ALLELE-SPECIFIC COPY NUMBER ESTIMATION BY WHOLE EXOME SEQUENCING

被引：5
|
作者：
Chen, Hao [1 ]
Jiang, Yuchao [2 ]
Maxwell, Kara N. [3 ]
Nathanson, Katherine L. [3 ]
Zhang, Nancy [2 ]
机构：
[1] Univ Calif Davis, Dept Stat, One Shields Ave, Davis, CA 95616 USA
[2] Univ Penn, Wharton Sch, Dept Stat, Philadelphia, PA 19104 USA
[3] Univ Penn, Perelman Sch Med, Philadelphia, PA 19104 USA
来源：
ANNALS OF APPLIED STATISTICS | 2017年 / 11卷 / 02期
关键词：
Allele-specific copy number; whole exome sequencing; tumor-normal pair; CIRCULAR BINARY SEGMENTATION;
D O I：
10.1214/17-AOAS1043
中图分类号：
O21 [概率论与数理统计]; C8 [统计学];
学科分类号：
020208 ; 070103 ; 0714 ;
摘要：
Whole exome sequencing is currently a technology of choice in large-scale cancer genomics studies, where the priority is to identify cancer-associated variants in coding regions. We describe a method for estimating allele-specific copy number using whole exome sequencing data from tumor and matched normal.
引用
下载
收藏
页码：1169 / 1192
页数：24
相关论文
共 50 条
  • [1] Allele-specific copy-number discovery from whole-genome and whole-exome sequencing
    Wang, WeiBo
    Wang, Wei
    Sun, Wei
    Crowley, James J.
    Szatkiewicz, Jin P.
    NUCLEIC ACIDS RESEARCH, 2015, 43 (14)
  • [2] RBV: Allele-specific copy-number validation of whole genome sequence and whole exome sequence data
    Whitford, W.
    Lehnert, K.
    Snell, R. G.
    Jacobsen, J. C.
    EUROPEAN JOURNAL OF HUMAN GENETICS, 2018, 26 : 705 - 706
  • [3] Copy number estimation from whole-exome sequencing in tumors
    Anderson, Shawn
    Che, Zhiwei
    Keshavan, Raja
    O'Hara, Andrea
    Lin, Dong
    Wang, Yuzhuo
    Collins, Colin
    Shams, Soheil
    CANCER RESEARCH, 2018, 78 (13)
  • [4] Allele-specific copy number profiling by next-generation DNA sequencing
    Chen, Hao
    Bell, John M.
    Zavala, Nicolas A.
    Ji, Hanlee P.
    Zhang, Nancy R.
    NUCLEIC ACIDS RESEARCH, 2015, 43 (04)
  • [5] Allele-specific copy number analysis of tumors
    Van Loo, Peter
    Nordgard, Silje H.
    Lingjaerde, Ole Christian
    Russnes, Hege G.
    Rye, Inga H.
    Sun, Wei
    Weigman, Victor J.
    Marynen, Peter
    Zetterberg, Anders
    Naume, Bjorn
    Perou, Charles M.
    Borresen-Dale, Anne-Lise
    Kristensen, Vessela N.
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (39) : 16910 - 16915
  • [6] Overcoming Challenges in Copy Number Estimation from Whole Exome Sequencing in Tumors
    Anderson, S.
    Che, Z.
    Keshavan, R.
    Venna, S.
    Collins, C.
    Shams, S.
    JOURNAL OF MOLECULAR DIAGNOSTICS, 2017, 19 (06): : 1035 - 1035
  • [7] Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data
    Favero, F.
    Joshi, T.
    Marquard, A. M.
    Birkbak, N. J.
    Krzystanek, M.
    Li, Q.
    Szallasi, Z.
    Eklund, A. C.
    ANNALS OF ONCOLOGY, 2015, 26 (01) : 64 - 70
  • [8] Allele-specific copy number analysis of breast carcinomas
    Van Loo, P.
    Nordgard, S.
    Lingjaerde, O. C.
    Russnes, H. G.
    Rye, I. H.
    Sun, W.
    Naume, B.
    Perou, C. M.
    Borresen-Dale, A. L.
    Kristensen, V. N.
    EJC SUPPLEMENTS, 2010, 8 (05): : 200 - 200
  • [9] Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing
    Weiner, Samson
    Li, Bingjun
    Nabavi, Sheida
    BIOINFORMATICS, 2024, 40 (08)
  • [10] Evaluation of somatic copy number estimation tools for whole-exome sequencing data
    Nam, Jae-Yong
    Kim, Nayoung K. D.
    Kim, Sang Cheol
    Joung, Je-Gun
    Xi, Ruibin
    Lee, Semin
    Park, Peter J.
    Park, Woong-Yang
    BRIEFINGS IN BIOINFORMATICS, 2016, 17 (02) : 185 - 192
12345