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Exome capture from saliva produces high quality genomic and metagenomic data Public Deposited

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https://ir.library.oregonstate.edu/concern/articles/dz010r753

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  • BACKGROUND: Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research. RESULTS: We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data. CONCLUSIONS: DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.
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  • Kidd et al.: Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics 2014 15:262. doi:10.1186/1471-2164-15-262
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  • 15
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  • B.M.H. and C.D.B. are supported by NIH grant R01HG003229. C.R.G. is supported by the UCSF Dissertation Year Fellowship and NIH grants T32GM007175 and T32HG000044. T.J.S and K.S.P. are supported by NSF grant DMS-1069303, the San Simeon Fund, and institutional funding from Gladstone Institutes. P.J.N, N.N-G and P.P. were supported by NIH grant AI17892. J.D.W. was supported by NIH grant R01HG400409. J.M.K was supported by NIH grant 1DP5OD009154. A.R.M. was supported by NIH training grant GM007790.
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  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2014-05-27T16:52:13Z No. of bitstreams: 4 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva.pdf: 1874711 bytes, checksum: 5519d8b6df7db4f88a2679f36e9c815b (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva_SupplementaryMaterial.pdf: 13085119 bytes, checksum: 2b093598b017da018f536facf5c10e29 (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva_TableS4.xls: 136192 bytes, checksum: 56372098a116337255d4886780208a99 (MD5)
  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2014-05-27T16:52:33Z (GMT) No. of bitstreams: 4 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva.pdf: 1874711 bytes, checksum: 5519d8b6df7db4f88a2679f36e9c815b (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva_SupplementaryMaterial.pdf: 13085119 bytes, checksum: 2b093598b017da018f536facf5c10e29 (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva_TableS4.xls: 136192 bytes, checksum: 56372098a116337255d4886780208a99 (MD5)
  • description.provenance : Made available in DSpace on 2014-05-27T16:52:33Z (GMT). No. of bitstreams: 4 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva.pdf: 1874711 bytes, checksum: 5519d8b6df7db4f88a2679f36e9c815b (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva_SupplementaryMaterial.pdf: 13085119 bytes, checksum: 2b093598b017da018f536facf5c10e29 (MD5) SharptonThomasMicrobiologyExomeCaptureSaliva_TableS4.xls: 136192 bytes, checksum: 56372098a116337255d4886780208a99 (MD5) Previous issue date: 2014-04-04

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