Annual Review of Genomics and Human Genetics - Volume 4, 2003
Volume 4, 2003
- Review Articles
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Genetics of Human Laterality Disorders: Insights from Vertebrate Model Systems
Vol. 4 (2003), pp. 1–32More LessMany internal organs in the vertebrate body are asymmetrically oriented along the left-right (L-R) body axis. Organ asymmetry and some components of the molecular signaling pathways that direct L-R development are highly conserved among vertebrate species. Although individuals with full reversal of organ L-R asymmetry (situs inversus totalis) are healthy, significant morbidity and mortality is associated with perturbations in laterality that result in discordant orientation of organ systems and complex congenital heart defects. In humans and other vertebrates, genetic alterations of L-R signaling pathways can result in a wide spectrum of laterality defects. In this review we categorize laterality defects in humans, mice, and zebrafish into specific classes based on altered patterns of asymmetric gene expression, organ situs defects, and midline phenotypes. We suggest that this classification system provides a conceptual framework to help consolidate the disparate laterality phenotypes reported in humans and vertebrate model organisms, thereby refining our understanding of the genetics of L-R development. This approach helps suggest candidate genes and genetic pathways that might be perturbed in human laterality disorders and improves diagnostic criteria.
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Race, Ancestry, and Genes: Implications for Defining Disease Risk
Vol. 4 (2003), pp. 33–67More LessGeneticists are interested in finding genes associated with disease. Because of widespread health disparities, race is a variable that is often said to be relevant in this context. The idea is that members of a preconceived “race” share common ancestry that may include genetic risk factors. Human variation has been shaped by the long-term processes of population history, and population samples that reflect that history carry statistical information about shared genetic variation or “ancestry.” But race is an elusive concept and a term difficult even to define rigorously. Unfortunately, these problems are neither new nor related to recent genetic knowledge. Race is also one of the most politically charged subjects in American life because its associated sociocultural component has notoriously led to categorical treatment that has been misleading and politically misused. There are ways in which the concept of race (whether or not the term is used) can be a legitimate tool in the search for disease-associated genes. But in that context race reflects deeply confounded cultural as well as biological factors, and a careful distinction must be made between race as a statistical risk factor and causal genetic variables.
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Gene Annotation: Prediction and Testing
Vol. 4 (2003), pp. 69–88More LessFifty years after the publication of DNA structure, the whole human genome sequence will be officially finished. This achievement marks the beginning of the task to catalogue every human gene and identify each of their function expression patterns. Currently, researchers estimate that there are about 30,000 human genes and approximately 70% of these can be automatically predicted using a combination of ab initio and similarity-based programs. However, to experimentally investigate every gene's function, the research community requires a high-quality annotation of alternative splicing, pseudogenes, and promoter regions that can only be provided by manual intervention. Manual curation of the human genome will be a long-term project as experimental data are continually produced to confirm or refine the predictions, and new features such as noncoding RNAs and enhancers have not been fully identified. Such a highly curated human gene-set made publicly available will be a great asset for the experimental community and for future comparative genome projects.
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The Drosophila Melanogaster Genome
Vol. 4 (2003), pp. 89–117More LessDrosophila's importance as a model organism made it an obvious choice to be among the first genomes sequenced, and the Release 1 sequence of the euchromatic portion of the genome was published in March 2000. This accomplishment demonstrated that a whole genome shotgun (WGS) strategy could produce a reliable metazoan genome sequence. Despite the attention to sequencing methods, the nucleotide sequence is just the starting point for genome-wide analyses; at a minimum, the genome sequence must be interpreted using expressed sequence tag (EST) and complementary DNA (cDNA) evidence and computational tools to identify genes and predict the structures of their RNA and protein products. The functions of these products and the manner in which their expression and activities are controlled must then be assessed—a much more challenging task with no clear endpoint that requires a wide variety of experimental and computational methods. We first review the current state of the Drosophila melanogaster genome sequence and its structural annotation and then briefly summarize some promising approaches that are being taken to achieve an initial functional annotation.
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Forensics and Mitochondrial DNA: Applications, Debates, and Foundations*
Vol. 4 (2003), pp. 119–141More LessDebate on the validity and reliability of scientific methods often arises in the courtroom. When the government (i.e., the prosecution) is the proponent of evidence, the defense is obliged to challenge its admissibility. Regardless, those who seek to use DNA typing methodologies to analyze forensic biological evidence have a responsibility to understand the technology and its applications so a proper foundation(s) for its use can be laid. Mitochondrial DNA (mtDNA), an extranuclear genome, has certain features that make it desirable for forensics, namely, high copy number, lack of recombination, and matrilineal inheritance. mtDNA typing has become routine in forensic biology and is used to analyze old bones, teeth, hair shafts, and other biological samples where nuclear DNA content is low. To evaluate results obtained by sequencing the two hypervariable regions of the control region of the human mtDNA genome, one must consider the genetically related issues of nomenclature, reference population databases, heteroplasmy, paternal leakage, recombination, and, of course, interpretation of results. We describe the approaches, the impact some issues may have on interpretation of mtDNA analyses, and some issues raised in the courtroom.
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Creationism and Intelligent Design
Vol. 4 (2003), pp. 143–163More LessCreationism, the rejection of evolution in favor of supernatural design, comes in many varieties besides the common young-earth Genesis version. Creationist attacks on science education have been evolving in the last few years through the alliance of different varieties. Instead of calls to teach “creation science,” one now finds lobbying for “intelligent design” (ID). Guided by the Discovery Institute's “Wedge strategy,” the ID movement aims to overturn evolution and what it sees as a pernicious materialist worldview and to renew a theistic foundation to Western culture, in which human beings are recognized as being created in the image of God. Common ID arguments involving scientific naturalism, “irreducible complexity,” “complex specified information,” and “icons of evolution,” have been thoroughly examined and refuted. Nevertheless, from Kansas to Ohio to the U.S. Congress, ID continues lobbying to teach the controversy, and scientists need to be ready to defend good evolution education.
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Peroxisome Biogenesis Disorders
Vol. 4 (2003), pp. 165–211More LessThe peroxisome biogenesis disorders (PBDs) comprise 12 autosomal recessive complementation groups (CGs). The multisystem clinical phenotype varies widely in severity and results from disturbances in both development and metabolic homeostasis. Progress over the last several years has lead to identification of the genes responsible for all of these disorders and to a much improved understanding of the biogenesis and function of the peroxisome. Increasing availability of mouse models for these disorders offers hope for a better understanding of their pathophysiology and for development of therapies that might especially benefit patients at the milder end of the clinical phenotype.
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Sequence Divergence, Functional Constraint, and Selection in Protein Evolution
Justin C. Fay, and Chung-I WuVol. 4 (2003), pp. 213–235More LessThe genome sequences of multiple species has enabled functional inferences from comparative genomics. A primary objective is to infer biological functions from the conservation of homologous DNA sequences between species. A second, more difficult, objective is to understand what functional DNA sequences have changed over time and are responsible for species' phenotypic differences. The neutral theory of molecular evolution provides a theoretical framework in which both objectives can be explicitly tested. Development of statistical tests within this framework has provided insight into the evolutionary forces that constrain and in some cases change DNA sequences and the resulting patterns that emerge. In this article, we review recent work on how functional constraint and changes in protein function are inferred from protein polymorphism and divergence data. We relate these studies to our understanding of the neutral theory and adaptive evolution.
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Molecular Pathogenesis of Pancreatic Cancer
Vol. 4 (2003), pp. 237–256More LessPancreatic cancer is an almost universally fatal disease, with a five-year survival rate of 5%. Research into both sporadic and inherited forms of pancreatic cancer has yielded tremendous advances in the understanding of this disease at the molecular level. Elucidating genetic alterations in pancreatic cancer has identified various abnormalities ranging from gross chromosomal abnormalities to point mutations, many of which influence the development and progression of pancreatic cancer. Identifying precursor lesions within pancreatic ducts has led to the formulation of a progression model of pancreatic cancer and subsequent identification of early- and late-stage changes leading to invasive cancer. Ultimately, understanding the genetic events underlying the development of pancreatic cancer may serve as a useful adjunct in the screening and treatment of patients suffering from, or at risk for, pancreatic cancer.
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The Inherited Basis of Diabetes Mellitus: Implications for the Genetic Analysis of Complex Traits
Vol. 4 (2003), pp. 257–291More LessDiabetes encompasses a heterogeneous group of diseases, each with a substantial genetic component. We review the division of diabetes into different subtypes based on clinical phenotype, the fruitful pursuit of genes underlying monogenic forms of the disease, the successes and drawbacks of whole-genome linkage scans in type 1 and type 2 diabetes, and the recent identification of several diabetes genes by large association studies. We use the lessons learned from this extensive body of evidence to illustrate general implications for the genetic analysis of complex traits.
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Patterns of Human Genetic Diversity: Implications for Human Evolutionary History and Disease
Vol. 4 (2003), pp. 293–340More LessSince the completion of the human genome sequencing project, the discovery and characterization of human genetic variation is a principal focus for future research. Comparative studies across ethnically diverse human populations and across human and nonhuman primate species is important for reconstructing human evolutionary history and for understanding the genetic basis of human disease. In this review, we summarize data on patterns of human genetic diversity and the evolutionary forces (mutation, genetic drift, migration, and selection) that have shaped these patterns of variation across both human populations and the genome. African population samples typically have higher levels of genetic diversity, a complex population substructure, and low levels of linkage disequilibrium (LD) relative to non-African populations. We discuss these differences and their implications for mapping disease genes and for understanding how population and genomic diversity have been important in the evolution, differentiation, and adaptation of humans.
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Human Nonsyndromic Sensorineural Deafness*
Vol. 4 (2003), pp. 341–402More LessGiven the unique biological requirements of sound transduction and the selective advantage conferred upon a species capable of sensitive sound detection, it is not surprising that up to 1% of the approximately 30,000 or more human genes are necessary for hearing. There are hundreds of monogenic disorders for which hearing loss is one manifestation of a syndrome or the only disorder and therefore is nonsyndromic. Herein we review the supporting evidence for identifying over 30 genes for dominantly and recessively inherited, nonsyndromic, sensorineural deafness. The state of knowledge concerning their biological roles is discussed in the context of the controversies within an evolving understanding of the intricate molecular machinery of the inner ear.
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Enzyme Therapy for Lysosomal Storage Disease: Principles, Practice, and Prospects
Vol. 4 (2003), pp. 403–436More LessOver the past three decades, enzyme therapy for lysosomal storage diseases has moved from an academic pursuit to direct delivery of effective clinical care for affected patients and families. This success is based on understanding the complexities of lysosomal biogenesis, lysosomal hydrolase sorting and hydrolytic requirements, and the target sites of pathology of these diseases. This article reviews these concepts and their application to the treatment of affected patients with Gaucher disease, Fabry disease, and mucopolysaccharidosis I. The principles, progress, and practice in these diseases provide prototypes for expansion of enzyme therapy to a growing set of these diseases.
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Nonsyndromic Seizure Disorders: Epilepsy and the Use of the Internet to Advance Research
Vol. 4 (2003), pp. 437–457More LessThe progress in understanding the genetics of nonsyndromic epilepsy is the direct result of dramatic advances made by the Human Genome Project. The development of thousands of precisely mapped genetic markers and the nearly complete sequencing of the entire human genome in 2001 allowed genetic researchers in epilepsy to identify many loci and genes as causal in inherited idiopathic epilepsy. This substantial increase in information has required the development of accurate and online bioinformatic databases. Only the Internet can enable such large amounts of precise DNA sequence information to be transferred to researchers. Along with the construction of these databases has been the development of efficient search algorithms for specific DNA sequences and genetic information. This article summarizes the effect that this burst of new genomic information has had on research aimed at discovering the underlying genetic factors for nonsyndromic epilepsy. Many of the web sites important to epilepsy gene discovery are listed and discussed in this article, including sites with extensive information on genetic markers, genetic analysis, gene sequence, gene expression, gene mutations, and DNA sequence variation. Continued acquisition of information on naturally occurring DNA sequence variants will greatly help research directed towards understanding the genetic susceptibility of the common, nonsyndromic epilepsies and will lead to the promise of personalized medicine.
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The Genetics of Narcolepsy
Vol. 4 (2003), pp. 459–483More Less▪ AbstractHuman narcolepsy is a genetically complex disorder. Family studies indicate a 20–40 times increased risk of narcolepsy in first-degree relatives and twin studies suggest that nongenetic factors also play a role. The tight association between narcolepsy-cataplexy and the HLA allele DQB1*0602 suggests that narcolepsy has an autoimmune etiology. In recent years, extensive genetic studies in animals, using positional cloning in dogs and gene knockouts in mice, have identified abnormalities in hypothalamic hypocretin (orexin) neurotransmission as key to narcolepsy pathophysiology. Though most patients with narcolepsy-cataplexy are hypocretin deficient, mutations or polymorphisms in hypocretin-related genes are extremely rare. It is anticipated that susceptibility genes that are independent of HLA and impinge on the hypocretin neurotransmitter system are isolated in human narcolepsy.
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Previous Volumes
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Volume 24 (2023)
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Volume 23 (2022)
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Volume 22 (2021)
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Volume 21 (2020)
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Volume 20 (2019)
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Volume 19 (2018)
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Volume 18 (2017)
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Volume 17 (2016)
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Volume 16 (2015)
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Volume 15 (2014)
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Volume 14 (2013)
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Volume 13 (2012)
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Volume 12 (2011)
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Volume 11 (2010)
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Volume 10 (2009)
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Volume 9 (2008)
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Volume 8 (2007)
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Volume 7 (2006)
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Volume 6 (2005)
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Volume 5 (2004)
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Volume 4 (2003)
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Volume 3 (2002)
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Volume 2 (2001)
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Volume 1 (2000)
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Volume 0 (1932)