Genome-wide analysis of loss of heterozygosity and copy number amplification in uterine leiomyomas using the 100K single nucleotide polymorphism array

Experimental and Molecular Pathology

Volumn 91, Issue 1, 2011, Pages 434-439

  Meadows, Kellen L ^a,b   Andrews, Danica M K ^a   Xu, Zongli ^a   Carswell, Gleta K ^a   Laughlin, Shannon K ^a,c   Baird, Donna D ^a   Taylor, Jack A ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b DUKE UNIVERSITY   (United States)

^c MAYO CLINIC   (United States)

Author keywords

Copy number amplification; LOH; Single nucleotide polymorphism array; Uterine leiomyoma

Indexed keywords

ARTICLE; CHROMOSOME 7Q; CHROMOSOME ANALYSIS; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA MICROARRAY; FEMALE; GENE FREQUENCY; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; HEMIZYGOSITY; HETEROZYGOSITY LOSS; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; MOLECULAR PATHOLOGY; PROMOTER REGION; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR VOLUME; UTERUS MYOMA;

CHROMOSOMES, HUMAN, PAIR 16; CHROMOSOMES, HUMAN, PAIR 3; CHROMOSOMES, HUMAN, PAIR 7; DNA COPY NUMBER VARIATIONS; FEMALE; GENE AMPLIFICATION; GENE DOSAGE; GENOMICS; HUMANS; LEIOMYOMA; LOSS OF HETEROZYGOSITY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; UTERINE NEOPLASMS;

EID: 79956218087     PISSN: 00144800     EISSN: 10960945     Source Type: Journal    
DOI: 10.1016/j.yexmp.2011.03.007     Document Type: Article

References (26)

1. Beroukhim R., Lin M., Park Y., Hao K., Zhao X., Garraway L.A., Fox E.A., Hochberg E.P., Mellinghoff I.K., Hofer M.D., Descazeaud A., Rubin M.A., Meyerson M., Wong W.H., Sellers W.R., Li C. Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput. Biol. 2006, 2:e41.
2. Canevari A.d.A., Pontes A., Rogatto S.R. Microallelotyping defines novel regions of loss of heterozygosity in uterine leiomyomas. Mol. Carcinog. 2005, 42:177-182.
3. Davis B.J., Haneke K.E., Miner K., Kowalik A., Barrett J.C., Peddada S., Baird D.D. The fibroid growth study: determinants of therapeutic intervention. J. Womens Health 2009, 18:725-732.
4. Baird D.D., Dunson D.B., Hill M.C., Cousins D., Schectman J.M. High cumulative incidence of uterine leiomyoma in black and white women: ultrasound evidence. Am. J. Obstet. Gynecol. 2003, 188(1):100-107.
5. Di X., Matsuzaki H., Webster T.A., Hubbell E., Liu G., Dong S., Bartell D., Huang J., Chiles R., Yang G., Shen M.M., Kulp D., Kennedy G.C., Mei R., Jones K.W., Cawley S. Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics 2005, 21:1958-1963.
6. Flake G.P., Andersen J., Dixon D. Etiology and pathogenesis of uterine leiomyomas: a review. Environ. Health Perspect. 2003, 111:1037-1054.
7. Flynn M., Jamison M., Datta S., Myers E. Health care resource use for uterine fibroid tumors in the United States. Am. J. Obstet. Gynecol. 2006, 195:955-964.
8. Hartmann K.E., Birnbaum H., Ben-Hamadi R., Wu E.Q., Farrell M.H., Spalding J., Stang P. Annual costs associated with diagnosis of uterine leiomyomata. Obstet. Gynecol. 2006, 108:930-937.
9. Hennig Y., Deichert U., Bonk U., Thode B., Bartnitzke S., Bullerdiek J. Chromosomal translocations affecting 12q14-15 but not deletions of the long arm of chromosome 7 associated with a growth advantage of uterine smooth muscle cells. Mol. Hum. Reprod. 1999, 5:1150-1154.
10. Huang J., Wei W., Zhang J., Liu G., Bignell G.R., Stratton M.R., Futreal P.A., Wooster R., Jones K.W., Shapero M.H. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum. Genomics 2004, 1:287-299.
11. Kataoka S., Yamada H., Hoshi N., Kudo M., Hareyama H., Sakuragi N., Fujimoto S. Cytogenetic analysis of uterine leiomyoma: the size, histopathology and GnRHa-response in relation to chromosome karyotype. Eur. J. Obstet. Gynecol. Reprod. Biol. 2003, 110:58-62.
12. Lee D.W., Ozminkowski R.J., Carls G.S., Wang S., Gibson T.B., Stewart E.A. The direct and indirect cost burden of clinically significant and symptomatic uterine fibroids. J. Occup. Environ. Med. 2007, 49:493-506.
13. Lengauer C., Kinzler K.W., Vogelstein B. Genetic instabilities in human cancers. Nature 1998, 396:643-649.
14. Levy B., Mukherjee T., Hirschhorn K. Molecular cytogenetic analysis of uterine leiomyoma and leiomyosarcoma by comparative genomic hybridization. Cancer Genet. Cytogenet. 2000, 121:1-8.
15. Lieberfarb M.E., Lin M., Lechpammer M., Li C., Tanenbaum D.M., Febbo P.G., Wright R.L., Shim J., Kantoff P.W., Loda M., Meyerson M., Sellers W.R. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res. 2003, 63:4781-4785.
16. Ligon A.H., Morton C.C. Genetics of uterine leiomyomata. Genes Chromosomes Cancer 2000, 28:235-245.
17. Lindblad-Toh K., Tanenbaum D.M., Daly M.J., Winchester E., Lui W.O., Villapakkam A., Stanton S.E., Larsson C., Hudson T.J., Johnson B.E., Lander E.S., Meyerson M. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat. Biotechnol. 2000, 18:1001-1005.
18. Mao X., Barfoot R., Hamoudi R.A., Easton D.F., Flanagan A.M., Stratton M.R. Allelotype of uterine leiomyomas. Cancer Genet. Cytogenet. 1999, 114:89-95.
19. Packenham J.P., du Manoir S., Schrock E., Risinger J.I., Dixon D., Denz D.N., Evans J.A., Berchuck A., Barrett J.C., Devereux T.R., Ried T. Analysis of genetic alterations in uterine leiomyomas and leiomyosarcomas by comparative genomic hybridization. Mol. Carcinog. 1997, 19:273-279.
20. Rein M.S., Powell W.L., Walters F.C., Weremowicz S., Cantor R.M., Barbieri R.L., Morton C.C. Cytogenetic abnormalities in uterine myomas are associated with myoma size. Mol. Hum. Reprod. 1998, 4:83-86.
21. Sandberg A.A. Updates on the cytogenetics and molecular genetics of bone and soft tissue tumors: leiomyoma. Cancer Genet. Cytogenet. 2005, 158:1-26.
22. Stewart E.A. Uterine fibroids. Lancet 2001, 357:293-298.
23. van der Heijden O., Chiu H.C., Park T.C., Takahashi H., LiVolsi V.A., Risinger J.I., Barrett J.C., Berchuck A., Evans A.C., Behbakht K., Menzin A.W., Liu P.C., Benjamin I., Morgan M.A., King S.A., Rubin S.C., Boyd J. Allelotype analysis of uterine leiomyoma: localization of a potential tumor suppressor gene to a 4-cM region of chromosome 7q. Mol. Carcinog. 1998, 23:243-247.
24. Vanharanta S., Wortham N.C., Laiho P., Sjoberg J., Aittomaki K., Arola J., Tomlinson I.P., Karhu A., Arango D., Aaltonen L.A. 7q deletion mapping and expression profiling in uterine fibroids. Oncogene 2005, 24:6545-6554.
25. Walker C.L., Stewart E.A. Uterine fibroids: the elephant in the room. Science 2005, 308:1589-1592.
26. Zhao X., Li C., Paez J.G., Chin K., Janne P.A., Chen T.H., Girard L., Minna J., Christiani D., Leo C., Gray J.W., Sellers W.R., Meyerson M. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 2004, 64:3060-3071.