Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls

被引：0
|
作者：
Alexandra R. Buckley
Kristopher A. Standish
Kunal Bhutani
Trey Ideker
Roger S. Lasken
Hannah Carter
Olivier Harismendy
Nicholas J. Schork
机构：
[1] University of California,Biomedical Sciences Graduate Program
[2] J. Craig Venter Institute,Bioinformatics and Systems Biology Sciences Graduate Program
[3] University of California,Division of Medical Genetics, Department of Medicine
[4] University of California San Diego,Moores Cancer Center
[5] University of California San Diego,Cancer Cell Map Initiative (CCMI)
[6] University of California San Diego,Microbial Genomics Program
[7] J. Craig Venter Institute,Division of Biomedical Informatics, Department of Medicine
[8] University of California San Diego,undefined
[9] The Translational Genomics Research Institute,undefined
来源：
BMC Genomics | / 18卷
关键词：
Cancer genomics; TCGA; Cancer germline; Whole exome sequencing; Variant calling; GATK; Batch effects; Whole genome amplification; Variant annotation; Genetic association testing;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
引用
收藏
相关论文
共 50 条
  • [41] Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns
    Yang, Xiaofei
    Gao, Lin
    Zhang, Shihua
    BRIEFINGS IN BIOINFORMATICS, 2017, 18 (05) : 761 - 773
  • [42] TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data
    Liao, Chenqi
    Wang, Xiong
    BMC BIOINFORMATICS, 2023, 24 (01)
  • [43] A pan-cancer analysis of the granzyme family based on the TCGA database and singlecell RNA sequencing data.
    Xu, Bin
    He, Junju
    Li, Jing
    Wu, Jie
    Zhang, Huibo
    Jin, Yan
    Yao, Yi
    Song, Qibin
    JOURNAL OF CLINICAL ONCOLOGY, 2022, 40 (16)
  • [44] Pan-cancer analysis reveals m6A modification is functionally important in cancer
    Zuo, Zhixiang
    Xie, Yubin
    Zheng, Yueyuan
    Nie, Peng
    Jiang, Shuai
    Zhao, Qi
    Miao, Yanyan
    Ren, Jian
    CANCER RESEARCH, 2018, 78 (13)
  • [45] Pan-cancer analysis reveals sex-specific signatures in the tumor microenvironment
    Han, Junwei
    Yang, Yang
    Li, Xiangmei
    Wu, Jiashuo
    Sheng, Yuqi
    Qiu, Jiayue
    Wang, Qian
    Li, Ji
    He, Yalan
    Cheng, Liang
    Zhang, Yan
    MOLECULAR ONCOLOGY, 2022, 16 (11) : 2153 - 2173
  • [46] Pan-cancer splicing analysis reveals shared drivers of malignant transformation and survival
    Bhattacharjee, Anukana
    Crowther, Audrey
    Li, Guangyuan
    Venkatasubramanian, Meenakshi
    Schnell, Dan
    Hay, Stuart
    Singh, Preeti
    Subramanian, Krithika R.
    Chetal, Kashish
    Chen, Xiaoting
    Kulkarni, Aishwarya
    Weirauch, Matthew T.
    Salomonis, Nathan
    CANCER RESEARCH, 2023, 83 (07)
  • [47] Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
    Varn, Frederick S.
    Wang, Yue
    Mullins, David W.
    Fiering, Steven
    Cheng, Chao
    CANCER RESEARCH, 2017, 77 (06) : 1271 - 1282
  • [48] Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function
    Cabanski, Christopher R.
    White, Nicole M.
    Dang, Ha X.
    Silva-Fisher, Jessica M.
    Rauck, Corinne E.
    Cicka, Danielle
    Maher, Christopher A.
    RNA BIOLOGY, 2015, 12 (06) : 628 - 642
  • [49] A Systematic Pan-Cancer Analysis of Genetic Heterogeneity Reveals Associations with Epigenetic Modifiers
    de Matos, Mafalda Ramos
    Posa, Ioana
    Carvalho, Filipa Sofia
    Morais, Vanessa Alexandra
    Grosso, Ana Rita
    de Almeida, Sergio Fernandes
    CANCERS, 2019, 11 (03)
  • [50] A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters
    Demircioglu, Deniz
    Cukuroglu, Engin
    Kindermans, Martin
    Nandi, Tannistha
    Calabrese, Claudia
    Fonseca, Nuno A.
    Kahles, Andre
    Kjong-Van Lehmann
    Stegle, Oliver
    Brazma, Alvis
    Brooks, Angela N.
    Ratsch, Gunnar
    Tan, Patrick
    Goke, Jonathan
    CELL, 2019, 178 (06) : 1465 - +
12345