biostudies-literatureUnknownChen DNIDA NIH HHSNIH HHSAffordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping-by-sequencing and more recently generated by low-coverage whole-genome-bioRxiv : the preprint server for biology2024.07.17.603984https://www.ebi.ac.uk/biostudies/studies/S-EPMC11275765biostudies-literatureA Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations.PMC11275765P50 DA037844S10 OD026929Okamoto FJohnson BBCohen KSanches TMPolesskaya OZiegler KSChen DLin BPeng BChitre ASCheng RPalmer AANguyen KHfalseA Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations.Affordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping-by-sequencing and more recently generated by low-coverage whole-genome-2024-01-01T00:00:00Z2024 Jul2026-04-07T15:02:04.741Z2025-04-03T23:55:49.499ZS-EPMC112757653907140510.1101/2024.07.17.603984