Cargando…

A practical method to detect SNVs and indels from whole genome and exome sequencing data

The recent development of massively parallel sequencing technology has allowed the creation of comprehensive catalogs of genetic variation. However, due to the relatively high sequencing error rate for short read sequence data, sophisticated analysis methods are required to obtain high-quality varia...

Descripción completa

Detalles Bibliográficos
Autores principales:	Shigemizu, Daichi, Fujimoto, Akihiro, Akiyama, Shintaro, Abe, Tetsuo, Nakano, Kaoru, Boroevich, Keith A., Yamamoto, Yujiro, Furuta, Mayuko, Kubo, Michiaki, Nakagawa, Hidewaki, Tsunoda, Tatsuhiko
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group 2013
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703611/ https://www.ncbi.nlm.nih.gov/pubmed/23831772 http://dx.doi.org/10.1038/srep02161

Ejemplares similares

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
por: Shigemizu, Daichi, et al.
Publicado: (2018)

Publisher Correction: IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
por: Shigemizu, Daichi, et al.
Publicado: (2018)

Performance comparison of four commercial human whole-exome capture platforms
por: Shigemizu, Daichi, et al.
Publicado: (2015)

Exome Analyses of Long QT Syndrome Reveal Candidate Pathogenic Mutations in Calmodulin-Interacting Genes
por: Shigemizu, Daichi, et al.
Publicado: (2015)

Stepwise iterative maximum likelihood clustering approach
por: Sharma, Alok, et al.
Publicado: (2016)

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes
por: Fujimoto, Akihiro, et al.
Publicado: (2016)

Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population
por: Wong, Jing Hao, et al.
Publicado: (2019)

DeepInsight: A methodology to transform a non-image data to an image for convolution neural network architecture
por: Sharma, Alok, et al.
Publicado: (2019)

A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations
por: Miya, Fuyuki, et al.
Publicado: (2015)

A comparison of machine learning classifiers for dementia with Lewy bodies using miRNA expression data
por: Shigemizu, Daichi, et al.
Publicado: (2019)

Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset
por: Domogala, Daniel D., et al.
Publicado: (2021)

Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer
por: Fujimoto, Akihiro, et al.
Publicado: (2021)

Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data
por: Shigemizu, Daichi, et al.
Publicado: (2020)

The Construction of Risk Prediction Models Using GWAS Data and Its Application to a Type 2 Diabetes Prospective Cohort
por: Shigemizu, Daichi, et al.
Publicado: (2014)

Detection of Disease-Causing SNVs/Indels and CNVs in Single Test Based on Whole Exome Sequencing: A Retrospective Case Study in Epileptic Encephalopathies
por: Sun, Dan, et al.
Publicado: (2021)

Low incidence of SNVs and indels in trio genomes of Cas9-mediated multiplex edited sheep
por: Wang, Xiaolong, et al.
Publicado: (2018)

Integrated Analysis of Whole Genome and Transcriptome Sequencing Reveals Diverse Transcriptomic Aberrations Driven by Somatic Genomic Changes in Liver Cancers
por: Shiraishi, Yuichi, et al.
Publicado: (2014)

Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
por: Fujimoto, Akihiro, et al.
Publicado: (2020)

Risk prediction models for dementia constructed by supervised principal component analysis using miRNA expression data
por: Shigemizu, Daichi, et al.
Publicado: (2019)

Integrated analysis of human genetic association study and mouse transcriptome suggests LBH and SHF genes as novel susceptible genes for amyloid-β accumulation in Alzheimer’s disease
por: Yamaguchi-Kabata, Yumi, et al.
Publicado: (2018)

The prediction models for postoperative overall survival and disease‐free survival in patients with breast cancer
por: Shigemizu, Daichi, et al.
Publicado: (2017)

Loss-of-function mutations in Zn-finger DNA-binding domain of HNF4A cause aberrant transcriptional regulation in liver cancer
por: Taniguchi, Hiroaki, et al.
Publicado: (2018)

MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning
por: Li, Chang, et al.
Publicado: (2022)

Circulating Tumor DNA Analysis for Liver Cancers and Its Usefulness as a Liquid Biopsy
por: Ono, Atsushi, et al.
Publicado: (2015)

Quantification of multicellular colonization in tumor metastasis using exome‐sequencing data
por: Nishino, Jo, et al.
Publicado: (2020)

Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix
por: Chandra, Abel, et al.
Publicado: (2019)

Empirical Bayes Estimation of Semi-parametric Hierarchical Mixture Models for Unbiased Characterization of Polygenic Disease Architectures
por: Nishino, Jo, et al.
Publicado: (2018)

Detection of structural variants and indels within exome data
por: Karakoc, Emre, et al.
Publicado: (2011)

Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through immune landscape analysis
por: Shigemizu, Daichi, et al.
Publicado: (2022)

Sudden death in epilepsy and ectopic neurohypophysis in Joubert syndrome 23 diagnosed using SNVs/indels and structural variants pipelines on WGS data: a case report
por: Sumathipala, Dulika, et al.
Publicado: (2020)

Classification and deep-learning–based prediction of Alzheimer disease subtypes by using genomic data
por: Shigemizu, Daichi, et al.
Publicado: (2023)

Arete – candidate gene prioritization using biological network topology with additional evidence types
por: Lysenko, Artem, et al.
Publicado: (2017)

Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions
por: Gambin, Tomasz, et al.
Publicado: (2020)

JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types
por: Akiyama, Shintaro, et al.
Publicado: (2021)

Whole-genome sequencing reveals novel ethnicity-specific rare variants associated with Alzheimer’s disease
por: Shigemizu, Daichi, et al.
Publicado: (2022)

Reducing INDEL calling errors in whole genome and exome sequencing data
por: Fang, Han, et al.
Publicado: (2014)

Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data
por: Kim, Bo-Young, et al.
Publicado: (2017)

An integrative machine learning approach for prediction of toxicity-related drug safety
por: Lysenko, Artem, et al.
Publicado: (2018)

DeepInsight-3D architecture for anti-cancer drug response prediction with deep-learning on multi-omics
por: Sharma, Alok, et al.
Publicado: (2023)

Clinical Implications of Noncoding Indels in the Surfactant-Encoding Genes in Lung Cancer
por: Nakagomi, Takahiro, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_0trh8aocr35ip3g40rtfuvomoq