ArticleGenome biology2011
Comparison of solution-based exome capture methods for next generation sequencing.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 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.
The trial behind it
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
136 citing papers in PubMed.
- The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2015Trial
- Trial
- Targeted resequencing reveals ALK fusions in non-small cell lung carcinomas detected by FISH, immunohistochemistry, and real-time RT-PCR: a comparison of four methods.BioMed research international · 2013Trial
- IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies.BioMed research international · 2013Trial
- A Practical Workflow for Correcting Kit-Specific Effects in Whole-Exome Sequencing Data.Methods and protocols · 2026Article
- Risk Haplotype of BTNL2 Predisposes Male Patients to NSTEMI: A Genetic and Functional Study.Research square · 2026Article
- Performance comparison of four exome capture platforms on DNBSEQ-Series high throughput sequencer.BMC genomics · 2025Article
- Non-truncating BMPR1A variants associated with familial colorectal cancer and adenomatous polyps.BMC cancer · 2025Article
- Germline Cancer Susceptibility Variants in Patients With Uveal Melanoma.Pigment cell & melanoma research · 2025Article
- Genome sequencing reveals CCDC88A variants in malformations of cortical development and immune dysfunction.Human molecular genetics · 2025Article
- Article
- Genes to therapy: a comprehensive literature review of whole-exome sequencing in neurology and neurosurgery.European journal of medical research · 2024Review
- Human whole-exome genotype data for Alzheimer's disease.Nature communications · 2024Article
- Genetic etiology of progressive pediatric neurological disorders.Pediatric research · 2024Article
- Novel insights into tumorigenesis revealed by molecular analysis of Lynch syndrome cases with multiple colorectal tumors.Frontiers in oncology · 2024Article
- Presentation and diagnosis of childhood-onset combined pituitary hormone deficiency: A single center experience from over 30 years.EClinicalMedicine · 2022Article
- Mapping transgene insertion sites reveals the α-Cre transgene expression in both developing retina and olfactory neurons.Communications biology · 2022Article
- Pharmacogenomics of celiprolol - evidence for a role of P-glycoprotein and organic anion transporting polypeptide 1A2 in celiprolol pharmacokinetics.Clinical and translational science · 2022Article
- Mono- and biallelic germline variants of DNA glycosylase genes in colon adenomatous polyposis families from two continents.Frontiers in oncology · 2022Article
- Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma.Nature communications · 2021Article
76 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
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTechniques enabling targeted re-sequencing of the protein coding sequences of the human genome on next generation sequencing instruments are of great interest. We conducted a systematic comparison of the solution-based exome capture kits provided by Agilent and Roche NimbleGen. A control DNA sample was captured with all four capture methods and prepared for Illumina GAII sequencing. Sequence data from additional samples prepared with the same protocols were also used in the comparison.
resultsWe developed a bioinformatics pipeline for quality control, short read alignment, variant identification and annotation of the sequence data. In our analysis, a larger percentage of the high quality reads from the NimbleGen captures than from the Agilent captures aligned to the capture target regions. High GC content of the target sequence was associated with poor capture success in all exome enrichment methods. Comparison of mean allele balances for heterozygous variants indicated a tendency to have more reference bases than variant bases in the heterozygous variant positions within the target regions in all methods. There was virtually no difference in the genotype concordance compared to genotypes derived from SNP arrays. A minimum of 11× coverage was required to make a heterozygote genotype call with 99% accuracy when compared to common SNPs on genome-wide association arrays.
conclusionsLibraries captured with NimbleGen kits aligned more accurately to the target regions. The updated NimbleGen kit most efficiently covered the exome with a minimum coverage of 20×, yet none of the kits captured all the Consensus Coding Sequence annotated exons.
Indexed as
Identifiers
What OpenQuestion holds
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.