How many cells are represented in a sample going through NGS
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10 months ago
erezts • 0

Hi,

When running an NGS we get tens or hundreds of reads. These reads are calls of amplified DNA fragments of the patient. My question is, how many cells have provided the DNA fragments? When extracting DNA and creating a library, HOW MANY CELLS HAVE PROVIDED THE DNA? Any articles, references and your answers will be welcomed.

Tnx

NGS exome sequencing • 317 views
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This is not really bioinformatics so it likely will get closed. The answer is "it depends" and the dependency is the number of cells the wetlab used to extract DNA (or RNA, or whatever you measure). Can be millions, thousands, or in case of single-cell technology a single one. You will need to read the method sections of the paper to find which assay and kit was used, and then read the respective manual to get an idea.

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10 months ago
Ventrilocus ▴ 160

It is easy to compute. You just need the ng of DNA input in the NGS experiment. For example, assume we input 250 ng of DNA (that is what is required in a standard WGS experiment*). Each cell contains 6 pg of DNA, hence, the number of cells is:

250 ng * (1000 pg / 1 ng) * (1 cell / 6 pg**) = 41,667.67 cells

*http://genomics.broadinstitute.org/products/whole-genome-sequencing

*The amount of 6 pg per cell can be estimated from: human genome is around 6200 Mbp, the average nucleotide molecular weight is about 660 g/bp mol and Avogadro's number is 6.022 10^23. Hence:

6200 Mbp * (10^6 bp/ 1 Mbp) * (1 bp mol/ 6.022 * 10^23 bp) * (660 g/ 1 bp mol) * (10^12 pg/ 1 g)= 6.795 pg

Of course, as stated by ATpoint in the comment, the amount of input DNA highly depends on the NGS experiment.

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