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In general, do standard whole genome sequencing techniques rely more on known chromosome counts, independently arrive at chromosome counts, and/or not directly address issues such as base number, aneuploidy, and polyploidy?

For example would have normal whole genome sequencing techniques detected that humans have 46 rather than 48 chromosomes?

Maybe a better way to put this question would be as follows:

Given the whole genome sequence for humans and a belief that chimpanzee had 46 chromosomes would whole genome sequencing of the chimpanzee most likely say

1) Here are the sequences for those 46 and by the way there was material left over.

2) Here is the best representation of all the chimpanzee's DNA mapped onto 46 chromosomes.

3) Here are the sequences for those 46 and chimpanzee's appear to have 48 chromosomes.

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What Biomed_guy says is basically the answer, I just wanted to clarify a bit. When you sequence DNA, you do something during the preparation of your DNA library to turn it into small fragments if it isn't already, like shearing the DNA. This gives you very small pieces of DNA that should still be quite unique when matched to reference genome.

But as previously answered, the determining factor for how DNA is then mapped is the reference genome you are using. So the answer is what you state in both 1 and 2. When trying to figure out what DNA you have, you start with a reference sequence which is all of the genomic DNA 'layed out' so that your fragments can then be compared against it and matched to a best fit region based on matching sequence. Anything that does not match the ref genome gets dumped into a 'junk' output file.

So conceptually, many gene sequences are highly conserved between humans and chimpanzees. This would mean that you could successfully align your sequences fragments to either genome. Importantly, this is number of chromosomes agnostic. It is the genes that matter.

Imagine that if Ras, Myc, and Erk are all on human chr 12 in humans, but split up in chimps so that Ras is on chr 12, Myc on Chr 13, and Erk on Chr 24, this would make no difference when you map back to the genome assuming the genes are conserved between human and chimp. If you have a sequenced fragment from human Myc that is the same as Chimp Myc, it would align to a location on chr 12 if you use human DNA as ref, or it would align to a location on chr 13 if you use Chimp as ref. Make sense?

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I'm pretty sure that it relies on a reference genome. As in, since the original human genome sequencing, most of the techniques used today rely on that original construction (with modifications).

That's how people use it to detect copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) with these sequencing techniques (and aneuploidy as well).

The reads from the sequencing run are compared to the reference genome and if statistically significant differences in the number of reads are seen, then they are noted as differences in the genome. If there is extra unmapped DNA, then it would likely just not know where to put it and call it "extra material".

So #1.

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You understand, it's not that chimps have lots of extra DNA that humans do not, they have two chromosomes which are fused in humans.

Theoretically, discrepancies between the reads and the reference could be discovered. Practically, with current short read technology, it would be difficult to sort out a discrepancy that involved a region of the genome that was repetitive, which the telomeres of the chimp 2A and 2B and the telomeric-like sequences in the regions where those fused in humans, would be.

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