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Definition of Genomics at the CAP and Glossary of Key Terms Author(s): Gail Habegger Vance MD, FCAP, George Fiedler, Tim Bragg, David Greenfeld, Jill Kaufman, PhD, Jodi Soriano, Nazneen Aziz, PhD, Fay Shamanski, PhD, Bernadine Prygrosky, Jeff McNeal, Patricia Vasalos, Stanley J. Robboy MD, FCAP, Karl V. Voelkerding MD, FCAP, Louis D. Wright Jr., MD, FCAP, Debra G.B. Leonard MD, PhD, FCAP, Walter H. Henricks MD, FCAP, Iris Schrijver MD, FCAP, Gregory J. Tsongalis, PhD College of American Pathologists | 325 Waukegan Rd. | Northfield, IL 60093 | 800-323-4040 | cap.org | Version 1 325 Waukegan Rd. |Northfield, IL 60093 t: 800-323-4040 | cap.org Version no. Definition of Genomics at the CAP and Glossary of Key Terms Genomics Definition for the CAP and Pathology The genome is the complete set of DNA within a single cell of an organism. Genomics – the study and application of recombinant DNA, mitochondrial DNA, pathogen DNA/RNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes. Genomics for the CAP - genomic medicine, molecular pathology, and clinical care based on genomic information. This includes the application and utility of large-scale genomic information management and data architecture in healthcare diagnostics in pursuit of efficient and cost-effective patient care and health outcomes at the level of individuals, institutions, populations, and communities. 1 Clinical Informatics - a discipline within informatics that we define as “the application of information management in healthcare in pursuit of safe, efficient, effective, and costeffective patient care and health outcomes at the level of individuals, institutions, 2 populations, and communities.” The term informatics is broad with many similar, but somewhat different, definitions. We chose the definition of informatics as the “science of information management” for the purposes of this strategy. 1 Definition proposed by Gail Habegger Vance, MD, FCAP and CAP’s Genomics Strategy Workgroup – endorsed by Advisory Group 2 Definition proposed by Andrew E. Horvath, MD, FCAP and Walter H. Henricks, MD, FCAP and CAP’s Informatics Strategy Workgroup – endorsed by Advisory Group © 2015 College of American Pathologists. All rights reserved. PAGE 2 Definition of Genomics at the CAP and Glossary of Key Terms Glossary of Key Terms and Phrases A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Allele: Alternative form of a genetic locus; a single allele for each locus is inherited from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes). Base pair (bp): Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs. Bioinformatics: The study of methods for storing, retrieving and analyzing biological data, such as nucleic acid (DNA/RNA) and protein sequence, structure, function, pathways (neural pathways included) and genetic interactions. It generates new knowledge that is useful in such fields as drug design and development of new software tools to create that knowledge. Bioinformatics also deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, structural biology, software engineering, data mining, image processing, modeling and simulation, discrete mathematics, control and system theory, circuit theory, and statistics. Complementary DNA (cDNA): DNA that is synthesized in the laboratory from a messenger RNA template. Chromosome: The self-replicating genetic structure of cells containing the cellular DNA that bears in its nucleotide sequence the linear array of genes. In prokaryotes, chromosomal DNA is circular, and the entire genome is carried on one chromosome. Eukaryotic genomes consist of a number of chromosomes whose DNA is associated with different kinds of proteins. © 2015 College of American Pathologists. All rights reserved. PAGE 3 Definition of Genomics at the CAP and Glossary of Key Terms Cis: Allele(s) on the same chromosome. Codon: The sequence of nucleotides, coded in triplets (codons) along the mRNA, that determines the sequence of amino acids in protein synthesis. A gene's DNA sequence can be used to predict the mRNA sequence, and the genetic code can in turn be used to predict the amino acid sequence. Copy number variant: The gene copy number (also "copy number variants" or CNVs) is the number of copies of a particular gene in the genotype of an individual. Deoxyribonucleic acid (DNA): An informational molecule encoding the genetic instructions used in the development and functioning of all known living organisms and many viruses. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. Genetic information is encoded as a sequence of nucleotides (guanine, adenine, thymine, and cytosine) recorded using the letters G, A, T, and C. Most DNA molecules are double-stranded helices, consisting of two long polymers of simple units called nucleotides, molecules with backbones made of alternating sugars (deoxyribose) and phosphate groups (related to phosphoric acid), with the nucleobases (G, A, T, C) attached to the sugars. DNA is well-suited for biological information storage, since the DNA backbone is resistant to cleavage and the double-stranded structure provides the molecule with a built-in duplicate of the encoded information. Epigenetics: Epigenetics is an emerging field of science that studies heritable changes caused by the activation and deactivation of genes without any change in the underlying DNA sequence of the organism. The word epigenetics is of Greek origin and literally means over and above (epi) the genome. Epigenome: The term epigenome is derived from the Greek word epi which literally means “above” the genome. The epigenome consists of chemical compounds that modify, or © 2015 College of American Pathologists. All rights reserved. PAGE 4 Definition of Genomics at the CAP and Glossary of Key Terms mark, the genome in a way that tells it what to do, where to do it, and when to do it. Different cells have different epigenetic marks. These epigenetic marks, which are not part of the DNA itself, can be passed on from cell to cell as cells divide, and from one generation to the next. Epistasis: Epistasis is a circumstance where the expression of one gene is affected by the expression of one or more independently inherited genes. For example, if the expression of gene #2 depends on the expression of gene #1, but gene #1 becomes inactive, then the expression of gene #2 will not occur. In this example, gene #1 is said to be epistatic to gene #2. Exon: The protein-coding DNA sequence of a gene. Exome: The part of the genome formed by exons, the coding portions of genes that are expressed to provide the genetic blueprint used in the synthesis of proteins and other functional gene products. Gene: The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product (i.e., a protein or RNA molecule). Gene expression: The process by which a gene's coded information is converted into the structures present and operating in the cell. Expressed genes include those that are transcribed into mRNA and then translated into protein and those that are transcribed into RNA but not translated into protein (e.g., transfer and ribosomal RNAs). Genetic Marker: A gene or other identifiable portion of DNA whose inheritance can be followed. © 2015 College of American Pathologists. All rights reserved. PAGE 5 Definition of Genomics at the CAP and Glossary of Key Terms Genome: The complete set of DNA within a single cell of an organism. Genomics: The study and application of recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes. Genomic Medicine: Medical practice driven by genomic information for the care of individual patients. Genotype: The genetic constitution of an organism, as distinguished from its physical appearance. Heterozygote: An organism that has two different alleles at one or more loci on homologous chromosomes. Homozygote: An organism that has two identical alleles of a gene. Insertion: A chromosome abnormality in which a piece of DNA is incorporated into a gene and thereby disrupts the gene's normal function. Karyogram: A photomicrograph of an individual's chromosomes arranged in a standard format showing the number, size, and shape of each chromosome type; used in lowresolution physical mapping to correlate gross chromosomal abnormalities with the characteristics of specific diseases. Microarray: Sets of miniaturized chemical reaction areas that may also be used to test DNA fragments, antibodies, or proteins all contained on a single platform. © 2015 College of American Pathologists. All rights reserved. PAGE 6 Definition of Genomics at the CAP and Glossary of Key Terms Monogenic disorder: A disorder caused by mutation of a single gene. Multiplexing: A laboratory approach that performs multiple sets of reactions in parallel (simultaneously); greatly increasing speed and throughput. Mutation: Any heritable change in DNA sequence. Nucleotide: A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). Thousands of nucleotides are linked to form a DNA or RNA molecule. Oligonucleotide: A molecule usually composed of 25 or fewer nucleotides; used as a DNA synthesis primer. Oncogene: A gene, one or more forms of which is associated with cancer. Many oncogenes are involved, directly or indirectly, in controlling the rate of cell growth. Pharmacogenomics: The study of the interaction of an individual's genetic makeup and response to a drug. Phenotype: The physical characteristics of an organism or the presence of a disease that may or may not be genetic. Polymerase chain reaction (PCR): A method for amplifying a DNA base sequence using a heat-stable polymerase and two 20-base primers, one complementary to the (+) strand at one end of the sequence to be amplified and one complementary to the (-) strand at the other end. © 2015 College of American Pathologists. All rights reserved. PAGE 7 Definition of Genomics at the CAP and Glossary of Key Terms Because the newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample. Polymorphism: Difference in DNA sequence among individuals that may underlie differences in health. Genetic variations occurring in more than 1% of a population would be considered useful polymorphisms for genetic linkage analysis. Primer: Short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase. Pseudogene: A sequence of DNA similar to a gene but nonfunctional; probably the remnant of a once-functional gene that accumulated mutations. Recombinant DNA (rDNA): DNA sequences that result from the use of laboratory methods (molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological organisms. Recombinant DNA is possible because DNA molecules from all organisms share the same chemical structure; they differ only in the sequence of nucleotides within that identical overall structure. Consequently, when DNA from a foreign source is linked to host sequences that can drive DNA replication and then introduced into a host organism, the foreign DNA is replicated along with the host DNA. Recessive gene: A gene which will be expressed only if there are 2 identical copies or, for a male, if one copy is present on the X chromosome. Sequencing methods: The processes and instrumentation for determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to © 2015 College of American Pathologists. All rights reserved. PAGE 8 Definition of Genomics at the CAP and Glossary of Key Terms determine the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA. These include chain termination methods such as Sanger sequencing, de novo methods such as Shotgun sequencing and Bridge polymerase chain reaction, and the Next Generation Sequencing methods such as single molecule real time sequencing (SMRT), heliscope single molecule sequencing, DNA nanoball sequencing, ion semiconductor sequencing, SOLiD sequencing by ligation, Illumina sequencing by reversible dye-terminators, pyrosequencing, and Polony sequencing. Sequence tagged site (STS): Short (200 to 500 base pairs) DNA sequence that has a single occurrence in the human genome and whose location and base sequence are known. Detectable by polymerase chain reaction, STSs are useful for localizing and orienting the mapping and sequence data reported from many different laboratories and serve as landmarks on the developing physical map of the human genome. Expressed sequence tags (ESTs) are STSs derived from cDNAs. Single-gene disorder: Hereditary disorder caused by a mutant allele of a single gene (e.g., Duchenne muscular dystrophy, retinoblastoma, sickle cell disease). Single Nucleotide Polymorphism: Single nucleotide polymorphisms (SNPs) are a type of polymorphism involving variation of a single base pair. Scientists are studying how single nucleotide polymorphisms, or SNPs (pronounced "snips"), in the human genome correlate with disease, drug response, and other phenotypes. Somatic cell genetic mutation: A change in the genetic structure that is neither inherited nor passed to offspring. Also called acquired mutations. Suppressor gene: A gene that can suppress the action of another gene. © 2015 College of American Pathologists. All rights reserved. PAGE 9 Definition of Genomics at the CAP and Glossary of Key Terms Tandem repeat sequences: Multiple copies of the same base sequence on a chromosome; used as markers in physical mapping. Trans: Allele on the other chromosome homolog. Transcription: The synthesis of an RNA copy from a sequence of DNA (a gene); the first step in gene expression. Transcriptome: The full complement of activated genes, mRNAs, or transcripts in a particular tissue at a particular time. Translation: The process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids. Translocation: A mutation in which a large segment of one chromosome breaks off and attaches to another chromosome. Variant: An alteration in the normal sequence of a gene, the significance of which is often unclear until further study of the genotype and corresponding phenotype occurs in a sufficiently large population. Complete gene sequencing often identifies numerous allelic variants (sometimes hundreds) for a given gene. © 2015 College of American Pathologists. All rights reserved. PAGE 10