Determination of genomic copy number with quantitative microsphere hybridization

Human Mutation

Volumn 27, Issue 4, 2006, Pages 376-386

  Newkirk, Heather L ^a   Rogan, Peter K ^a   Miralles, Mauricio ^a   Knoll, Joan H M ^a,b  

^a UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

^b CHILDREN S MERCY HOSPITAL   (United States)

Author keywords

ABL1; Copy number; Flow cytometry; Microsphere; Mutation detection; PMP22; TEKT3

Indexed keywords

GENE PRODUCT; GENOMIC DNA; MICROSPHERE; NUCLEOTIDE; PHYCOERYTHRIN; POLYSTYRENE; STREPTAVIDIN;

ABL1 GENE; ALLELE; ARTICLE; CELL LINE; CHROMOSOME 17P; CHROMOSOME 17Q; CHROMOSOME 9Q; CHROMOSOME DUPLICATION; CHROMOSOME TRANSLOCATION; CHRONIC MYELOID LEUKEMIA; CLINICAL ARTICLE; CONJUGATION; CONTROLLED STUDY; CYTOGENETICS; DNA EXTRACTION; DNA HYBRIDIZATION; FLOW CYTOMETRY; FLUORESCENCE; GENE; GENE AMPLIFICATION; GENE DELETION; GENE MUTATION; GENE NUMBER; GENOME; HEREDITARY MOTOR SENSORY NEUROPATHY; HOXB1 GENE; HUMAN; HUMAN CELL; MOLECULAR PROBE; PMP22 GENE; PRIORITY JOURNAL; QUANTITATIVE MICROSPHERE HYBRIDIZATION; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; TEKT3 GENE;

CELL LINE; CHARCOT-MARIE-TOOTH DISEASE; CHROMOSOME ABERRATIONS; CHROMOSOME DELETION; CHROMOSOMES, HUMAN, PAIR 19; CHROMOSOMES, HUMAN, PAIR 9; DNA PROBES; GENE DOSAGE; GENOME, HUMAN; GENOMICS; HUMANS; MICROSPHERES; NUCLEIC ACID HYBRIDIZATION; SENSITIVITY AND SPECIFICITY; TRISOMY;

EID: 33645829845     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20312     Document Type: Article

References (32)

1. Bagwell CB, Baker D, Whetstone S, Munson M, Hitchcox S, Ault KA, Lovett EJ. 1989. A simple and rapid method for determining the linearity of a flow cytometer amplification system. Cytometry 10:689-694.
2. Borucki MK, Reynolds J, Call DR, Ward TJ, Page B, Kadushin J. 2005. Suspension microarray with dendrimer signal amplification allows direct and high-throughput subtyping of Listeria monocytogenes from genomic DNA. J Clin Microbiol 43:3255-3259.
3. Brown RD, Zarbo RJ, Linden MD, Torres FX, Nakleh RE, Schultz D, Mackowiak PG. 1994. Two-color multiparametric method for flow cytometric DNA analysis. Standardization of spectral compensation. Am J Clin Pathol 101:630-637.
4. Coder DM, Redelman D, Vogt RF. 1994. Computing the central location of immunofluorescence distributions: logarithmic data transformations are not always appropriate. Cytometry 18:75-78.
5. Dunbar S, Godbout R, Newkirk H, Hetzel J. 2003. Microsphere suspension array technology for SNP detection in cattle. IEEE Eng Med Biol Mag 22:158-162.
6. Earley M, Vogt RJ, Shapiro H, Mandy F, Kellar K, Bellisario R, Pass K, Marti G, Stewart C, Hannon W. 2002. Report from a workshop on multianalyte microsphere. Cytometry 50:239-242.
7. Fulton RJ, McDade RL, Smith PL, Kienker LJ, Kettman JR Jr. 1997. Advanced multiplexed analysis with the FlowMetrix system. Clin Chem 43:1749-1756.
8. Hadd AG, Laosinchai-Wolf W, Novak CR, Badgett MR, Isgur LA, Goldrick M, Walkerpeach CR. 2004. Microsphere bead arrays and sequence validation of 5/7/9 T genotypes for multiplex screening of cystic fibrosis polymorphisms. J Mol Diagn 6:348-355.
9. Inoue K, Dewar K, Katsanis N, Reiter LT, Lander ES, Devon KL, Wyman DW, Lupski JR, Birren B. 2001. The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes. Genome Res 11:1018-1033.
10. ISCN. 2005. An international system for human cytogenetic nomenclature. Shaffer LG, Tommerup N, editors. Basel, Switzerland: S. Karger, p 55-84, 104-111.
11. Kellar K, Iannone M. 2002. Multiplexed microsphere-based flow cytometric assays. Exp Hematol 30:1227-1237.
12. Kirkwood TBL. 1979. Geometric means and measures of dispersion [Letter]. Biometrics 35:908-909.
13. Knoll JH, Lichter P. 1994. In situ hybridization to metaphase chromosomes and interphase nuclei. In: Dracopoli NC, Haines JL, Korf BR, Moir DT, Morton CC, Seidman CE, Seidman JG, Smith DR, editors. Current protocols in human genetics, vol. 1, unit 4-3 [Revised 2005]. New York: Green-Wiley.
14. Knoll JH, Rogan PK. 2003. Sequence-based, in situ detection of chromosomal abnormalities at high resolution. Am J Med Genet 121:245-257.
15. Knoll JHM, Rogan PK. 2004. Single copy genomic hybridization probes and method of generating same. US Patent No. 6,828,097.
16. Lewin B. 1980. DNA sequence organization: nonrepetitive and repetitive DNA. Gene expression 2 - eucaryotic chromosomes, 2nd edition. New York: Wiley-Interscience Publication, p 503-530.
17. Little SE, Vuononvirta R, Reis-Filho JS, Natrajan R, Iravani M, Fenwick K, Mackay A, Ashworth A, Pritchard-Jones K, Jones C. 2006. Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics 87:298-306.
18. Lowe M, Spiro A, Summers AO, Wireman J. 2001. Multiplexed identification and quantification of analyte DNAs in environmental samples using microspheres and flow cytometry. In: Spencer JFT, Spencer ALR, editors. Methods in biotechnology: environmental biology: methods and protocols. Totowa, NJ: Humana Press, p 51-74.
19. Lupski JR, Oca-Luna RMd, Slaugenhaupt S, Pentao L, Guzzetta V, Trask BJ, Saucedo-Cardenas O, Barker DF, Killian JM, Garcia CA, Chakravariti A, Patel PI. 1991. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 66:219-232.
20. ot-1 DNA: mitigation of this effect. Nucleic Acids Res 14; 33:e191.
21. Oostlander AE, Meijer GA, Ylstra B. 2004. Microarray-based comparative genomic hybridization and its applications in human genetics. Clin Genet 66:488-495.
22. Rockenbauer E, Petersen K, Vogel U, Bolund L, Kolvraa S, Nielsen KV, Nexo BA. 2005. SNP genotyping using microsphere-linked PNA and flow cytometric detection. Cytometry A 64:80-86.
23. Rogan PK, Cazcarro PM, Knoll JH. 2001. Sequence-based design of single-copy genomic DNA probes for fluorescence in situ hybridization. Genome Res 11:1086-1094.
24. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. 2002. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30:e57.
25. Sekar M, Bloch W, John PS. 2005. Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres. Nucleic Acids Res 33:366-375.
26. Shaffer LG, Bejjani BA. 2004. A cytogeneticist's perspective on genomic microarrays. Hum Reprod Update 10:221-226.
27. Sinclair P, Nacheva E, Leversha M, Telford N, Chang J, Reid A, Bench A, Champion K, Huntly B, Green A. 2000. Large deletions at the t(9;22) breakpoint are common and may identify a poor-prognosis subgroup of patients with chronic myeloid leukemia. Blood 95:738-743.
28. Southern EM. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503-518.
29. Studer M, Lumsden A, Ariza-McNaughton L, Bradley A, Krumlauf R. 1996. Altered segmental identity and abnormal migration of motor neurons in mice lacking Hoxb-1. Nature 384:630-634.
30. Vignali D. 2000. Multiplexed particle-based flow cytometric assays. J Immunol Methods 243:243-255.
31. White LM, Rogan PK, Nichols RD, Wu BL, Korf B, Knoll JH. 1996. Allele-specific replication of 15q11-q13 loci: a diagnostic test for detection of uniparental disomy. Am J Hum Genet 59:423-430.
32. White SJ, Breuning MH, den Dunnen JT. 2004. Detecting copy number changes in genomic DNA: MAPH and MLPA. Methods Cell Biol 75:751-768.