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What does sequencing "the human genome" mean? Don't individuals have unique genomes?

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Certainly individuals have unique genomes. The human genome sequencing project used DNA from a handful of volunteers, and the reference human genome that resulted from this project can be thought of as an "average" genome for those individuals. Where sequences differed between the individuals, a representative consensus sequence was chosen. Hence, the sequence of a gene from a given individual may not perfectly match the reference genome, although mostly the differences are small: genetic difference between humans is estimated to be around 0.1 --- 0.4%, which means a few million base pairs in total.

As DNA sequencing is nowadays orders of magnitude cheaper, genomes for larger number of individuals are being sequenced; see for example the 1000 genomes project.

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  • $\begingroup$ A good start to an answer - might you want to talk about SNPs and gene variants (various blood groups, for instance) to get into a little more detail? $\endgroup$ – MattDMo Jun 28 '16 at 1:25
  • $\begingroup$ What percent of genome same for each individuals and What is the maximum number of genetically unique individuals that human genome allows? $\endgroup$ – Abu sayed Jun 28 '16 at 4:00
  • $\begingroup$ @Abusayed added a point about % differences. Theoretically I guess there are 4^(3*10^9) possible genomes with 3 billion base pairs, but of course it doesn't work like that :) But still there is enough variation that there is virtually no chance of encountering two completely identical genomes by chance. $\endgroup$ – Roland Jun 28 '16 at 6:09
  • $\begingroup$ @MattDMo, feel free to edit if you want. It was a short, focused question though and I didn't want to respond with a population genetics lecture ;) $\endgroup$ – Roland Jun 28 '16 at 6:12
  • $\begingroup$ @Abu sayed: You might also be interested in these two facts: 1. The human reference genome's current release is version 20 (hg38). 2. Every newborn carries about 60-100 (which is not much at all) new private SNV due to mutations in the parents germline. $\endgroup$ – AlexDeLarge Jun 28 '16 at 8:22
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I think there are two concepts that you need to understand to understand what "sequence the human genome" mean; within vs between species variation and genome consensus

Within vs between species variation

There is indeed variation in the human population. We are not clones of each other. One can for example consider the average number of pairwise differences as a statistics of variation. Consider the two following sequences

  • ATCAATTCAGAA
  • AGCAATTAAGAA

Here, there are 2 pairwise differences. One can average the number of pairwise differences among any pair of individuals to get the average number of pairwise differences. The average number of pairwise differences within species is much lower than the average number of pairwise differences among species. It therefore makes sense to consider a standard genome of a species as variation within the species is negligible compared to variation among species.

Genome consensus

In order to obtain the "human genome", we samples DNA from a number of people, sequence them and then try to form a consensus among al these slightly different genomes. You can think of this consensus as some kind of average genome. Consider for example the following sequences:

  • AATGCA
  • AATGCA
  • AATGTA
  • AATGCA
  • AATGCG
  • AATGCA
  • AATGCA
  • ATTGCA
  • AATGCA

Sure, there is some variation but a priori AATGCA seems to be a good consensus.

Interestingly, it is very likely nobody on earth has the exact same genome as the consensus genome just. One simple reason is that there are sequencing errors occuring at a known rate but the other reason is that as sequences becomes long enough (the whole genome), every single individual carries at least one rare mutation that will not end up in the consensus.

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