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利用亲属关系划分法（PREPARE）从现存群体重建历史谱系。

Historical pedigree reconstruction from extant populations using PArtitioning of RElatives (PREPARE).

作者信息

Shem-Tov Doron, Halperin Eran

机构信息

The Balvatnic School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

The Balvatnic School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel; International Computer Science Institute, Berkeley, California, United States of America; Molecular Microbiology and Biotechnology Department, Tel-Aviv University, Tel-Aviv, Israel.

出版信息

PLoS Comput Biol. 2014 Jun 19;10(6):e1003610. doi: 10.1371/journal.pcbi.1003610. eCollection 2014 Jun.

DOI:10.1371/journal.pcbi.1003610
PMID:24945698
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4063675/
Abstract

Recent technological improvements in the field of genetic data extraction give rise to the possibility of reconstructing the historical pedigrees of entire populations from the genotypes of individuals living today. Current methods are still not practical for real data scenarios as they have limited accuracy and assume unrealistic assumptions of monogamy and synchronized generations. In order to address these issues, we develop a new method for pedigree reconstruction, [Formula: see text], which is based on formulations of the pedigree reconstruction problem as variants of graph coloring. The new formulation allows us to consider features that were overlooked by previous methods, resulting in a reconstruction of up to 5 generations back in time, with an order of magnitude improvement of false-negatives rates over the state of the art, while keeping a lower level of false positive rates. We demonstrate the accuracy of [Formula: see text] compared to previous approaches using simulation studies over a range of population sizes, including inbred and outbred populations, monogamous and polygamous mating patterns, as well as synchronous and asynchronous mating.

摘要

遗传数据提取领域最近的技术进步使得从当今在世个体的基因型重建整个人口的历史谱系成为可能。当前的方法在实际数据场景中仍然不实用，因为它们的准确性有限，并且假设了不切实际的一夫一妻制和同步世代的假设。为了解决这些问题，我们开发了一种新的谱系重建方法，[公式：见正文]，该方法基于将谱系重建问题表述为图着色的变体。新的表述使我们能够考虑先前方法忽略的特征，从而能够重建多达五代的历史，与现有技术相比，假阴性率有一个数量级的提高，同时保持较低的假阳性率水平。我们通过在一系列种群规模上进行模拟研究，包括近交和远交种群、一夫一妻制和一夫多妻制交配模式以及同步和异步交配，证明了[公式：见正文]与先前方法相比的准确性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/de7809ee9d5c/pcbi.1003610.g014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/a14371188627/pcbi.1003610.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/7108cbcfc3f9/pcbi.1003610.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/f940f101671c/pcbi.1003610.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/0c93d07a6c8a/pcbi.1003610.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/8c55b4b83513/pcbi.1003610.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/743107e286ea/pcbi.1003610.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/54cf3cb60e16/pcbi.1003610.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/b54d37d42420/pcbi.1003610.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/28076c215c7f/pcbi.1003610.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/6a53b522019a/pcbi.1003610.g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/9aa64e67ba49/pcbi.1003610.g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/eeced1ceb11a/pcbi.1003610.g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/bab5f7da1609/pcbi.1003610.g013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/de7809ee9d5c/pcbi.1003610.g014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/a14371188627/pcbi.1003610.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/7108cbcfc3f9/pcbi.1003610.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/f940f101671c/pcbi.1003610.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/0c93d07a6c8a/pcbi.1003610.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/8c55b4b83513/pcbi.1003610.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/743107e286ea/pcbi.1003610.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/54cf3cb60e16/pcbi.1003610.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/b54d37d42420/pcbi.1003610.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/28076c215c7f/pcbi.1003610.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/6a53b522019a/pcbi.1003610.g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/9aa64e67ba49/pcbi.1003610.g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/eeced1ceb11a/pcbi.1003610.g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/bab5f7da1609/pcbi.1003610.g013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/35e6/4063675/de7809ee9d5c/pcbi.1003610.g014.jpg

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4
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5
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8
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9
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