Backcross-to-Congenic Calculator

Backcross-to-Congenic Basics

Move a single gene, transgene, or chromosomal region from a donor strain onto a recipient strain background, *without* dragging along thousands of donor SNPs that could confound your phenotype.

1. Cross donor $\times$ recipient → F1 (50% recipient genome, all heterozygous at the target locus) 2. Backcross F1 carrier $\times$ recipient → BC1 (75% recipient on average) 3. Genotype the offspring, pick carriers, repeat 4. After ~10 backcrosses, the donor genome outside the target locus is <0.1% 5. Intercross two carriers to get a homozygous congenic stock

recipient proportion = 1 − (donor at start) $\times$ (0.5)^N. With F1 starting at 50% recipient, donor halves every generation. Geometric, not linear.

A "knock-out on a 129 background" is a different mouse than the same knock-out on a B6 background. Behavioral, immunological, and metabolic phenotypes can flip sign on a different background. If you want your paper to replicate, your KO needs to be on the background everyone else uses — usually B6.

Speed Congenic with Marker-Assisted Selection

Conventional backcrossing wastes time because you pick carriers blind. Even after 5 generations, the carrier you bred from might happen to have an unlucky 35% donor background — pulling the average back up.

Genotype 96-384 SNP markers spaced across the genome on every potential breeder. Pick the carrier whose *background* is most recipient — the one that "won" the random shuffle that generation. Markel et al. (1997) showed this gets you N10-equivalent in 4-5 generations instead of 10.

• SNP panel per breeder per generation: ~$50-100
• Per generation, 10-20 breeders typed: $500-2000
• Total speed congenic: $3000-10000
• Saved per-diem (5 generations × 11 weeks × ~$1.50/cage/day $\times$ ~10 cages): ~$5,000
• Saved postdoc time: 1+ year of waiting → priceless

If your target locus is on a chromosome with already-low recipient density, MAS gains less. If the line is a permanent backbone strain (not a one-shot project), the time savings dominate.