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Deep Sequencing
In genetics, coverage is one of several measures of the depth or completeness of DNA sequencing, and is more specifically expressed in any of the following terms: *Sequence coverage (or depth) is the number of unique reads that include a given nucleotide in the reconstructed sequence. Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. *Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of genome size. *Genomic coverage, the percentage of all base pairs or loci of the genome covered by sequencing. Sequence coverage Rationale Even though the sequencing accuracy for each individual nucleotide is very high, the very large number of nucleotides in the genome means that if an individual genome is only sequenced once, there will be a significant number of sequencing errors. Furthermore, many positions in a genome contain rare single-nucleotide polymorphisms (SNPs). Hence to distingu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNA-Seq
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome. RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/ SNPs and changes in gene expression over time, or differences in gene expression in different groups or treatments. In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling. RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries. Recent advances in RNA-Seq include single cell sequencing, bulk RNA sequencing, 3' mRNA-sequencing, in situ sequencing of fixed tissue, and native RNA molecule sequencin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Human Genome Research Institute
The National Human Genome Research Institute (NHGRI) is an institute of the National Institutes of Health, located in Bethesda, Maryland. NHGRI began as the Office of Human Genome Research in The Office of the Director in 1988. This Office transitioned to the National Center for Human Genome Research (NCHGR), in 1989 to carry out the role of the NIH in the International Human Genome Project (HGP). The HGP was developed in collaboration with the United States Department of Energy (DOE) and began in 1990 to sequence the human genome. In 1993, NCHGR expanded its role on the NIH campus by establishing the Division of Intramural Research (DIR) to apply genome technologies to the study of specific diseases. In 1996, the Center for Inherited Disease Research (CIDR) was also established (co-funded by eight NIH institutes and centers) to study the genetic components of complex disorders. In 1997 the United States Department of Health and Human Services (DHHS) renamed NCHGR the National Hum ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Whole Genome Sequencing
Whole genome sequencing (WGS), also known as full genome sequencing or just genome sequencing, is the process of determining the entirety of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondrial DNA, mitochondria and, for plants, in the chloroplast. Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014. In the future of personalized medicine, whole genome sequence data may be an important tool to guide therapeutic intervention. The tool of DNA sequencing, gene sequencing at Single-nucleotide polymorphism, SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response. Whole genome sequencing should not be confused with DNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Sequencing Theory
DNA sequencing theory is the broad body of work that attempts to lay analytical foundations for determining the order of specific nucleotides in a sequence of DNA, otherwise known as DNA sequencing. The practical aspects revolve around designing and optimizing sequencing projects (known as "strategic genomics"), predicting project performance, troubleshooting experimental results, characterizing factors such as sequence bias and the effects of software processing algorithms, and comparing various sequencing methods to one another. In this sense, it could be considered a branch of systems engineering or operations research. The permanent archive of work is primarily mathematical, although numerical calculations are often conducted for particular problems too. DNA sequencing theory addresses ''physical processes'' related to sequencing DNA and should not be confused with theories of analyzing resultant DNA sequences, e.g. sequence alignment. Publications sometimes do not make a careful ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base Calling
Base calling is the process of assigning nucleobases to chromatogram peaks, light intensity signals, or electrical current changes resulting from nucleotides passing through a nanopore. One computer program for accomplishing this job is Phred, which is a widely used base calling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy. Base callers for Nanopore sequencing use neural networks trained on current signals obtained from accurate sequencing data. Base calling accuracy Base calling can be assessed by two metrics, read accuracy and consensus accuracy. Read accuracy refers to the called base's accuracy to a known reference. Consensus accuracy refers to how accurate a consensus sequence is compared to overlapping reads from the same genetic locus In genetics, a locus (: loci) is a specific, fixed position on a chromosome where a particular gene or genetic marker is located. Each chromosome carries many genes, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Whole Genome Sequencing
Whole genome sequencing (WGS), also known as full genome sequencing or just genome sequencing, is the process of determining the entirety of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondrial DNA, mitochondria and, for plants, in the chloroplast. Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014. In the future of personalized medicine, whole genome sequence data may be an important tool to guide therapeutic intervention. The tool of DNA sequencing, gene sequencing at Single-nucleotide polymorphism, SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response. Whole genome sequencing should not be confused with DNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological properties, and its behavior. An organism's phenotype results from two basic factors: the expression of an organism's genetic code (its genotype) and the influence of environmental factors. Both factors may interact, further affecting the phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978 and again in his 1982 book '' The Extended Phenotype'' suggested that one can regard bird nests and other built structures such as caddisfly larva cases and beaver dams ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcriptome
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term ''transcriptome'' is a portmanteau of the words ''transcript'' and ''genome''; it is associated with the process of transcript production during the biological process of transcription. The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. Single-cell transcriptomics allows tracking of transcript change ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians, Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Phenotypic trait, Trait inheritance and Molecular genetics, molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the Cell (bi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Single-nucleotide Polymorphism
In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently large fraction of the population (e.g. 1% or more), many publications do not apply such a frequency threshold. For example, a Guanine, G nucleotide present at a specific location in a reference genome may be replaced by an Adenine, A in a minority of individuals. The two possible nucleotide variations of this SNP – G or A – are called alleles. SNPs can help explain differences in susceptibility to a wide range of diseases across a population. For example, a common SNP in the Factor H, CFH gene is associated with increased risk of age-related macular degeneration. Differences in the severity of an illness or response to treatments may also be manifestations of genetic variations caused by SNPs. For example, two ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondrial DNA, mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplast DNA, chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been Whole-genome sequencing, sequenced and various regions have been annotated. The first genome to be sequenced was that of the virus φX174 in 1977; the first genome sequence of a prokaryote (''Haemophilus influenzae'') was published in 1995; the yeast (''Saccharomyces cerevisiae'') genome was the first eukaryotic genome to be sequenced in 1996. The Human Genome Project ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
