Genomic and medical data refers to an area within

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 ...

that concerns the recording,

sequencing In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...

and analysis of an organism's

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 ...

Background

Genomics 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, ...

is a concept that was first developed by

Fred Sanger Frederick Sanger (; 13 August 1918 – 19 November 2013) was a British biochemist who received the Nobel Prize in Chemistry twice. He won the 1958 Chemistry Prize for determining the amino acid sequence of insulin and numerous other prot ...

who first sequenced the complete

of a

virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...

and of a

mitochondrion A mitochondrion () is an organelle found in the cell (biology), cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosine tri ...

. The term genomics was first coined in 1986 by Tom Roderick, a geneticist at the

Jackson Laboratory The Jackson Laboratory (often abbreviated as JAX) is an independent, non-profit biomedical research institution which was founded by Clarence Cook Little in 1929. It employs over 3,000 employees in Bar Harbor, Maine; Sacramento, California; F ...

in Maine, during a meeting about the mapping of the human genome. The genome is the entire

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

content that is present within one cell of an organism. Experts in genomics strive to determine consummate

DNA sequences A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the ...

and perform

genetic mapping Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be sepa ...

to help understand disease.

involves the study of all genes at the DNA (deoxyribonucleic Acid),

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

(messenger ribonucleic acid), and proteome level as well as the cellular or tissue level.

Open source tools for medical data

OMOP: It is an acronym for Observational Medical Outcomes Partnership. The OMOP research program was initially established under Foundation for

NIH The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in 1887 and is part of the United States Department of Health and Human Service ...

) and created first version of OMOP

common data model A common data model (CDM) can refer to any standardised data model which allows for data and information exchange between different applications and data sources. Common data models aim to standardise logical infrastructure so that related applica ...

. The common data model was able to accommodate observational data of different types (both claims and

electronic health record An electronic health record (EHR) is the systematized collection of electronically stored patient and population health information in a digital format. These records can be shared across different health care settings. Records are shared thro ...

s). It has a single common infrastructure that can accommodate both of the types from different sources around the world. It has successfully developed and executed large-scale statistical analyses capable of enabling active drug safety surveillance across prescription medications. OHDSI: It stands for Observational Health Data Sciences and Informatics and was initiated in 2013. It is a multi-stakeholder, interdisciplinary collaborative that is striving to bring out the value of observational health data through large-scale analytics. The main objective of OHDSI is to establish a research community for observational health data sciences that enables active engagement across multiple disciplines spanning multiple stakeholder groups. OpenClinica: It is the world's most widely used,

open-source software Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

for clinical research. First released in 2005, OpenClinica is designed to meet the diverse needs of modern research environments. It is built as a lightweight, extensible, and modular application. The software is web based and users can access it with a standard web browser and internet connection.

OpenEHR openEHR is an open standard specification in health informatics that describes the management and storage, retrieval and exchange of health data in electronic health records (EHRs). In openEHR, all health data for a person is stored in a "one lifet ...

: It is an open standard specification in

health informatics Health informatics combines communications, information technology (IT), and health care to enhance patient care and is at the forefront of the medical technological revolution. It can be viewed as a branch of engineering and applied science. ...

that describes the management and storage, retrieval and exchange of health data in electronic health records. In OpenEHR, all health data for a person is stored in a "one lifetime", vendor-independent, person-centered EHR. Clinical3PO: clinical3po is an open source big data environment for the Veteran Affairs informatics and computing infrastructure, enables scalable markup of electronic health record events to be used for predictive analysis.

Open Source tools for Genetic Data

Beacon Project: Beacon Project is an open web service that tests the willingness of international sites to share genetic data. It is being implemented on the websites of the world's top genomic research organizations. Matchmaker Exchange: Matchmaker Exchange is a federated network of databases whose goal is to find genetic causes of rare diseases by matching similar

phenotypic 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 propert ...

and genotypic profiles. BRCA Challenge: The BRCA Challenge aims to advance understanding of the genetic basis of breast and other cancers using data from around the world.

Gather and use genetic data in health care

More and more people are getting their DNA sequenced, but the use of genetic data to inform medical decisions is lagging. More than a decade since the

Human Genome Project The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...

was declared complete, fewer than 60 genetic variants are deemed worthy for use in clinical care, most for severe conditions in very young children. These genetic variants can guide medical decisions. Genomic data alone is not very useful, but needs to be examined in the right context in research and healthcare Some health-care organizations are working out ways to collect evidence from ongoing care to improve patient outcomes. Such efforts systematically analyze clinical data from peer-reviewed literature and introduce selected findings into clinical care. Then they track and evaluate outcomes. One of the best examples of such a 'learning health-care system' is the

Geisinger Health System Geisinger Health System (GHS) is a regional health care provider to central, south-central and northeastern Pennsylvania. Headquartered in Danville, Pennsylvania, Geisinger services over 3 million patients in 45 counties. Geisinger operates ten ...

, which serves 2.6 million patients in Pennsylvania. Once diagnosed with chronic conditions such as diabetes, heart failure or depression, patients' care and outcomes are monitored. Metrics such as hospitalization rates are used to recommend that certain individuals receive coordinated attention from a team of specialists including mental-health practitioners and nutritionists. Over three years, this reduced hospital admissions by 18% and seemed to reduce spending by 7%.

References

{{Reflist, 30em Genomics