title: DASAF: An R Package for Deep Sequencing-Based Detection of Fetal Autosomal Abnormalities from Maternal Cell-Free DNA.
abstract: Background. With the development of massively parallel sequencing (MPS), noninvasive prenatal diagnosis using maternal cell-free DNA is fast becoming the preferred method of fetal chromosomal abnormality detection, due to its inherent high accuracy and low risk. Typically, MPS data is parsed to calculate a risk score, which is used to predict whether a fetal chromosome is normal or not. Although there are several highly sensitive and specific MPS data-parsing algorithms, there are currently no tools that implement these methods. Results. We developed an R package, detection of autosomal abnormalities for fetus (DASAF), that implements the three most popular trisomy detection methods-the standard Z-score (STDZ) method, the GC correction Z-score (GCCZ) method, and the internal reference Z-score (IRZ) method-together with one subchromosome abnormality identification method (SCAZ). Conclusions. With the cost of DNA sequencing declining and with advances in personalized medicine, the demand for noninvasive prenatal testing will undoubtedly increase, which will in turn trigger an increase in the tools available for subsequent analysis. DASAF is a user-friendly tool, implemented in R, that supports identification of whole-chromosome as well as subchromosome abnormalities, based on maternal cell-free DNA sequencing data after genome mapping.
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, China.
authors.forename: Baohong
authors.identifier: 0000-0002-6029-7462
authors.initials: B
authors.lastname: Liu
authors.affiliation: Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Tang
authors.affiliation: Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai 200235, China; EG Information Technology Enterprise (EGI), Basepair Biotechonology. Co. Ltd., Suzhou 215123, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Qiu
authors.affiliation: EG Information Technology Enterprise (EGI), Basepair Biotechonology. Co. Ltd., Suzhou 215123, China.
authors.forename: Chunmei
authors.initials: C
authors.lastname: Tao
authors.affiliation: Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai 200235, China; EG Information Technology Enterprise (EGI), Basepair Biotechonology. Co. Ltd., Suzhou 215123, China.
authors.forename: Junhui
authors.initials: J
authors.lastname: Gao
authors.affiliation: EG Information Technology Enterprise (EGI), Basepair Biotechonology. Co. Ltd., Suzhou 215123, China.
authors.forename: Mengmeng
authors.initials: M
authors.lastname: Ma
authors.affiliation: EG Information Technology Enterprise (EGI), Basepair Biotechonology. Co. Ltd., Suzhou 215123, China.
authors.forename: Tingyan
authors.initials: T
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, China.
authors.forename: JianPing
authors.initials: J
authors.lastname: Cai
authors.affiliation: Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai 200235, China.
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai 200235, China; EG Information Technology Enterprise (EGI), Basepair Biotechonology. Co. Ltd., Suzhou 215123, China.
authors.forename: Guohui
authors.identifier: 0000-0002-2888-1335
authors.initials: G
authors.lastname: Ding
mesh_terms: D002474:Cell-Free System; D002869:Chromosome Aberrations / Q000196:embryology*; D004247:DNA / Q000032:analysis* / Q000235:genetics*; D030541:Databases, Genetic; D005260:Female; D005333:Fetus / Q000473:pathology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011247:Pregnancy; D012015:Reference Standards; D012984:Software; D013997:Time Factors
chemical_list: D004247:DNA