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Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)?

After that is done, it the complete genome can be stored and once the new genes (and their purposes are confirmed) are discovered, the scientist can simply go back to a previously sequenced data and to find it this particular person has this new gene or not.

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3 Answers 3

up vote 5 down vote accepted

A single run of sequencing won't cover the entire genome, in most cases. That's why they do multiple rounds in order to increase horizontal (covering more regions of genome) and vertical (a.k.a depth; more reads per locus so that you can be more confident) coverage.

Edit by dd3: In the cases where "a new gene is discovered", i.e. genome reannotation, it is possible to go back and look at previously stored sequence data to find out what alleles a person has (everyone has every gene, unless they have a deletion that spans the full length of the gene). This is a bioinformatics project, and if you are interested in learning more, I would recommend searching for recent publications on genome reannotation and remapping of sequence reads.

Whole genome sequencing is generally not recommended for prognosis of a specific disease like breast cancer. The common approach is to do a PCR of the biomarker loci and if necessary do a Sanger sequencing. However, if you have the money you can get your whole genome sequencing done :P

The number of runs required to increase the depth varies for different genomic regions. This article says that CpG islands require more runs. According to this article, the depth should be >3 per genotype marker.

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@WYSIWIG... Thank you. But how does it work in practice. Let's say someone wants to be tested for probalility of occuring a breast cancer. In that case - will only a particular region of genome be sequenced to find if a BRCA1 gene is ok? Please excusing me for a naive questions - but how many runs (approximately) are required to sequence the whole human genome? –  Mitten Apr 23 '13 at 4:42
    
edited the answer.. the comment was getting too long.. :) –  WYSIWYG Apr 23 '13 at 4:56
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for many of the technologies in use today, 30x coverage can still be problematic. Should mention that the sequencers have biases which systematically give hard to interpret or easily misinterpretable data. but given this, the data could and should be reused if its a whole genome sequence. –  shigeta Apr 23 '13 at 20:41
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coverage is an estimate of the number of times each individual base in the target sequence has been sequenced. so 30x coverage means you would have produced an assembled sequence where 30 sequencer outputs would contain an average base. the coverage needs to be so deep because the short sequences from the sequencer (a few hundred bases) there is some uncertainty in each sequence, errors in sequencing, and the resulting difficulty placing any given sequence. this paper might help:ncbi.nlm.nih.gov/pubmed/23393025 –  shigeta Apr 24 '13 at 12:59
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@Mitten: Coverage (vertical coverage) as I mentioned previously, is number of reads that map to a region of the genome. We generally look at the average coverage throughout the genome. –  WYSIWYG Apr 24 '13 at 12:59

Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)?

Likely, yes. But I think you vastly overestimate how often this is done. If someone gets their DNA "sequenced" at 23andMe, for example, they are not getting their whole genome sequenced. They are getting individual bits believed to be possibly clinically relevant sequenced. It's a different technology than you would use to get the whole genome. A whole mammalian genome is really big, therefore kind of expensive to sequence, and is mostly non-coding DNA of questionable relevance. Therefore you can just genotype the exact bases of interest, or maybe do exome capture, which gets you full sequence for the 1% or so of the genome that is currently annotated to be coding. Obviously either of those approaches would no be all-inclusive, so one might wish to redo them at a later date with new targeted regions of interest.

Even if you did get a whole genome done with current technology, right now it has limitations, namely read length, that make it hard to work out certain details. I could easily see someone needing to redo a genome using a longer read technology, when that technology arrives.

Also, we aren't really discovering that many new genes. Certainly not protein-coding ones. What is more likely is that we discover that variants in this or that gene might be clinically relevant to some health parameter.

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Apart from what WYSIWYG said. It might also be the case that you need to re-sequence because you're interested in seeing the changes that might have occurred since the last sequencing. Remember that cells keep dividing and therefore changing, so the DNA is slightly different from one cell to another (and from one population of cells or tissues to another). Single-cell sequencing is almost here. The obvious example here is a tumour. It helps knowing what happened and if possible detect the driver (or drivers) mutation (cancer cells tend to increase their mutation rate).

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