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Are sites with multiple single nucleotide variants in cancer genomes a consequence of drivers, hypermutable sites or sequencing errors?

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posted on 2023-06-09, 02:59 authored by Thomas C A Smith, Antony CarrAntony Carr, Adam Eyre-WalkerAdam Eyre-Walker
Across independent cancer genomes it has been observed that some sites have been recurrently hit by single nucleotide variants (SNVs). Such recurrently hit sites might be either (i) drivers of cancer that are postively selected during oncogenesis, (ii) due to mutation rate variation, or (iii) due to sequencing and assembly errors. We have investigated the cause of recurrently hit sites in a dataset of >3 million SNVs from 507 complete cancer genome sequences. We find evidence that many sites have been hit significantly more often than one would expect by chance, even taking into account the effect of the adjacent nucleotides on the rate of mutation. We find that the density of these recurrently hit sites is higher in non-coding than coding DNA and hence conclude that most of them are unlikely to be drivers. We also find that most of them are found in parts of the genome that are not uniquely mappable and hence are likely to be due to mapping errors. In support of the error hypothesis, we find that recurently hit sites are not randomly distributed across sequences from different laboratories. We fit a model to the data in which the rate of mutation is constant across sites but the rate of error varies. This model suggests that ~4% of all SNVs are errors in this dataset, but that the rate of error varies by thousands-of-fold between sites.

History

Publication status

  • Published

File Version

  • Published version

Journal

PeerJ

ISSN

2167-8359

Publisher

PeerJ

Volume

4

Page range

1-15

Article number

e2391

Department affiliated with

  • Evolution, Behaviour and Environment Publications

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2016-09-20

First Open Access (FOA) Date

2016-09-20

First Compliant Deposit (FCD) Date

2016-09-20

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