Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data,especially when the data sets are large and complex. Bioinformatics uses biology,chemistry,physics,computer science,computer programming,information engineering,mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can some times referred to as computational biology,however this distinction between the two terms is often disputed. To some,the term computational biology refers to building and using models of biological systems.
The human genome is a complete set of nucleic acid sequences for humans,encoded as the DNA within each of the 24 distinct chromosomes in the cell nucleus. A small DNA molecule is found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA,such as that for ribosomal RNA,transfer RNA,ribozymes,small nuclear RNAs,and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements,DNA playing structural and replicatory roles,such as scaffolding regions,telomeres,centromeres,and origins of replication,plus large numbers of transposable elements,inserted viral DNA,non-functional pseudogenes and simple,highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA,such as pseudogenes,but there is no firm consensus on the total amount of junk DNA.
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.
Computational biology refers to the use of data analysis,mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science,biology,and big data,the field also has foundations in applied mathematics,chemistry,and genetics. It differs from biological computing,a subfield of computer science and engineering which uses bioengineering to build computers.
Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species,spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparison of whole genome sequences provides a highly detailed view of how organisms are related to each other at the gene level. By comparing whole genome sequences,researchers gain insights into genetic relationships between organisms and study evolutionary changes. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore,Comparative genomics provides a powerful tool for studying evolutionary changes among organisms,helping to identify genes that are conserved or common among species,as well as genes that give unique characteristics of each organism. Moreover,these studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms.
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 National Human Genome Research Institute (NHGRI) is an institute of the National Institutes of Health,located in Bethesda,Maryland.
Personalized medicine,also referred to as precision medicine,is a medical model that separates people into different groups—with medical decisions,practices,interventions and/or products being tailored to the individual patient based on their predicted response or risk of disease. The terms personalized medicine,precision medicine,stratified medicine and P4 medicine are used interchangeably to describe this concept,though some authors and organizations differentiate between these expressions based on particular nuances. P4 is short for "predictive,preventive,personalized and participatory".
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.
The Cancer Genome Project is part of the cancer,aging,and somatic mutation research based at the Wellcome Trust Sanger Institute in the United Kingdom. It aims to identify sequence variants/mutations critical in the development of human cancers. Like The Cancer Genome Atlas project within the United States,the Cancer Genome Project represents an effort in the War on Cancer to improve cancer diagnosis,treatment,and prevention through a better understanding of the molecular basis of the disease. The Cancer Genome Project was launched by Michael Stratton in 2000,and Peter Campbell is now the group leader of the project. The project works to combine knowledge of the human genome sequence with high throughput mutation detection techniques.
Personal genomics or consumer genetics is the branch of genomics concerned with the sequencing,analysis and interpretation of the genome of an individual. The genotyping stage employs different techniques,including single-nucleotide polymorphism (SNP) analysis chips,or partial or full genome sequencing. Once the genotypes are known,the individual's variations can be compared with the published literature to determine likelihood of trait expression,ancestry inference and disease risk.
Computational epigenetics uses statistical methods and mathematical modelling in epigenetic research. Due to the recent explosion of epigenome datasets,computational methods play an increasing role in all areas of epigenetic research.
The 1000 Genomes Project (1KGP),taken place from January 2008 to 2015,was an international research effort to establish the most detailed catalogue of human genetic variation at the time. Scientists planned to sequence the genomes of at least one thousand anonymous healthy participants from a number of different ethnic groups within the following three years,using advancements in newly developed technologies. In 2010,the project finished its pilot phase,which was described in detail in a publication in the journal Nature. In 2012,the sequencing of 1092 genomes was announced in a Nature publication. In 2015,two papers in Nature reported results and the completion of the project and opportunities for future research.
Whole genome sequencing (WGS) is the process of determining the entirety,or nearly 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 mitochondria and,for plants,in the chloroplast.
DNA encryption is the process of hiding or perplexing genetic information by a computational method in order to improve genetic privacy in DNA sequencing processes. The human genome is complex and long,but it is very possible to interpret important,and identifying,information from smaller variabilities,rather than reading the entire genome. A whole human genome is a string of 3.2 billion base paired nucleotides,the building blocks of life,but between individuals the genetic variation differs only by 0.5%,an important 0.5% that accounts for all of human diversity,the pathology of different diseases,and ancestral story. Emerging strategies incorporate different methods,such as randomization algorithms and cryptographic approaches,to de-identify the genetic sequence from the individual,and fundamentally,isolate only the necessary information while protecting the rest of the genome from unnecessary inquiry. The priority now is to ascertain which methods are robust,and how policy should ensure the ongoing protection of genetic privacy.
A plant genome assembly represents the complete genomic sequence of a plant species,which is assembled into chromosomes and other organelles by using DNA fragments that are obtained from different types of sequencing technology.
Dr. Krystal Tsosie (Diné) is a Navajo geneticist and bioethicist at Arizona State University and activist for Indigenous data sovereignty. She is also an educator and an expert on genetic and social identities. Her advocacy and academic work in ameliorating disparities in genetics through community-based participatory research has been covered by various national news sources,including The New York Times,Nova,The Washington Post,NPR,The Atlantic,Forbes, and The Boston Globe.
The UC Santa Cruz Genomics Institute is a public research institution based in the Jack Baskin School of Engineering at the University of California,Santa Cruz. The Genomics Institute's scientists and engineers work on a variety of projects related to genome sequencing,computational biology,large data analytics,and data sharing. The institute also maintains a number of software tools used by researchers worldwide,including the UCSC Genome Browser,Dockstore,and the Xena Browser.
Personalized genomics is the human genetics-derived study of analyzing and interpreting individualized genetic information by genome sequencing to identify genetic variations compared to the library of known sequences. International genetics communities have spared no effort from the past and have gradually cooperated to prosecute research projects to determine DNA sequences of the human genome using DNA sequencing techniques. The methods that are the most commonly used are whole exome sequencing and whole genome sequencing. Both approaches are used to identify genetic variations. Genome sequencing became more cost-effective over time,and made it applicable in the medical field,allowing scientists to understand which genes are attributed to specific diseases.
