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蓝海人类学在线 Ryan WEI's Forum of Anthropology

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常染色体遗传标记TMRCA估算方法汇总ing

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发表于 2013-5-17 13:32 | 显示全部楼层 |阅读模式
最近发现疾病潜能相关的基因越来越好玩,但可惜大多数研究者的目的在于医学相关,对于历史演化相关的人类学方向内容很少关注,也极少计算TMRCA,不过因为hapmap等数据库在,相当一部分基因的种系差异还是很明显,具有人类学分析的潜在价值。我在琢磨是否可以根据已公布的数据,选取通用算法,自己算一下。汇集文献报道的相关算法信息。
比如最近关注乳腺癌相关基因,
BRCA1
5382insC p.s.朱莉是不是因为这个基因把乳腺切了?


On the origin and diffusion of BRCA1 c.5266dupC
(5382insC) in European populations



Age estimates using single markers method
In an attempt to corroborate age estimate results obtained using the maximum
likelihood method described above, we also estimated the time since MCRA
using four markers (D17S1299, D17S1801, D17S951 and D17S1861) analyzed
individually in three populations (Czech/Slovak, Polish and Danes) where we
had the largest number of families with known phase for the markers linked to
the mutation. The single marker method was implemented as described
previously in Greenwood et al.11 The Labuda correction for population-growth
rate was assumed to be 1.5 and applied as previously described. Because this
method does not consider marker mutations, which likely have a significant
role in a region where there is documented recombination suppression such as
BRCA1,9 this method will not be as well-suited to our dataset as the maximum
likelihood method, but can nevertheless serve to test the robustness of our
original estimates.





11、Greenwood CM, Sun S, Veenstra J et al: How old is this mutation? – a study of three Ashkenazi Jewish founder mutations.



发表于 2013-6-6 09:49 | 显示全部楼层
想不到Bioconductor已经发展到2.12版了,了不起。请教老永有没有使用过这种工具啊? 如用过,效果如何?
 楼主| 发表于 2013-6-6 10:58 | 显示全部楼层
这段事情超多,还没研究呢,不过,我最近的确觉得医学、潜能相关的snp大有意思,基本极少从人类学角度聊,可惜了。
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