Exome capture from saliva produces high quality genomic and metagenomic data.

TitleExome capture from saliva produces high quality genomic and metagenomic data.
Publication TypeJournal Article
Year of Publication2014
AuthorsKidd, JM, Sharpton, TJ, Bobo, D, Norman, PJ, Martin, AR, Carpenter, ML, Sikora, M, Gignoux, CR, Nemat-Gorgani, N, Adams, A, Guadalupe, M, Guo, X, Feng, Q, Li, Y, Liu, X, Parham, P, Hoal, EG, Feldman, MW, Pollard, KS, Wall, JD, Bustamante, CD, Henn, BM
JournalBMC Genomics
Volume15
Pagination262
Date Published2014
ISSN1471-2164
KeywordsExome, Genome, Human, Genomics, Genotype, High-Throughput Nucleotide Sequencing, HLA Antigens, Humans, Metagenomics, Microbiota, Molecular Sequence Data, Mouth, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Receptors, KIR, Saliva
Abstract

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.

DOI10.1186/1471-2164-15-262
Alternate JournalBMC Genomics
PubMed ID24708091
PubMed Central IDPMC4051168
Grant List1DP5OD009154 / OD / NIH HHS / United States
AI17892 / AI / NIAID NIH HHS / United States
DP5 OD009154 / OD / NIH HHS / United States
GM007790 / GM / NIGMS NIH HHS / United States
P30 CA124435 / CA / NCI NIH HHS / United States
R01HG003229 / HG / NHGRI NIH HHS / United States
R01HG400409 / HG / NHGRI NIH HHS / United States
T32 GM007790 / GM / NIGMS NIH HHS / United States
T32GM007175 / GM / NIGMS NIH HHS / United States
T32HG000044 / HG / NHGRI NIH HHS / United States