PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County

BMC Medical Genetics

Research Article

Toni I Pollin¹  Jeffrey R O'Connell²  Woei-Jyh Lee³  Richa Agarwala³  Alejandro A Schäffer³ 

[1] Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, 660 W. Redwood Street, 21201, Baltimore, Maryland, USA;Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, 660 W. Redwood Street, 21201, Baltimore, Maryland, USA;Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Avenue, 20705, Beltsville, Maryland, USA;National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, Maryland, USA;

关键词: Kinship Coefficient;    Large Pedigree;    Pedigree Structure;    Utility Program;    Nemaline Myopathy;   

DOI  :  10.1186/1471-2350-11-68

 received in 2009-12-04, accepted in 2010-05-02,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundBecause they are a closed founder population, the Old Order Amish (OOA) of Lancaster County have been the subject of many medical genetics studies. We constructed four versions of Anabaptist Genealogy Database (AGDB) using three sources of genealogies and multiple updates. In addition, we developed PedHunter, a suite of query software that can solve pedigree-related problems automatically and systematically.MethodsWe report on how we have used new features in PedHunter to quantify the number and expected genetic contribution of founders to the OOA. The queries and utility of PedHunter programs are illustrated by examples using AGDB in this paper. For example, we calculated the number of founders expected to be contributing genetic material to the present-day living OOA and estimated the mean relative founder representation for each founder. New features in PedHunter also include pedigree trimming and pedigree renumbering, which should prove useful for studying large pedigrees.ResultsWith PedHunter version 2.0 querying AGDB version 4.0, we identified 34,160 presumed living OOA individuals and connected them into a 14-generation pedigree descending from 554 founders (332 females and 222 males) after trimming. From the analysis of cumulative mean relative founder representation, 128 founders (78 females and 50 males) accounted for over 95% of the mean relative founder contribution among living OOA descendants.Discussion/ConclusionsThe OOA are a closed founder population in which a modest number of founders account for the genetic variation present in the current OOA population. Improvements to the PedHunter software will be useful in future studies of both the OOA and other populations with large and computerized genealogies.

【 授权许可】

Unknown   
© Lee et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. 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.