Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals
Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (S...
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BioMed Central
2014-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-12-165.pdf |
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| author | Kichan Lee Seonggyun Han Yeonjeong Tark Sangsoo Kim |
| author_facet | Kichan Lee Seonggyun Han Yeonjeong Tark Sangsoo Kim |
| author_sort | Kichan Lee |
| collection | DOAJ |
| description | Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available. |
| format | Article |
| id | doaj-art-9adabcea65824dacb16b04c6eb15cfbd |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2014-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-9adabcea65824dacb16b04c6eb15cfbd2025-02-02T01:09:39ZengBioMed CentralGenomics & Informatics1598-866X2234-07422014-12-0112416517010.5808/GI.2014.12.4.165101Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean IndividualsKichan Lee0Seonggyun Han1Yeonjeong Tark2Sangsoo Kim3Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea.Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.http://genominfo.org/upload/pdf/gni-12-165.pdfgenome-wide association studyhaplotypesKoreaNGSphasingsingle-nucleotide polymorphism |
| spellingShingle | Kichan Lee Seonggyun Han Yeonjeong Tark Sangsoo Kim Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals Genomics & Informatics genome-wide association study haplotypes Korea NGS phasing single-nucleotide polymorphism |
| title | Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals |
| title_full | Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals |
| title_fullStr | Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals |
| title_full_unstemmed | Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals |
| title_short | Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals |
| title_sort | short reads phasing to construct haplotypes in genomic regions that are associated with body mass index in korean individuals |
| topic | genome-wide association study haplotypes Korea NGS phasing single-nucleotide polymorphism |
| url | http://genominfo.org/upload/pdf/gni-12-165.pdf |
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