions) :

Fill out our sample submission form
Send it via email : contact us
Print out the form and include it with your samples
Send your samples to us
Label your tubes/plates correctly : see details here
Adhere to the corresponding transport conditions listed under Sample types
Indicate if we can discard your samples after completion of project

3

Submission form

Your experiment starts

Now it is up to us... We will start your experiment as soon as possible.

When expedited, the turn-around-time (TAT) is 1 month
For standard requests the turn-around-time (TAT) is 2 months

The standard TAT is generally overestimated, but this extended timeframe allows us to : combine similar requests of multiple scientists and to repeat the experiment in case of issues.

Please refrain from contacting us in case the pre-agreed TAT didn't expire yet.

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Related tests

Human genome sequencing

For germline genetic testing, full human genome sequencing is becoming mainstream. Find out more here.

Non-Invasive Prenatal Testing (NIPT)

Identify fetal aneuploidies and even microdeletions and -duplications in the maternal blood

Sars-Cov2 sequencing

Sequence the full Sars-Cov2 genome to assess the evolution of the virus within the population

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