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To obtain a high complexity library of ligation products that will ensure high resolution and depth of data, a sample of 20–25 million cells is required as input for Hi-C. [3] [4] Primary human samples, which may be available only in fewer cell numbers, could be used for standard Hi-C library preparation with as low as 1–5 million cells. [4]
Chromosomes at various stages of mitosis.Karyograms are generally made by chromosomes in prometaphase or metaphase. During these phases, the two copies of each chromosome (connected at the centromere) will look as one unless the image resolution is high enough to distinguish the two.
Low-resolution physical mapping is typically capable of resolving DNA ranging from one base pair to several mega bases. In this category, most mapping methods involve generating a somatic cell hybrid panel, which is able to map any human DNA sequences, the gene of interest [clarification needed], to specific chromosomes of animal cells, such as those of mice and hamsters. [4]
There are two distinctive mapping approaches used in the field of genome mapping: genetic maps (also known as linkage maps) [7] and physical maps. [3] While both maps are a collection of genetic markers and gene loci, [8] genetic maps' distances are based on the genetic linkage information, while physical maps use actual physical distances usually measured in number of base pairs.
Chromosome conformation capture-on-chip (4C) (also known as circular chromosome conformation capture) captures interactions between one locus and all other genomic loci. It involves a second ligation step, to create self-circularized DNA fragments, which are used to perform inverse PCR. Inverse PCR allows the known sequence to be used to ...
High-resolution banding involves the staining of chromosomes during prophase or early metaphase (prometaphase), before they reach maximal condensation. Because prophase and prometaphase chromosomes are more extended than metaphase chromosomes, the number of bands observable for all chromosomes ( bands per haploid set , bph; "band level ...
As of 2006, even high-resolution CGH arrays are accurate to detect structural variations (SV) at resolution of 200 bp. [16] This method allows one to identify new recurrent chromosome changes such as microdeletions and duplications in human conditions such as cancer and birth defects due to chromosome aberrations. Figure 2.
Optical mapping [1] is a technique for constructing ordered, genome-wide, high-resolution restriction maps from single, stained molecules of DNA, called "optical maps". By mapping the location of restriction enzyme sites along the unknown DNA of an organism, the spectrum of resulting DNA fragments collectively serves as a unique "fingerprint" or "barcode" for that sequence.