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21st Jan 2013
An algorithm and Web sleuthing has led researchers to discover the hidden identities of anonymous DNA donors.
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Author: John Bohannon -
21st Jan 2013
Relatives provide the basic material for the study of inheritance of human disease. However, the methodologies for the estimation of heritability and the interpretation of the results have been controversial. The debate arises from the plethora of methods used, the validity of the methodological assumptions and the inconsistent and sometimes erroneous genetic interpretations made.
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14th Jan 2013
A wealth of microarray gene expression data and a growing volume of RNA sequencing data are now available in public databases. The authors look at how these data are being used and discuss considerations for how such data should be analysed and deposited and how data reuse could be improved.
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21st Dec 2012
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5th Nov 2012
Abstract: By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing.
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30th Oct 2012
Three papers characterizing human germline mutation rates bolster evidence for a relatively low rate of base substitution in modern humans and highlight a central role for paternal age in determining rates of mutation. These studies represent the advent of a transformation in our understanding of mutation rates and processes, which may ultimately have public health implications.
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12th Oct 2012
Alterations in the human microbiome are increasingly being linked to diseases, but new methods are needed to probe these links more quickly and in more detail. The publication of the first metagenome-wide association (MGWA) study — which identifies changes in the microbial composition of the gut that are associated with type 2 diabetes (T2D) — is an important step towards these goals.
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12th Oct 2012
Genome-wide association studies (GWASs) of mice provide an alternative means of identifying genes and genetic variants that are important for human physiology and disease. This Review describes the various resources and strategies for GWASs of mice, emphasizing their advantages and pitfalls relative to human studies.
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20th Sep 2012
by Norman R. Drinkwater, Michael N. Gould
More information...The construction in the 1990s of high density genetic maps of the mouse and rat based on simple sequence length polymorphisms led to an explosion of activity directed toward the identification of quantitative trait loci (QTLs) that control a broad array of normal and abnormal biology. More than 3,900 mouse and nearly 1,000 rat QTLs have been mapped by linkage analysis in studies of, among others, behavior, bone morphogenesis, cardiovascular function, and metabolism, as well as diseases including arthritis, diabetes, and cancer.
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11th Sep 2012
As the list of genetic variants that are implicated in disease gets longer, the challenge is to understand how they contribute to disease phenotypes. A recent study describes a high-throughput yeast system for detecting the effects of disease alleles on protein stability.
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11th Sep 2012
Recent measurements of the human mutation rate using next-generation sequencing have revealed a value of approximately half of that previously derived from fossil calibration. Here, the authors discuss the implications of this revised mutation rate in relation to our understanding of human evolution.
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6th Sep 2012
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification.
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5th Sep 2012More information...
Background: Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data.
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23rd Aug 2012
Mutations generate sequence diversity and provide a substrate for selection.
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20th Aug 2012
Several computational methods have been developed for predicting the effects of rapidly expanding variation data. Comparison of the performance of tools has been very difficult as the methods have been trained and tested with different datasets. Until now, unbiased and representative benchmark datasets have been missing. We have developed a benchmark database suite, VariBench, to overcome this problem. VariBench contains datasets of experimentally verified high quality variation data carefully chosen from literature and relevant databases.
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17th Aug 2012Areas of life sciences research that were previously distant from each other in ideology, analysis practices and toolkits, such as microbial ecology and personalized medicine, have all embraced techniques that rely on next-generation sequencing instruments. Yet the capacity to generate the data greatly outpaces our ability to analyse it. Existing sequencing technologies are more mature and accessible than the methodologies that are available for individual researchers to move, store, analyse and present data in a fashion that is transparent and reproducible.More information...
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14th Aug 2012
The importance for research and clinical utility of mutation databases, as well as the issues and difficulties entailed in their construction, is discussed within the Human Variome Project. While general principles and standards can apply to most human diseases, some specific questions arise when dealing with the nature of genetic neurological disorders. So far, publically accessible mutation databases exist for only about half of the genes causing neurogenetic disorders; and a considerable work is clearly still needed to optimize their content.
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14th Aug 2012More information...
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24th Jul 2012
Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved “open consent” process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods.
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23rd Jul 2012
Gonçalo Abecasis, Jonathan Marchini and colleagues report a pre-phasing strategy for genotype imputation in GWAS, which they show maintains accuracy while substantially lowering computational costs. Their approach has been implemented in both MACH and IMPUTE 2.0 software.
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July 2012
- Including known covariates can reduce power to detect genetic effects in case-control studies
- De novo mutations in human genetic disease
- Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO)
- Human Genetic Variation, Shared and Private
- Computational tools for prioritizing candidate genes: boosting disease gene discovery
- Human variome project country nodes: Documenting genetic information within a country
June 2012
- Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain
- Informed consent: A broken contract
- Analysis of case-control association studies with known risk variants
- Mutation mapping and identification by whole genome sequencing [METHOD]
- Biorepositories: Building better biobanks
- Whole-Genome Sequencing: The New Standard of Care?
May 2012
- Dealing with Data: A Case Study on Information and Data Management Literacy
- Exploring the variation within
- Exome sequencing and the genetic basis of complex traits
- Solving bottlenecks in data sharing in the life sciences
- A new approach for detecting low-level mutations in next-generation sequence data
- Human genetics: Not-so-rare gene variants
- Human genetics: Fruits of exome sequencing for autism
- Locus-specific mutation databases for neurodegenerative brain diseases