Using GWAS Data to Identify Copy Number Variants Contributing to Common Complex Diseases

Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional variation. Consequently, most modern genome-wide association studies test CNVs along with SNPs, after inferring copy number status from the data generated by high-throughput genotyping platforms. Here we give an overview of CNV genomics in humans, highlighting patterns that inform methods for identifying CNVs. We describe how genotyping signals are used to identify CNVs and provide an overview of existing statistical models and methods used to infer location and carrier status from such data, especially the most commonly used methods exploring hybridization intensity. We compare the power of such methods with the alternative method of using tag SNPs to identify CNV carriers. As such methods are only powerful when applied to common CNVs, we describe two alternative approaches that can be informative for identifying rare CNVs contributing to disease risk. We focus particularly on methods identifying de novo CNVs and show that such methods can be more powerful than case-control designs. Finally we present some recommendations for identifying CNVs contributing to common complex disorders.Comment: Published in at http://dx.doi.org/10.1214/09-STS304 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Mixing Rates of Random Walks with Little Backtracking

Many regular graphs admit a natural partition of their edge set into cliques of the same order such that each vertex is contained in the same number of cliques. In this paper, we study the mixing rate of certain random walks on such graphs and we generalize previous results of Alon, Benjamini, Lubetzky and Sodin regarding the mixing rates of non-backtracking random walks on regular graphs.Comment: 31 pages; to appear in the CRM Proceedings Series, published by the American Mathematical Society as part of the Contemporary Mathematics Serie

Magnetic fields in Bok globules: Multi-wavelength polarimetry as tracer across large spatial scales

[abridged] The role of magnetic fields in the process of star formation is a matter of continuous debate. Clear observational proof of the general influence of magnetic fields on the early phase of cloud collapse is still pending. First results on Bok globules with simple structures indicate dominant magnetic fields across large spatial scales (Bertrang+2014). The aim of this study is to test the magnetic field influence across Bok globules with more complex density structures. We apply near-infrared polarimetry to trace the magnetic field structure on scales of 10^4-10^5au in selected Bok globules. The combination of these measurements with archival data in the optical and sub-mm wavelength range allows us to characterize the magnetic field on scales of 10^3-10^6au. We present polarimetric data in the near-infrared wavelength range for the three Bok globules CB34, CB56, and [OMK2002]18, combined with archival polarimetric data in the optical wavelength range for CB34 and CB56, and in the sub-millimeter wavelength range for CB34 and [OMK2002]18. We find a strong polarization signal (P>2%) in the near-infrared and strongly aligned polarization segments on large scales (10^4-10^6au) for all three globules. This indicates dominant magnetic fields across Bok globules with complex density structures. To reconcile our findings in globules, the lowest mass clouds known, and the results on intermediate (e.g., Taurus) and more massive (e.g., Orion) clouds, we postulate a mass dependent role of magnetic fields, whereby magnetic fields appear to be dominant on low and high mass but rather sub-dominant on intermediate mass clouds.Comment: 7 pages, 6 figures; Accepted by A&