Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition
Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype bloc...
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BioMed Central
2016-12-01
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| Series: | Genomics & Informatics |
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| author | Sun Ah Kim Yun Joo Yoo |
| author_facet | Sun Ah Kim Yun Joo Yoo |
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| description | Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP) markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study. |
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| institution | Kabale University |
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| publishDate | 2016-12-01 |
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| spelling | doaj-art-84c2895f192744ebb7ff396cc879bb572025-02-03T01:40:35ZengBioMed CentralGenomics & Informatics1598-866X2234-07422016-12-0114419620410.5808/GI.2016.14.4.196174Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block PartitionSun Ah Kim0Yun Joo Yoo1Department of Mathematics Education, Seoul National University, Seoul 08826, Korea.Department of Mathematics Education, Seoul National University, Seoul 08826, Korea.Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP) markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study.http://genominfo.org/upload/pdf/gni-14-196.pdf1,000 Genomes Projecthaplotypeshaplotype blocklinkage disequilibrium |
| spellingShingle | Sun Ah Kim Yun Joo Yoo Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition Genomics & Informatics 1,000 Genomes Project haplotypes haplotype block linkage disequilibrium |
| title | Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition |
| title_full | Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition |
| title_fullStr | Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition |
| title_full_unstemmed | Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition |
| title_short | Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition |
| title_sort | effects of single nucleotide polymorphism marker density on haplotype block partition |
| topic | 1,000 Genomes Project haplotypes haplotype block linkage disequilibrium |
| url | http://genominfo.org/upload/pdf/gni-14-196.pdf |
| work_keys_str_mv | AT sunahkim effectsofsinglenucleotidepolymorphismmarkerdensityonhaplotypeblockpartition AT yunjooyoo effectsofsinglenucleotidepolymorphismmarkerdensityonhaplotypeblockpartition |