ATTACHMENT 1_SOW_1232SA26Q1231.pdf
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- Attached to
- Khufu - Hybrid Capture Genotyping Service Federal contract opportunity
- Solicitation number
- 1232SA26Q1231
About this file
This is a Statement of Work for a collaborative Sorghum genomics project involving USDA, Twist Bioscience, and HudsonAlpha Institute for Biotechnology. The project delivers high-quality genotype data supporting genetic diversity and breeding objectives through community-driven target design and high-throughput genotyping using custom hybrid capture technology.
The scope encompasses two primary components: Khufu hybrid capture genotyping for 120 samples per 96-well plate, which includes DNA extraction, library preparation, enrichment pooling, sequencing, and variant calling with deliverables in HapMap format; and Twist FlexPrep and enrichment panel design and printing for 120 samples. USDA leads community engagement and provides samples and metadata; Twist Bioscience designs, validates, and supplies custom capture panels along with discounted FlexPrep UltraHigh-Throughput Library Prep Kits; HudsonAlpha calibrates Sorghum-specific laboratory and sequencing workflows, performs DNA extraction using plant-optimized methods to overcome polysaccharide and polyphenolic content challenges, prepares sequencing libraries, executes target enrichment and sequencing on the Illumina NovaSeq X platform with paired-end 150 bp reads, and conducts bioinformatic processing through the Khufu platform. Deliverables include demultiplexed FASTQ files via secure transfer, HapMap files with imputed genotypes via electronic delivery, and a quality control summary report in PDF format.
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| File | Type | Posted |
|---|---|---|
| Solicitation_1232SA26Q1231.pdf |
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Statement of Work (SOW)
USDA / Twist Bioscience / HudsonAlpha Sorghum Genomics Project — Community-Driven Target Design and High-Throughput Genotyping via Custom Hybrid Capture
Participating Organizations:
● USDA (Doreen Ware Lab): Community coordination, target specification, and sample provision.
● Twist Bioscience: Probe design, printing, validation, and provision of FlexPrep Ultra- High-Throughput Library Prep Kits at a reduced cost.
● HudsonAlpha Institute for Biotechnology: Experimental execution including calibration of all plant-specific protocols for Sorghum seeds and optimization of sequencing methods.
1. Project Overview
This collaborative project combines community coordination by USDA, probe manufacturing by Twist Bioscience, and HudsonAlpha’s Sorghum-optimized sequencing and analysis workflows.
It will deliver high-quality genotype data supporting genetic diversity and breeding objectives.
2. Scope of Work Khufu – Hybrid capture genotyping 120 quantity - per 96-well plate. Includes DNA extraction, Library prep, enrichment pooling, Sequencing and variant calling at the sample volume and panel size indicated in the quote header. Deliverables are genotype calls and imputation in hapmap format
Twist flex prep and enrichment panel 120 quantity- flex prep kits and panel design and printing for the sample volume and panel size indicated at the quote header
2.1 Community-Driven Probe Design (USDA and Twist Bioscience)
● USDA collects community input to define target genes, variants, and loci of interest.
● Twist Bioscience designs, refines, and validates the hybrid-capture probe panel to match these specifications.
● HudsonAlpha receives the validated panel and optimizes capture conditions for the Sorghum genome.
2.2 DNA Extraction (HudsonAlpha)
● HudsonAlpha extracts DNA from Sorghum seeds using calibrated, plant-optimized methods developed to overcome high polysaccharide and polyphenolic content. The number of seeds representing each sample would be optimized to the project needs taking into account sample genetic variability with technical constraints.
2.3 Library Preparation (HudsonAlpha)
● HudsonAlpha prepares sequencing libraries using the Twist FlexPrep UHT Library Prep Kit. Library prep parameters are adjusted and validated for Sorghum DNA characteristics.
2.4 Target Enrichment and Sequencing (HudsonAlpha)
● Captured libraries are sequenced on the Illumina NovaSeq X platform with paired-end 150 bp reads using HudsonAlpha’s optimized sequencing conditions for plant genomes.
Coverage is optimized to the unique on/ off target enrichment of the panel, cost, scale and quality of results.
2.5 Bioinformatics Processing (HudsonAlpha)
● Data are processed through the Khufu bioinformatics platform to generate FASTQ and HapMap variant data using pipelines tuned for Sorghum. The deliverables would be optimized to fit the community needs represented by USDA.
3. Deliverables Deliverable Description Format / Delivery
Raw sequence data
Demultiplexed FASTQ files Secure transfer
Variant data HapMap files with imputed genotypes Electronic delivery
Summary report Quality control metrics and project overview PDF
4. Responsibilities
● USDA: Leads community engagement, defines genomic targets, provides samples and metadata.
● Twist Bioscience: Designs and verifies custom capture panels; supplies discounted FlexPrep kits.
● HudsonAlpha: Calibrates all Sorghum-specific lab and sequencing workflows; performs sequencing and bioinformatic analysis.
| Statement of Work (SOW) |
| USDA / Twist Bioscience / HudsonAlpha Sorghum Genomics Project — Community-Driven Target Design and High-Throughput Genotyping via Custom Hybrid Capture |
| 1. Project Overview |
| 2. Scope of Work |
| 3. Deliverables |
| 4. Responsibilities |
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