Series |

Study designs

Good experiments start with good planning. The analysis of genetic and molecular information involves increasingly sophisticated tools and methodologies, many of which are advancing at a fast pace. The articles in this series provide detailed advice on the most appropriate and up-to-date means for designing experiments, with the aim of helping researchers to maximise the value of their data.

Content

This Review outlines a broad, universal framework for systems biology applied to infectious disease research. From study design and omics data collection, analysis, visualization and interpretation to translational outcomes, the authors illustrate how systems biology can provide insights into host–pathogen relationships for the betterment of human health.

Review Article | | Nature Reviews Genetics

The increased adoption of DNA sequencing in genetic association studies is uncovering a wide range of population genetic variation, including rare genetic variants. Although this rarity limits the statistical power of associating individual rare variants with phenotypes, this Review discusses the diverse methods for leveraging the collective effects of rare variants in order to uncover important roles in complex traits, particularly human diseases.

Review Article | | Nature Reviews Genetics

Various types of observational studies can provide statistical associations between factors, such as between an environmental exposure and a disease state. This Review discusses the various genetics-focused statistical methodologies that can move beyond mere associations to identify (or refute) various mechanisms of causality, with implications for responsibly managing risk factors in health care and the behavioural and social sciences.

Review Article | | Nature Reviews Genetics

The rapid development of CRISPR-based gene manipulation has enabled various approaches for high-throughput functional genomics. This Review guides users through the practicalities of CRISPR-based functional genomics screens, including study design options, best-practice approaches, pitfalls to avoid and data analysis strategies.

Review Article | | Nature Reviews Genetics

Advances in genome sequencing, editing and synthetic biology have enhanced the feasibility of large-scale genome engineering, termed genome writing. In this Opinion article, Chari and Church discuss the strengths and limitations of diverse strategies for genome writing, including extensively modifying existing genomes versus synthesizing genomesde novo, and they provide future visions for writing large genomes.

Opinion | | Nature Reviews Genetics

Although it has been known for decades that RNA is subjected to numerous covalent modifications, there has been a recent surge in interest driven by sequencing-based transcriptome-wide detection methods and the realization that RNA modifications have important roles in diverse biological processes. This Review describes the range of detection strategies for RNA modifications, their particular strengths and limitations, and how responsible and complementary application of these techniques will be required to ensure the quality and interpretability of the rapidly accumulating data sets.

Review Article | | Nature Reviews Genetics

The use of phylogenetics in cancer genomics is increasing owing to a growing appreciation of the importance of evolutionary theory to cancer progression. The authors provide guidance on the design and analysis of tumour phylogeny studies by surveying the range of phylogenetic methods and tools available to the cancer researcher and discussing their key applications and the unsolved problems in the field.

Review Article | | Nature Reviews Genetics

To characterize the genetic underpinnings of speciation, genome scans can identify genomic regions that differ between divergent populations of wild organisms. In this Review, Wolf and Ellegren describe the methodological details of these approaches and how genomic islands of differentiation should be interpreted cautiously in the search for 'speciation genes'. They also discuss methodological best practice that takes into consideration genomic differentiation occurring through speciation-independent evolutionary processes.

Review Article | | Nature Reviews Genetics

Loss-of-function (LOF) approaches are powerful experimental tools for characterizing gene functions. However, emerging discrepancies when genes are investigated using different tools or organisms has triggered debate about how such LOF results should be biologically interpreted. In this Review, experts from varied fields discuss how understanding the underlying features of each LOF approach can provide explanations for different experimental outcomes and can guide their optimal and reliable application.

Review Article | | Nature Reviews Genetics

A genome sequence is only useful once the information encoded in it can be deciphered. In this Review, Mudge and Harrow describe the latest approaches to higher eukaryote gene annotation, including making the best use of complex transcriptome data sets, integrating evidence for functionality and extending annotations to encompass regulatory features.

Review Article | | Nature Reviews Genetics

Considerable resources are required to gain maximal insights into the diverse big data sets in biomedicine. In this Review, the authors discuss how crowdsourcing, in the form of collaborative competitions (known as Challenges), can engage the scientific community to provide the diverse expertise and methodological approaches that can robustly address some of the most pressing questions in genetics, genomics and biomedical sciences.

Review Article | | Nature Reviews Genetics

Phenotypic data from electronic health records and epidemiological studies can be exploited to study the impact of genetic variation on the phenome. This Review highlights challenges that need to be overcome for the characterization of the complex human genome–phenome relationship using phenome-wide association studies (PheWAS).

Review Article | | Nature Reviews Genetics

Technical differences between the many variant methods that are based on restriction site-associated DNA sequencing (RADseq) lead to trade-offs in experimental design and analysis. Here, the authors comprehensively review the various RADseq approaches and provide general considerations for designing a RADseq study.

Review Article | | Nature Reviews Genetics

Directed evolution uses laboratory-based evolution to enhance the properties of biomolecules, primarily to generate proteins with optimized or novel activities. This Review discusses the diverse range of technologies for the directed evolution of proteins, particularly methods for generating diversity in the gene library and approaches for screening and selecting for variants with desired properties. The relative strengths and limitations of these approaches are highlighted to guide readers to appropriate strategies.

Review Article | | Nature Reviews Genetics

Before genome-wide association studies, linkage analysis was the primary approach used for genetic mapping of complex traits in humans. Now, with the widespread application of whole-genome sequencing (WGS), linkage analysis based on WGS data is emerging as a useful tool for the identification of susceptibility genes for human disease. This Review reiterates the main principles of linkage analysis and provides guidelines for performing linkage analysis on WGS data.

Review Article | | Nature Reviews Genetics

Heritability estimates provide a useful means of understanding the genetic and environmental contributions to phenotypic variance. The authors define heritability, discuss how to estimate and interpret it in the context of disease and examine how biases in heritability estimates arise.

Review Article | | Nature Reviews Genetics

In addition to somatic mutations in tumours, inherited genetic variants can influence how a patient with cancer responds to drug treatment. This Review considers best practice in design and analysis for pharmacogenomic studies to identify such variants, potentially leading to personalized oncology.

Review Article | | Nature Reviews Genetics

Twin studies have long been used for dissecting the relative contributions of genetics and other factors to various phenotypes. This Review discusses how these traditional studies are now being integrated with modern omics technologies to provide a wide range of biological insights.

Review Article | | Nature Reviews Genetics

Biological processes are inherently dynamic and therefore capturing data about gene expression at multiple time points can provide valuable insights into biological systems. This Review discusses experimental and analytical considerations for studies of gene expression dynamics, and the possibilities for integration with other data sets.

Review Article | | Nature Reviews Genetics

Phylogenetic analysis is pervading every field of biological study. The authors review and assess the main methods of phylogenetic analysis — including parsimony, distance, likelihood and Bayesian methods — and provide guidance for selecting the most appropriate approach and software package.

Review Article | | Nature Reviews Genetics

This Review describes how genome-wide analyses have provided various insights into the most lethal malarial parasite,Plasmodium falciparum, including determinants of antimalarial drug resistance. The authors also propose how genetic tools can be refined to monitor future therapeutic interventions.

Review Article | | Nature Reviews Genetics

Although genome sequencing is becoming routine, genome annotation is becoming increasingly challenging. The authors provide an overview of the steps and software tools that are available for annotating eukaryotic genomes, and describe the best practices for sharing, quality checking and updating the annotation.

Review Article | | Nature Reviews Genetics

Computer simulations can be valuable components of studies in many fields, including population genetics, evolutionary biology, genetic epidemiology and ecology. The recent increase in the available range of software packages is now making simulation an accessible option for researchers with limited bioinformatics experience.

Review Article | | Nature Reviews Genetics

Studies of the composition, dynamics and function of the human microbiome have taken off in the past two years thanks to the development of new sequencing technologies and advanced algorithms. This article provides a guide to the experimental and analytical best practices in this flourishing field.

Review Article | | Nature Reviews Genetics

Although many studies claim to have detected an adaptive allele, this label is not always applied rigorously. The authors argue that obtaining direct evidence that specific alleles are adaptive requires approaches which functionally connect genotype, phenotype and fitness.

Review Article | | Nature Reviews Genetics

Exome sequencing is a powerful approach for accelerating the discovery of the genes underlying Mendelian disorders and, increasingly, of genes underlying complex traits. This Review describes the experimental and analytical options for applying exome sequencing and the key challenges in using this approach.

Review Article | | Nature Reviews Genetics

Advances in sequencing technologies, assembly algorithms and computing power are making it feasible to assemble the entire transcriptome from short RNA reads. The article reviews the transcriptome assembly strategies, their advantages and limitations and how to apply them effectively.

Review Article | | Nature Reviews Genetics

The increased genetic diversity in populations with recent ancestry from more than one continent may help in the identification of genetic variants underlying disease risk. This Progress article discusses recent developments in methods to study complex traits in these admixed populations, including combining SNP and admixture association signals.

Progress | | Nature Reviews Genetics

Technological advances now allow large-scale studies of human disease-associated epigenetic variation, specifically variation in DNA methylation. Such epigenome-wide association studies present novel opportunities, but, as discussed here, they also create new challenges that are not encountered in genome-wide association studies.

Review Article | | Nature Reviews Genetics

Identity by descent (IBD) — the probability that two alleles descended from a common ancestor — is used in fundamental applications such as gene mapping and estimating heritability. The authors offer a solution to the confusion between IBD and identity by state (IBS) that is caused by the common practice of using dense SNPs to estimate IBD.

Opinion | | Nature Reviews Genetics

This article reviews the increasing range of genome-scale methods that are being used to analyse eukaryotic DNA replication. Studies in different species and of replication timing or origin location have yielded varying degrees of success; technical hurdles remain, but important biological insights have been gained.

Review Article | | Nature Reviews Genetics

Cancer is fundamentally a disease of the genome and so high-throughput sequencing technologies offer great potential for improving our understanding of the biology and treatment of cancer. Experimental strategies, computational approaches and cancer-specific considerations for detecting different types of genomic alterations are discussed.

Review Article | | Nature Reviews Genetics

Despite the yield of genome-wide association studies, the variants identified explain little of the heritability of most complex diseases. This unexplained heritability could be partly due to gene–environment (G×E) interactions. This Review provides a guide to designs and analytical approaches for studying specific G×E interactions.

Review Article | | Nature Reviews Genetics

Genome-wide association studies are not widespread in Africa, partly because of the challenges of dealing with population structure and high genomic diversity. New approaches in statistical imputation and whole-genome sequencing are now set to exploit these features for fine mapping causal variants.

Review Article | | Nature Reviews Genetics

There is an increasing demand for next-generation sequencing technologies that rapidly deliver high volumes of accurate genome information at a low cost. This Review provides a guide to the features of the different platforms, and describes the recent advances in this fast-moving area.

Review Article | | Nature Reviews Genetics

Bayesian analyses are increasingly being used in genetics, particularly in the context of genome-wide association studies. This article provides a guide to using Bayesian analyses for assessing single-SNP associations and highlights the advantages of these methods compared with standard frequentist analyses.

Review Article | | Nature Reviews Genetics

Coupling next-generation sequencing to chromatin immunoprecipitation has transformed the resolution and genomic coverage of DNA-binding protein and nucleosome mapping studies. However, successful ChIP–seq requires careful consideration of the experimental and analytical approaches; this Review evaluates the current strategies and challenges.

Review Article | | Nature Reviews Genetics

Mapping genetic variants that cause changes in transcript levels is a new tool that can give insight into the biology of disease risk loci identified by genome-wide association studies; here the potential power and technical challenges of this approach are discussed.

Review Article | | Nature Reviews Genetics

The development of high-throughput DNA sequencing methods provides a new method for mapping and quantifying transcriptomes — RNA sequencing (RNA-Seq). This article explains how RNA-Seq works, the challenges it faces and how it is changing our view of eukaryotic transcriptomes.

Innovation | | Nature Reviews Genetics

RNAi, a common gene knockdown technique, has been widely used in a variety of genetic screens. As part of our 'art and design of genetic screens' series, the authors discuss RNAi assay design and analytical approaches for large-scale screening experiments in cells and whole-animal experiments.

Review Article | | Nature Reviews Genetics