Nội dung được dịch bởi AI, chỉ mang tính chất tham khảo
Các phương pháp phi tham số cho phân tích vi mạch tác nhân đơn sắc
Tóm tắt
Phân tích dữ liệu vi mạch oligonucleotide trong giám sát và phát hiện tác nhân gây bệnh là một nhiệm vụ đầy thách thức. Nồng độ mẫu mục tiêu, độ toàn vẹn của axit nucleic và thành phần axit nucleic của vật chủ có thể có ảnh hưởng sâu sắc đến phân phối tín hiệu. Phân tích khám phá sự phân phối tín hiệu phát quang trong các mẫu lâm sàng đã tiết lộ những sai lệch so với tính bình thường, gợi ý rằng các phương pháp không phụ thuộc vào phân phối nên được áp dụng. Giá trị dự đoán dương tính và tỷ lệ dương tính giả đã được xem xét để đánh giá tính hữu ích của ba phương pháp phi tham số đã được thiết lập cho việc phân tích dữ liệu lai vi rút: (1) Mann-Whitney U, (2) hệ số tương quan Spearman và (3) kiểm định chi-bình phương. Trong ba kiểm định này, kiểm định chi-bình phương cho thấy tính hữu dụng nhất. Việc chấp nhận việc sử dụng vi mạch cho chẩn đoán lâm sàng định kỳ sẽ yêu cầu công nghệ này phải đi kèm với các phương pháp phân tích đơn giản nhưng đáng tin cậy. Chúng tôi báo cáo rằng việc thực hiện kiểm định chi-bình phương của chúng tôi đã mang lại sự kết hợp của tỷ lệ dương tính giả thấp và độ chính xác dự đoán cao.
Từ khóa
#vi mạch oligonucleotide #phân tích dữ liệu #phương pháp phi tham số #kiểm định chi-bình phương #chẩn đoán lâm sàngTài liệu tham khảo
Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL: Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci USA 2002, 99(24):15687–15692. 10.1073/pnas.242579699
Lin FM, Huang HD, Chang YC, Tsou AP, Chan PL, Wu LC, Tsai MF, Horng JT: Database to dynamically aid probe design for virus identification. IEEE Trans Inf Technol Biomed 2006, 10(4):705–713. 10.1109/TITB.2006.874202
Chou CC, Lee TT, Chen CH, Hsiao HY, Lin YL, Ho MS, Yang PC, Peck K: Design of microarray probes for virus identification and detection of emerging viruses at the genus level. BMC Bioinformatics 2006, 7: 232. 10.1186/1471-2105-7-232
Chizhikov V, Wagner M, Ivshina A, Hoshino Y, Kapikian AZ, Chumakov K: Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J Clin Microbiol 2002, 40(7):2398–2407. 10.1128/JCM.40.7.2398-2407.2002
Laassri M, Chizhikov V, Mikheev M, Shchelkunov S, Chumakov K: Detection and discrimination of orthopoxviruses using microarrays of immobilized oligonucleotides. J Virol Methods 2003, 112(1–2):67–78. 10.1016/S0166-0934(03)00193-9
Mehlmann M, Dawson ED, Townsend MB, Smagala JA, Moore CL, Smith CB, Cox NJ, Kuchta RD, Rowlen KL: Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus. J Clin Microbiol 2006, 44(8):2857–2862. 10.1128/JCM.00135-06
Jabado OJ, Liu Y, Conlan S, Quan PL, Hegyi H, Lussier Y, Briese T, Palacios G, Lipkin WI: Comprehensive viral oligonucleotide probe design using conserved protein regions. Nucleic Acids Res 2008, 36(1):e3. 10.1093/nar/gkm1106
Wilson WJ, Strout CL, DeSantis TZ, Stilwell JL, Carrano AV, Andersen GL: Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol Cell Probes 2002, 16(2):119–127. 10.1006/mcpr.2001.0397
Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD: Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res 2004, 14(3):398–405. 10.1101/gr.2141004
Lin B, Wang Z, Vora GJ, Thornton JA, Schnur JM, Thach DC, Blaney KM, Ligler AG, Malanoski AP, Santiago J, et al.: Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res 2006, 16(4):527–535. 10.1101/gr.4337206
Sulaiman IM, Tang K, Osborne J, Sammons S, Wohlhueter RM: GeneChip resequencing of the smallpox virus genome can identify novel strains: a biodefense application. J Clin Microbiol 2007, 45(2):358–363. 10.1128/JCM.01848-06
Assarsson E, Greenbaum JA, Sundstrom M, Schaffer L, Hammond JA, Pasquetto V, Oseroff C, Hendrickson RC, Lefkowitz EJ, Tscharke DC, et al.: Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci USA 2008, 105(6):2140–2145. 10.1073/pnas.0711573105
Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, et al.: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24(9):1151–1161. 10.1038/nbt1239
Townsend MB, Dawson ED, Mehlmann M, Smagala JA, Dankbar DM, Moore CL, Smith CB, Cox NJ, Kuchta RD, Rowlen KL: Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance. J Clin Microbiol 2006, 44(8):2863–2871. 10.1128/JCM.00134-06
Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL: E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol 2005, 6(9):R78. 10.1186/gb-2005-6-9-r78
Watson M, Dukes J, Abu-Median AB, King DP, Britton P: DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data. Genome Biol 2007, 8(9):R190. 10.1186/gb-2007-8-9-r190
Wiesinger-Mayr H, Vierlinger K, Pichler R, Kriegner A, Hirschl AM, Presterl E, Bodrossy L, Noehammer C: Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition. BMC Microbiol 2007, 7: 78. 10.1186/1471-2180-7-78
Wong CW, Heng CL, Wan Yee L, Soh SW, Kartasasmita CB, Simoes EA, Hibberd ML, Sung WK, Miller LD: Optimization and clinical validation of a pathogen detection microarray. Genome Biol 2007, 8(5):R93. 10.1186/gb-2007-8-5-r93
Rehrauer H, Schonmann S, Eberl L, Schlapbach R: PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. Bioinformatics 2008, 24(16):i83–89. 10.1093/bioinformatics/btn269
Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB: Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 2002, 18(11):1454–1461. 10.1093/bioinformatics/18.11.1454
Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America 2003, 100(16):9440–9445. 10.1073/pnas.1530509100
Palacios G, Quan PL, Jabado OJ, Conlan S, Hirschberg DL, Liu Y, Zhai J, Renwick N, Hui J, Hegyi H, et al.: Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis 2007, 13(1):73–81. 10.3201/eid1301.060837
Quan PL, Palacios G, Jabado OJ, Conlan S, Hirschberg DL, Pozo F, Jack PJ, Cisterna D, Renwick N, Hui J, et al.: Detection of Respiratory Viruses and Subtype Identification of Influenza A Viruses by GreeneChipResp Oligonucleotide Microarray. J Clin Microbiol 2007, 45(8):2359–2364. 10.1128/JCM.00737-07
Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, et al.: EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res 2006, (34 Database):D10–15. 10.1093/nar/gkj130
Bao Y, Federhen S, Leipe D, Pham V, Resenchuk S, Rozanov M, Tatusov R, Tatusova T: National center for biotechnology information viral genomes project. J Virol 2004, 78(14):7291–7298. 10.1128/JVI.78.14.7291-7298.2004
Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658–1659. 10.1093/bioinformatics/btl158
Berger JA, Hautaniemi S, Jarvinen AK, Edgren H, Mitra SK, Astola J: Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 2004, 5: 194. 10.1186/1471-2105-5-194
Rash S, Gusfield D: String barcoding: uncovering optimal virus signatures. In RECOMB '02: Proceedings of the sixth annual international conference on Computational biology: April 18–21, 2002 2002. Washington, DC, USA: ACM Press, New York, NY; 2002:254–261. full_text
Jafari P, Azuaje F: An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors. BMC Med Inform Decis Mak 2006, 6: 27. 10.1186/1472-6947-6-27
Daniel WW: Biostatistics, a foundation for analysis in the health sciences. 4th edition. New York: Wiley; 1987.
Nefzger MD, Drasgow J: The Needless Assumption of Normality in Pearson-Tau. American Psychologist 1957, 12(5):623–625. 10.1037/h0048216
Kristiansson E, Sjogren A, Rudemo M, Nerman O: Quality optimised analysis of general paired microarray experiments. Stat Appl Genet Mol Biol 2006., 5: Article10 Article10
Held GA, Grinstein G, Tu Y: Modeling of DNA microarray data by using physical properties of hybridization. Proc Natl Acad Sci USA 2003, 100(13):7575–7580. 10.1073/pnas.0832500100
Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF: Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res 2003, 31(14):4211–4217. 10.1093/nar/gkg476
Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 1995, 57(1):289–300.
Storey JD: A direct approach to false discovery rates. Journal of the Royal Statistical Society Series B-Statistical Methodology 2002, 64: 479–498. 10.1111/1467-9868.00346
Giles PJ, Kipling D: Normality of oligonucleotide microarray data and implications for parametric statistical analyses. Bioinformatics 2003, 19(17):2254–2262. 10.1093/bioinformatics/btg311
Huang S, Qu Y: The loss in power when the test of differential expression is performed under a wrong scale. J Comput Biol 2006, 13(3):786–797. 10.1089/cmb.2006.13.786
Sasaki D, Kondo S, Maeda N, Gingeras TR, Hasegawa Y, Hayashizaki Y: Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signals. Genomics 2007, 89(4):541–551. 10.1016/j.ygeno.2006.12.013
Leiske DL, Karimpour-Fard A, Hume PS, Fairbanks BD, Gill RT: A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray. BMC Genomics 2006, 7: 72. 10.1186/1471-2164-7-72
Fan J, Niu Y: Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Bioinformatics 2007, 23(18):2391–2398. 10.1093/bioinformatics/btm361
Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, et al.: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 2001, 19(4):342–347. 10.1038/86730
Naef F, Lim DA, Patil N, Magnasco M: DNA hybridization to mismatched templates: a chip study. Phys Rev E Stat Nonlin Soft Matter Phys 2002, 65(4 Pt 1):040902.
Hekstra D, Taussig AR, Magnasco M, Naef F: Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res 2003, 31(7):1962–1968. 10.1093/nar/gkg283
Levy JA: Three new human herpesviruses (HHV6, 7, and 8). Lancet 1997, 349(9051):558–563. 10.1016/S0140-6736(97)80119-5
Jung SH, Jang W: How accurately can we control the FDR in analyzing microarray data? Bioinformatics 2006, 22(14):1730–1736. 10.1093/bioinformatics/btl161