mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation.

IF 4.4 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Bioinformatics Pub Date : 2023-09-02 DOI:10.1093/bioinformatics/btad565

Mercedeh Movassagh, Steven J Schiff, Joseph N Paulson

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Abstract

Motivation: In recent years, significant strides have been made in the field of genomics, with the commencement of large-scale studies aimed at collecting host mutational profiles and microbiome data. The amalgamation of host gene mutational profiles in both healthy and diseased subjects with microbial abundance data holds immense promise in providing insights into several crucial research questions, including the development and progression of diseases, as well as individual responses to therapeutic interventions. With the advent of sequencing methods such as 16s ribosomal RNA (rRNA) sequencing and whole genome sequencing, there is increasing evidence of interplay of human genetics and microbial communities. Quantitative trait loci associated with microbial abundance (mbQTLs), are genetic variants that influence the abundance of microbial populations within the host.

Results: Here, we introduce mbQTL, the first R package integrating 16S ribosomal RNA (rRNA) sequencing and single-nucleotide variation (SNV) and single-nucleotide polymorphism (SNP) data. We describe various statistical methods implemented for the identification of microbe-SNV pairs, relevant statistical measures, and plot functionality for interpretation.

Availability and implementation: mbQTL is available on bioconductor at https://bioconductor.org/packages/mbQTL/.

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mbQTL：一个用于微生物数量性状基因座（QTL）估计的R/Bioconductor软件包。

动机：近年来，随着旨在收集宿主突变谱和微生物组数据的大规模研究的开始，基因组学领域取得了重大进展。将健康和患病受试者的宿主基因突变谱与微生物丰度数据相结合，有望深入了解几个关键的研究问题，包括疾病的发展和进展，以及个体对治疗干预的反应。随着16s核糖体RNA（rRNA）测序和全基因组测序等测序方法的出现，越来越多的证据表明人类遗传学和微生物群落之间存在相互作用。与微生物丰度相关的数量性状基因座（mbQTL）是影响宿主内微生物种群丰度的遗传变异。结果：在这里，我们介绍了第一个整合16S核糖体RNA（rRNA）测序、单核苷酸变异（SNV）和单核苷酸多态性（SNP）数据的R包mbQTL。我们描述了用于鉴定微生物SNV对的各种统计方法、相关统计测量以及用于解释的绘图功能。可用性和实施：mbQTL可在生物导管上获得，网址为https://bioconductor.org/packages/mbQTL/.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics 生物-生化研究方法

CiteScore

11.20

自引率

5.20%

发文量

753

审稿时长

2.1 months

期刊介绍： The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.