Supply of Laboratory Equipment(Part XLII RT-PCR, PCR, Gel Documentation system, Genome Sequencer and Nucleicacid bioanlayzer) for SES of the Republic of Uzbekistan.

New amendment added #3: to amend Section_III_Returnable_Bidding_Forms_Form D_Technical Bid Form

New amendment added #2: extends the tender deadline by one additional week to allow suppliers sufficient time to adapt to the amended requirements. 

New clarification added: Q7  : Lot 4Paragraph 9: “Maximum number of paired-end reads of DNA fragments from one reaction module (flow cell).”Question : The current wording is based on the terminology used in sequencing-by-synthesis (SBS) systems, which measure performance in paired-end reads per flow cell. However, other globally recognized next-generation sequencing (NGS) technologies, such as semiconductor sequencing, DNA nanoball sequencing, or nanopore sequencing, use different read structures and data metrics (e.g., single-end reads, total bases generated, or total reads per chip), while achieving equivalent or higher throughput and accuracy.To ensure technological neutrality and fair competition, we propose revising the specification as follows:“The system shall provide a high number of sequencing reads per run (in single-end or paired-end configuration), comparable to the performance achieved by modern high-throughput platforms capable of paired-end sequencing of DNA fragments on a single reaction module (flow cell) or equivalent consumable.”A7 : Lot 4. Line no 9. will be amended to address your request and shall read as follows: "Maximum number of sequencing reads per run from a single reaction module (flow cell) shall be approximately 25–30 million paired-end reads or an equivalent number of single-end reads generated by alternative sequencing technologies"Q8 : Question: Lot 1Paragraph 1: Rotary cycler for RT-PCR and real-time detection , open to any reagents intended for medical diagnostics and compatible with consumables from other manufacturersQuestion:  The specification’s reference to a “rotary cycler” describes a specific design principle used by certain manufacturers (e.g., air-based rotary systems), which may inadvertently limit participation to a single or a few suppliers. However, block-based thermal cyclers and rotary air-based cyclers achieve the same diagnostic purpose and meet all required parameters for real-time PCR and medical diagnostics when designed to comply with relevant standards (ISO 13485, CE IVD, etc.).To ensure technological neutrality and broader competition, we propose that the specification be rephrased as follows:“Real-time PCR system with a thermal cycling mechanism (rotary or block-based) suitable for quantitative PCR and RT-PCR applications, open to reagents intended for medical diagnostics and compatible with consumables from multiple manufacturers.”A8 :Lot1. Line 1. the Section_III_Returnable_Bidding_Forms_Form D_Technical Bid Form will be amended as follows: Real-time PCR system with a thermal cycling mechanism (rotary or block-based) suitable for quantitative PCR and RT-PCR applications, open to reagents intended for medical diagnostics and compatible with consumables from multiple manufacturers.”Q9 :  LOT 1 : Paragraph 3: “Thermal cycler for real-time PCR reactions: 36 positions for 0.2 ml tubes and 72 positions for 0.1 ml strip tubes.”Question : The current wording refers to a specific tube and strip configuration (36 × 0.2 mL and 72 × 0.1 mL), which is characteristic of certain rotary cycler Rotor-Gene Q which limits participation of other suppliers.To ensure technological neutrality and compliance with international procurement best practices, we propose the following inclusive rephrasing:“Thermal cycler for real-time PCR reactions, designed to accommodate small reaction volumes in individual tubes, strip tubes, or plates, with a total capacity of at least 36 to 96 reaction positions. Equivalent configurations and consumable formats shall be accepted, provided that they ensure accurate temperature control and fluorescence detection in real time.”A9 : Lot 1. The systems offering equal or greater capacity (e.g., up to 96 positions), and demonstrating equivalent or superior temperature control and fluorescence detection, will be considered fully compliant or exceeding the specification. Line 3. the Section_III_Returnable_Bidding_Forms_Form D_Technical Bid Form will be amended as follows:  Thermal cycler for real-time PCR reactions: capable of accommodating small reaction volumes in individual tubes, strip tubes, or plates, with a total capacity of at least 36 to 96 reaction positions, ensuring accurate temperature control and real-time fluorescence detection.Q10: Lot 1Paragraph 7: The sample movement speed (up and down) is maximum more than 12°C/s.Question : The maximum ramp rate (temperature increase/decrease speed) in real-time PCR instruments directly affects temperature accuracy, stability, and reproducibility during amplification cycles. While higher ramp rates may reduce run time, they can also compromise uniform temperature control and increase variability between wells, particularly during annealing and extension phases.Leading international manufacturers — such as Thermo Fisher Scientific, QIAGEN, Bio-Rad, and Agilent — have optimized their real-time PCR systems with moderate ramp rates (5–7°C/s) to ensure better precision, stable temperature transitions, and consistent amplification results, especially for diagnostic and quantitative applications.Therefore, we propose to rephrase the specification as follows to ensure competitive neutrality:“The sample ramp rate (temperature increase/decrease speed) shall ensure accurate and stable temperature control during amplification cycles, with a maximum ramp rate of up to 12°C/s or as optimized by the manufacturer to achieve precise and reproducible results.”A10: Lot1. Line 7. the Section_III_Returnable_Bidding_Forms_Form D_Technical Bid Form will be amended as follows: The sample movement speed (up and down) is  maximum 5-7 °C/s or better. The offer that is equivalent or exceeds the requirement is considered substantially compliant. Q11: Lot 1Paragraph 13: Sample volume 5-100 µLQuestion :  Most instruments such as Thermo Fisher Scientific (Applied Biosystems QuantStudio 5, QIAGEN Rotor-Gene Q (Rotary System), Agilent AriaMx Real-Time PCR System,Roche LightCycler 480 II and etc. allow flexibility from 10 to 100 µL, depending on plate type and assay conditions.To ensure broader participation of multiple suppliers, we kindly request that the sample volume criterion be amended to 10–100 µL.A11:  Lot1. Line 13. the Section_III_Returnable_Bidding_Forms_Form D_Technical Bid Form will be amended as follows, Sample volume 10-100 µLQ12: Greetings, We are interested in participating in this project. We kindly request an extension in the submission deadline for 1 week to provide you with our best offer.A12: The tender will be extended by a Week. Q13: regarding the Lot #4 Full-genome sequencer for high-throughput massive parallel sequencing, complete with starter kit,  we would like you to clarify: does 'starter kit' refer to sequencing kit only? does it incude any application kit?A13: For the purposes of this tender, the “starter kit” refers to the set of reagents and consumables provided by the manufacturer to enable the initial operation of the sequencer, including, but not necessarily limited to:- Sequencing kits required to perform the first runs;- Basic consumables necessary for instrument setup and verification;- Any additional components explicitly provided by the manufacturer to allow immediate operation upon delivery.

New clarification added: Q3: Lot 4Paragraph 1: The system for high-throughput nucleic acid sequencing is designed to decipher the primary DNA sequence by synthesis using fluorescently labeled nucleotides, with simultaneous recording of the fluorescent signal from the nucleotide incorporated into the synthesized chain, followed by image recognition and data conversion into digital format.Question : We note that the current wording appears to reflect one specific sequencing technology — namely, sequencing by synthesis (SBS) — which may inadvertently limit participation to a restricted group of suppliers using this exact approach. We therefore suggest the following neutralized wording for this section:“A system for high-throughput nucleic acid sequencing designed to determine the primary DNA sequence using any suitable sequencing technology (e.g., sequencing by synthesis, ligation, nanopore, or other high-accuracy parallel methods), with real-time or sequential detection of incorporated bases and digital data output.”A3: Lot. 4. To allow wider competition, Line no.3 of the Section_III_Returnable_Bidding_Forms_Form D_Technical Bid Form will be amended as follows: "The sequencing system shall utilize a validated high-throughput next-generation sequencing (NGS) technology that enables massively parallel determination of DNA sequences by synthesis, ligation, or single-molecule real-time detection, with automated signal or image acquisition and conversion into digital format."Q4: Question: Lot 4Paragraph 6: The ability to perform the procedure of generating molecular clusters and sequencing within a single device, in a fully automated mode, without removing/installing the reaction module (flow cell)Question : As we note that the current wording applies to one system that meets the integrated workflow requirement is the Illumina NextSeq 1000/2000 (or other Illumina platforms) which carries out cluster generation and sequencing in a unified workflow and which unintentionally restrict participation to a limited number of suppliers and it should be noted that some advanced sequencing platforms utilize a separated or modular workflow — where cluster (or template) generation and sequencing are performed in distinct steps or modules.This separated workflow offers several important advantages, including:Elimination of cross-contamination between runs due to independent handling of clustering and sequencing reagents;Improved maintenance and flexibility, allowing replacement of flow cells and modules without affecting sequencing performance;Compatibility with a wider range of sequencing chemistries and automation options.Based on the above, and to ensure technological neutrality and compliance with open competition principles, we kindly propose the following rephrased and more inclusive wording:“The sequencing system shall allow either an integrated or a separated workflow for molecular cluster (or template) generation and sequencing, provided that the process is automated, minimizes user intervention, and prevents cross-contamination between runs.”A4: Lot 4. Line no.6 of the Section_III_Returnable_Bidding_Forms_Form D_Technical Bid Form will be amended as follows: "The sequencing system may allow either an integrated or a separated (modular) workflow for molecular cluster (or template) generation and sequencing, provided that the process is automated, minimizes user intervention, and prevents cross-contamination between runs."Q5: Question: Lot 4Paragraph 7: The maximum time required for a complete instrument operation cycle in the highest performance mode, including the generation of molecular clustersQuestion : The mentioned criteria — combining molecular cluster generation and sequencing in a single operation cycle — is specific to certain sequencing platforms (e.g., those using the sequencing-by-synthesis approach with onboard cluster generation). However, many globally recognized next-generation sequencing (NGS) systems achieve equivalent throughput and accuracy through alternative, modular workflows, where cluster or template generation is performed automatically but in a separate integrated step.Therefore, to maintain technological neutrality and encourage broad participation from various leading NGS manufacturers, we propose the following rephrased specification:“The maximum time required for a complete sequencing run in the highest performance mode (including, where applicable, molecular cluster or template generation) shall be clearly indicated by the manufacturer. Both integrated and modular automated workflows shall be accepted, provided that they ensure full automation and high-throughput performance.”This revision maintains the technical intent — high-throughput sequencing with efficient automation — while allowing equivalent systems using different but equally validated technologies to participate.A5: Lot 4. Line no 7. The intent of this requirement is to establish the maximum time required for a complete sequencing cycle, including, where applicable, molecular cluster or template generation, regardless of whether these processes are carried out within an integrated system or a modular automated workflow, which shall not exceed 48 hours in the highest performance mode. This requirement will be revised accordingly.Q6:Question: Lot 4Paragraph 8: Maximum throughput per run of the instrument when sequencing fragments of 2x150 nucleotide pairs from both ends on a single reaction module (flow cell)QUestion:  The specification as currently written directly refers to the “2×150 bp paired-end sequencing” mode, which is specific terminology associated primarily with the sequencing-by-synthesis (SBS) technology used by certain manufacturers (e.g., Illumina). However, many globally recognized high-throughput sequencing systems (Ion Torrent Genexus System, DNBSEQ-G400 / G99, PromethION 24 / 48)  use different read configurations or sequencing chemistries that achieve equivalent or superior throughput, accuracy, and read length, even if the nomenclature differs.To ensure technological neutrality, we propose that the clause be reformulated as follows:“The system shall ensure high-throughput sequencing per run, capable of producing comparable data output to paired-end sequencing with 150-base-pair reads (2×150 bp) or equivalent configurations, on a single flow cell or reaction module.”A6: Lot 4. Line no 8. will be amended to address your request and shall read as follows: "Maximum throughput per run at maximal read length, at least 15 Gb"

New amendment added #1: This amendment modifies LOT 4, Requirement Lines 20 and 21, and extends the tender deadline by one additional week to allow suppliers sufficient time to adapt to the new requirements.

New clarification added: Q 1 : For lot 4 ,specifically for term 20 and 21, they are only illumina owned, and any other sequencers do not have. Can this be acceptable that these two parameters unqualified? Or does this tender only accept illumina sequencer?A1 : As per Lot 4, technical specifications requested in lines 20 and 21, suppliers are encouraged to offer equivalent alternative solutions for these parameters. Technical specifications will be amended to address the request.Q2 : Regarding the technical specification iof Lot 4 Full-genome Sequencer, we hereby submit a written request for clarification.Line 20: The ability to archive data in ORA format with data compression efficiency exceeding gzip by at least 4.9 times.Item 20: Based on market research, the ORA compression algorithm used in gene sequencers produced by Illumina, Inc. is exclusive to the Illumina brand. Among other leading global brands, gene sequencers manufactured by Shenzhen MGI Tech Co., Ltd. and Thermo Fisher Scientific Inc., as well as other brands, all utilize the gzip compression format. The gzip format is a universal compression algorithm with broad compatibility and lower demands on computer performance. It is supported by almost all operating systems and numerous applications. In contrast, the ORA compression algorithm can only be processed using Illumina-specific tools, limiting end-user flexibility. Additionally, a drawback of the ORA compression algorithm is that it generates less output data. Therefore, we consider this specification to be exclusive, as only one brand of gene sequencer can meet it. We recommend modifying the parameter to require data archiving capability in either ORA or Gzip format.A2: As per Lot 4, technical specifications requested in line 20, suppliers are encouraged to offer equivalent alternative solutions for requested parameters. Therefore technical specifications for Lot #4, line 20 will be amended as follows: 'The ability to archive data in ORA or gzip format'.