ArticleBMC genomics2019
SMaSH: Sample matching using SNPs in humans.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed, 22 citations in OpenAlex.
- SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin.bioRxiv : the preprint server for biology · 2025Article
- Genotyping from targeted NGS data based on a small set of SNPs correctly matches patient samples.BMC research notes · 2025Article
- Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors.Cancer research · 2025Article
- Screening a new set of microhaplotypes in exonic regions for sample identity testing and paternity testing during whole exome sequencing analysis.International journal of legal medicine · 2025Article
- Considerations for the development of iPSC-derived cell therapies: a review of key challenges by the JSRM-ISCT iPSC Committee.Cytotherapy · 2024Review
- Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments.Cell reports. Medicine · 2024Article
- Development of a coding SNP panel for tracking the origin of whole-exome sequencing samples.BMC genomics · 2024Article
- A multi-omics dataset for the analysis of frontotemporal dementia genetic subtypes.Scientific data · 2023Article
- Regulatory considerations for developing a phase I investigational new drug application for autologous induced pluripotent stem cells-based therapy product.Stem cells translational medicine · 2021Review
- Article
- The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundInadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotide polymorphisms (SNPs), omics data types often only provide low to moderate coverage, thus requiring integration of evidence from a large number of SNPs to determine if two samples derive from the same individual or not.
methodsWe select about six thousand SNPs in the human genome and develop a Bayesian framework that is able to robustly identify sample matches between next generation sequencing data sets.
resultsWe validate our approach on a variety of data sets. Most importantly, we show that our approach can establish identity between different omics data types such as Exome, RNA-Seq, and MethylCap-Seq. We demonstrate how identity detection degrades with sample quality and read coverage, but show that twenty million reads of a fairly low quality RNA-Seq sample are still sufficient for reliable sample identification.
conclusionOur tool, SMASH, is able to identify sample mismatches in next generation sequencing data sets between different sequencing modalities and for low quality sequencing data.
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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.