David Fredman

Complex SNP-related sequence variation in segmental genome duplications.

There is uncertainty about the true nature of predicted single-nucleotide polymorphisms (SNPs) in segmental duplications (duplicons) and whether these markers genuinely exist at increased density as indicated in public databases. We explored these issues by genotyping 157 predicted SNPs in duplicons and control regions in normal diploid genomes and fully homozygous complete hydatidiform moles. Our data identified many true SNPs in duplicon regions and few paralogous sequence variants. Twenty-eight percent of the polymorphic duplicon sequences we tested involved multisite variation, a new type of polymorphism representing the sum of the signals from many individual duplicon copies that vary in sequence content due to duplication, deletion or gene conversion. Multisite variations can masquerade as normal SNPs when genotyped. Given that duplicons comprise at least 5% of the genome and many are yet to be annotated in the genome draft, effective strategies to identify multisite variation must be established and deployed.

SNP association studies in Alzheimer's disease highlight problems for complex disease analysis

Genetic linkage and association analyses are two distinct approaches to understanding the genetic etiology of complex disease. Association analysis has become particularly popular in recent times, but the true utility of the strategy remains uncertain. To try to gain better insight into the relevant issues, we have used genetic association analysis to explore the etiology of Alzheimers disease. Our empirical findings supplement the theoretical debate, illustrating the general doubtfulness of previous positive findings and the limited ability of typical association studies based on candidate genes to discern true medium-sized signals from false positives. Improvements in genotyping technologies and increasing the number of SNPs tested, without sophisticated allowance for all other issues, could simply lead to an unmanageable overload of false-positive signals, themselves obscuring true disease associations.

Mobile-Phone Dispatch of Laypersons for CPR in Out-of-Hospital Cardiac Arrest

BACKGROUND Cardiopulmonary resuscitation (CPR) performed by bystanders is associated with increased survival rates among persons with out-of-hospital cardiac arrest. We investigated whether rates of bystander-initiated CPR could be increased with the use of a mobile-phone positioning system that could instantly locate mobile-phone users and dispatch lay volunteers who were trained in CPR to a patient nearby with out-of-hospital cardiac arrest. METHODS We conducted a blinded, randomized, controlled trial in Stockholm from April 2012 through December 2013. A mobile-phone positioning system that was activated when ambulance, fire, and police services were dispatched was used to locate trained volunteers who were within 500 m of patients with out-of-hospital cardiac arrest; volunteers were then dispatched to the patients (the intervention group) or not dispatched to them (the control group). The primary outcome was bystander-initiated CPR before the arrival of ambulance, fire, and police services. RESULTS A total of 5989 lay volunteers who were trained in CPR were recruited initially, and overall 9828 were recruited during the study. The mobile-phone positioning system was activated in 667 out-of-hospital cardiac arrests: 46% (306 patients) in the intervention group and 54% (361 patients) in the control group. The rate of bystander-initiated CPR was 62% (188 of 305 patients) in the intervention group and 48% (172 of 360 patients) in the control group (absolute difference for intervention vs. control, 14 percentage points; 95% confidence interval, 6 to 21; P<0.001). CONCLUSIONS A mobile-phone positioning system to dispatch lay volunteers who were trained in CPR was associated with significantly increased rates of bystander-initiated CPR among persons with out-of-hospital cardiac arrest. (Funded by the Swedish Heart-Lung Foundation and Stockholm County; ClinicalTrials.gov number, NCT01789554.).

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources

HGVbase (Human Genome Variation database; http://hgvbase.cgb.ki.se, formerly known as HGBASE) is an academic effort to provide a high quality and non-redundant database of available genomic variation data of all types, mostly comprising single nucleotide polymorphisms (SNPs). Records include neutral polymorphisms as well as disease-related mutations. Online search tools facilitate data interrogation by sequence similarity and keyword queries, and searching by genome coordinates is now being implemented. Downloads are freely available in XML, Fasta, SRS, SQL and tagged-text file formats. Each entry is presented in the context of its surrounding sequence and many records are related to neighboring human genes and affected features therein. Population allele frequencies are included wherever available. Thorough semi-automated data checking ensures internal consistency and addresses common errors in the source information. To keep pace with recent growth in the field, we have developed tools for fully automated annotation. All variants have been uniquely mapped to the draft genome sequence and are referenced to positions in EMBL/GenBank files. Data utility is enhanced by provision of genotyping assays and functional predictions. Recent data structure extensions allow the capture of haplotype and genotype information, and a new initiative (along with BiSC and HUGO-MDI) aims to create a central repository for the broad collection of clinical mutations and associated disease phenotypes of interest.

Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3

Genome-wide association studies identified noncoding SNPs associated with type 2 diabetes and obesity in linkage disequilibrium (LD) blocks encompassing HHEX-IDE and introns of CDKAL1 and FTO [Sladek R, et al. (2007) Nature 445:881–885; Steinthorsdottir V, et al. (2007) Nat. Genet 39:770–775; Frayling TM, et al. (2007) Science 316:889–894]. We show that these LD blocks contain highly conserved noncoding elements and overlap with the genomic regulatory blocks of the transcription factor genes HHEX, SOX4, and IRX3. We report that human highly conserved noncoding elements in LD with the risk SNPs drive expression in endoderm or pancreas in transgenic mice and zebrafish. Both HHEX and SOX4 have recently been implicated in pancreas development and the regulation of insulin secretion, but IRX3 had no prior association with pancreatic function or development. Knockdown of its orthologue in zebrafish, irx3a, increased the number of pancreatic ghrelin-producing epsilon cells and decreased the number of insulin-producing β-cells and glucagon-producing α-cells, thereby suggesting a direct link of pancreatic IRX3 function to both obesity and type 2 diabetes.

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes☆

Pan-vertebrate developmental cis-regulatory elements are discernible as highly conserved noncoding elements (HCNEs) and are often dispersed over large areas around the pleiotropic genes whose expression they control. On the loci of two developmental transcription factor genes, SOX3 and PAX6, we demonstrate that HCNEs conserved between human and zebrafish can be systematically and reliably tested for their regulatory function in multiple stable transgenes in zebrafish, and their genomic reach estimated with confidence using synteny conservation and HCNE density along these loci. HCNEs of both human and zebrafish function as specific developmental enhancers in zebrafish. We show that human HCNEs result in expression patterns in zebrafish equivalent to those in mouse, establishing zebrafish as a suitable model for large-scale testing of human developmental enhancers. Orthologous human and zebrafish enhancers underwent functional evolution within their sequence and often directed related but non-identical expression patterns. Despite an evolutionary distance of 450 million years, one pax6 HCNE drove expression in identical areas when comparing zebrafish vs. human HCNEs. HCNEs from the same area often drive overlapping patterns, suggesting that multiple regulatory inputs are required to achieve robust and precise complex expression patterns exhibited by developmental genes.

HGVbase: a curated resource describing human DNA variation and phenotype relationships

The Human Genome Variation Database (HGVbase; http://hgvbase.cgb.ki.se) has provided a curated summary of human DNA variation for more than 5 years, thus facilitating research into DNA sequence variation and human phenotypes. The database has undergone many changes and improvements to accommodate increasing volumes and new types of data. The focus of HGVbase has recently shifted towards information on haplotypes and phenotypes, relationships between phenotypes and DNA variation, and collaborative efforts to provide a global resource for genome-phenome data. Open sharing and precise phenotype definitions are necessary to advance the current understanding of common diseases that are typified by complex aetiologies, small genetic effect sizes and multiple confounding factors that obscure positive study results. Association data will increasingly be collected as part of this new project thrust. This report describes the evolving features of HGVbase, and covers in detail the technological choices we have made to enable efficient storage and data mining of increasingly large and complex data sets.

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes.

Metazoan genomes contain arrays of highly conserved noncoding elements (HCNEs) that span developmental regulatory genes and define regulatory domains. We describe Ancora http://ancora.genereg.net, a web resource that provides data and tools for exploring genomic organization of HCNEs for multiple genomes. Ancora includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains.

Recurrent Horizontal Transfer of Bacterial Toxin Genes to Eukaryotes

In this work, we report likely recurrent horizontal (lateral) gene transfer events of genes encoding pore-forming toxins of the aerolysin family between species belonging to different kingdoms of life. Clustering based on pairwise similarity and phylogenetic analysis revealed several distinct aerolysin sequence groups, each containing proteins from multiple kingdoms of life. These results strongly support at least six independent transfer events between distantly related phyla in the evolutionary history of one protein family and discount selective retention of ancestral genes as a plausible explanation for this patchy phylogenetic distribution. We discuss the possible roles of these proteins and show evidence for a convergent new function in two extant species. We hypothesize that certain gene families are more likely to be maintained following horizontal gene transfer from commensal or pathogenic organism to its host if they 1) can function alone; and 2) are immediately beneficial for the ecology of the organism, as in the case of pore-forming toxins which can be utilized in multicellular organisms for defense and predation.

Mobile phone technology identifies and recruits trained citizens to perform CPR on out-of-hospital cardiac arrest victims prior to ambulance arrival

AIM In a two-parted study, evaluate a new concept were mobile phone technology is used to dispatch lay responders to nearby out-of-hospital cardiac arrests (OHCAs). METHODS Mobile phone positioning systems (MPS) can geographically locate selected mobile phone users at any given moment. A mobile phone service using MPS was developed and named Mobile Life Saver (MLS). Simulation study: 25 volunteers named mobile responders (MRs) were connected to MLS. Ambulance time intervals from 22 consecutive OHCAs in 2005 were used as controls. The MRs randomly moved in Stockholm city centre and were dispatched to simulated OHCAs (identical to controls) if they were within a 350 m distance. Real life study: during 25 weeks 1271-1801 MRs trained in CPR were connected to MLS. MLS was activated at the dispatch centre in parallel with ambulance dispatch when an OHCA was suspected. The MRs were dispatched if they were within 500 m from the suspected OHCA. RESULTS Simulation study: mean response time for the MRs compared to historical ambulance time intervals was reduced by 2 min 20s (44%), p<0.001, (95% CI, 1 min 5s - 3 min 35s). The MRs reached the simulated OHCA prior to the historical control in 72% of cases. Real life study: the MLS was triggered 92 times. In 45% of all suspected and in 56% of all true OHCAs the MRs arrived prior to ambulance. CPR was performed by MRs in 17% of all true OHCAs and in 30% of all true OHCAs if MRs arrived prior to ambulance. CONCLUSION Mobile phone technology can be used to identify and recruit nearby CPR-trained citizens to OHCAs for bystander CPR prior to ambulance arrival.