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. 2015 Mar 15;16:27. doi: 10.1186/s12863-015-0184-1

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© Kember et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Flowchart outlining the quality control and analysis pipeline of this study. SNP data from the control and Old Order Amish populations was used to call CNVs using the PennCNV program. The pedigree structure in the Amish allowed family based calls to be made, and the CNV frequency in the control data allowed us to determine whether the Amish CNV calls were common, rare, or exclusive to the Amish population. We sought to determine CNVs in bipolar individuals, burden in individuals, and CNVs in disease loci. In addition, we utilized the whole genome sequence data to find CNVs and SNPs within the same gene in the same individual.