Lab capability build
Assay Internalization Plan
Crop focus · Corn & soy Discovery · Illumina chip array Production · KASP Main partner · LGC Biosearch Guided by · External consultant Horizon · 44–72 weeks

Own the path from chip genotypes to locked KASP assays

A phased plan for a wet-lab team that already runs KASP production, but has not ordered assays or owned upstream SNP selection. The chip array wet lab can stay outsourced. LGC Biosearch carries the assay design and validation load early, then ownership moves to the team one step at a time: ordering → LGC-validated assays → in-house validation → SNP selection → primer design.

Context

Until now, the upstream steps (chip analysis, SNP selection, assay design and validation) were handled outside the lab, and primers arrived ready for production. Clients still need variety purity and variety identification projects. The lab now wants to own more of that chain, starting from provider-generated chip data, without a single big-bang cutover.

An external consultant sets the learning and practice path, and hands over simple tools (for example, chip array data → SNP shortlist). LGC Biosearch provides KASP assay design and validation services. The lab team runs the wet lab, makes the pass/fail calls, and delivers to clients. See who does what →

End state

When a client requests variety ID or purity work, the lab can:

  1. Send DNA/leaf to a chip service provider — the array run can stay external
  2. Receive the genotype matrix / VCF
  3. Select a discriminating SNP panel with internal tools + checklist
  4. Design or order KASP assays
  5. Validate assays in-house
  6. Lock primers and deliver production genotyping
Phase roadmap
Phase 0 · Learn to orderPhase 1 · KOD via LGCPhase 2 · KBD + in-house validation Phase 3 · Chip data → SNP shortlistPhase 4 · Primer designPhase 5 · Steady state

Tip: click a phase box to jump to its tab. On a phone, scroll the chart sideways.

LGC Biosearch: main service provider & transition guardrails

LGC supplies KASP chemistry and assay design, and the lab already works with KASP, so LGC is the natural main provider. Two of its services define the first three phases:

Phase 1

KOD · KASP on Demand

  • LGC designs, validates and optimises the assay in its own lab
  • Needs at least 22 and up to 94 of the lab's DNA samples (non-human species)
  • LGC sends the genotyping results for the lab's confirmation before shipping the assay mix
  • LGC states a working assay is guaranteed, or no charge
  • Higher cost per assay, lowest risk. Used for learning and for hard or high-stakes SNPs.
Phases 2–3

KBD · KASP by Design

  • LGC designs only (Kraken software); no wet-lab validation before delivery
  • The lab validates the assay itself, on its own samples and instrument
  • Lower cost per assay, so it becomes the default once the lab can judge results
  • Failed assays go back to LGC for redesign, or up to KOD
Why LGC is also the transition guardrail
  • Safety net: in KOD, someone else carries the risk of a non-working assay while the team is still learning.
  • Ready-made pass/fail standard: LGC validates against stated criteria (no-template controls negative, distinct clusters, call rate above 90%, minor allele frequency above 2% unless the allele is known to be rare). The team adopts these as its first written gate.
  • Escalation path: if an in-house design or validation fails, the SNP goes back to LGC, so client projects do not stall.
  • One step at a time: LGC leads in Phase 1, shares in Phases 2–3, then handles only hard SNPs and overflow in Phases 4–5.
  • Final contingency: the Germany sister lab stays available as a last resort if a problem cannot be solved by the lab, LGC and the external consultant.

Service terms and sample requirements are from LGC's public pages (KOD, KBD, assay design). Confirm current terms in the LGC quote.

End-state process and when the lab takes each step
Client requestChip array runGenotype dataSNP shortlist Assay designValidationLock primersProduction KASP
Three parties

External consultant

Sets the learning path, writes templates, hands over simple tools, reviews at phase gates.

LGC Biosearch

Designs and validates KASP assays (KOD), designs only (KBD), supplies assay mix and support.

Lab team

Runs the wet lab, makes pass/fail decisions, owns the client delivery and the SOPs.

Roadmap at a glance
PhaseFocusLGC serviceDurationOwnership shift
0 · Learn to orderOrder + run known assaysForms, quotes, assay mix4–6 wkOrdering
1 · KODSNP list → LGC designs + validates → deliverKOD6–8 wkRequest to production
2 · KBD + in-house validationLGC designs, lab validates and locksKBD (+ KOD for exceptions)6–10 wkWet QC judgment
3 · Chip → SNP shortlistInternal marker selectionKBD8–12 wkAnalytics
4 · Primer designEasy SNPs in-houseHard SNPs only8–12 wkDesign
5 · Steady stateRoutine service ownershipOverflow12–24 wkFull process
Jump to a phase

Tools from the external consultant

  • Assay order packager (Phase 1) — SNP table → LGC submission sheet + assay inventory IDs
  • Validation scorecard (Phase 2) — plate results → pass/fail + failure codes
  • Chip SNP selector (Phase 3) — genotypes + replicates → ranked discriminating panel + QC report
  • Flank + Primer3 designer (Phase 4) — reference flanks, nearby-SNP mask, order export

Costs are planning ranges in USD and will vary by array type, sample volume, and vendor quotes. External consultant lines are a planning placeholder: $150/hr × 2 hr/week = $300/week, so each phase's consultant cost is its duration in weeks × $300 (about $13.2–21.6k across all phases). Replace with the agreed engagement terms. Prefer buying certainty early (KOD, chip provider, consultant review) while the team builds judgment.