Long Non Coding Rna And Small Rna Sequencing For Identification Of Rna Biomarkers For Radiation Biodosimetry

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The U S Department Of Health And Human Services Dhhs National Institutes Of Health Nih National Cancer Institute Nci Center For Cancer Research Ccr Radiation Oncology Branch Rob Experimental Therapeutics Section Ets Intends To Procure On A Sole Source Basis Services For Long Non Coding Rna And Small Rna Sequencing For Identification Of Rna Biomarkers For Radiation Biodosimetry From Novogene Corporation Inc 823 Anchorage Place Suite 105 Chula Vista Ca 91914 4534 United States The Response Close Date Of The Notice For This Requirement Is In Accordance With Far 5 203 B This Acquisition Will Be Processed Under Far Part 12 Acquisition For Commercial Items And Will Be Made Pursuant To The Authority In Far Part 13 106 1 B 1 And Is Exempt From The Requirements Of Far Part 6 The North American Industry Classification System Naics Code Is 541380 And The Business Size Standard Is 16 5 1 0 Background Radiological Attacks And Nuclear Detonations Can Cause Mass Casualties Victims May Have Received Substantial Radiation Doses And May Not Immediately Exhibit Visible Symptoms Of Radiation Sickness Victims With Whole Body Or Substantial Partial Body Exposure Gt 2 Gray Gy Will Require Immediate Treatment Within 24 Hours To Mitigate Radiation Injury While Others Will Require Both Intermediate And Long Term Management For Possible Injury To The Marrow Gastrointestinal Tract Lung And Other Organs Early Prediction Of Possible Acute Intermediate And Delayed Effects Will Enable Timely Therapeutic Interventions Which Will Not Only Reduce Death But Also Improve Quality Of Life For The Victims To That End The Nci Has Designed This Study To Explore Both Long Non Coding And Small Rnas Which Change In Response To Radiation Using High Throughput Ngs Sequencing Platforms 1 1 Objective The U S Department Of Health And Human Services Dhhs National Institutes Of Health Nih National Cancer Institute Nci Center For Cancer Research Ccr Radiation Oncology Branch Rob Experimental Therapeutics Section Ets Requires Microrna Mirna Expression Information Through Small Rna Sequencing Small Rna Seq And Long Non Coding Rna Lncrna And Mrna Expression Information Through Lncrna Sequencing Lncrna Seq To Identify Biomarker Signatures Of General Radiation Exposure And Organ Specific Radiation Injury 2 0 Scope This Project Involves Mrna And Lncrna Seq 216 Samples And Small Rna Seq 96 Samples Of 312 Total Samples It Is A Multi Step Process With Each Step Dependent On Successful Completion Of The Former The Project Workflow Shall Consist Of The Following Preparation Of Cdna Libraries For Both Mrna Lncrna Seq And Small Rna Seq Rna Quality Control For All Samples Before And After Library Preparation Performance Of Rna Seq Workflows Mrna Lncrna Seq For 216 Samples Using An Illumina Platform Small Rna Seq For 96 Samples Including Clustering Prior To Sequencing Using An Illumina Platform Quality Control Of All Reads Alignment Of Reads To Reference Genome Data Analysis For Identification Of Differentially Expressed Coding And Non Coding Rnas 3 0 Contract Requirements And Personnel Qualifications The Contractor Shall Perform The Following Tasks 3 1Mrna And Lncrna Sequencing Of 216 Samples 3 1 1 Total Rna Sample Quality Control 3 1 1 1 Assessment Of Rna Sample Purity By Measuring Absorbance At Wavelengths Of 230Nm 260Nm And 280Nm Using A Nanodrop Spectrophotometer The Samples Must Meet The Following Criteria 3 1 1 1 1 260 280 Ratio 2 0 3 1 1 1 2 260 230 Ratio 1 8 3 1 1 2 Agarose Gel Electrophoresis On 1 Gels To Ensure No Rna Degradation And No Contamination 3 1 1 3 Assessment Of Rna Integrity Using An Agilent 2100 Bioanalyzer The Sample Must Meet The Following Criteria 3 1 1 3 1 Rna Integrity Number Rin 8 3 1 2 Library Construction 3 1 2 1 Purification With Oligo Dt Beads And Fragmentation Of Mrna And Lncrna From Total Rna To Prepare Samples For Complementary Dna Cdna Synthesis 3 1 2 2 Cdna Synthesis 3 1 2 2 1 Reverse Transcription Of Rna Fragments Into First Strand Cdna Using Reverse Transcriptase Enzymes And Random Primers 3 1 2 2 2 Removal Of Rna Template And Synthesis Of A Second Cdna Strand Using A Custom Illumina Second Strand Synthesis Buffer Dntpsm Rnase H And Escheria Coli Polymerase I Resulting In Double Stranded Cdna 3 1 2 2 3 Purification And Terminal Repair To Remove Overhanging Nucleotides And Ensure Each Strand Of Cdna Contains 5 Phosphate And 3 Hydroxyl Groups 3 1 2 2 4 Addition Of An A Nucleotide To The 3 End Of Fragments A Tailing To Prevent Fragments From Ligating To One Another During Ligation 4 1 2 2 5 3 1 2 2 5 Ligation Of Sequencing Adaptors To Enable Specific Amplification 3 1 2 2 6 Size Selection Of Fragments 150 200 Base Pairs Bp And Polymerase Chain Reaction Pcr Enrichment To Amplify Sequences With Adapters 3 1 3 Library Quality Control 3 1 3 1 Quantification Of Cdna Using A Qubit 2 0 Fluorometer To Ensure Library Meets The Following Criteria 3 1 3 1 1 Concentration 20 Ng l 3 1 3 1 2 Total 100Ng 3 1 3 2 Dilution Of Sample To 1 Ng l Followed By Assessment Of Purity Using An Agilent 2100 Bioanalyzer To Ensure The Following Criteria 3 1 3 2 1 Fragments Between 400 Bp And 5000Bp 3 1 3 2 2 Main Peak At Approximately 2000Bp 3 1 3 3 Quantitative Pcr To Quantify Samples To Greater Accuracy And Ensure The Following Criteria 3 1 3 3 2 Library Activity Gt 2Nm 3 1 4 Sequencing Using Illumina Platforms And The Following Parameters 3 1 4 1 Read Length 125 150Bp Paired End Reads 3 1 4 2 Sequencing Depth 15 20G Raw Reads Per Sample 3 1 4 3 Data Quality 80 Of Bases With Q30 Percentage Of Bases With Correct Base Recognition Rates Greater Than 99 9 In Total Bases 3 1 5Data Analysis 3 1 5 1 Quality Control To Obtain Clean Data By Filtering Data As Follows 3 1 5 1 1 Discard Reads With Adapter Contamination 3 1 5 1 2 Discard Reads Comprised Of Gt 10 Uncertain Nucleotides 3 1 5 1 3 Discard Reads In Which Gt 50 Is Comprised Of Nucleotides With A Base Quality Lt 20 3 1 5 2 Map Reads To Reference Genomes 3 2 Small Rna Sequencing Of 96 Samples 3 2 1 Total Rna Sample Quality Control 3 2 1 1 Assessment Of Rna Sample Purity By Measuring Absorbance At Wavelengths Of 230Nm 260Nm And 280Nm Using A Nanodrop Spectrophotometer The Samples Must Meet The Following Criteria 3 2 1 1 1 260 280 Ratio 2 0 3 2 1 1 2 260 230 Ratio 1 8 3 2 1 2 Agarose Gel Electrophoresis On 1 Gels To Ensure No Rna Degradation And No Contamination 3 2 1 3 Assessment Of Rna Integrity Using An Agilent 2100 Bioanalyzer The Sample Must Meet The Following Criteria 3 2 1 3 1 Rin 8 3 2 2 Library Construction 3 2 2 1 Library Prep For Small Rna Sequencing Using Nebnext Multiplex Small Rna Library Prep Set For Illumina Including The Following Steps 3 2 2 1 1Ligation Of Adapters To The 3 End Of All Mirnas Small Interfering Rnas Sirnas And Piwi Interacting Rnas Pirnas 3 2 2 1 2 Hybridization Of Excess Adapter Into A Double Stranded Molecule To Prevent Adapter Dimer Formation In Subsequent Steps 3 2 2 1 3 Ligation Of Adapters To The 5 End Of All Mirnas Sirnas And Pirnas 3 2 2 1 4 First Strand Cdna Synthesis Using Reverse Transcriptase 3 2 2 1 5 Pcr Amplification Followed By Purification On 8 Polyacrylamide Gel 100V 80 Min 3 2 2 1 6 Recovery Of Dna Fragments Of 140 160Bp Length Of Small Non Coding Rnas Plus 3 And 5 Adaptors And Dissolution In 8 l Elution Buffer 3 2 3Library Quality Control 3 2 3 1 Assessment Of Library Purity Using Agilent 2100 Bioanalyzer With Dna High Sensitivity Chips 3 2 4Clustering And Sequencing Using Illumina Platforms And The Following Parameters 3 2 4 1 Clustering Of Index Coded Samples On A Cbot Cluster Generation System Using Truseq Sr Cluster Kit V3 Cbot Hs Illumina 3 2 4 2 Read Length 50Bp Single End Reads 3 2 4 3 Sequencing Depth 10 Million Raw Reads Per Sample 3 2 4 4 Data Quality 85 Of Bases With Q30 Or Higher 3 2 5Data Analysis 3 2 5 1 Quality Control To Obtain Clean Data By Filtering Data As Follows 3 2 5 1 1 Discard Reads With Adapter Contamination 3 2 5 1 2 Discard Reads Comprised Of Gt 10 Uncertain Nucleotides 3 2 5 1 3 Discard Reads In Which Gt 50 Is Comprised Of Nucleotides With A Base Quality Lt 20 3 2 5 2 Map Reads To Reference Genomes 4 0 Type Of Order This Is A Firm Fixed Price Purchase Order 4 1 Non Severable Services This Is A Non Severable Firm Fixed Price Purchase Order The Services Specified In Each Contract Line Item Clin Have Been Determined To Be Non Severable Services A Specific Undertaking Or Entire Job With A Defined End Product Of Value To The Government 5 0 Period Of Performance The Anticipated Period Of Performance Shall Be For One 1 12 Month Base Period 6 0 Place Of Performance All Work Shall Be Performed At The Contractor S Facility 7 0 Reports And Deliverables All Written Drafts And Final Deliverable Products Shall Be Submitted As An Electronic Copy In The Form Of Pdf Files Excel Workbooks Or Text Files For Review And Comment By The Government S Technical Point Of Contact Tpoc For A Review Period Not To Exceed Thirty 30 Days Final Copies Of Approved Drafts Shall Be Delivered To The Tpoc Within Ten 10 Business Days After Receipt Of The Government S Comments Deliverable 1 Task 3 1 Lncrna And Mrna Sequencing Data For 216 Samples Shall Be Due Within 6 Months After Award Deliverable 2 Task 3 2 Mirna Sequencing Data For 96 Samples Shall Be Due Within 6 Months After Award 8 0 Unique Qualifications Of The Contractor In Fiscal Year 2019 Nci Ccr Rob Ets Conducted Pilot Studies Using Mrna And Mirna Sequencing Services With Novogene Corporation Inc Under Purchase Order 75N91019p00752 Which Had A Period Of Performance Of 09 19 2019 Through 12 18 2019 The Sequencing Data Under The Previous Purchase Order Award Has Been Unparalleled With Respect To Quality Control Accuracy And Reproducibility Ets Has Validated The Results From The Preliminary Services And Have Found 100 Accuracy Of The Data Provided To Expand And Complete The Ongoing Research The Mirna Mrna Sequencing Analysis For The Current Requirement Must Be Compatible With Previous Findings Provided By Novogene Due To Variability And Limited Size Of Samples The Ability To Generate Consistent Results From Difficult Sample Conditions Is Required For The Requested Services Changing Variables At This Time Would Be Detrimental To Current Gene Expression Studies Performed At The Nci And Therefore A Change In Vendor Would Provide Results That Are Not Scientifically Comparable To Previous Findings And Would Disrupt The Overall Body Of Research This Notice Is Not A Request For Competitive Quotations However If Any Interested Party Especially A Small Business Believes It Can Meet The Above Requirement It May Submit A Proposal Or Quote For The Government To Consider The Response And Any Other Information Furnished Must Be In Writing And Must Contain Material In Enough Detail To Allow Nci To Determine If The Party Can Perform The Requirement All Responses And Questions Must Be Submitted Via Email To Adam Hernandez Contract Specialist At Adam Hernandez Nih Gov Responses Are Due No Later Than 11 00 A M Est Wednesday April 29 2020 04 29 2020 A Determination By The Government Not To Compete This Proposed Requirement Based Upon Responses To This Notice Is Solely Within The Discretion Of The Government Information Received Will Be Considered Solely For Determining Whether To Conduct A Competitive Procurement To Receive An Award Contractors Must Be Registered And Have Valid Certification In The System For Award Management Sam Through Sam Gov And Have Representations And Certifications Filled Out Reference 75N91020q00053 On All Correspondence

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