| Item type |
文献 / Documents(1) |
| 公開日 |
2023-08-22 |
| アクセス権 |
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アクセス権 |
open access |
| 資源タイプ |
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資源タイプ識別子 |
http://purl.org/coar/resource_type/c_6501 |
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資源タイプ |
journal article |
| 出版社版DOI |
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識別子タイプ |
DOI |
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関連識別子 |
https://doi.org/10.1186/1471-2105-8-200 |
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言語 |
ja |
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関連名称 |
10.1186/1471-2105-8-200 |
| 出版タイプ |
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|
出版タイプ |
VoR |
|
出版タイプResource |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| タイトル |
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|
タイトル |
Evaluation of sample size effect on the identification of haplotype blocks |
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言語 |
en |
| 著者 |
オサベ, ダイ
棚橋, 俊仁
ノムラ, キョウコ
シノハラ, シュウイチ
ナカムラ, ナオト
吉川, 敏一
塩田, 洋
Keshavarz, Parvaneh
長﨑, 裕加
クニカ, キヨシ
森谷, 眞紀
井上, 寛
板倉, 光夫
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| 抄録 |
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内容記述タイプ |
Abstract |
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内容記述 |
Background: Genome-wide maps of linkage disequilibrium (LD) and haplotypes have been created for different populations. Substantial sharing of the boundaries and haplotypes among populations was observed, but haplotype variations have also been reported across populations. Conflicting observations on the extent and distribution of haplotypes require careful examination. The mechanisms that shape haplotypes have not been fully explored, although the effect of sample size has been implicated. We present a close examination of the effect of sample size on haplotype blocks using an original computational simulation.
Results: A region spanning 19.31 Mb on chromosome 20q was genotyped for 1,147 SNPs in 725 Japanese subjects. One region of 445 kb exhibiting a single strong LD value (average |D'|; 0.94) was selected for the analysis of sample size effect on haplotype structure. Three different block definitions (recombination-based, LD-based, and diversity-based) were exploited to create simulations for block identification with θ value from real genotyping data. As a result, it was quite difficult to estimate a haplotype block for data with less than 200 samples. Attainment of a reliable haplotype structure with 50 samples was not possible, although the simulation was repeated 10,000 times.
Conclusion: These analyses underscored the difficulties of estimating haplotype blocks. To acquire a reliable result, it would be necessary to increase sample size more than 725 and to repeat the simulation 3,000 times. Even in one genomic region showing a high LD value, the haplotype block might be fragile. We emphasize the importance of applying careful confidence measures when using the estimated haplotype structure in biomedical research. |
|
言語 |
en |
| 書誌情報 |
en : BMC Bioinformatics
巻 8,
p. 200,
発行日 2007-06-14
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| 収録物ID |
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収録物識別子タイプ |
ISSN |
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収録物識別子 |
14712105 |
| 収録物ID |
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収録物識別子タイプ |
NCID |
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収録物識別子 |
AA12034719 |
| 出版者 |
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出版者 |
BioMed Central |
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言語 |
en |
| 出版者 |
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出版者 |
Springer Nature |
|
言語 |
en |
| 権利情報 |
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|
言語 |
en |
|
権利情報 |
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| EID |
|
|
識別子 |
398874 |
|
識別子タイプ |
URI |
| 言語 |
|
|
言語 |
eng |
bmcb_8_200.pdf (1.46 MB)
