PMID- 29385401
OWN - NLM
STAT- MEDLINE
DCOM- 20190712
LR  - 20230201
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 34
IP  - 12
DP  - 2018 Jun 15
TI  - Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data 
      by jointly modelling somatic copy number alterations and heterozygous germline 
      single-nucleotide-variants.
PG  - 2004-2011
LID - 10.1093/bioinformatics/bty043 [doi]
AB  - MOTIVATION: Tumor purity and ploidy have a substantial impact on next-gen 
      sequence analyses of tumor samples and may alter the biological and clinical 
      interpretation of results. Despite the existence of several computational methods 
      that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome 
      Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast 
      and fully-automated method that works in a wide range of sequencing coverage, 
      level of tumor purity and level of intra-tumor heterogeneity, is still missing. 
      RESULTS: We describe a computational method called Accurity that infers tumor 
      purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy 
      number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs 
      and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both 
      in silico and real sequencing data demonstrated that Accurity is highly accurate 
      and robust, even in low-purity, high-ploidy and low-coverage settings in which 
      several existing methods perform poorly. Accounting for tumor purity and ploidy, 
      Accurity significantly increased signal/noise gaps between different copy 
      numbers. We are hopeful that Accurity is of clinical use for identifying cancer 
      diagnostic biomarkers. AVAILABILITY AND IMPLEMENTATION: Accurity is implemented 
      in C++/Rust, available at http://www.yfish.org/software/. SUPPLEMENTARY 
      INFORMATION: Supplementary data are available at Bioinformatics online.
FAU - Luo, Zhihui
AU  - Luo Z
AD  - State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 
      Chinese Academy of Sciences, Shanghai, China.
FAU - Fan, Xinping
AU  - Fan X
AD  - State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 
      Chinese Academy of Sciences, Shanghai, China.
AD  - University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, China.
FAU - Su, Yao
AU  - Su Y
AD  - State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 
      Chinese Academy of Sciences, Shanghai, China.
FAU - Huang, Yu S
AU  - Huang YS
AD  - State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 
      Chinese Academy of Sciences, Shanghai, China.
AD  - University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Algorithms
MH  - Computational Biology/methods
MH  - Computer Simulation
MH  - *DNA Copy Number Variations
MH  - Germ-Line Mutation
MH  - High-Throughput Nucleotide Sequencing/methods
MH  - Humans
MH  - Neoplasms/*genetics
MH  - *Ploidies
MH  - *Software
MH  - Whole Genome Sequencing/*methods
PMC - PMC9881684
EDAT- 2018/02/01 06:00
MHDA- 2019/07/13 06:00
PMCR- 2018/01/27
CRDT- 2018/02/01 06:00
PHST- 2016/09/05 00:00 [received]
PHST- 2018/01/26 00:00 [accepted]
PHST- 2018/02/01 06:00 [pubmed]
PHST- 2019/07/13 06:00 [medline]
PHST- 2018/02/01 06:00 [entrez]
PHST- 2018/01/27 00:00 [pmc-release]
AID - 4827681 [pii]
AID - bty043 [pii]
AID - 10.1093/bioinformatics/bty043 [doi]
PST - ppublish
SO  - Bioinformatics. 2018 Jun 15;34(12):2004-2011. doi: 10.1093/bioinformatics/bty043.