In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun.
Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.
The Joint Genome Institute (JGI) is a scientific user facility for integrative genomic science at Lawrence Berkeley National Laboratory. The mission of the JGI is to advance genomics research in support of the United States Department of Energy's (DOE) missions of energy and the environment. It is one of three national scientific user facilities supported by the Office of Biological and Environmental Research (BER) within the Department of Energy's Office of Research. These BER facilities are part of a more extensive network of 28 national scientific user facilities that operate at the DOE national laboratories.
Molecular cytogenetics combines two disciplines, molecular biology and cytogenetics, and involves the analysis of chromosome structure to help distinguish normal and cancer-causing cells. Human cytogenetics began in 1956 when it was discovered that normal human cells contain 46 chromosomes. However, the first microscopic observations of chromosomes were reported by Arnold, Flemming, and Hansemann in the late 1800s. Their work was ignored for decades until the actual chromosome number in humans was discovered as 46. In 1879, Arnold examined sarcoma and carcinoma cells having very large nuclei. Today, the study of molecular cytogenetics can be useful in diagnosing and treating various malignancies such as hematological malignancies, brain tumors, and other precursors of cancer. The field is overall focused on studying the evolution of chromosomes, more specifically the number, structure, function, and origin of chromosome abnormalities. It includes a series of techniques referred to as fluorescence in situ hybridization, or FISH, in which DNA probes are labeled with different colored fluorescent tags to visualize one or more specific regions of the genome. Introduced in the 1980s, FISH uses probes with complementary base sequences to locate the presence or absence of the specific DNA regions. FISH can either be performed as a direct approach to metaphase chromosomes or interphase nuclei. Alternatively, an indirect approach can be taken in which the entire genome can be assessed for copy number changes using virtual karyotyping. Virtual karyotypes are generated from arrays made of thousands to millions of probes, and computational tools are used to recreate the genome in silico.
New England Biolabs (NEB) is an American life sciences company which produces and supplies recombinant and native enzyme reagents for life science research. It also provides products and services supporting genome editing, synthetic biology and next-generation sequencing. NEB also provides free access to research tools such as REBASE, InBASE, and Polbase.
Chromosome conformation capture techniques are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genomic loci that are nearby in 3-D space, but may be separated by many nucleotides in the linear genome. Such interactions may result from biological functions, such as promoter-enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. Interaction frequencies may be analyzed directly, or they may be converted to distances and used to reconstruct 3-D structures.
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele.
The Earth Microbiome Project (EMP) was an initiative founded by Janet Jansson, Jack Gilbert, and Rob Knight in 2010 to collect natural samples and analyze microbial life around the globe.
Wang Jun is a Chinese scientist, founder and CEO of iCarbonX, and former CEO of the Beijing Genomics Institute.
Single cell epigenomics is the study of epigenomics in individual cells by single cell sequencing. Since 2013, methods have been created including whole-genome single-cell bisulfite sequencing to measure DNA methylation, whole-genome ChIP-sequencing to measure histone modifications, whole-genome ATAC-seq to measure chromatin accessibility and chromosome conformation capture.
Second Genome is a venture capital funded, life sciences research company based in South San Francisco. The company's focus is on the development and exploitation of a research platform which facilitates the identification and elucidation of relationships between human physiology and the human microbiota, and it has a long term goal of becoming a drug development company. The name "second genome" comes from the notion that humans have, effectively, two genomes: the native human genome, and the more diverse set of genomes carried by the human microbiota.
Nikos Kyrpides is a Greek-American bioscientist who has worked on the origins of life, information processing, bioinformatics, microbiology, metagenomics and microbiome data science. He is a senior staff scientist at the Berkeley National Laboratory, head of the Prokaryote Super Program and leads the Microbiome Data Science program at the US Department of Energy Joint Genome Institute.
The Philippine Genome Center (PGC) is a multi-disciplinary research facility in Quezon City, Metro Manila, Philippines which specializes in genomics.
Clinical metagenomic next-generation sequencing (mNGS) is the comprehensive analysis of microbial and host genetic material in clinical samples from patients by next-generation sequencing. It uses the techniques of metagenomics to identify and characterize the genome of bacteria, fungi, parasites, and viruses without the need for a prior knowledge of a specific pathogen directly from clinical specimens. The capacity to detect all the potential pathogens in a sample makes metagenomic next generation sequencing a potent tool in the diagnosis of infectious disease especially when other more directed assays, such as PCR, fail. Its limitations include clinical utility, laboratory validity, sense and sensitivity, cost and regulatory considerations.
Hi-C is a high-throughput genomic and epigenomic technique to capture chromatin conformation (3C). In general, Hi-C is considered as a derivative of a series of chromosome conformation capture technologies, including but not limited to 3C, 4C, and 5C. Hi-C comprehensively detects genome-wide chromatin interactions in the cell nucleus by combining 3C and next-generation sequencing (NGS) approaches and has been considered as a qualitative leap in C-technology development and the beginning of 3D genomics.
Proximity ligation-assisted chromatin immunoprecipitation sequencing (PLAC-seq) is a chromatin conformation capture(3C)-based technique to detect and quantify genomic chromatin structure from a protein-centric approach. PLAC-seq combines in situ Hi-C and chromatin immunoprecipitation (ChIP), which allows for the identification of long-range chromatin interactions at a high resolution with low sequencing costs. Mapping long-range 3-dimensional(3D) chromatin interactions is important in identifying transcription enhancers and non-coding variants that can be linked to human diseases.
Pore-C is a genomic technique which utilizes chromatin conformation capture (3C) and Oxford Nanopore Technologies' (ONT) long-read sequencing to characterize three-dimensional (3D) chromatin structure. To characterize concatemers, the originators of Pore-C developed an algorithm to identify alignments that are assigned to a restriction fragment; concatemers with greater than two associated fragments are deemed high order. Pore-C attempts to improve on previous 3C technologies, such as Hi-C and SPRITE, by not requiring DNA amplification prior to sequencing. This technology was developed as a simpler and more easily scalable method of capturing higher-order chromatin structure and mapping regions of chromatin contact. In addition, Pore-C can be used to visualize epigenomic interactions due to the capability of ONT long-read sequencing to detect DNA methylation. Applications of this technology include analysis of combinatorial chromatin interactions, the generation of de novo chromosome scale assemblies, visualization of regions associated with multi-locus histone bodies, and detection and resolution of structural variants.
