Quality Control of High‐Throughput Biological Data

Williams, Paul D.

doi:10.1002/9780470567647.ch3

Cited by 2 publications

(3 citation statements)

References 14 publications

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“…On average, each RNA sample yielded approximately 3-5 x 10 7 reads. Subsequently, each FASTQ file underwent quality assessment using the FASTQC tool 80 . Before alignment to the reference genome, raw Upset plots were prepared with package UpSetR (version 1.4.0) 85 .…”

Section: Bulk Rnaseqmentioning

confidence: 99%

Persistent alveolar bronchiolization, interstitial fibrosis and impaired lung function post-exercise are features of long-COVID in SARS-CoV-2-Delta variant infected aged hamsters

Baumgärtner,

Heydemann,

Ciurkiewicz

et al. 2024

Preprint

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Long-term consequences of SARS-CoV-2 infection affect the life quality of millions of people and pose a heavy burden on the public health sector. The underlying causes, pathomechanisms and morphological correlates are still largely unknown and further research in appropriate animal models is needed. The goal of the study was to characterize the trajectory of lung regeneration over a period of 112 days in the hamster model by combining morphological, transcriptome analysis and functional readouts. We demonstrate that in the acute phase, SARS-CoV-2 Delta-infected, male, aged hamsters show a severe impairment of lung function in a resting state. In the chronic phase of the disease, similar impairments are appreciable until 7 weeks post infection only after exercise on a rodent treadmill. The hamster model recapitulates chronic pulmonary fibrotic changes observed in many patients with respiratory long COVID, but does not show extra-pulmonary long term lesions. We show that sub-pleural and interstitial pulmonary fibrosis as well as alveolar bronchiolization persist until 112 dpi. Interestingly, CK8+ alveolar differentiation intermediate (ADI) cells are becoming less prominent in the alveolar proliferation areas from 28 dpi on. Instead, CK14+ airway basal cells and SCGB1A1+ club cells, expressing cell proliferation markers, mainly populate alveolar bronchiolization areas at later time-points. We postulate that pulmonary fibrosis and SCGB1A1+ club cell rich areas of alveolar bronchiolization represent potential risk factors for other diseases in long-COVID survivors.

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Section: Bulk Rnaseqmentioning

confidence: 99%

Persistent alveolar bronchiolization, interstitial fibrosis and impaired lung function post-exercise are features of long-COVID in SARS-CoV-2-Delta variant infected aged hamsters

Baumgärtner,

Heydemann,

Ciurkiewicz

et al. 2024

Preprint

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“…Dadas as complexidades das etapas de alinhamento e descoberta de variantes, além da preocupação sempre presente em se garantir a qualidade das análises in silico realizadas [43,44]. O desenvolvimento e aplicação de protocolos em bioinformática para análise dos dados são essenciais para lidar com o alto volume de dados gerados e realizar a ligação entre o experimento biológico e a interpretação dos dados gerados: representam assim uma excelente oportunidade para desenvolvimento.…”

Section: Análises De Bioinformáticaunclassified

“…Foram utilizados programas como o FastQC (0.11.3) [44] e Rqc (1.2.0) [43], que fornecem informações sobre estatísticas básicas das sequências; qualidade; conteúdo de GC; distribuição do tamanho das sequências; níveis de duplicação das sequências; e sequências sobre-representadas.…”

Section: Controle De Qualidade Pré Alinhamentounclassified

Aplicação de protocolos e métodos em bioinformática para análise de sequenciamento de exomas humanos

Borges¹

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Background:The technical advances in sequencing made in less than a decade associated with the development and low costs of high throughput sequencing techniques allow their application in genomic medicine. Therefore, Whole Exome Sequencing (WES), which corresponds to less than 2% of the entire genome, emerges as a cost-effective tool that aims to identify variants related to human diseases. Bioinformatics is fundamental to process the big volume of data and link the obtained results with the biology. Objective: We aim to apply and evaluate protocols and applications designed for WES data analysis on human subjects. We also intend to apply and enhance protocols and applications designed to predict variants as potentially pathological from WES data. Materials and Methods: We used the following tools: FastQC, Rqc, BWA, Picard, GATK e VEP. We applied them to exome data, determining variation in quality profiles, local realignment, quality recalibration and variant calls. We also evaluated whether or not technical and population differences affect the depth profiles of samples from the 1000 Genomes Project. Results: We applied our protocol on 27 samples, resulting in pre and postalignment quality control charts. Local realignment took place at more than 15% of the exome definition, extending to more than 79% of sequences. Quality recalibration minimized per cycle variation. In total, 72% of the sequences were paired against the genome, nevertheless 46% extended off-target. The mean coverage was 59X for the exome. We also detected that depth tends to vary based on technical and population differences between samples. Conclusion: We applied x a variant-calling workflow that accounts for sequence quality, the alignment against the genome, local realignment, quality recalibration and annotation. In addition, we concluded that depth depends on technical and population differences, showing that genomic complexity may interfere with the capturing phase, affecting downstream analyses.

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Quality Control of High‐Throughput Biological Data

Cited by 2 publications

References 14 publications

Persistent alveolar bronchiolization, interstitial fibrosis and impaired lung function post-exercise are features of long-COVID in SARS-CoV-2-Delta variant infected aged hamsters

Persistent alveolar bronchiolization, interstitial fibrosis and impaired lung function post-exercise are features of long-COVID in SARS-CoV-2-Delta variant infected aged hamsters

Aplicação de protocolos e métodos em bioinformática para análise de sequenciamento de exomas humanos

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