SciClone protocols

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SciClone specifications

Information


Unique identifier OMICS_05106
Name SciClone
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Version 1.1.0
Stability Stable
Requirements
IRanges, ggplot2, sciclone
Maintained Yes

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Documentation


Maintainers


  • person_outline Li Ding <>
  • person_outline Chris Miller <>

Additional information


The Genome Institute, Washington University, St. Louis, MO, USA; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University, St. Louis, MO, USA; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, USA; Massachusetts General Hospital, Boston, MA, USA; Liggins Institute, Auckland, New Zealand

Publication for SciClone

SciClone in pipelines

 (7)
2018
PMCID: 5880262
PMID: 29440180
DOI: 10.1101/mcs.a002444

[…] the heterogeneity of each tumor specimen and compared it to the others in the series. here, copy-number-neutral variants and their attendant vafs were clustered in five dimensions using the sciclone algorithm v1.1 () (parameters: minimumdepth = 300, maximumclusters=15), followed by phylogeny reconstruction with clonevol ()., somatic mutations and rna-seq data from tumors were input […]

2017
PMCID: 5522415
PMID: 28733645
DOI: 10.1038/s41467-017-00182-7

[…] from ingwat of 2/3 individual mice. rna-seq libraries were prepared with polya selection using 500 ng of total rna and the illumina truseq stranded rna reagents (illumina; san diego, ca, usa) on a sciclone liquid handling robot (perkinelmer; waltham, ma, usa) using a perkinelmer-developed automated script. cluster generation was performed with the resulting libraries using the illumina truseq […]

2017
PMCID: 5655919
PMID: 28748566
DOI: 10.1111/bjh.14863

[…] ng spriworks fragment library cartridges i (beckman coulter, brea, ca, usa) with a size selection of 200–400 bp. from september 2015, the trimming, 3’‐adenylation and adaptor ligations were done on a sciclone g3 robot (perkin elmer, waltham, ma, usa) using illumina‐compatible kapa library dna adaptors (roche diagnostics, basel, switzerland). sequencing was performed as paired‐end sequencing, 2 × 1 […]

2017
PMCID: 5698805
PMID: 29177109
DOI: 10.4172/2161-0460.1000355

[…] the sureselect human all exon 50mb kit (agilent technologies) and the paired-end multiplexed sequencing library kit (illumina). exome capture and sequence library construction was performed on a sciclone g3 ngs workstation (caliper life sciences) and dna was tested for uniform enrichment of targets with qpcr following established protocols provided by agilent. two exome sample libraries […]

2016
PMCID: 4980485
PMID: 27502118
DOI: 10.1038/ncomms12498

[…] by applying unsupervised hierarchical clustering on a matrix of sample-by-sample correlations derived from gene expression (fpkm) values ()., the clonal architecture of each tumour was inferred with sciclone (version 1.0.7; ref. ), using default parameters except for copynumbermargins set to 0.25. the median vaf of each subclone was used as input for clonevol (https://github.com/hdng/clonevol), […]


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SciClone in publications

 (132)
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] integrity number was determined using the experion automated electrophoresis system (bio-rad). rna-seq libraries were prepared with truseq stranded mrna lt sample preparation kit (illumina) using sciclone and zephyr liquid handling robotics (perkinelmer). sequencing libraries were pooled, diluted, and sequenced on an illumina hiseq 3000 using 50 bp single-read chemistry. base calls provided […]

PMCID: 5907387
PMID: 29669589
DOI: 10.1186/s40168-018-0450-3

[…] by the samples barcoding in dual index (nextera xt index kit v2 from illumina) and an amplification (12 pcr cycles). after pcr, the library was purified using ampure beads (beckman coulter) on a sciclone robotic platform from perkin elmer. the quality and quantity of each library were evaluated using the labchip gx touch (capillary electrophoresis method from perkin elmer)., libraries […]

PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] quality control (qc) was performed on all the samples at ncgr upon receipt and all samples passed. rna-seq libraries were prepared and bar-coded using the maestro-based truseq rna application on the sciclone ngs platform (perkinelmer, ma, usa), a robotics system developed and validated for automated library preparation. the maestro-based truseq rna application provided a pre-programmed solution […]

PMCID: 5880262
PMID: 29440180
DOI: 10.1101/mcs.a002444

[…] in lats1 and map4k3 (; )., to characterize the changing clonal architecture of this tumor, the variant allele fractions of copy-number neutral snvs were clustered in five dimensions using the sciclone algorithm (a). eight clusters were detected, and the mutation spectrum for each was identified. the first recurrent tumor after radiation therapy was dominated by cluster 2, which emerged […]

PMCID: 5865165
PMID: 29572477
DOI: 10.1038/s41598-018-22882-w

[…] at previously optimized densities into 384-well ultra-low attachment plates (#3827, corning). cells were treated the following day with a 7 point 3-fold dilution series, 5.4 µm to 7.4 nm using a sciclone alh 3000 liquid handling robot. changes in cell viability were assayed at 72 hours using the cell titre glo 3d assay (#g9683, promega), luminescence reads were performed on a synergymx plate […]


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SciClone institution(s)
Supported by NHGRI grant U01HG006517, NHGRI grant U54HG003079, an International Myeloma Foundation Brian D. Novis research grant, Barnes-Jewish Hospital Foundation grant 7603-55, NIH/NCI SPORE in Leukemia grant P50CA171063, NIH/NCI grant 1K12CA167540, and Clinical and Translational Award from the NIH National Center for Advancing Translational Sciences grant UL1 TR000448.

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