Exome capture from saliva produces high quality genomic and metagenomic data

BMC Genomics

Brenna M Henn^1,11  Carlos D Bustamante³  Jeffrey D Wall¹  Katherine S Pollard⁴  Marcus W Feldman⁷  Eileen G Hoal^1,10  Peter Parham⁹  Xiao Liu⁵  Yingrui Li⁵  Qiang Feng⁵  Xiaosen Guo⁵  Moraima Guadalupe²  Alexandra Adams³  Neda Nemat-Gorgani⁹  Christopher R Gignoux⁶  Martin Sikora³  Meredith L Carpenter³  Alicia R Martin³  Paul J Norman⁹  Dean Bobo^1,11  Thomas J Sharpton^1,12  Jeffrey M Kidd⁸ 

[1] Institute for Human Genetics, and the Departments of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA;Agilent Technologies, Genomics Division, Cedar Creek, TX 78612, USA;Department of Genetics, Stanford University, Stanford, CA 94305, USA;The J. David Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA;Translational Medicine, BGI – Shenzhen, Shenzhen, China;Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, CA 94143, USA;Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA;Departments of Human Genetics, and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA;Department of Structural Biology, Stanford University, Stanford, CA 94305, USA;Stellenbosch University, Tygerberg, South Africa;Department of Ecology and Evolution, Stony Brook University, Life Sciences Bldg, Room 640, Stony Brook, NY 11794, USA;Departments of Microbiology, and Statistics, Oregon State University, Corvallis, OR 97331, USA

关键词: Microbiome;    Metagenomics;    Genetic diversity;    KhoeSan;    Exomes;   

Others  :  1217535
DOI  :  10.1186/1471-2164-15-262

 received in 2014-03-18, accepted in 2014-03-28,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Kidd et al.; licensee BioMed Central Ltd.

【 图 表 】

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