Official name: Danmarks Tekniske Universitet — DTU
National registration number: 30060946
Postal address: Anker Engelunds Vej 1
Town: Kgs. Lyngby
NUTS code: DK012 Københavns omegn
Postal code: 2800
Country: Denmark
Contact person: Mikkel Bjerregaard Jensen
E-mail: mbjje@dtu.dk
Telephone: +45 45252525
Internet address(es):
Main address: http://www.dtu.dk

Body governed by public law

Education

Procurement of Illumina Nextseq 550 Sequencing System Including Bronze Support Plan

38430000 Detection and analysis apparatus

Supplies

1) NextSeq 550 System (SY-415-1002);

2) 1 year bronze service contract for the NextSeq 550 system.

This contract is divided into lots: no

Value excluding VAT: 300 000.00 GBP

38000000 Laboratory, optical and precision equipments (excl. glasses)

38400000 Instruments for checking physical characteristics

38900000 Miscellaneous evaluation or testing instruments

NUTS code: DK012 Københavns omegn

DTU has been tasked through funds from the Fleming Fund (UKAID) to establish regional reference centres for whole genome sequencing in Africa. This includes establishing a centre at the National Institute for Communicable Diseases (NICD) in South Africa. In order to fulfill their role as a reference centre for the Southern African region, NICD needs a well-established sequencing plat-form/technology for sequencing pathogenic bacteria, in addition to alleviate some of the massive sequencing pressure and need for timely SARS-CoV-2 sequencing. After reviewing the specifications on other sequencing platforms, the conclusion is that only the Illumina NextSeq system can cover the specific sequencing needs at NICD, as a NextSeq system has the needed sequencing capacity.

Price

Options: no

The procurement is related to a project and/or programme financed by European Union funds: no

Negotiated procedure without prior publication

Explanation:

Context:

The regional whole genome sequencing reference centre at NICD, Johannesburg, South Africa needs a well-established WGS platform/technology to sequence bacterial pathogens to fulfil their role as the regional WGS reference centre for Southern Africa, in addition to alleviate some of the massive sequencing pressure and need for timely SARS-CoV-2 sequencing.

Requirements/specifications:

1) Short read technology which corresponds to read sizes ranging between 75 to 150 bases and insert sizes of 200-300 bp combined with high accuracy nucleotide calling of app 99 %;

2) Sequencing-by-synthesis system (SBS);

3) Medium yield of 16-120 (Gb);

4) High throughput of about 200 isolates per run;

5) Not a requirement to have a rapid turnaround;

6) Vital to have a low error rate to avoid re-runs and misinterpretations;

7) Output data needs to be applicable to the analytic workflow applied by NICD (CGE Bacterial Analysis Pipeline, Enterobase);

8) Need of a service contract to cover: coverage of parts, reagents replacement, remote technical support, on-site application support, and protection of costly repairs.

Justifications:

1) Long-read sequencing platforms will not be considered due to the high error rate between 10 %-13 % by the two long-read platforms available: the Pacific Biosciences (PacBio) suite and the Oxford Nanopore Technologies (ONT) suite;

2) Currently, only two available sequencing-by-ligation (SBL) platforms exist and both have a lower yield than required as well as problems sequencing palindromic sequences. Thus, SBL will not be considered;

3) Only Illumina Nextseq meet the required medium yield range of 16-120 Gb. The other available platforms provide either a too small or high a yield;

4) Only Illumina Nextseq and Hiseq meets the required high throughput of about 200 isolates per run. The other available platforms provide a too little throughput from single isolate up to 50 strains;

5) Illumina platforms have an error rate of app. 99 %. A low error rate is vital for accurate identification of genes and mutations as well as phylogeny of bacteria. The long read technology platforms all have much higher error rates (10 %-13 %) which complicate an accurate analysis. Thus, data often are merged with Illumina data to make up for the errors for further analysis. In addition, Thermo Fisher platforms have problems with especially in homo-polymeric regions, leading to difficulties for de novo assemblies complicating an accurate analysis;

9) The analytic workflow (software) applied by NICD (CGE Bacterial Analysis Pipeline and Enterobase) is based on the output from Illumina technologies, thus, only fully applicable to Il-lumina platforms. In order to be able to analyse and compare data from non-Illumina technologies, considerable rewrites, coding and revalidation would be needed;

10) Its vital that platforms are regularly serviced to warrant the high accuracy to ensure high quality genomic data for the analysis. To the best of our knowledge, only Illumina offers service contracts. Only Illumina can support Illumina platforms;

11) Of the different Illumina systems, the Nextseq is the only fit for a regional pathogen sequencing centre, due to the HiSeq system being more applicable for larger genomes (human or eukartotic), whereas the MiSeq and MiniSeq instruments has a lower sequence capacity than needed at the regional WGS centre. Thus, only Illumina can supply NICD with the specific short-read WGS platform that they require.

The procurement is covered by the Government Procurement Agreement: yes

05/02/2021

The contract has been awarded to a group of economic operators: no

Official name: Separations
Town: Randburg
NUTS code: 00 Not specified
Country: South Africa

The contractor/concessionaire will be an SME: no

Total value of the contract/lot/concession: 300 000.00 GBP

Official name: Klagenævnet for Udbud
Postal address: Nævnenes hus, Toldboden 2
Town: Viborg
Postal code: 8800
Country: Denmark
E-mail: klfu@erst.dk
Telephone: +45 35291000
Internet address: http://www.klfu.dk

Precise information on deadline(s) for review procedures:

Complaint regarding pre-qualification:

Complaint regarding pre-qualification must be submitted no later than 20 calendar days after notification has been sent to the concerned candidates informing them who has been selected, if the notification includes the grounds for the decision, cf. lov om Klagenævnet for Udbud (Complaints Board for Tenders) § 7, Section 1.

Complaint regarding award of contract:

Complaint regarding the award of a contract must be submitted no later than 45 calendar days from the date after the contracting authority has published a notice in the European Union Official Journal informing that the contracting authority has awarded/concluded a contract, cf. lov om Klagenævnet for Udbud (Complaints Board for Tenders) § 7, Section 2, No 1.

Complaint regarding award of a contract under a framework agreement with a reopening of the competition (mini-tender):

Complaint regarding the award of a contract under a framework agreement with a reopening of the competition must be submitted no later than 30 calendar days from the date after the contracting authority has notified the concerned tenderers that a contract based on a framework agreement with a reopening of the competition has been awarded/concluded, if the notification includes the grounds for the decision, cf. lov om Klagenævnet for Udbud (Complaints Board for Tenders) § 7, Section 2, No 2.

Complaint regarding the award of a framework agreement:

Complaint regarding the award of a contract must be submitted no later than 6 months from the date after the contracting authority has notified the concerned candidates and tenderers that a framework agreement has been concluded, cf. lov om Klagenævnet for Udbud (Complaints Board for Tenders) § 7, Section 2, No 3.

Complaint regarding direct award of contract:

Complaint that the contracting authority, contrary to the Public Procurement Act, has concluded a contract without prior publication of a contract notice in the European Union Official Journal must be submitted no later than 30 calendar days from the date after a contract award notice has been published by the contracting authority in the European Union Official Journal and that contract award notice includes the grounds for the decision to award the contract directly, cf. lov om Klagenævnet for Udbud (Complaints Board for Tenders) § 7, section 3.

Compliant regarding public procurements below the EU threshold:

Complaint regarding violation of public procurements below the EU threshold must be submitted no later than 45 calendar days from the date after the contracting authority has notified the tenderers about the award of contract, if this notification includes the grounds for the decision; and no later than 6 months from the date after the contracting authority has notified the concerned candidates and tenderers that a framework agreement has been concluded, if the notification includes the grounds for the decision, cf. lov om Klagenævnet for Udbud (Complaints Board for Tenders) § 7, section 4, No 1 and 2. Compliant regarding pre-qualification on procurement below the EU threshold must be submitted no later than 20 calendar days from the date after the contracting authority has sent a notification to the concerned candidates who has been selected and this notification includes the grounds for the decision, cf. lov om Klagenævnet for Udbud (Complaints Board for Tenders)) § 7, Section 5.

Official name: Konkurrence- og Forbrugerstyrelsen
Postal address: Carl Jacobsens Vej 35
Town: Valby
Postal code: 2500
Country: Denmark
E-mail: kfst@kfst.dk
Telephone: +45 41715000
Internet address: http://www.kfst.dk

05/02/2021