Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

Distributed Grid Experiences in CMS DC04

In March-April 2004 the CMS experiment undertook a Data Challenge (DC04). During the previous 8 months CMS undertook a large simulated event production. The goal of the challenge was to run CMS reconstruction for sustained period at 25Hz in put rate, distribute the data to the CMS Tier-1 centers and analyze them at remote sites. Grid environments developed in Europe by the LHC Computing Grid (LCG) and in the US with Grid2003 were utilized to complete the aspects of the challenge. A description of the experiences, successes and lessons learned from both experiences with grid infrastructure is presented

Role of Tier-0, Tier-1 and Tier-2 Regional Centers in CMS DC04

The CMS 2004 Data Challenge (DC04) was devised to test several key aspects of the CMS Computing Model in three ways: by trying to sustain a 25 Hz reconstruction rate at the Tier-0; by distributing the reconstructed data to six Tier-1 Regional Centers (CNAF in Italy, FNAL in US, GridKA in Germany, IN2P3 in France, PIC in Spain, RAL in UK) and handling catalogue issues; by redistributing data to Tier-2 centers for analysis. Simulated events, up to the digitization step, were produced prior to the DC as input for the reconstruction in the Pre-Challenge Production (PCP04). In this paper, the model of the Tier-0 implementation used in DC04 is described, as well as the experience gained in using the newly developed data distribution management layer, which allowed CMS to successfully direct the distribution of data from Tier-0 to Tier-1 sites by loosely integrating a number of available Grid c omponents. While developing and testing this system, CMS explored the overall functionality and limits of each component, in any of the different implementations which were deployed within DC04. The role of Tier-1's is presented and discussed, from the import of reconstructed data from Tier-0, to the archiving on to the local mass storage system (MSS) and the data distribution management to Tier-2's for analysis. Participating Tier-1's differed in available resources, set-up and configuration: a critical evaluation of the results and performances achieved adopting different strategies in the organization and management of each Tier-1 center to support CMS DC04 is presented

Bunched beam test of the CMS drift tubes local muon trigger

The 40 MHz bunched muon beam set up at CERN was used in May 2003 to make a full test of the drift tubes local muon trigger. The main goal of the test was to prove that the integration of the various devices located on a muon chamber was adequately done both on the hardware and software side of the system. Furthermore the test provided complete information about the general performance of the trigger algorithms in terms of efficiency and noise. Data were collected with the default configuration of the trigger devices and with several alternative configurations at various angles of incidence of the beam. Tests on noise suppression and di-muon trigger capability were performed