Guide Dictionary of DNA and Genome Technology, Second Edition

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This approach has been used for mendelian disorders as well as complex traits genome-wide association study [GWAS]. Genomic inflation factor: A mathematical term from genetic epidemiology used to control for population stratification in GWAS. Genomic medicine: A term used to describe medical advances and approaches based on human genomic information, sometimes referred to as personalized or precision medicine. Genomics: The study of genes and their function.

Genotype: The specific set of 2 alleles inherited at a genetic locus. Haplotype: The combination of linked marker alleles may be polymorphisms or mutations for a given region of DNA on a single chromosome. The HapMap is a key resource for finding genes affecting health, disease, and responses to drugs and environmental factors. The first release of the HapMap was made in Heterologous expression: A research technique that causes a protein to be produced in a cell that does not normally make ie, express that protein. Heterotetrameric, homotetrameric, and heteromultimeric ion channels: Ion channels made up of different combinations of protein subunits; 4 different subunits heterotetrameric , 4 of the same subunit homotetrameric , and 2 or more different subunits heteromultimeric.

Heterozygous heterozyosity : Having 2 unlike alleles at a particular locus. Homozygous homozygosity : Having 2 like or identical alleles at a particular locus in a diploid genome. Human Genome Project: Collective name for several projects begun in by the US Department of Energy DOE to create an ordered set of DNA segments from known chromosomal locations, develop new computational methods for analyzing genetic map and DNA sequence data, and develop new techniques and instruments for detecting and analyzing DNA.

The first draft of the human genome DNA sequence, produced by the efforts of the Human Genome Project, was completed in The Human Genome Project officially ended in April The ability of complementary stretches of DNA or RNA to hybridize with each other is dependent on the base-pair sequence. Identity by descent IBD : The property of 2 or more alleles that are identical to an ancestral allele, used in gene association studies.

Imputation: A statistical method for inferring genotypes that are not directly measured. Library: A complete set of clones that contains all the genetic material from an organism, tissue, or specific cell type at a specific stage of development. Linkage: Two loci genes or other designated DNA sequence that reside close enough to each other that recombination crossing over rarely occurs between them.

Alleles at the 2 loci do not assort independently at meiosis but are likely to be inherited together. Linkage disequilibrium LD : Refers to alleles at loci close enough together that they remain inherited together through many generations because their extreme close proximity makes recombination crossing over between them highly unlikely.

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Locus plural loci : The physical site on a chromosome occupied by a particular gene or other identifiable DNA sequence characteristic. Megabase: One million base pairs. Mendelian disorder single-gene disorder : A trait or disease that follows the patterns of inheritance that suggest the trait or disease is determined by a gene at a single locus.

Metagenomics: Study of a collection of genetic material genomes from a mixed community of organisms. Metagenomics usually refers to the study of microbial communities. Methylation: Covalent attachment of methyl groups to DNA, usually at cytosine bases.

Dictionary of DNA and Genome Technology by Paul Singleton -

Methylation can reduce transcription from a gene and is a mechanism in X-chromosome inactivation and imprinting. Microarray: A technology used to study many genes simultaneously, usually consisting of an ordered microscopic pattern of known nucleic acid sequences on a glass slide. In a common type of microarray, a sample of DNA or RNA is added to the slide and sequence-dependent binding is measured using sensitive fluorescent detection methods. Minor allele: The allele of a biallelic polymorphism that is less frequent in the study population.

Missense mutation: A mutation that is typically the change of a single nucleotide that results in the substitution of one amino acid for another in the final gene product. Mutation: Any alteration of a gene or genetic material from its natural state. Generally, mutations refer to changes that alter the gene in a negative sense causing the protein product of the gene to have an altered function.

Nonsense mutation: Any mutation that results directly in the formation of a stop codon. Nonsynonymous variant: A polymorphism that results in a change in the amino acid sequence of a protein and therefore may affect the function of the protein. Oncogene: A gene, 1 or more forms of which is associated with cancer. Many oncogenes are involved, directly or indirectly, in controlling the rate of cell growth.

Patch-clamp technique: A laboratory technique in electrophysiology that allows the study of single or multiple ion channels in cells. Penetrance: The proportion of individuals of a given genotype who show any evidence of the associated phenotype. Pharmacogenetic polymorphism: Genetic variants that alter the way an individual metabolizes or responds to a specific medication. Pharmacogenomics: Study of genes related to genetic controlled variation in drug responses.

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Phenotype: The total observable nature of an individual, resulting from interaction of the genotype with the environment. Plasmid: Circular extrachromosomal DNA molecules in bacteria that can independently reproduce. Plasmids can be used as vectors in recombinant DNA research, and they can contain genes important to bacterial virulence such as antibiotic resistance in nature. Polymorphism: Difference in DNA sequence among individuals that may underlie differences in health.

The vast majority of DNA polymorphisms are benign and not associated with a detectable phenotype. Population stratification also population structure : A form of confounding in genetic association studies caused by genetic differences between cases and controls unrelated to disease but due to sampling them from populations of different ancestries.

Proband: The affected person whose disorder, or concern about a disorder, brings a family or pedigree to be genetically evaluated. More than 1 promoter may be present in a gene and may give rise to different versions of the protein. Prophage: The genome of a bacteriophage when it is integrated into the host bacterial genome or a plasmid. Illumina Solexa and Roche sequencing has also been used to characterise the genomes of cotton [ 44 ]. Roche sequencing has been used to survey the genome of Miscanthus [ 45 ], while Sanger, Illumina Solexa and Roche sequencing is being used to interrogate the banana genome [ 46 ].

Ossowski et al. As well as finding over potential errors in the reference genome sequence, they identified more than unique SNPs and almost 80 1—3 bp indels. Longer indels are more difficult to identify from short read data without the use of paired reads, however, they did identify more than 3. The re-sequencing of rice and Medicago truncatula has also been undertaken using the Illumina Solexa for SNP discovery [ 48 , 49 ]. As increasing numbers of reference genomes become available, it is expected that whole genome re-sequencing of crop genomes will become common, providing insights into crop genome structure and diversity.

While Brassica shares extensive synteny with Arabidopsis thaliana , there is not enough similarity at the microsynteny level to approach Brassica genome sequencing as a re-sequencing of Arabidopsis. It is expected that the combination of the BAC sequence data and the assembled contigs from the Illumina GAII data will lead to the release of a high quality genome sequence during The large cereal genomes remain elusive, but the advances in technology are starting to make de novo sequencing of these genomes feasible. Roche has been applied for the sequencing of complex BACs from barley [ 50 , 51 ] and this has been complemented by repeat characterisation using WGS Illumina Solexa data [ 52 ].

However, the size of the wheat genome is much larger 17 Mbp than related cereal genomes such as barley Hordeum vulgare , Mbp , rye Secale cereale , Mbp and oat Avena sativa , 11 Mbp. The size and hexaploid nature of the wheat genome creates significant problems in elucidating its genome sequence and it may take several years before sequencing technology is fast and cheap enough to readily determine the whole genome sequence.

A total of 68 BAC clones of a 3B chromosome specific BAC library [ 53 ] have been fingerprinted and there are plans to sequence a minimal tiling path of BACs for this chromosome using Roche technology. Expectations are that by the end of , the majority of the gene-rich regions of hexaploid wheat will have been sequenced.

However, these expectations are likely to be modified by the rapid changes in sequencing technology and the ever-reducing cost of producing sequence data. The advances in genome sequencing technology have provided a means to sequence increasingly large and complex genomes. Data generation is now no longer limiting complex genome sequencing, and the sequencing and re-sequencing of previously intractable plant genomes is now becoming feasible. The ability to analyse and assemble this data is currently limited by a lack of dedicated bioinformatics tools that are designed to cope with the repetitive nature of many crop genomes.

We have also seen that with the release of each new assembly tool we see an improvement, even for static datasets, in assembly statistics. These include amongst others: an increase in contig sizes, a decrease in the total number of contigs and a decrease in the number of assembly errors. While it has not been formally proven that complex repeats can always be resolved from the data currently produced simply using novel algorithms, newer algorithms have continually demonstrated improvements in the overall quality of assemblies and this is largely due to the ever increasing sophistication in their methods of handling repeats.

However sophisticated the current methods for handling repeats are now, they still represent a nascent stage in the evolution of these algorithms. There are many directions this improvement can take and we are confident that the greatest increases in the ability to accurately resolve repeat structures in crop genome assemblies will stem from improvements made to the assembly algorithms. Improvements in data quality and quantity will of course also assist in producing better assemblies. As improved algorithms are developed, it may be expected that the sequencing of large and complex genomes will become commonplace, and following the research path of mammalian genomics, focus will move to the detection of sequence variation and the association of this variation with important agronomic traits, with downstream applications for crop improvement.

The size of many plant genomes combined with the large number of repetitive elements and polyploidy creates a challenge for traditional genome sequencing methods. Current sequencing and assembly approaches cannot produce a finished genome for large and complex cereal genomes. Novel approaches will be required to enable the sequencing of complex plant genomes using second or third-generation sequencing data. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide.

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Volume Article Contents. De novo sequencing of plant genomes using second-generation technologies Michael Imelfort. Oxford Academic. Google Scholar. David Edwards. Cite Citation. Permissions Icon Permissions. Abstract The ability to sequence the DNA of an organism has become one of the most important tools in modern biological research.

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Search ADS. Initial sequencing and analysis of the human genome vol , pg , Transposable element distribution, abundance and role in genome size variation in the genus Oryza. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Recent developments of the cucumber genome initiative—an international effort to unlock the genetic potential of an orphan crop using novel genomic technology. Google Preview.

Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand. De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Van Tassell. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.

Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. From cot curves to genomics. How gene cloning established new concepts in plant biology. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. The complete genome of an individual by massively parallel DNA sequencing. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. The golden delicious apple genome: an international whole genome sequencing initiative.

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety.

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Analysis of genome structure and organization in banana Musa acuminata using sequencing. Genome-wide detection of single nucleotide polymorphisms in diverse rice accessions. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Published by Oxford University Press. For Permissions, please email: journals. Issue Section:. Download all figures. View Metrics.

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Dictionary of DNA and genome technology / Paul Singleton.

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How to sequence the human genome - Mark J. Kiel

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