Sequence-based, in situ detection of chromosomal abnormalities at high resolution

American Journal of Medical Genetics

Volumn 121 A, Issue 3, 2003, Pages 245-257

  Knoll, Joan H M ^a,b   Rogan, Peter K ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY SCHOOL OF MEDICINE   (United States)

^b CHILDREN S MERCY HOSPITAL   (United States)

Author keywords

Chromosomal breakpoints; Cytogenetic abnormalities; DNA sequence analysis; genomic rearrangement; Fluorescence in situ hybridization; Single copy DNA probes

Indexed keywords

ARTICLE; CHROMOSOME 1; CHROMOSOME 15; CHROMOSOME 15Q; CHROMOSOME 17; CHROMOSOME 22; CHROMOSOME 2Q; CHROMOSOME 4; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; CHROMOSOME REARRANGEMENT; CHROMOSOME SIZE; CHRONIC MYELOID LEUKEMIA; DNA FLANKING REGION; DNA PROBE; EUCHROMATIN; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DELETION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENE TRANSLOCATION; GENETIC CODE; GENOME; HUMAN; HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; SMITH MAGENIS SYNDROME; SOUTHERN BLOTTING;

EID: 0042695871     PISSN: 15524825     EISSN: None     Source Type: Journal    
DOI: 10.1002/ajmg.a.20123     Document Type: Article

References (28)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
2. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. 2002. Recent segmental duplications in the human genome. Science 297:1003-1013.
3. Bi W, Yan J, Stankiewicz P, Park SS, Walz K, Boerkoel CF, Potocki L, Shaffer LG, Devriendt K, Nowaczyk MJ, Inoue K, Lupski JR. 2002. Genes in a refined Smith-Magenis syndrome critical deletion interval on chromosome 17p11.2 and the syntenic region of the mouse. Genome Res 12(5):713-728.
4. Buiting K, Lich C, Cottrell S, Barnicoat A, Horsthemke B. 1999. A 5-kb imprinting center deletion in a family with Angelman syndrome reduces the shortest region of deletion overlap to 880 bp. Hum Genet 105:665-666.
5. Cassidy SB, Dykens E, Williams CA. 2000. Prader-Willi and Angelman syndromes: Sister imprinted disorders. Am J Med Genet 97:136-146.
6. Chen KS, Manian P, Koeuth T, Potocki L, Zhao Q, Chinault AC, Lee CC, Lupski JR. 1997. Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat Genet 17:154-163.
7. Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ. 2001. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409(6822):953-958.
8. Christian SL, McDonough J, Liu Cy CY, Shaikh S, Vlamakis V, Badner JA, Chakravarti A, Gershon ES. 2002. An evaluation of the assembly of an approximately 15-Mb region on human chromosome 13q32-q33 linked to bipolar disorder and schizophrenia. Genomics 79(5):635-656.
9. Craig JM, Kraus J, Cremer T. 1997. Removal of repetitive sequences from FISH probes using PCR-assisted affinity chromatography. Hum Genet 100:472-476.
10. Florijn RJ, Bonden LA, Vrolijk H, Wiegant J, Vaandrager JW, Baa F, den Dunnen JT, Tanke JJ, van Ommen GJ, Raap AK. 1995. High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes. Hum Mol Genet 4:831-836.
11. Francke U. 1999. Williams-Beuren syndrome: Genes and mechanisms. Hum Mol Genet 8:1947-1954.
12. Frangiskakis JM, Ewart AK, Morris CA, Mervis CB, Bertrand J, Robinson BF, Klein BP, Ensing GJ, Everett LA, Green ED, Proschel C, Gutowski NJ, Noble M, Atkinson DL, Odelberg SJ, Keating MT. 1996. LIM-kinase1 hemizygosity implicated in impaired visuospatial constructive cognition. Cell 12:86:59-69.
13. Fuscoe JC, Collins CC, Pinkel D, Gray JW. 1989. An efficient method for selecting unique-sequence clones from DNA libraries and its application to fluorescent staining of human chromosome 21 using in situ hybridization. Genomics 5:100-109.
14. Kent WJ. 2002. BLAT - The BLAST-like alignment tool. Genome Res 12:656-664.
15. Knoll JHM, 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. New York: Green-Wiley, Unit 4.3.
16. Knoll JH, Nicholls RD, Magenis RE, Graham JM Jr, Lalande M, Latt SA. 1989. Angelman and Prader-Willi syndromes share a common chromosome 15 deletion but differ in parental origin of the deletion. Am J Med Genet 32:285-290.
17. Korenberg JR, Chen XN, Sun Z, Shi ZY, Ma S, Vataru E, Yimlamai D, Weissenbach JS, Shizuya H, Simon MI. 1999. Human genome anatomy: BACs integrating the genetic and cytogenetic maps for bridging genome and biomedicine. Genome Res 9:994-1001.
18. Leblanc T, Berger R. 1997. Molecular cytogenetics of childhood acute myelogenous leukemias. Eur J Haematol 59:1-13.
19. Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC. 1988. Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80:224-234.
20. Nicholls RD, Knoll JH, Glatt K, Hersh JH, Brewster TD, Graham JM Jr, Wurster-Hill D, Wharton R, Latt SA. 1989. Restriction fragment length polymorphisms within proximal 15q and their use in molecular cytogenetics and the Prader-Willi syndrome. Amer J Med Genet 33:66-77.
21. Ohta T, Gray TA, Rogan PK, Buiting K, Gabriel JM, Saitoh S, Muralidhar B, Bilienska B, Krajewska-Walasek M, Driscoll DJ, Horsthemke B, Butler MJ, Nicholls RD. 1999. Imprinting-mutation mechanisms in Prader-Willi syndrome. Am J Hum Genet 64:397-413.
22. Osborne LR, Martindale D, Scherer SW, Shi XM, Huizenga J, Heng HH, Costa T, Pober B, Lew L, Brinkman J, Rommens J, Koop B, Tsui LC. 1996. Identification of genes from a 500-kb region at 7q11.23 that is commonly deleted in Williams syndrome patients. Genomics 36:328-336.
23. Pinkel D, Landegent J, Collins C, Fuscoe J, Segraves R, Lucas J, Gray J. 1988. Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 and translocations of chromosome 4. Proc Natl Acad Sci USA 85:9138-9142.
24. Rogan PK, Cazcarro P, Knoll JHM. 2001. Sequence-based desgin of single-copy genomic DNA probes for fluorescence in situ hybridization. Genome Research 11:1086-1094.
25. Saitoh S, Buiting K, Rogan PK, Buxton JL, Driscoll DJ, Arnemann J, Konig R, Malcolm S, Horsthemke B, Nicholls RD. 1996. Minimal definition of the imprinting center and fixation of chromosome 15q11-q13 epigenotype by imprinting mutations. Proc Natl Acad Sci USA 93:7811-7815.
26. Sealey PG, Whittaker PA, Southern EM. 1985. Removal of repeated sequences from hybridization probes. Nucl Acids Res 13:1905-1922.
27. Trask B, Fertitta A, Christensen M, Youngblom J, Bergmann A, Copeland A, de Jong P, Mohrenweiser H, Olsen A, Carrano A. 1993. Fluorescence in situ hybridization mapping of human chromosome 19: Cytogenetic band location of 540 cosmids and 70 genes or DNA markers. Genomics 15:133-145.
28. White LM, Rogan PK, Nicholls RD, Wu BL, Korf B, Knoll JHM. 1996. Allele-specific replication of 15q11-q13 loci: a diagnostic test for detection of uniparental disomy. Am J Hum Genet 59:423-430.