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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Related Experiment Video

Updated: Apr 18, 2026

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
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Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing.

Sydney B Blattman1, Nabih Maslah1,2, Austin A Varela1

  • 1Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.

Biorxiv : the Preprint Server for Biology
|April 17, 2026
PubMed
Summary
This summary is machine-generated.

Genotyping in Fixed Transcriptomes (GIFT) links genetic mutations to cell states in thousands of cells. This new method reveals how mutations like JAK2V617 drive disease in myeloproliferative neoplasms.

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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations
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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Single-cell transcriptomics offers insights into cell heterogeneity.
  • Linking transcriptional states to somatic mutations in single cells remains a challenge.
  • Existing platforms have limitations in simultaneous genetic and transcriptomic profiling.

Purpose of the Study:

  • Introduce Genotyping in Fixed Transcriptomes (GIFT), a novel assay.
  • Enable simultaneous detection of genetic variants and transcriptome profiles in single cells.
  • Facilitate clonal lineage tracing and genotype-to-phenotype relationship resolution.

Main Methods:

  • Developed a novel assay (GIFT) using gapfilling reactions between ssDNA probes.
  • Barcodes native transcript sequences for highly specific mutation detection.
  • Achieved high genotyping accuracy (>99%) and flexible capture of hundreds of mutations per cell.
  • Applied GIFT to profile over 700,000 cells from myeloproliferative neoplasm (MPN) patients.

Main Results:

  • Demonstrated GIFT's scalability and accuracy, including in FFPE tissues.
  • Revealed mutation-dependent hematopoietic responses to inflammation in MPNs.
  • Identified an allelic dose gradient of interferon-associated programs linked to JAK2V617.
  • Showcased GIFT's ability to trace clonal lineages and link genotype to phenotype.

Conclusions:

  • GIFT overcomes technical limitations in single-cell mutation and transcriptome analysis.
  • Enables comprehensive cell state measurements and clonal lineage tracing at single-cell resolution.
  • Provides new insights into genotype-to-phenotype relationships in complex diseases like MPNs.