ArticleHuman immunology2015
Impact of three Illumina library construction methods on GC bias and HLA genotype calling.
Article in Human immunology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed.
- Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.BMC genomics · 2025Article
- Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine.Medical principles and practice : international journal of the Kuwait University, Health Science Centre · 2024Review
- Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors.PeerJ · 2024Article
- The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content.Frontiers in microbiology · 2022Article
- Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures.BMC genomics · 2021Article
- Advances and opportunities in malaria population genomics.Nature reviews. Genetics · 2021Review
- A long road/read to rapid high-resolution HLA typing: The nanopore perspective.Human immunology · 2021Review
- Variants at the ASIP locus contribute to coat color darkening in Nellore cattle.Genetics, selection, evolution : GSE · 2021Article
- Fast and inexpensive whole-genome sequencing library preparation from intact yeast cells.G3 (Bethesda, Md.) · 2021Article
- Article
- Development of a sequencing system for spatial decoding of DNA barcode molecules at single-molecule resolution.Communications biology · 2020Article
- Reply to Li et al., "GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently AffectApplied and environmental microbiology · 2020Article
- GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently AffectApplied and environmental microbiology · 2020Article
- Article
- German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing.Frontiers in microbiology · 2020Article
- High-throughput DNA sequencing technologies for water and wastewater analysis.Science progress · 2019Review
- Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.Genome research · 2019Article
- Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing.BMC genomics · 2019Article
- Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation.Frontiers in public health · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Next-generation sequencing (NGS) is increasingly recognized for its ability to overcome allele ambiguity and deliver high-resolution typing in the HLA system. Using this technology, non-uniform read distribution can impede the reliability of variant detection, which renders high-confidence genotype calling particularly difficult to achieve in the polymorphic HLA complex. Recently, library construction has been implicated as the dominant factor in instigating coverage bias. To study the impact of this phenomenon on HLA genotyping, we performed long-range PCR on 12 samples to amplify HLA-A, -B, -C, -DRB1, and -DQB1, and compared the relative contribution of three Illumina library construction methods (TruSeq Nano, Nextera, Nextera XT) in generating downstream bias. Here, we show high GC% to be a good predictor of low sequencing depth. Compared to standard TruSeq Nano, GC bias was more prominent in transposase-based protocols, particularly Nextera XT, likely through a combination of transposase insertion bias being coupled with a high number of PCR enrichment cycles. Importantly, our findings demonstrate non-uniform read depth can have a direct and negative impact on the robustness of HLA genotyping, which has clinical implications for users when choosing a library construction strategy that aims to balance cost and throughput with data quality.
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.