ReviewCancer informatics2014
Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.
Review in Cancer informatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
85 citing papers in PubMed.
- Detection of germline variants in human population chronically exposed to high level natural background radiation in Kerala coast.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2026Article
- Tutorial for variant interrogation in tumor samples.PLoS computational biology · 2026Article
- Advances in Biotechnological GABA Production: Exploring Microbial Diversity, Novel Food Substrates, and Emerging Market Opportunities.International journal of molecular sciences · 2025Review
- Development of an in vitro method to assess the immunogenicity of biologics in the prevention of infectious diseases.Immunologic research · 2025Article
- PathVar: A Customisable NGS Variant Calling Algorithm Implicates Novel Candidate Genes and Pathways in Hemiplegic Migraine.Clinical genetics · 2025Article
- Article
- From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases.Diagnostics (Basel, Switzerland) · 2024Review
- Omics Biology in Diagnosis of Diseases: Towards Empowering Genomic Medicine from an Evolutionary Perspective.Life (Basel, Switzerland) · 2024Article
- Whole exome sequencing in energy deficiency inborn errors of metabolism: A systematic review.Molecular genetics and metabolism reports · 2024Review
- NGS-Based Identification of Two NovelInternational journal of molecular sciences · 2024Article
- Detection of common pathogenesis of rheumatoid arthritis and atherosclerosis via microarray data analysis.Heliyon · 2024Article
- Multi‑dimensional analysis reveals NCKAP5L is a promising biomarker for the diagnosis and prognosis of human cancers, especially colorectal cancer.Oncology letters · 2024Article
- In silico bioprospecting of receptors associated with the mechanism of action of Rondonin, an antifungal peptide from spiderIn silico pharmacology · 2024Article
- Biology-aware mutation-based deep learning for outcome prediction of cancer immunotherapy with immune checkpoint inhibitors.NPJ precision oncology · 2023Article
- Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss.PLoS genetics · 2023Article
- Identification of Lncrna-Mrna Networks in Hepg2 Cells uponIranian journal of public health · 2023Article
- A conditional knockout rat resource of mitochondrial protein-coding genes via a DdCBE-induced premature stop codon.Science advances · 2023Article
- Protocol to benchmark gene expression signature scoring techniques for single-cell RNA sequencing data in cancer.STAR protocols · 2022Article
- Characterization of driver mutations in Chinese non-small cell lung cancer patients using a novel targeted sequencing panel.Journal of thoracic disease · 2022Article
- Fusion Gene Detection Using Whole-Exome Sequencing Data in Cancer Patients.Frontiers in genetics · 2022Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, pre-processing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.