ISO/TS 4425:2023 ゲノミクス情報学 — 臨床大規模並列 DNA シーケンスのマイクロサテライト不安定性 (MSI) 情報を記述するデータ要素とそのメタデータ | ページ 6

3.1

biological specimen

biospecimen

specimen

sample of tissue, body fluid, food, or other substance that is collected or acquired to support the assessment, diagnosis, treatment, mitigation or prevention of a disease, disorder or abnormal physical state, or its symptoms

[SOURCE:ISO/TS 20428:2017, 3.34]

3.2

clinical sequencing

next generation sequencing or later sequencing technologies with human samples for clinical practice and clinical trials

[SOURCE:ISO/TS 20428:2017, 3.5]

3.3

deletion

contiguous removal of one or more bases from a genomic sequence

[SOURCE:ISO/IEC 23092-2:2020, 3.4]

3.4

deoxyribonucleic acid

DNA

molecule that encodes genetic information in the nucleus of cells

[SOURCE:ISO 25720:2009, 4.7]

3.5

DNA sequencing

determining the order of nucleotide bases (adenine, guanine, cytosine and thymine) in a molecule of DNA

Note 1 to entry: Sequence is generally described from the 5' end.

[SOURCE:ISO 17822:2020, 3.19]

3.6

exome

part of the genome formed by exons

[SOURCE:ISO/TS 20428:2017, 3.13]

3.7

gene

basic unit of hereditary material that encodes and controls the expression of a protein or protein subunit

3.8

indel

insertion (3.9) or/and deletion (3.3)

[SOURCE:ISO/TS 20428:2017, 3.18]

3.9

insertion

contiguous addition of one or more bases into a genomic sequence

[SOURCE:ISO/IEC 23092-2:2020, 3.18]

3.10

microsatellite

repetitive DNA elements, also known as simple sequence repeats (SSR), consisting of short in tandem repeat motifs of one to a few nucleotides that tend to occur in non-coding DNA of eukaryotic genomes and that are sometimes referred to as variable number of tandem repeats (VNTRs)

3.11

microsatellite instability

MSI

condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR)

3.12

DNA mismatch repair

MMR

system for recognizing and repairing erroneous insertion, deletion, and misincorporation of bases that can rise during DNA replication and recombination, as well as repairing some forms of DNA damage

3.13

nucleotide

monomer of a nucleic acid polymer such as DNA or RNA

Note 1 to entry: Nucleotides are denoted as letters ('A' for adenine; 'C' for cytosine; 'G' for guanine; 'T' for thymine which only occurs in DNA; and 'U' for uracil, which only occurs in RNA). The chemical formula for a specific DNA or RNA molecule is given by the sequence of its nucleotides, which can be represented as a string over the alphabet ('A',' C',' G', 'T') in the case of DNA, and a string over the alphabet ('A', 'C', 'G', 'U') in the case of RNA. Bases with unknown molecular composition are denoted with 'N'.

[SOURCE:ISO/IEC 23092-2:2020, 3.20]

3.14

polymerase chain reaction

PCR

in vitro enzymatic technique to increase the number of copies of a specific DNA fragment by several orders of magnitude

[SOURCE:ISO 16577:2022, 3.6.47]

3.15

quality score

Phred quality score

Q score

sequencing quality score of a given nucleotide base

Note 1 to entry:Q is defined by the following equation: Q = -10log10(e) ここで, e is the estimated probability of the base call being wrong.

Note 2 to entry: A quality score of 20 represents an error rate of 1 in 100, with a corresponding call accuracy of 99 %.

Note 3 to entry: Higher quality scores indicate a smaller probability of error. Lower quality scores can result in a significant portion of the reads being unusable. Low quality scores may also indicate false-positive variant calls, resulting in inaccurate conclusions.

[SOURCE:ISO 20397-2:2021, 3.30]

3.16

read type

type of run in the sequencing instrument

Note 1 to entry: It can be either single-end or paired-end.

Note 2 to entry: Single-end: Single read runs the sequencing instrument reads from one end of a fragment to the other end.

Note 3 to entry: Paired-end: Paired-end runs read from one end to the other and then starts another round of reading from the opposite end.

[SOURCE:ISO/TS 20428:2017, 3.27]

3.17

reference sequence

nucleic acid sequence with biological relevance

Note 1 to entry: Each reference sequence is indexed by a one-dimensional integer coordinate system whereby each integer within range identifies a single nucleotide. Coordinate values can only be equal to or larger than zero. The coordinate system in the context of this standard is zero-based (i.e., the first nucleotide has coordinate 0, and it is said to be at position 0) and linearly increases within the string from left to right.

[SOURCE:ISO/IEC 23092-1:2020, 3.22]

3.18

read

sequence read

fragmented nucleotide sequences that are used to reconstruct the original sequence for next-generation sequencing technologies

[SOURCE:ISO/TS 20428:2017, 3.26]

3.19

variation

sequence variation

DNA sequence variation

differences of DNA sequence among individuals in a population

[SOURCE:ISO 25720:2009, 4.8]

3.20

small indel

insertion (3.9) or deletion (3.3) of 2 nucleotides to 100 nucleotides

[SOURCE:ISO/TS 20428:2017, 3.32]

3.21

subject of care

person who uses, or is a potential user of, a healthcare service

[SOURCE:ISO/TS 22220:2011, 3.2, modified — Note to entry and second preferred term deleted.]

3.22

target capture

method to capture genomic regions of interest from a DNA sample prior to sequencing

[SOURCE:ISO/TS 20428:2017, 3.36]

3.23

targeted sequencing

technique used for sequencing only selected/targeted genomic regions of interest from a DNA sample

[SOURCE:ISO/TS 22692:2020, 3.22, modified — Note to entry and second preferred term deleted.]

3.24

whole exome sequencing

WES

technique for sequencing the exomes of the protein-coding genes in a genome

3.25

whole genome sequencing

WGS

technique that determines the complete DNA sequence of an organism's genome at a single time

[SOURCE:ISO/TS 20428:2017, 3.39]