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TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data

Wei, Lin; Jin, Zhilin; Yang, Shengjie; Xu, Yanxun; Zhu, Yitan; Ji, Yuan
Motivation:The Cancer Genome Atlas (TCGA) program has produced huge amounts of cancer genomics data providing unprecedented opportunities for research. In 2014, we developed TCGA-Assembler, a software pipeline for retrieval and processing of public TCGA data. In 2016, TCGA data were transferred from the TCGA data portal to the Genomic Data Commons (GDCs), which is supported by a different set of data storage and retrieval mechanisms. In addition, new proteomics data of TCGA samples have been generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, which were not available for downloading through TCGA-Assembler. It is desirable to acquire and integrate data from both GDC and CPTAC. Results:We develop TCGA-assembler 2 (TA2) to automatically download and integrate data from GDC and CPTAC. We make substantial improvement on the functionality of TA2 to enhance user experience and software performance. TA2 together with its previous version have helped more than 2000 researchers from 64 countries to access and utilize TCGA and CPTAC data in their research. Availability of TA2 will continue to allow existing and new users to conduct reproducible research based on TCGA and CPTAC data. Availability and implementation:http://www.compgenome.org/TCGA-Assembler/ or https://github.com/compgenome365/TCGA-Assembler-2. Contact:zhuyitan@gmail.com or koaeraser@gmail.com. Supplementary information:Supplementary data are available at Bioinformatics online.
PMCID:5925773
PMID: 29272348
ISSN: 1367-4811
CID: 4961982

modSaRa: a computationally efficient R package for CNV identification

Xiao, Feifei; Niu, Yue; Hao, Ning; Xu, Yanxun; Jin, Zhilin; Zhang, Heping
Summary/UNASSIGNED:Chromosomal copy number variation (CNV) refers to a polymorphism that a DNA segment presents deletion or duplication in the population. The computational algorithms developed to identify this type of variation are usually of high computational complexity. Here we present a user-friendly R package, modSaRa, designed to perform copy number variants identification. The package is developed based on a change-point based method with optimal computational complexity and desirable accuracy. The current version of modSaRa package is a comprehensive tool with integration of preprocessing steps and main CNV calling steps. Availability and Implementation/UNASSIGNED:modSaRa is an R package written in R, C ++ and Rcpp and is now freely available for download at http://c2s2.yale.edu/software/modSaRa . Contact/UNASSIGNED:heping.zhang@yale.edu. Supplementary information/UNASSIGNED:Supplementary data are available at Bioinformatics online.
PMCID:5860124
PMID: 28453611
ISSN: 1367-4811
CID: 4961972

Protein-resistant polyurethane by sequential grafting of poly(2-hydroxyethyl methacrylate) and poly(oligo(ethylene glycol) methacrylate) via surface-initiated ATRP

Jin, Zhilin; Feng, Wei; Zhu, Shiping; Sheardown, Heather; Brash, John L
Protein-resistant polyurethane (PU) surfaces were prepared by sequentially grafting poly(2-hydroxyethyl methacrylate) (poly(HEMA)) and poly(oligo(ethylene glycol) methacrylate) (poly(OEGMA)) via surface-initiated atom transfer radical polymerization (s-ATRP). The chain lengths of poly(HEMA) and poly(OEGMA) were regulated via the ratio of monomer to sacrificial initiator in solution. The surfaces were characterized by water contact angle and X-ray photoelectron spectroscopy (XPS). The protein resistant properties of the surfaces were assessed by single and binary adsorption experiments with fibrinogen (Fg), lysozyme (Lys), and lactalbumin (Lac). The adsorption of all three proteins on the sequentially grafted poly(HEMA)-poly(OEGMA) surfaces (PU/PH/PO) was greatly reduced compared with the unmodified PU. Adsorption decreased with increasing poly(OEGMA) chain length. On the PU/PH/PO surface with longest poly(OEGMA) chain length (∼100), the decrease in Lys adsorption was in the range of 95-98% and the decrease in Fg and Lac adsorption was >99% compared with the unmodified PU. Adsorption from binary protein solutions showed that the PU/PH/PO surfaces resisted these proteins more or less equally, that is, independent of protein size.
PMID: 20939048
ISSN: 1552-4965
CID: 4961962

Protein-resistant materials via surface-initiated atom transfer radical polymerization of 2-methacryloyloxyethyl phosphorylcholine

Jin, Zhilin; Feng, Wei; Zhu, Shiping; Sheardown, Heather; Brash, John L
Poly(2-methacryloyloxyethyl phosphorylcholine) (poly(MPC)) was grafted from various polymeric substrates to prepare protein-resistant materials. The poly(MPC) chain length was adjusted via the ratio of monomer to sacrificial initiator in solution. The surfaces were characterized by water contact angle and X-ray photoelectron spectroscopy (XPS). The protein-resistant properties of the poly(MPC)-grafted surfaces were evaluated by single adsorption experiments with fibrinogen and lysozyme. It was shown that the simple three-step grafting method could be applied to modify various biomaterial surfaces including polyurethane and silicones. The adsorption of fibrinogen and lysozyme to the modified surfaces was greatly reduced compared to the unmodified surfaces, and adsorption decreased with increasing poly(MPC) chain length. On polyurethane film grafted with poly(MPC) of chain length 100, the reduction in adsorption was approx. 96% for lysozyme and approx. 99% for fibrinogen.
PMID: 20534188
ISSN: 1568-5624
CID: 4961952

Protein-resistant polyurethane via surface-initiated atom transfer radical polymerization of oligo(ethylene glycol) methacrylate

Jin, Zhilin; Feng, Wei; Zhu, Shiping; Sheardown, Heather; Brash, John L
Protein-resistant polyurethane (PU) surfaces were prepared by surface-initiated simultaneous normal and reverse atom transfer radical polymerization (s-ATRP) of poly(oligo(ethylene glycol) methacrylate) (poly (OEGMA)). Oxygen plasma treatment was employed for initial activation of the PU surface. The grafted polymer chain length was adjusted by varying the molar ratio of monomer to sacrificial initiator in solution from 5:1 to 200:1. The modified PU surfaces were characterized by water contact angle, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). Protein adsorption experiments from tris-buffered saline (TBS) and plasma were carried out to evaluate the protein-resistance of the surfaces. Adsorption from single and binary protein solutions as well as from plasma was significantly reduced after modification. Adsorption decreased with increasing poly(OEGMA) chain length. Fibrinogen (Fg) adsorption on the 200:1 monomer/initiator surface was in the range of 3-33 ng/cm(2) representing 96-99% reduction compared with the unmodified PU. Fg adsorption from 0.01-10% plasma was as low as 1-5 ng/cm(2). Moreover, binary protein adsorption experiments using Fg and lysozyme (Lys) showed that protein size is a factor in the protein resistance of these surfaces.
PMID: 19148931
ISSN: 1552-4965
CID: 4961932

Protein-resistant polyurethane prepared by surface-initiated atom transfer radical graft polymerization (ATRgP) of water-soluble polymers: effects of main chain and side chain lengths of grafts

Jin, Zhilin; Feng, Wei; Beisser, Kristen; Zhu, Shiping; Sheardown, Heather; Brash, John L
Water-soluble poly(oligo(ethylene glycol) methacrylate) (poly(OEGMA)) with various main chain and side chain lengths were grafted to polyurethane (PU) surface by surface-initiated atom transfer radical graft polymerization (s-ATRgP). The polymer main chain length was varied by varying the molar ratio of monomer to free initiator in solution (typically 5:1, 50:1, 100:1). Three different side chain lengths were obtained using different OEGMA monomers (MW 300, 475, 1100 g/mol). Water contact angle and X-ray photoelectron spectroscopy (XPS) were used to characterize the modified PU surfaces. The respective effects of poly(OEGMA) main chain and side chain lengths on fibrinogen (Fg) and lysozyme (Lys) adsorption were investigated in single protein systems at room temperature in TBS, pH 7.4. The poly(OEGMA)-grafted PU surfaces were found to be highly protein-resistant, with reductions of Fg and Lys adsorption in the range of 84-98% and 67-91%, respectively, compared to the unmodified PU surface. The adsorption of both proteins decreased with increasing poly(OEGMA) main chain length for a given side chain length (number of EO units). For a given main chain length, the Fg adsorption level did not change significantly with increasing side chain length. However, Lys adsorption increased with increasing side chain length, possibly due to decreasing graft density as monomer size and footprint on the surface increase. Adsorption resistance was generally greater for the bigger protein.
PMID: 19150594
ISSN: 1873-4367
CID: 4961942