Population history modulates the fitness effects of Copy Number Variation in the Roma.
Journal
Human genetics
ISSN: 1432-1203
Titre abrégé: Hum Genet
Pays: Germany
ID NLM: 7613873
Informations de publication
Date de publication:
Sep 2023
Sep 2023
Historique:
received:
17
04
2023
accepted:
02
06
2023
medline:
25
8
2023
pubmed:
14
6
2023
entrez:
13
6
2023
Statut:
ppublish
Résumé
We provide the first whole genome Copy Number Variant (CNV) study addressing Roma, along with reference populations from South Asia, the Middle East and Europe. Using CNV calling software for short-read sequence data, we identified 3171 deletions and 489 duplications. Taking into account the known population history of the Roma, as inferred from whole genome nucleotide variation, we could discern how this history has shaped CNV variation. As expected, patterns of deletion variation, but not duplication, in the Roma followed those obtained from single nucleotide polymorphisms (SNPs). Reduced effective population size resulting in slightly relaxed natural selection may explain our observation of an increase in intronic (but not exonic) deletions within Loss of Function (LoF)-intolerant genes. Over-representation analysis for LoF-intolerant gene sets hosting intronic deletions highlights a substantial accumulation of shared biological processes in Roma, intriguingly related to signaling, nervous system and development features, which may be related to the known profile of private disease in the population. Finally, we show the link between deletions and known trait-related SNPs reported in the genome-wide association study (GWAS) catalog, which exhibited even frequency distributions among the studied populations. This suggests that, in general human populations, the strong association between deletions and SNPs associated to biomedical conditions and traits could be widespread across continental populations, reflecting a common background of potentially disease/trait-related CNVs.
Identifiants
pubmed: 37311904
doi: 10.1007/s00439-023-02579-5
pii: 10.1007/s00439-023-02579-5
pmc: PMC10449987
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1327-1343Subventions
Organisme : Agencia Estatal de Investigación
ID : CGL2016-75389-P
Organisme : Agencia Estatal de Investigación
ID : PID2019-106485GB-I00/AEI/10.13039/501100011033
Organisme : Agencia Estatal de Investigación
ID : CEX2018-000792-M
Organisme : Agència de Gestió d'Ajuts Universitaris i de Recerca
ID : 2017SGR00702
Informations de copyright
© 2023. The Author(s).
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