ArticleNature genetics2014
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Article in Nature genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 654 papers, 1 of them a synthesis that pooled it.
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
654 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases.Nature communications · 2025Pooled it
- Phase II Study of Adavosertib in Patients With Tumors Containing BRCA1 and BRCA2 Mutations: Results From the NCI-MATCH ECOG-ACRIN Cancer Research Group (EAY131) Subprotocol Z1I.JCO precision oncology · 2026Trial
- Tumor ecosystem and microbiome features associated with efficacy and resistance to avelumab plus chemoradiotherapy in head and neck cancer.Nature cancer · 2026Trial
- Nivolumab plus ipilimumab induce hyper-progression in renal medullary carcinoma: results of a phase II trial and preclinical evidence.Nature communications · 2025Trial
- Molecularly matched targeted therapies plus radiotherapy in glioblastoma: the phase 1/2a NNature medicine · 2025Trial
- Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial.Nature medicine · 2023Trial
- Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Trial
- Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (International journal of molecular sciences · 2026Article
- Landscape of parental postzygotic mutations across >11,000 rare disease trios.American journal of human genetics · 2026Article
- Pipettes and Pipelines: The Weapons of Omics Sciences for a New Age of Clinical Studies.Current issues in molecular biology · 2026Review
- Transcriptomic analysis of tissue-resident memory T cells of the fallopian tube reveals a precursor immune surveillance network for ovarian cancer prevention.Nature communications · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Non-BRCA germline pathogenic variants and response to neoadjuvant systemic therapy in triple-negative breast cancer patients enrolled in a prospective clinical trial.Breast cancer research and treatment · 2026Article
- Article
- A three generation family with VACTERL association is found to have a rare form of diamond-blackfan anaemia.European journal of human genetics : EJHG · 2026Article
- Ancient regulatory evolution shapes individual language abilities in present-day humans.Science advances · 2026Article
- Genome-wide identification of eQTL-associated lncRNAs in melon and their role in fruit cracking.Scientific reports · 2026Article
- Unique sex chromosome translocations and evolutionary strata in two Sylvioidea songbird families.BMC genomics · 2026Article
- Microglandular adenosis, triple negative breast carcinoma and DNA repair defects.Journal of clinical pathology · 2026Article
- Multi-layered molecular profiling informs the diagnosis and targeted therapy of desmoplastic small round cell tumor.Nature communications · 2026Article
594 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
9 authors.
Funding
Abstract
High-throughput DNA sequencing technology has transformed genetic research and is starting to make an impact on clinical practice. However, analyzing high-throughput sequencing data remains challenging, particularly in clinical settings where accuracy and turnaround times are critical. We present a new approach to this problem, implemented in a software package called Platypus. Platypus achieves high sensitivity and specificity for SNPs, indels and complex polymorphisms by using local de novo assembly to generate candidate variants, followed by local realignment and probabilistic haplotype estimation. It is an order of magnitude faster than existing tools and generates calls from raw aligned read data without preprocessing. We demonstrate the performance of Platypus in clinically relevant experimental designs by comparing with SAMtools and GATK on whole-genome and exome-capture data, by identifying de novo variation in 15 parent-offspring trios with high sensitivity and specificity, and by estimating human leukocyte antigen genotypes directly from variant calls.
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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.