Editing Karyotype (section)

== Human karyogram ==
[[File:DNA human male chromosomes.gif|thumb|Micrographic karyogram of a human male. See section text for details.]]
[[File:Human karyotype with bands and sub-bands.png|thumb|370px|Schematic karyogram of a human. Even at low magnification, it gives an overview of the [[human genome]], with numbered chromosome pairs, its main changes during the [[cell cycle]] (top center), and the [[human mitochondrial genetics|mitochondrial genome]] to scale (at bottom left). See section text for more details.]]
Both the micrographic and schematic karyograms shown in this section have a standard chromosome layout, and display darker and lighter regions as seen on [[G banding]], which is the appearance of the chromosomes after treatment with [[trypsin]] (to partially digest the chromosomes) and [[Staining (biology)|staining]] with [[Giemsa stain]]. Compared to darker regions, the lighter regions are generally more [[Transcription (biology)|transcriptionally]] active, with a greater ratio of [[coding DNA]] versus [[non-coding DNA]], and a higher [[GC content]].<ref name=Romiguier2017>{{cite journal| author=Romiguier J, Roux C| title=Analytical Biases Associated with GC-Content in Molecular Evolution. | journal=Front Genet | year= 2017 | volume= 8 | issue=  | pages= 16 | pmid=28261263 | doi=10.3389/fgene.2017.00016 | pmc=5309256 | doi-access=free }} </ref>

Both the micrographic and schematic karyograms show the normal human [[diploid]] karyotype, which is the typical composition of the [[genome]] within a normal cell of the human body, and which contains 22 pairs of [[Autosome|autosomal]] chromosomes and one pair of [[sex chromosomes]] (allosomes). A major exception to diploidy in humans is [[gamete]]s (sperm and egg cells) which are haploid with 23 unpaired chromosomes, and this [[ploidy]] is not shown in these karyograms. The micrographic karyogram is converted into [[grayscale]], whereas the schematic karyogram shows the purple hue as typically seen on Giemsa stain (and is a result of its azure B component, which stains DNA purple).<ref>{{cite book|author=K. Lew|title=Comprehensive Sampling and Sample Preparatio. Chapter: 3.05 - Blood Sample Collection and Handling|publisher=Academic Press|year=2012|isbn=9780123813749|url=https://www.sciencedirect.com/science/article/pii/B9780123813732000685}}</ref>

The schematic karyogram in this section is a graphical representation of the idealized karyotype. For each chromosome pair, the scale to the left shows the length in terms of million [[base pairs]], and the scale to the right shows the designations of the [[Locus (genetics)|bands and sub-bands]]. Such bands and sub-bands are used by the [[International System for Human Cytogenomic Nomenclature]] to describe locations of [[#Chromosome abnormalities|chromosome abnormalities]]. Each row of chromosomes is vertically aligned at [[centromere]] level.

===Human chromosome groups===
Based on the karyogram characteristics of size, position of the [[centromere]] and sometimes the presence of a [[chromosomal satellite]] (a segment distal to a [[secondary constriction]]), the human chromosomes are classified into the following groups:<ref>{{cite journal|last1=Erwinsyah |first1=R. |author2=Riandi |last3=Nurjhani |first3=M.|name-list-style=amp|year=2017|title=Relevance of human chromosome analysis activities against mutation concept in genetics course|journal=IOP Conference Series: Materials Science and Engineering|volume=180 |page=012285 |doi=10.1088/1757-899x/180/1/012285|s2cid=90739754 |doi-access=free}}</ref>
{|class=wikitable
! Group
! Chromosomes
! Features
|- style="background:lavenderblush"
| '''A'''
| 1–3
| Large, metacentric or submetacentric
|- style="background:honeydew"
| '''B'''
| 4-5
| Large, submetacentric
|- style="background:lightyellow"
| '''C'''
| 6–12, X
| Medium-sized, submetacentric
|- style="background:linen"
| '''D'''
| 13–15
| Medium-sized, acrocentric, with [[satellite chromosome|satellite]]
|- style="background:lightcyan"
| '''E'''
| 16–18
| Small, metacentric or submetacentric
|- style="background:lavender"
| '''F'''
| 19–20
| Very small, metacentric
|- style="background:lavenderblush"
| '''G'''
| 21–22, Y
| Very small, acrocentric (and 21, 22 with [[satellite chromosome|satellite]])
|}

Alternatively, the human genome can be classified as follows, based on pairing, sex differences, as well as location within the [[cell nucleus]] versus inside [[mitochondria]]:
* 22 homologous [[autosomal]] chromosome pairs (chromosomes 1 to 22). [[Homologous chromosome|Homologous]] means that they have the same genes in the same loci, and autosomal means that they are not sex chromomes.
* Two [[sex chromosome]] (in green rectangle at bottom right in the schematic karyogram, with adjacent silhouettes of typical representative [[phenotype]]s): The most common karyotypes for [[females]] contain two [[X chromosome]]s and are denoted 46,XX; [[Male|males]] usually have both an X and a [[Y chromosome]] denoted 46,XY. However, approximately 0.018% percent of humans are [[intersex]], sometimes due to variations in sex chromosomes.<ref>{{cite journal |url=https://pubmed.ncbi.nlm.nih.gov/12476264/#:~:text=Applying%20this%20more%20precise%20definition,Sterling%20s%20estimate%20of%201.7%25. |title=How Common is Intersex? |year=2002 |pmid=12476264 |last1=Sax |first1=L. |journal=Journal of Sex Research |volume=39 |issue=3 |pages=174–178 |doi=10.1080/00224490209552139 |s2cid=33795209 }}</ref>
* The [[Human mitochondrial genetics|human mitochondrial genome]] (shown at bottom left in the schematic karyogram, to scale compared to the nuclear DNA in terms of [[base pair]]s), although this is not included in micrographic karyograms in clinical practice. Its genome is relatively tiny compared to the rest.

===Copy number===
[[File:Animal cell cycle-en.svg|thumb|The [[cell cycle]]]]
Schematic karyograms generally display a DNA copy number corresponding to the [[G0 phase|G<sub>0</sub> phase]] of the cellular state (outside of the replicative [[cell cycle]]) which is the most common state of cells. The schematic karyogram in this section also shows this state. In this state (as well as during the G<sub>1</sub> phase of the [[cell cycle]]), each cell has two autosomal chromosomes of each kind (designated 2n), where each chromosome has one copy of each [[Locus (genetics)|locus]], making a total copy number of two for each locus (2c). At top center in the schematic karyogram, it also shows the chromosome 3 pair after having undergone [[DNA synthesis]], occurring in the [[S phase]] (annotated as S) of the cell cycle. This interval includes the [[G2 phase|G<sub>2</sub> phase]] and [[metaphase]] (annotated as "Meta."). During this interval, there is still 2n, but each chromosome will have two copies of each locus, wherein each [[sister chromatid]] (chromosome arm) is connected at the centromere, for a total of 4c.<ref name="pmid30202427">{{cite journal| author=Gomes CJ, Harman MW, Centuori SM, Wolgemuth CW, Martinez JD| title=Measuring DNA content in live cells by fluorescence microscopy. | journal=Cell Div | year= 2018 | volume= 13 | issue=  | pages= 6 | pmid=30202427 | doi=10.1186/s13008-018-0039-z | pmc=6123973 | doi-access=free }} </ref> The chromosomes on micrographic karyograms are in this state as well, because they are generally micrographed in metaphase, but during this phase the two copies of each chromosome are so close to each other that they appear as one unless the image resolution is high enough to distinguish them. In reality, during the G<sub>0</sub> and G<sub>1</sub> phases, nuclear DNA is dispersed as [[chromatin]] and does not show visually distinguishable chromosomes even on micrography.

The copy number of the [[Human mitochondrial genetics|human mitochondrial genome]] per human cell varies from 0 (erythrocytes)<ref name="pmid3178814">{{cite journal| author=Shuster RC, Rubenstein AJ, Wallace DC| title=Mitochondrial DNA in anucleate human blood cells. | journal=Biochem Biophys Res Commun | year= 1988 | volume= 155 | issue= 3 | pages= 1360–5 | pmid=3178814 | doi=10.1016/s0006-291x(88)81291-9 | pmc= | url=https://pubmed.ncbi.nlm.nih.gov/3178814  }} </ref> up to 1,500,000 ([[Egg cell|oocytes]]), mainly depending on the number of mitochondria per cell.<ref name="pmid28721182">{{cite journal| author=Zhang D, Keilty D, Zhang ZF, Chian RC| title=Mitochondria in oocyte aging: current understanding. | journal=Facts Views Vis Obgyn | year= 2017 | volume= 9 | issue= 1 | pages= 29–38 | pmid=28721182 | doi= | pmc=5506767 }} </ref>