A Genetic Database for Anthropology

在过去的十年里，人类基因组上可用的数据量几乎呈爆炸式增长。关于人类基因组的数据可以帮助我们了解人类进化史，包括我们作为一个物种与其他类人猿的关系，以及反映人类历史的更近的人类群体之间的关系。从我们对人类基因组的了解中获得的信息也与许多社会科学有关。然而，几乎没有可用的基础设施来帮助在人类基因组数据和来自社会科学的数据之间提供接口。与历史学、历史人口学、语言学、医学人类学、法医人类学和种族研究等相关的一个领域是存在于人类群体中的基因频率变异。当前群体中的基因频率变异是这些群体历史上所有因素的净遗传效应：相对内婚制与外婚制、过去和现在的种群规模、相对内婚制的时间长度、起源、选择等。目前，在大部分人类基因组中检测到的现代DNA多态的基因频率变异信息没有集中的位置。与这种资源最接近的是ALFRED的当前实现，即可在网络上访问的等位基因频率数据库http://alfred.med.yale.edu/alfred/index.asp.该项目将进一步发展阿尔弗雷德，使其成为人类学遗传学领域和上述其他社会科学领域的资源。该数据库将包含多个遗传基因座(包括功能基因和匿名基因座)和多个群体的基因频率数据。每个频率都将详细描述/定义所使用的方案所研究的多态位点以及所研究的特定人群的特定样本。DNA序列一级多态的分子定义将与分子数据库和种群描述(名称、语言、地点等)相联系。发展将涉及三个方面：有计划地持续积累来自当前文献和过去15年左右的基因频率数据；加强设计和实施(硬件和软件)，以便能够对因特网上的查询作出有力和快速的反应；在分子方面实现与相关人类基因组学数据库的互连，在人口/社会科学方面实现与人种学和其他数据库的互连。增强后的数据库将提供许多功能。它将成为本科生和研究生的教育资源。它将是一个跨学科的研究资源，提供参考基因频率，用于与新数据进行比较。它将推动不同实验室未来的数据收集工作集中在那些早期研究表明将提供关于特定研究问题的最佳信息的遗传标记上。它将通过特定的社会/文化变量，如语言、地理位置、人口规模等，提供进入遗传学/基因组学世界的入口。相反，它将提供与人类学遗传学家需要的有关人口的民族学和历史数据的链接，以解释他们收集的基因频率数据。作为基因组学数据库和相关社会科学之间的桥梁，该数据库将为现代研究日益跨学科的性质提供基础设施。

The past decade has seen a virtual explosion in the amount of data available on the human genome. Data on the human genome can be used to help us understand human evolutionary history, including both our relationship as a species to other great apes and much more recent relationships among human populations reflecting their histories. Information derived from our knowledge of the human genome is also relevant to many of the social sciences. Yet, there is little infrastructure available to help provide an interface between data on the human genome and data derived from the social sciences. One area of particular relevance to history, historical demography, linguistics, medical anthropology, forensic anthropology, and ethnic studies, among others, is the gene frequency variation that exists among human populations. Gene frequency variation among current populations is the net genetic effect of all of the factors in the history of those populations: relative endogamy versus exogamy, past and present population sizes, length of time relatively endogamous, origins, selection, etc.Currently there is no centralized location for information on gene frequency variation for the modern DNA polymorphisms detected in the bulk of the human genome. The closest approximation to such a resource is the current implementation of ALFRED, the web-accessible ALlele FREquency Database http://alfred.med.yale.edu/alfred/index.asp. This project will further develop ALFRED to serve as a resource for the anthropological genetics field and the other social science areas noted above. The database will contain gene frequency data for multiple genetic loci (both functional genes and anonymous loci) and multiple populations. Each frequency will have detailed descriptions/definitions of both the polymorphic site studied with protocols used as well as the specific sample of the specific population studied. The molecular definition of the polymorphism at the DNA sequence level will be linked to the molecular databases and the description of the population (name, language, location, etc.) will be linked to at least one ethnographic database.Development will involve three aspects: curated on-going accumulation of gene frequency data from the current literature and that of the past 15 or so years, enhancement of the design and implementation (hardware and software) to allow robust and rapid response to queries over the internet, and implementation of interconnections to relevant human genomics databases on the molecular side and to ethnographic and other databases on the population/social science side. The enhanced database will serve many functions. It will be an educational resource at both the undergraduate and graduate levels. It will be an inter-disciplinary research resource providing reference gene frequencies for comparison with new data. It will provide impetus to focus future data collection efforts in diverse labs on those genetic markers that early studies suggest will provide the best information on specific research questions. It will provide entree to the genetics/genomics world via specific social/cultural variables such as language, geographic location, population size, etc. Conversely, it will provide links to relevant ethnologic and historical data on populations that anthropological geneticists need in order to interpret the gene frequency data they collect. As a bridge between the genomics databases and the relevant social sciences the database will provide infrastructure to the increasingly interdisciplinary nature of modern research.