A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database: CNV extraction, transformation, and loading AI (CNV-ETLAI)
Tài liệu tham khảo
Manning, 2010, Professional Practice and Guidelines Committee. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities, Genet. Med., 12, 742, 10.1097/GIM.0b013e3181f8baad
Miller, 2010, Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies, Am. J. Hum. Genet., 86, 749, 10.1016/j.ajhg.2010.04.006
Robson, 2017, Efficacy Mech. Eval., 4
Wu, 2017, The clinical use of chromosomal microarray analysis in detection of fetal chromosomal rearrangements: a study from China Mainland, Eur. J. Obstet. Gynecol. Reprod. Biol., 212, 44, 10.1016/j.ejogrb.2017.03.007
Rickman, 2005, Prenatal diagnosis by array-CGH, Eur. J. Med. Genet., 48, 232, 10.1016/j.ejmg.2005.03.003
Lee, 2012, Clinical utility of array comparative genomic hybridisation for prenatal diagnosis: a cohort study of 3171 pregnancies, BJOG, 119, 614, 10.1111/j.1471-0528.2012.03279.x
Levy, 2018, Prenatal diagnosis by chromosomal microarray analysis, Fertil. Steril., 109, 201, 10.1016/j.fertnstert.2018.01.005
Levy, 2019, Are all chromosome microarrays the same? What clinicians need to know, Prenat. Diagn., 39, 157, 10.1002/pd.5422
MacDonald, 2014, The Database of Genomic Variants: a curated collection of structural variation in the human genome, Nucleic Acids Res., 42, D986, 10.1093/nar/gkt958
Firth, 2009, DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources, Am. J. Hum. Genet., 84, 524, 10.1016/j.ajhg.2009.03.010
Landrum, 2014, ClinVar: public archive of relationships among sequence variation and human phenotype, Nucleic Acids Res., 42, D980, 10.1093/nar/gkt1113
Rehm, 2015, ClinGen–the clinical genome resource, N. Engl. J. Med., 372, 2235, 10.1056/NEJMsr1406261
Siva, 2008, 1000 Genomes project, Nat. Biotechnol., 26, 256, 10.1038/nbt0308-256b
Collins, 2020, A structural variation reference for medical and population genetics, Nature, 581, 444, 10.1038/s41586-020-2287-8
Sudmant, 2015, Global diversity, population stratification, and selection of human copy-number variation, Science, 349, 10.1126/science.aab3761
Nowakowska, 2017, Clinical interpretation of copy number variants in the human genome, J. Appl. Genet., 58, 449, 10.1007/s13353-017-0407-4
Haeussler
Meyer, 2013, The UCSC Genome Browser database: extensions and updates 2013, Nucleic Acids Res., 41, D64, 10.1093/nar/gks1048
Levenshtein, 1965, Binary codes capable of correcting deletions, insertions, and reversals, Sov. Phys. Dokl., 163, 845
R. Liu, J.X. McKie, PyMuPDF. http://pymupdf.readthedocs.io/en/latest/ (Up-dated on Sep 2021).
Sandler, 2018, MobilenetV2: inverted residuals and linear bottlenecks, IEEE Comput. Soc. Conf. Comput. Vis. Pattern Recogn., 4510
Paszke, 2019, PyTorch: an imperative style, high-performance deep learning library, Adv. Neural Inf. Process. Syst., 32, 8026
Kingma, 2014, Adam: a method for stochastic optimization, ArXiv, 1412.6980
2020
E. Loper, S. Bird, NLTK: the Natural Language Toolkit. arXiv Preprint Cs/0205028. 2002 May 17.
Tilkov, 2010, Node. js: using JavaScript to build high-performance network programs, IEEE Internet Comput., 14, 80, 10.1109/MIC.2010.145
Robinson, 2020, igv. js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV), bioRxiv
Riggs, 2020, Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen), Genet. Med., 22, 245, 10.1038/s41436-019-0686-8
Grande, 2015, Genomic microarray in fetuses with increased nuchal translucency and normal karyotype: a systematic review and meta-analysis, Ultrasound Obstet. Gynecol., 46, 650, 10.1002/uog.14880
Brady, 2014, A prospective study of the clinical utility of prenatal chromosomal microarray analysis in fetuses with ultrasound abnormalities and an exploration of a framework for reporting unclassified variants and risk factors, Genet. Med., 16, 469, 10.1038/gim.2013.168
Xia, 2020, Application of chromosome microarray analysis in prenatal diagnosis, BMC Pregnancy Childbirth, 20, 696, 10.1186/s12884-020-03368-y
Qiu, 2012, CNVD: text mining-based copy number variation in disease database, Hum. Mutat., 33, E2375, 10.1002/humu.22163
Yang, 2018, Constructing a database for the relations between CNV and human genetic diseases via systematic text mining, BMC Bioinf., 19, 528, 10.1186/s12859-018-2526-2
Farré, 2013, Recombination rates and genomic shuffling in human and chimpanzee-a new twist in the chromosomal speciation theory, Mol. Biol. Evol., 30, 853, 10.1093/molbev/mss272