Abstract：
:In many cancers, incidence, treatment efficacy and overall prognosis vary between geographic populations. Studies disentangling the contributing factors may help in both understanding cancer biology and tailoring therapeutic interventions. Ancestry estimation in such studies should preferably be driven by genomic data, due to frequently missing or erroneous self-reported or inferred metadata. While respective algorithms have been demonstrated for baseline genomes, such a strategy has not been shown for cancer genomes carrying a substantial somatic mutation load. We have developed a bioinformatics tool for the assignment of population groups from genome profiling data for both unaltered and cancer genomes. Despite extensive somatic mutations in the cancer genomes, consistency between germline and cancer data reached of 97% and 92% for assignment into 5 and 26 ancestral groups, respectively. Comparison with self-reported meta-data estimated a matching rate between 88-92%, mostly limited by interpretation of self-reported ethnicity labels compared to the standardized mapping output. Our SNP2pop application allows to assess population information from SNP arrays as well as sequencing platforms and to estimate the population structure in cancer genomics projects, to facilitate research into the interplay between ethnicity-related genetic background, environmental factors and somatic mutation patterns in cancer biology.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Huang Q,Baudis Mdoi
10.1038/s41598-020-61854-xsubject
Has Abstractpub_date
2020-03-16 00:00:00pages
4846issue
1issn
2045-2322pii
10.1038/s41598-020-61854-xjournal_volume
10pub_type
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep24304
更新日期：2016-04-14 00:00:00
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pub_type： 杂志文章
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更新日期：2016-06-29 00:00:00
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pub_type： 杂志文章
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pub_type： 杂志文章
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更新日期：2016-07-29 00:00:00
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pub_type： 杂志文章
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2015-06-10 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2015-01-08 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2015-12-15 00:00:00
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pub_type： 杂志文章
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更新日期：2017-03-03 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2017-01-20 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2019-09-16 00:00:00
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pub_type： 杂志文章
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更新日期：2020-07-27 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2017-10-12 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2017-09-12 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2016-02-16 00:00:00
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pub_type： 杂志文章
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更新日期：2017-10-12 00:00:00
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journal_title：Scientific reports
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journal_title：Scientific reports
pub_type： 杂志文章,随机对照试验
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更新日期：2018-04-27 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep41817
更新日期：2017-02-02 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2020-12-15 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
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更新日期：2017-10-16 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep37394
更新日期：2016-11-22 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep43430
更新日期：2017-03-03 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-34505-5
更新日期：2018-11-02 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-41407-7
更新日期：2019-03-21 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-50441-4
更新日期：2019-09-27 00:00:00
