FadE: whole genome methylation analysis for multiple sequencing platforms

被引:1
|
作者
Souaiaia, Tade [2 ]
Zhang, Zheng [1 ]
Chen, Ting [2 ]
机构
[1] Life Technol Corp, Foster City, CA 94404 USA
[2] Univ So Calif, Program Computat Biol & Bioinformat, Los Angeles, CA 90089 USA
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
ALIGNMENT;
D O I
10.1093/nar/gks830
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
DNA methylation plays a central role in genomic regulation and disease. Sodium bisulfite treatment (SBT) causes unmethylated cytosines to be sequenced as thymine, which allows methylation levels to reflected in the number of 'C'-'C' alignments covering reference cytosines. Di-base color reads produced by lifetech's SOLiD sequencer provide unreliable results when translated to bases because single sequencing errors effect the downstream sequence. We describe FadE, an algorithm to accurately determine genome-wide methylation rates directly in color or nucleotide space. FadE uses SBT unmethylated and untreated data to determine background error rates and incorporate them into a model which uses Newton-Raphson optimization to estimate the methylation rate and provide a credible interval describing its distribution at every reference cytosine. We sequenced two slides of human fibroblast cell-line bisulfite-converted fragment library with the SOLiD sequencer to investigate genome-wide methylation levels. FadE reported widespread differences in methylation levels across CpG islands and a large number of differentially methylated regions adjacent to genes which compares favorably to the results of an investigation on the same cell-line using nucleotide-space reads at higher coverage levels, suggesting that FadE is an accurate method to estimate genome-wide methylation with color or nucleotide reads. http://code.google.com/p/fade/.
引用
收藏
页数:9
相关论文
共 50 条
  • [21] Whole genome sequencing in patients with multiple primary tumors
    Wallander, K.
    Nilsson, D.
    Tham, E.
    EUROPEAN JOURNAL OF HUMAN GENETICS, 2018, 26 : 587 - 588
  • [22] Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms
    Arora, Kanika
    Shah, Minita
    Johnson, Molly
    Sanghvi, Rashesh
    Shelton, Jennifer
    Nagulapalli, Kshithija
    Oschwald, Dayna M.
    Zody, Michael C.
    Germer, Soren
    Jobanputra, Vaidehi
    Carter, Jade
    Robine, Nicolas
    SCIENTIFIC REPORTS, 2019, 9 (1)
  • [23] Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms
    Kanika Arora
    Minita Shah
    Molly Johnson
    Rashesh Sanghvi
    Jennifer Shelton
    Kshithija Nagulapalli
    Dayna M. Oschwald
    Michael C. Zody
    Soren Germer
    Vaidehi Jobanputra
    Jade Carter
    Nicolas Robine
    Scientific Reports, 9
  • [24] Whole genome DNA methylation sequencing of the chicken retina, cornea and brain
    Isac Lee
    Bejan A. Rasoul
    Ashton S. Holub
    Alannah Lejeune
    Raymond A. Enke
    Winston Timp
    Scientific Data, 4
  • [25] Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Bright, A. Taylor
    Tewhey, Ryan
    Abeles, Shira
    Chuquiyauri, Raul
    Llanos-Cuentas, Alejandro
    Ferreira, Marcelo U.
    Schork, Nicholas J.
    Vinetz, Joseph M.
    Winzeler, Elizabeth A.
    BMC GENOMICS, 2012, 13
  • [26] Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    A Taylor Bright
    Ryan Tewhey
    Shira Abeles
    Raul Chuquiyauri
    Alejandro Llanos-Cuentas
    Marcelo U Ferreira
    Nicholas J Schork
    Joseph M Vinetz
    Elizabeth A Winzeler
    BMC Genomics, 13
  • [27] Whole Genome DNA Methylation Analysis of Commpass Identifies Biomarkers of Multiple Myeloma Survival
    Barwick, Benjamin G.
    Auclair, Daniel
    Blanski, Alex
    Kirchhoff, Meghan
    Docter, Brianne
    Rohrer, Daniel C.
    Keats, Jonathan J.
    Lonial, Sagar
    Boise, Lawrence H.
    Vertino, Paula M.
    BLOOD, 2018, 132
  • [28] Whole-genome bisulfite sequencing identifies HDAC3-mediated DNA methylation in multiple myeloma
    Ogiya, Daisuke
    Ohguchi, Hiroto
    Liu, Jiye
    Kurata, Keiji
    Adamia, Sophia
    Hideshima, Teru
    Anderson, Kenneth C.
    CLINICAL LYMPHOMA MYELOMA & LEUKEMIA, 2019, 19 (10): : E72 - E72
  • [29] BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
    Luli S. Zou
    Michael R. Erdos
    D. Leland Taylor
    Peter S. Chines
    Arushi Varshney
    Stephen C. J. Parker
    Francis S. Collins
    John P. Didion
    BMC Genomics, 19
  • [30] BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
    Zou, Luli S.
    Erdos, Michael R.
    Taylor, D. Leland
    Chines, Peter S.
    Varshney, Arushi
    Parker, Stephen C. J.
    Collins, Francis S.
    Didion, John P.
    BMC GENOMICS, 2018, 19