Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome.

Yining Yao,Chengchen Shao,Zhihan Zhou,Kuan Sun,Qiqun Tang,Qinrui Yang,Xiaoqin Qian,Jianhui Xie

doi:10.3389/fgene.2021.809815

Yining Yao, Chengchen Shao + Show 6 more

Open Access

https://doi.org/10.3389/fgene.2021.809815

Copy DOI

Abstract

Multiple mutational events of insertion/deletion occurring at or around InDel sites could form multi-allelic InDels and multi-InDels (abbreviated as MM-InDels), while InDels with random DNA sequences could imply a unique mutation event at these loci. In this study, preliminary investigation of MM-InDels with random sequences was conducted using high-throughput phased data from the 1000 Genomes Project. A total of 3,599 multi-allelic InDels and 6,375 multi-InDels were filtered with multiple alleles. A vast majority of the obtained MM-InDels (85.59%) presented 3 alleles, which implies that only one secondary insertion or deletion mutation event occurred at these loci. The more frequent presence of two adjacent InDel loci was observed within 20 bp. MM-InDels with random sequences presented an uneven distribution across the genome and showed a correlation with InDels, SNPs, recombination rate, and GC content. The average allelic frequencies and prevalence of multi-allelic InDels and multi-InDels presented similar distribution patterns in different populations. Altogether, MM-InDels with random sequences can provide useful information for population resolution.

Highlights

Insertion/deletion polymorphisms (InDels) could be generated by the insertion or deletion of short DNA sequences and are thought to be bi-allelic (Bhangale et al, 2005)
The enrichment of neighboring polymorphisms has been reported in the human genome (Hodgkinson and EyreWalker, 2010), which is in line with our observation
Previous studies suggested that MM-InDels containing two InDels have three instead of four alleles (Huang et al, 2014; Li et al, 2021), which is in line with our observation

Summary

Introduction

Insertion/deletion polymorphisms (InDels) could be generated by the insertion or deletion of short DNA sequences and are thought to be bi-allelic (Bhangale et al, 2005). According to the insertion or the deletion of DNA length and sequence types, InDels could be classified into insertions or deletions of single base pairs, expansions of monomeric base pairs or multi-base pairs of 2- to 15-bp repeat units, transposon insertions, and those containing apparently random DNA sequences (Mills et al, 2006). InDels could be caused by an insertion or a deletion mutation event in the genome across human history and are informative about human evolution and migration (Pereira et al, 2012). The expansions of short DNA sequences account for a large part of InDels, which might

Methods

Results

Conclusion