Statistical modeling on human microbiome sequencing data

Dongyang Yang; Wei Xu; Dongyang Yang; Wei Xu

doi:10.3934/bdia.2019001

Big Data and Information Analytics

2019, Volume 4, Issue 1: 1-12. doi: 10.3934/bdia.2019001

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Research article

Statistical modeling on human microbiome sequencing data

Dongyang Yang ¹,
Wei Xu ^{1,2
,
,}

1.
Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
2.
Department of Biostatistics, Princess Margeret Cancer Centre, Toronto, Canada

Received: 30 November 2019 Accepted: 23 December 2019 Published: 31 December 2019

Research studies have shown that human microbiome is associated with many diseases through the linkage between bacterial taxa and environmental and genetic factors. Typical human microbiome sequencing data that obtained by next generation sequencing technologies of the 16S rRNA gene are high dimensional and sparse because most taxa are not shared among the samples. As a result, the data is often over-dispersed and with excess zeros. These features rise statistical challenges for compositional data analysis. We review the recent statistical methodology development for this setting. In particular, we summarize some current popular parametric probability models including the cases when repeated measurements of the microbiome are applicable. Multivariate analyses methods that are based on distance measurement for testing differences between microbes community are introduced. Statistical models which are developed to assess the association between genetic variants on X-chromosome and microbial components are highlighted. We discuss some applications on analysis of the association of host genome, microbial compositions and human diseases. Despite sophisticated approaches to statistical analysis of taxa count data, we suggest some future research directions on how to classify and predict clinical outcomes with microbial compositions.
- big data,
- statistical modeling,
- human microbiome,
- sequencing data,
- genomics,
- data mining
Citation: Dongyang Yang, Wei Xu. Statistical modeling on human microbiome sequencing data[J]. Big Data and Information Analytics, 2019, 4(1): 1-12. doi: 10.3934/bdia.2019001

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Abstract

Research studies have shown that human microbiome is associated with many diseases through the linkage between bacterial taxa and environmental and genetic factors. Typical human microbiome sequencing data that obtained by next generation sequencing technologies of the 16S rRNA gene are high dimensional and sparse because most taxa are not shared among the samples. As a result, the data is often over-dispersed and with excess zeros. These features rise statistical challenges for compositional data analysis. We review the recent statistical methodology development for this setting. In particular, we summarize some current popular parametric probability models including the cases when repeated measurements of the microbiome are applicable. Multivariate analyses methods that are based on distance measurement for testing differences between microbes community are introduced. Statistical models which are developed to assess the association between genetic variants on X-chromosome and microbial components are highlighted. We discuss some applications on analysis of the association of host genome, microbial compositions and human diseases. Despite sophisticated approaches to statistical analysis of taxa count data, we suggest some future research directions on how to classify and predict clinical outcomes with microbial compositions.

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