Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice.
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ABSTRACT:
SUBMITTER: Lobo AK
PROVIDER: S-EPMC8527510 | biostudies-literature | 2021 Oct
REPOSITORIES: biostudies-literature
Publications
Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice.
Lobo Alexandra K AK Traeger Lindsay L LL Keller Mark P MP Attie Alan D AD Rey Federico E FE Broman Karl W KW
G3 (Bethesda, Md.) 20211001 11
In a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, we identified three sets of sample mix-ups (two pairs and one trio) as well as at least 15 microbiome samples that appear to be mixtures of pairs of mice. The microbiome data consisted of shotgun sequencing reads from fecal DNA, used to characterize the gut microbial communities present in these mice. These sequence reads included sufficient reads derived from the host mouse to identify the i ...[more]
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