The Human Genome Variation database of Genotype to Phenotype information (HGVbaseG2P) is a new central database for summary-level findings produced by human genetic association studies, both large and small. Such a database is needed so that researchers have an easy way to access all the available association study data relevant to their genes, genome regions or diseases of interest. Such a depository will allow true positive signals to be more readily distinguished from false positives (type I error) that fail to consistently replicate. In this paper we describe how HGVbaseG2P has been constructed, and how its data are gathered and organized. We present a range of user-friendly but powerful website tools for searching, browsing and visualizing G2P study findings. HGVbaseG2P is available at http://www.hgvbaseg2p.org.

BackgroundFor many analytical methods the efficiency of DNA amplification varies across the genome and between samples. The most affected genome regions tend to correlate with high C + G content, however this relationship is complex and does not explain why the direction and magnitude of effects varies considerably between samples.ResultsHere, we provide evidence that sequence elements that are particularly high in C + G content can remain annealed even when aggressive melting conditions are applied. In turn, this behavior creates broader ‘Thermodynamically Ultra-Fastened’ (TUF) regions characterized by incomplete denaturation of the two DNA strands, so reducing amplification efficiency throughout these domains.ConclusionsThis model provides a mechanistic explanation for why some genome regions are particularly difficult to amplify and assay in many procedures, and importantly it also explains inter-sample variability of this behavior. That is, DNA samples of varying quality will carry more or fewer nicks and breaks, and hence their intact TUF regions will have different lengths and so be differentially affected by this amplification suppression mechanism – with ‘higher’ quality DNAs being the most vulnerable. A major practical consequence of this is that inter-region and inter-sample variability can be largely overcome by employing routine fragmentation methods (e.g. sonication or restriction enzyme digestion) prior to sample amplification.

Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linkedAccess" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service.

'MegaPlex PCR' is a robust technology for highly multiplexed amplification of specific DNA sequences. It uses target-specific pairs of PCR primers that are physically separated by surface immobilization. Initial surface-based amplification cycles are then coupled to efficient solution-phase PCR using one common primer pair. We demonstrate this method by coamplifying and genotyping 75 unselected human single-nucleotide polymorphism (SNP) loci.The key challenge in developing a high-multiplex amplification procedure is preventing excessive off-target priming by the many primers in the reaction [1][2][3] . Several previously developed methods use surface immobilization of primer pairs as a way to separate reactions and thus limit primerdimer formation [4][5][6] , but drawbacks of these methods include inefficient amplification, loss of reactants from the surface and considerable primer-dimer formation within pairs of primers.MegaPlex PCR likewise uses physical separation of primer pairs to prevent their interaction, but it additionally includes 'common sequences' at the 5′ ends of the surface primers so that early-stage amplicons can be moved into the solution phase for co-amplification by highly efficient and unbiased PCR using a single common primer pair [6][7][8] (Fig. 1). To reduce primer-dimer formation, MegaPlex PCR uses surface primers that are made partially double-stranded by base-pairing their common 5′ sequences with complementary 'barrier oligonucleotides'. A detailed methods description is available in Supplementary Methods online.During the development of MegaPlex PCR we evaluated a range of targets, input DNAs and reaction conditions. We used membrane arrays and microbeads as binding surfaces, with the beads now routinely attached to microtiter plate wells to provide a platform compatible with automation.Using the microbead support we found MegaPlex PCR to be effective with as little as 200 ng of human genomic DNA, and in various 15-plex reactions it recovered many different target sequences of up to at least 500 bp in size, with little bias against larger amplicons ( Supplementary Fig. 1 online). As occasional targets (~1/10 in preliminary studies) generated severe primer-dimer artifacts, regardless of the multiplex level of the experiment, optimization of MegaPlex PCR was required. One option was the exclusion of these targets by empirical or computational prefiltering, but we selected a modification that avoided the need for target preselection.This modification involves enriching the input genomic DNA for sequences of interest via a crude solution-phase multiplex PCR using specific primers for all the amplification targets. The primer sequences for this can match the specific portions of those on the solid surface, or they can be designed to prime slightly outside these sites in the genomic DNA. This strategy is used routinely in digital molecular counting and genome mapping studies that use limiting-dilution samples, with multiplexing up to at least 1,200 (ref. 9). Although this is less specific ...