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Updated: Jan 8, 2026
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Development and validation of a dual-purpose 60K single nucleotide polymorphism chip for simultaneous genotyping of
Jinhyeong Kim1, Eunjin Cho2, Minjun Kim3
1Department of Animal Science, Chungnam National University, Daejeon, Korea.
Objective:
Chickens and ducks represent the most important poultry species within the livestock industry. However, the availability of single nucleotide polymorphism (SNP) chips for these species is limited, and development of separate chips for each species requires considerable expense. To address this limitation, we developed the first poultry SNP chip applicable to both species simultaneously. The 60K SNP chip comprises 30,816 SNPs for chickens and 35,209 SNPs for ducks. The performance of the chip was evaluated using non-pooled datasets (chicken only and duck only) and a pooled dataset combining chicken and duck DNA to verify that genotyping accuracy was maintained without crossspecies interference.
Methods:
DNA was extracted from 28 Korean native chickens and 28 Korean native ducks. Genotyping was performed using the Illumina platform, employing chicken-only, duck-only, and pooled chicken-duck SNP panels. Genotype accuracy and concordance were evaluated with PLINK. Sample and SNP quality were assessed in accordance with the Illumina genotyping protocol. Principal component analysis (PCA) was conducted to evaluate and compare the chicken-duck pooled dataset with the non-pooled datasets.
Results:
The mean genotype concordance of non-pooled (chicken only and duck only) datasets exceeded 99%, while concordance between non-pooled and chicken-duck pooled datasets surpassed 97.8%. All datasets satisfied quality thresholds for call rate, GenCall score, 10% GenCall score, and cluster separation. PCA revealed consistent clustering patterns, with no significant differences observed between non-pooled and pooled datasets.
Conclusion:
The first, at the best of our knowledge, poultry SNP chip incorporating chicken-duck pooled samples, has been successfully developed and validated. This chip provides reliable genotyping performance for both species and presents a cost-effective option for large-scale SNP chip development in the livestock industry.
