Quack: A quality assurance tool for high throughput sequence data

Thrash, Adam; Arick, Mark A.; Peterson, Daniel G.

doi:10.1016/j.ab.2018.01.028

Cited by 1,295 publications

(1,402 citation statements)

References 4 publications

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“…SSCS and DCS consensus formation was performed in Galaxy [ 95 ] using the Du Novo pipeline (version 2.14) including error correction of barcode sequences ( S1 Fig ) [ 51 , 52 ]. Quality of the sequencing reads was verified using FastQC [ 96 ]. Errors in barcode sequences were corrected, allowing up to three mismatches and requiring a minimum mapping quality of 20.…”

Section: Methodsmentioning

confidence: 99%

Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues

et al. 2020

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Mutations create genetic variation for other evolutionary forces to operate on and cause numerous genetic diseases. Nevertheless, how de novo mutations arise remains poorly understood. Progress in the area is hindered by the fact that error rates of conventional sequencing technologies (1 in 100 or 1,000 base pairs) are several orders of magnitude higher than de novo mutation rates (1 in 10,000,000 or 100,000,000 base pairs per generation). Moreover, previous analyses of germline de novo mutations examined pedigrees (and not germ cells) and thus were likely affected by selection. Here, we applied highly accurate duplex sequencing to detect low-frequency, de novo mutations in mitochondrial DNA (mtDNA) directly from oocytes and from somatic tissues (brain and muscle) of 36 mice from two independent pedigrees. We found mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo. Mutation frequencies and patterns differed between germline and somatic tissues and among mtDNA regions, suggestive of distinct mutagenesis mechanisms. Additionally, we discovered a more pronounced genetic drift of mitochondrial genetic variants in the germline of older versus younger mice, arguing for mtDNA turnover during oocyte meiotic arrest. Our study deciphered for the first time the intricacies of germline de novo mutagenesis using duplex sequencing directly in oocytes, which provided unprecedented resolution and minimized selection effects present in pedigree studies. Moreover, our work provides important information about the origins and accumulation of mutations with aging/maturation and has implications for delayed reproduction in modern human societies. Furthermore, the duplex sequencing method we optimized for single cells opens avenues for investigating low-frequency mutations in other studies.

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Section: Methodsmentioning

confidence: 99%

Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues

et al. 2020

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“…The following workflow was used in bioinformatic analyses of the RNA-seq data: QC check (fastQC) ➔ alignment (Hisat2) ➔ featureCounts (subread) ➔ Differential gene expression analysis (DESeq2) ➔ Pathway Enrichment, GO analysis (Bioconductor clusterProfiler). To ensure the quality of RNA-seq data, fastq files were subjected to fastQC ( 37 ) to check their quality and changes after adaptor and quality trim. MultiQC ( 38 ) was then utilized to analyze and integrate the QC reports ( Figure S1 ).…”

Section: Methodsmentioning

confidence: 99%

Perinatal Exposure to Nicotine Alters Sperm RNA Profiles in Rats

et al. 2022

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Perinatal exposure to smoking has been associated with childhood asthma, one of the most common pediatric conditions affecting millions of children globally. Of great interest, this disease phenotype appears heritable as it can persist across multiple generations even in the absence of persistent exposure to smoking in subsequent generations. Although the molecular mechanisms underlying childhood asthma induced by perinatal exposure to smoking or nicotine remain elusive, an epigenetic mechanism has been proposed, which is supported by the data from our earlier analyses on germline DNA methylation (5mC) and histone marks (H3 and H4 acetylation). To further investigate the potential epigenetic inheritance of childhood asthma induced by perinatal nicotine exposure, we profiled both large and small RNAs in the sperm of F1 male rats. Our data revealed that perinatal exposure to nicotine leads to alterations in the profiles of sperm-borne RNAs, including mRNAs and small RNAs, and that rosiglitazone, a PPARγ agonist, can attenuate the effect of nicotine and reverse the sperm-borne RNA profiles of F1 male rats to close to placebo control levels.

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“…A workflow was created to filter the results, to view the sequenced sites, and the observed heteroplasmic frequencies at these sites. Quality of the sequencing reads was checked using FASTQC [22]. Reads were mapped to the human reference genome (hg38) using BWA-MEM [23].…”

Section: (D) Mtdna Mapping and Variant Callingmentioning

confidence: 99%

Pronounced somatic bottleneck in mitochondrial DNA of human hair

Barrett

Arbeithuber

Zaidi

et al. 2019

Phil. Trans. R. Soc. B

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Heteroplasmy is the presence of variable mitochondrial DNA (mtDNA) within the same individual. The dynamics of heteroplasmy allele frequency among tissues of the human body is not well understood. Here, we measured allele frequency at heteroplasmic sites in two to eight hairs from each of 11 humans using next-generation sequencing. We observed a high variance in heteroplasmic allele frequency among separate hairs from the same individual—much higher than that for blood and cheek tissues. Our population genetic modelling estimated the somatic bottleneck during embryonic follicle development of separate hairs to be only 11.06 (95% confidence interval 0.6–34.0) mtDNA segregating units. This bottleneck is much more drastic than somatic bottlenecks for blood and cheek tissues (136 and 458 units, respectively), as well as more drastic than, or comparable to, the germline bottleneck (equal to 25–32 or 7–10 units, depending on the study). We demonstrated that hair undergoes additional genetic drift before and after the divergence of mtDNA lineages of individual hair follicles. Additionally, we showed a positive correlation between donor's age and variance in heteroplasmy allele frequency in hair. These findings have important implications for forensics and for our understanding of mtDNA dynamics in the human body.This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.

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Quack: A quality assurance tool for high throughput sequence data

Cited by 1,295 publications

References 4 publications

Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues

Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues

Perinatal Exposure to Nicotine Alters Sperm RNA Profiles in Rats

Pronounced somatic bottleneck in mitochondrial DNA of human hair

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