Inference of kinship coefficients from Korean SNP genotyping data
2
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals.
Abstract
The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals.
참고문헌 (16)
- Budowle, B., "Forensically relevant SNP classes", Biotechniques, 44, pp.603~610 (2008)
- Wheeler, D. A., "The complete genome of an individual by massively parallel DNA sequencing", Nature, 452, pp.872~876 (2008)
- Ginsburg, G. S., "Personalized medicine: revolutionizing drug discovery and patient care", Trends. Biotechnol, 19, pp.491~496 (2001)
- Kim, S., "SNP genotyping: technologies and biomedical applications", Annu. Rev. Biomed. Eng, 9, pp.289~320 (2007)
- Barrett, J. C., "Evaluating coverage of genome-wide association studies", Nat. Genet, 38, pp.659~662 (2006)
- Sahana, G., "Comparison of association mapping methods in a complex pedigreed population", Genet. Epidemiol, 34, pp.455~462 (2010)
- Botstein, D., "Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease", Nat. Genet, 33, pp.228~237 (2003)
- Kirkpatrick, B., "Haplotype inference in complex pedigrees", J. Comput. Biol, 17, pp.269~280 (2010)
- Lin, S., "Comparisons of methods for linkage analysis and haplotype reconstruction using extended pedigree data", BMC. Genet, 6(Suppl 1), pp.S76~ (2005)
- Takahata, N., "Polymorphism and balancing selection at major histocompatibility complex loci", Genetics, 130, pp.925~938 (1992)
- Dupanloup, I., "Inferring admixture proportions from molecular data: extension to any number of parental populations", Mol. Biol. Evol, 18, pp.672~675 (2001)
- Seung Hwan Paik, "Linkage and association scan for tanning ability in an isolated Mongolian population", BMB Reports, 44(11), pp.741~746 (2011), 생화학분자생물학회
- Gao, X., "Human population structure detection via multilocus genotype clustering", BMC Genet, 8, pp.34~ (2007)
- Dankyu Yoon, "Replication of genome-wide association studies on asthma and allergic diseases in Korean adult population", BMB Reports, 45(5), pp.305~310 (2012), 생화학분자생물학회[DOI]
- Balani, S. K., "Strategy of utilizing in vitro and in vivo ADME tools for lead optimization and drug candidate selection", Curr. Top. Med. Chem, 5, pp.1033~1038 (2005)
- Day, I. N., "dbSNP in the detail and copy number complexities", Hum. Mutat, 31, pp.2~4 (2010)