ArticleNature methods2016
Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- An expanded role for single-cell chemical genomics profiling in drug discovery.The Biochemical journal · 2026Review
- De Novo Detection of Clonal Structure and Evolution in Single-Cell and Spatial Transcriptomes.International journal of molecular sciences · 2025Article
- Scalable co-sequencing of RNA and DNA from individual nuclei.Nature methods · 2025Article
- HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling.Genome biology · 2024Article
- Analyzing the functional effects of DNA variants with gene editing.Cell reports methods · 2024Review
- De novo detection of somatic mutations in high-throughput single-cell profiling data sets.Nature biotechnology · 2024Article
- Spatially resolved transcriptomics: advances and applications.Blood science (Baltimore, Md.) · 2023Review
- Identification of a novel gene signature in second-trimester amniotic fluid for the prediction of preterm birth.Scientific reports · 2022Article
- Integrated genomic, transcriptomic and metabolomic analysis reveals MDH2 mutation-induced metabolic disorder in recurrent focal segmental glomerulosclerosis.Frontiers in immunology · 2022Article
- SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platform.Genome biology · 2021Article
- Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines.Genomics, proteomics & bioinformatics · 2021Review
- Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects.International journal of legal medicine · 2020Review
- GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions.Frontiers in bioengineering and biotechnology · 2020Article
- Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method.Scientific reports · 2019Article
- Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.Nature protocols · 2018Article
- Article
- Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI).Science (New York, N.Y.) · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Paired DNA and RNA profiling is increasingly employed in genomics research to uncover molecular mechanisms of disease and to explore personal genotype and phenotype correlations. Here, we introduce Simul-seq, a technique for the production of high-quality whole-genome and transcriptome sequencing libraries from small quantities of cells or tissues. We apply the method to laser-capture-microdissected esophageal adenocarcinoma tissue, revealing a highly aneuploid tumor genome with extensive blocks of increased homozygosity and corresponding increases in allele-specific expression. Among this widespread allele-specific expression, we identify germline polymorphisms that are associated with response to cancer therapies. We further leverage this integrative data to uncover expressed mutations in several known cancer genes as well as a recurrent mutation in the motor domain of KIF3B that significantly affects kinesin-microtubule interactions. Simul-seq provides a new streamlined approach for generating comprehensive genome and transcriptome profiles from limited quantities of clinically relevant samples.
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Registered trials
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