ArticleGenome research2016
SMASH, a fragmentation and sequencing method for genomic copy number analysis.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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.
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Who cites it
21 citing papers in PubMed, 28 citations in OpenAlex.
- Trial
- A High-Fidelity and Ancestrally Inclusive Patient-Derived Organoid Platform Resolves Cancer Cell Plasticity in Uterine Carcinosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Modeling and targeting general and chromosome-specific aneuploidy in cancer.Genes & development · 2025Review
- Nanopore-based random genomic sampling for intraoperative molecular diagnosis.Genome medicine · 2025Article
- Prenatal Counseling and Diagnosis of COX20 Gene-Related Mitochondrial Complex IV Deficiency: A Case Report and Literature Review.International journal of women's health · 2025Article
- Aneuploidy in human cancer: new tools and perspectives.Trends in genetics : TIG · 2023Review
- Oncogene-like addiction to aneuploidy in human cancers.Science (New York, N.Y.) · 2023Article
- Oncogene-like addiction to aneuploidy in human cancers.bioRxiv : the preprint server for biology · 2023Article
- Patient-Derived Triple-Negative Breast Cancer Organoids Provide Robust Model Systems That Recapitulate Tumor Intrinsic Characteristics.Cancer research · 2022Article
- High resolution copy number inference in cancer using short-molecule nanopore sequencing.Nucleic acids research · 2021Article
- Article
- Detection of Copy Number Variants by Short Multiply Aggregated Sequence Homologies.The Journal of molecular diagnostics : JMD · 2020Article
- Article
- Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer.Developmental cell · 2020Article
- Parallel Tests of Whole Exome Sequencing and Copy Number Variant Sequencing Increase the Diagnosis Yields of Rare Pediatric Disorders.Frontiers in genetics · 2020Article
- Micronuclei-based model system reveals functional consequences of chromothripsis in human cells.eLife · 2019Article
- SMURF-seq: efficient copy number profiling on long-read sequencers.Genome biology · 2019Article
- DNA copy number variations in children with vesicoureteral reflux and urinary tract infections.PloS one · 2019Article
- Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders.Frontiers in genetics · 2019Article
- Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer.Cancer research · 2018Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Copy number variants (CNVs) underlie a significant amount of genetic diversity and disease. CNVs can be detected by a number of means, including chromosomal microarray analysis (CMA) and whole-genome sequencing (WGS), but these approaches suffer from either limited resolution (CMA) or are highly expensive for routine screening (both CMA and WGS). As an alternative, we have developed a next-generation sequencing-based method for CNV analysis termed SMASH, for short multiply aggregated sequence homologies. SMASH utilizes random fragmentation of input genomic DNA to create chimeric sequence reads, from which multiple mappable tags can be parsed using maximal almost-unique matches (MAMs). The SMASH tags are then binned and segmented, generating a profile of genomic copy number at the desired resolution. Because fewer reads are necessary relative to WGS to give accurate CNV data, SMASH libraries can be highly multiplexed, allowing large numbers of individuals to be analyzed at low cost. Increased genomic resolution can be achieved by sequencing to higher depth.
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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.