Small insertions and deletions (INDELs) in human genomes

Mullaney, Julienne M.; Mills, Ryan E.; Pittard, W. Stephen; Devine, Scott E.

doi:10.1093/hmg/ddq400

Cited by 305 publications

(245 citation statements)

References 42 publications

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“…Indel variation is common even within a single species (Mullaney et al, 2010) and thus it should be no surprise that restriction site associated libraries often sample regions containing such variation. Within repetitive DNA elements (i.e., simple sequence repeats, microsatellites) indels can arise rapidly through slipped-strand mispairing during DNA replication (Levinson and Gutman, 1987), giving rise to single or often tandem repeat nucleotide differences between taxa.…”

Section: Radseq At the Phylogenetic Scalementioning

confidence: 99%

PyRAD: assembly ofde novoRADseq loci for phylogenetic analyses

Eaton

2013

Preprint

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Restriction-site associated genomic markers are a powerful tool for investigating evolutionary questions at the population level, but are limited in their utility at deeper phylogenetic scales where fewer orthologous loci are typically recovered across disparate taxa. While this limitation stems in part from mutations to restriction recognition sites that disrupt data generation, an alternative source of data loss comes from the failure to identify homology during bioinformatic analyses. Clustering methods that allow for lower similarity thresholds and the inclusion of indel variation will perform better at assembling RADseq loci at the phylogenetic scale.PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic data sets. It utilizes a wrapper around an alignment-clustering algorithm which allows for indel variation within and between samples, as well as for incomplete overlap among reads (e.g., paired-end). Here I compare PyRAD with the program Stacks in their performance analyzing a simulated RADseq data set that includes indel variation. Indels disrupt clustering of homologous loci in Stacks but not in PyRAD, such that the latter recovers more shared loci across disparate taxa. I show through re-analysis of an empirical RADseq data set that indels are a common feature of such data, even at shallow phylogenetic scales. PyRAD utilizes parallel processing as well as an optional hierarchical clustering method which allow it to rapidly assemble phylogenetic data sets with hundreds of sampled individuals. Availability:Software is written in Python and freely available at http://www.dereneaton.com/software/ Supplement:Scripts to completely reproduce all simulated and empirical analyses are available in the Supplementary Materials.

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Section: Radseq At the Phylogenetic Scalementioning

confidence: 99%

PyRAD: assembly ofde novoRADseq loci for phylogenetic analyses

Eaton

2013

Preprint

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“…Most indels range between 2-16 bases in length (Mullaney, et al,2010) (also referred to as micro-indels) and their frequency has been shown to vary across the genome with lower rate in conserved and functional regions and an increased rate in hot spots for genetic variation. The average indel rate is approximately one indel in 5.1 to 13.2 kb of DNA (Mills et al, 2006).…”

Section: Insertions and Deletions (Indels)mentioning

confidence: 99%

“…Increasing the read length has also been shown to improve micro-indel (<10 bases) detection sensitivity without significantly affecting specificity, demonstrating a more efficient method for increasing coverage than simply producing more reads. Paired-end reads -Indel detection greatly improves when based on paired end reads deep sequencing data (Mullaney et al, 2010). Both alignment (Li and Durbin, 2009; and variant detection tools (Kai Ye et al, 2009) utilize paired-end reads so that one of the reads is used to pinpoint the pair's loci in the reference while the other read can be subjected to gapped alignment and indel inference.…”

Section: Insertions and Deletions (Indels)mentioning

confidence: 99%

Deep Sequencing Data Analysis: Challenges and Solutions

Isakov¹,

Shomron²

2011

Bioinformatics - Trends and Methodologies

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“…Polymorphisms in mature and/or pre-miR sequences may affect miR biogenesis and be associated with the development of various types of cancer (17)(18)(19)(20)(21). Small insertions and deletion (indels) polymorphisms are one of the most common genetic alterations in the human genome that influence human traits and diseases (22,23). There is limited information regarding the association between pre-miR-3131 polymorphisms and cancer risk.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of a 3-base pair indel polymorphism within pre-microRNA-3131 in patients with prostate cancer using mismatch polymerase chain reaction-restriction fragment length polymorphism

Hashemi

Bahari

Sattarifard

et al. 2017

Molecular and Clinical Oncology

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Abstract. The present study aimed to examine the impact of a 3-bp indel (rs57408770) polymorphism within the pre-microRNA (miR)-3131 polymorphism on prostate cancer (PCa) risk in a sample of an Iranian population. In total, 340 subjects, including 177 patients with PCa and 170 patients with benign prostatic hyperplasia, were enrolled in the present case-control study. A mismatch polymerase chain reaction-restriction fragment length polymorphism method was designed for genotyping the 3-bp indel (rs57408770) polymorphism. The present findings demonstrated that the indel variant significantly increased the risk of PCa in codominant [odds ratio (OR)=2.23, 95% confidence interval (CI)=1.13-4.37; P=0.021, insertion (ins)/ins vs. deletion (del)/del] and recessive (OR=2.33, 95% CI=1.25-4.36; P=0.009, ins/ins vs. del/del + del/ins). In conclusion, to the best of our knowledge, the present findings for the first time proposed that a 3-bp indel variant of miR-3131 may be a risk factor for susceptibility to PCa in a sample of an Iranian population. Further studies with different ethnicities and larger sample sizes are required to validate the present findings. IntroductionProstate cancer (PCa), the second most common malignancy in men, is the fifth leading cause of cancer-related mortality among men globally (1). The incidence rate of PCa in Iran is lower than that in the rest of the world (2-4). Despite the high prevalence of PCa, little is known about the mechanisms underlying the development and progression of PCa. It has been proposed that genomic and environmental factors contribute to the development and progression of PCa (5-8). Twin studies have indicated that 42% of the variation in PCa risk may be attributed to genetics (9). Single nucleotide polymorphisms (SNPs), the most common type of genetic variation in the human genome, have been demonstrated to be associated with the risk of developing PCa (10-12).MicroRNA (miR) are small, non-coding, endogenous, single-stranded RNA molecules that are ~22 nucleotides in length (13,14). They regulate gene expression by directing sequence-specific degradation or inhibiting translation of target mRNA (13,14). Mounting evidence has suggested that mutation or SNPs in miR genes may affect target-binding activity, expression, or processes of mature miR, thus affecting the expression of their target genes (15,16). Polymorphisms in mature and/or pre-miR sequences may affect miR biogenesis and be associated with the development of various types of cancer (17-21). Small insertions and deletion (indels) polymorphisms are one of the most common genetic alterations in the human genome that influence human traits and diseases (22,23). There is limited information regarding the association between pre-miR-3131 polymorphisms and cancer risk. Recently, Wang et al (20) investigated the impact of a 3-bp indel polymorphism (rs57408770) in pre-miR-3131 on hepatocellular carcinoma (HCC) and observed that the insertion (ins) allele significantly increased the risk of HCC in a Chinese population. ...

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Small insertions and deletions (INDELs) in human genomes

Cited by 305 publications

References 42 publications

PyRAD: assembly ofde novoRADseq loci for phylogenetic analyses

PyRAD: assembly ofde novoRADseq loci for phylogenetic analyses

Deep Sequencing Data Analysis: Challenges and Solutions

Evaluation of a 3-base pair indel polymorphism within pre-microRNA-3131 in patients with prostate cancer using mismatch polymerase chain reaction-restriction fragment length polymorphism

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