PRSS1 genotype is associated with prognosis in patients with pancreatic ductal adenocarcinoma

Wu, Huasheng; Ding, Fadian; Chen, Xijun; Chen, Shaoqin; Shi, Zhen; Liu, Qicai; Zheng, Zhenhua; Chen, Youting

doi:10.3892/ol.2019.11097

Cited by 2 publications

(2 citation statements)

References 21 publications

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“…In PDAC-1 and PDAC-2 we see shared copy number loss of tumor supressor genes CDKN2A, SMAD4 and BRCA2 25 , 29 . In PDAC-2 we observed a subclonal amplification of PRSS1 , a mutation that was fixed within our sampling for PDAC-1 and is associated with tumor size, tumor node metastasis rate 30 . This suggests that while the lines have the same origin, each culture captured different subsets of tumor clonal populations.…”

Section: Resultsmentioning

confidence: 61%

High-content single-cell combinatorial indexing

Mulqueen

Pokholok²,

O’Connell

et al. 2021

Nat Biotechnol

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Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but produces sparse coverage in terms of usable reads per cell. We develop symmetrical strand sci (‘s3’), a uracil-based adapter switching approach that improves the rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-ATAC) in human cortical and mouse whole brain tissues, with mouse datasets demonstrating a 6-to-13-fold improvement in usable reads per cell compared with other available methods. Application of s3 to single-cell whole genome sequencing (s3-WGS) and to whole genome plus chromatin conformation (s3-GCC) yields 148 and 14.8 fold improvements, respectively, in usable reads per cell compared with sci-DNA-seq and sci-HiC. We show that s3-WGS and s3-GCC resolve subclonal genomic alterations in patient-derived pancreatic cancer cell lines. We expect that the s3 platform will be compatible with other transposase-based techniques, including sci-MET or CUT&Tag.

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Section: Resultsmentioning

confidence: 61%

High-content single-cell combinatorial indexing

Mulqueen

Pokholok²,

O’Connell

et al. 2021

Nat Biotechnol

View full text Add to dashboard Cite

show abstract

“…In PDAC-1 and PDAC-2 we see shared copy number loss of tumor suppressor genes CDKN2A, SMAD4 and BRCA2 25,27 . In PDAC-2 we observed a subclonal amplification of PRSS1, a mutation that was fixed within our sampling for PDAC-1 and is associated with tumor size and a higher tumor node metastasis (TNM) stage 28 . This suggests that while the lines have the same origin, each culture captured different subsets of tumor clonal populations.…”

mentioning

confidence: 73%

High-content single-cell combinatorial indexing

Mulqueen

Pokholok

O’Connell

et al. 2021

Preprint

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Single-cell genomics assays have emerged as a dominant platform for interrogating complex biological systems. Methods to capture various properties at the single-cell level typically suffer a tradeoff between cell count and information content, which is defined by the number of unique and usable reads acquired per cell. We and others have described workflows that utilize single-cell combinatorial indexing (sci)1, leveraging transposase-based library construction2 to assess a variety of genomic properties in high throughput; however, these techniques often produce sparse coverage for the property of interest. Here, we describe a novel adaptor-switching strategy, ‘s3’, capable of producing one-to-two order-of-magnitude improvements in usable reads obtained per cell for chromatin accessibility (s3-ATAC), whole genome sequencing (s3-WGS), and whole genome plus chromatin conformation (s3-GCC), while retaining the same high-throughput capabilities of predecessor ‘sci’ technologies. We apply s3 to produce high-coverage single-cell ATAC-seq profiles of mouse brain and human cortex tissue; and whole genome and chromatin contact maps for two low-passage patient-derived cell lines from a primary pancreatic tumor.

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PRSS1 genotype is associated with prognosis in patients with pancreatic ductal adenocarcinoma

Cited by 2 publications

References 21 publications

High-content single-cell combinatorial indexing

High-content single-cell combinatorial indexing

High-content single-cell combinatorial indexing

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