Genome-wide discovery of chromosomal copy number variants in human amniotic cell using array-based comparative genomic hybridization

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• 作者：Sang Min Lee (1) (2)
  Young Rok Seo (1) (2) (3)
  Min Hyung Jung (4)
  
• 关键词：Comparative Genomic Hybridization (CGH) ; G ; banding analysis ; Copy Number Variant (CNV) ; Copy Number Variant Region (CNVR) ; Prenatal diagnosis
• 刊名：Molecular & Cellular Toxicology
• 出版年：2011
• 出版时间：September 2011
• 年：2011
• 卷：7
• 期：3
• 页码：311-321
• 全文大小：494KB
• 参考文献：1. Wang, Y., Smith, K., Waldman, B. C. & Waldman, A. S. Depletion of the bloom syndrome helicase stimulates homology-dependent repair at double-strand breaks in human chromosomes. / DNA Repair (Amst) 10: 416鈥?26 (2011). CrossRef
  2. Reardon, W. / et al. Mutations in the fibroblast growth factor receptor 2 gene cause Crouzon syndrome. / Nat Genet 8:98鈥?03 (1994). CrossRef
  3. Nancy, J., Roizen, N. J. & Patterson, D. Down鈥檚 syndrome. / THE LANCET 361:1281鈥?289 (2003). CrossRef
  4. Manuela, A. / et al. Prenatal PAH exposure is associated with chromosome-specific aberrations in cord blood. / Mutation Research 703:108鈥?14 (2010).
  5. Yan, J. B. / et al. Rapid screening for chromosomal aneuploidies using array-MLPA. / BMC Med Genet 12:68 (2011). CrossRef
  6. Ness, G. O. & Houge, G. Diagnosis of cryptic chromosome aberrations. / Tidsskr Nor Laegeforen 123:2418鈥?421 (2003).
  7. Shinawi, M. & Cheung, S. W. The array CGH and its clinical applications. / Drug Discov Today 13:760鈥?70 (2008). CrossRef
  8. Kallioniemi, A. / et al. Comparative genomic hybridization: a powerful new method for cytogenetic analysis of solid tumors. / Science 258:818鈥?21 (1992). CrossRef
  9. Bejjani, B. A. / et al. Use of targeted array-basedCGH for the clinical diagnosis of chromosomal imbalance: is less more? / Am J Med Genet 134:259鈥?67 (2005). CrossRef
  10. Wong, A. / et al. Detection and calibration of microdeletions and microduplications by array-based comparative genomic hybridization and its applicability to clinical genetic testing. / Genet Med 7:264鈥?71 (2005). CrossRef
  11. Vissers, L. E. / et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. / Am J Hum Genet 73:1261鈥?270 (2003). CrossRef
  12. Ness, G. O., Lyb忙k, H., Arnes, J. & R酶dahl, E. Chromosomal Imbalances in Lymphoid Tumors of the Orbit. / IOVS 43:9鈥?4 (2002).
  13. Woo, H. I. / et al. Clinical, biochemical and genetic analyses in two Korean patients with medium-chain acyl-CoA dehydrogenase deficiency. / Korean J Lab Med 31:54鈥?0 (2011). CrossRef
  14. Sun, W. / et al. PPM1A and PPM1B act as IKKbeta phosphatases to terminate TNFalpha-induced IKKbeta-NF-kappaB activation. / Cell Signal 21:95鈥?02 (2009). CrossRef
  15. Parvari, R. / et al. The 2p21 deletion syndrome: characterization of the transcription content. / Genomics 86: 195鈥?11 (2005). CrossRef
  16. Deshmukh, N. / et al. Potentially harmful advantage to athletes: a putative connection between UGT2B17 gene deletion polymorphism and renal disorders with prolonged use of anabolic androgenic steroids. / SATPP 29: 1鈥? (2010).
  17. Yang, T. L. / et al. Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. / Am J Hum Genet 83:663鈥?74 (2008). CrossRef
  18. Yamamoto, Y. / et al. Gain of 5p15.33 is associated with progression of bladder cancer. / Oncology 72:132鈥?38 (2007). CrossRef
  19. Rouleau, C. / et al. Sudden infant death syndrome (SIDS): characteristics of deaths since the fall in SIDS in the French region of Languedoc-Roussillon. / Arch Dis Child 94:894鈥?96 (2009). CrossRef
  20. Akhurst, R. J. TGF beta signaling in health and disease. / Nat Genet 36:790鈥?92 (2004). CrossRef
  21. Boileau, C., Jondeau, G., Mizuguchi, T. & Matsumoto, N. Molecular genetics of Marfan sydrome. / Curr Opin Cardiol 20:194鈥?00 (2005). CrossRef
  22. Roberts, A. B. & Wakefield, L. M. The two faces of transforming growth factor beta in carcinogenesis. / Proc Natl Acad Sci 100:8621鈥?623 (2003). CrossRef
  23. Waite, K. A. & Eng, C. From developmental disorder to heritable cancer: it鈥檚 all in the BMP/TGF-beta family. / Nat Rev Genet 4:763鈥?73 (2003). CrossRef
  24. L茅vesque, E., Beaulieu, M., Guillemette, C., Hum, D. W. & B茅langer, A. Effect of fibroblastic growth factors (FGF) on steroid UDP-glucuronosyltransferase expression and activity in the LNCaP cell line. / J Steroid Biochem Mol Biol 64:43鈥?8 (1998). CrossRef
  25. Mart铆, S. B., Cichon, S., Propping, P. & N枚then, M. Metabotropic glutamate receptor 3 (GRM3) gene variation is not associated with schizophrenia or bipolar affective disorder in the German population. / Am J Med Genet 114:46鈥?0 (2002). CrossRef
  26. Chisamore, M. J., Cunningham, M. E., Flores, O., Wilkinson, H. A. & Chen, J. D. Characterization of a novel small molecule subtype specific estrogen-related receptor alpha antagonist in MCF-7 breast cancer cells. / PLoS One 4:e5624 (2009). CrossRef
  27. Liu, H. / et al. Calcitonin receptor-mediated CFTR activation in human intestinal epithelial cells. / J Cell Mol Med doi: 10.1111/j.1582-4934.2011.01264.x (2011).
  
• 作者单位：Sang Min Lee (1) (2)
  Young Rok Seo (1) (2) (3)
  Min Hyung Jung (4)
  
  1. Department of Life Science, Dongguk University-Seoul, 26 Pil-dong 3-ga, Junggu, Seoul, 100-715, Korea
  2. Institute of Environmental Medicine for Green Chemistry, Dongguk University-Seoul, 26 Pil-dong 3-ga, Junggu, Seoul, 100-715, Korea
  3. Department of Pharmacology, Medical Research Center (MRC), 1 Hoegi-dong, Dongdaemun-gu, Seoul, 130-701, Korea
  4. Department of Obstetric and Gynecology, School of Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul, 130-701, Korea
  

文摘

Chromosome aberrations (CA) are associated with several genetic heredity diseases. Of concerns, prenatal diagnosis or cytogenetic screening was administered to determine if there are chromosome abnormalities, genetic diseases, or birth defects in a fetus or embryo. It is very useful to diagnose high-risk pregnancies so that delivery can be scheduled. However, conventional G-banding technique which is generally applied in CA detection for prenatal diagnosis has limit on exploit of copy number variants (CNVs) due to low resolution and tedious multiple processes. Instead, array comparative genomic hybridization (aCGH) technology enabling incremented high-resolution, even in microscale segmental CNVs, can be considered as an alternative approach for improving prenatal diagnosis. In this study, our aCGH (Illumina Infinium Human 370Quad-Duo; coverage of SNP tag and CNV regions) was used to identify copy number variations from genomic DNA in human amniotic cell specimens. The aCGH results revealed various karyotypes of CNVs including loss, homozygous loss, gain, high copy gain, and copy neutral LOH whereas using conventional Gbanding only one benign cytogenetic CNV was observed in one case study. The aCGH was compatible to define small-scale chromosomal imbalances segment that were undetectable risk segment by G-banding. In contrast, abnormal G-banded karyotypes as balanced rearrangements were hidden from detection by aCGH analysis. This indicates that even though the aCGH enables us more advantage in detection of unbalanced CNVs at small-size regions with relatively high resolution, combination of both techniques is still required for efficient evaluation of various CNVs (both balanced and unbalanced ones). The aCGH also provides detailed database of copy number variant regions (CNVRs) in each chromosome. Interestingly, CNVRs containing important genes (ACADM, PPM1B, UGT2B17 and ZDHHC11) were discovered from our data, in which their defects or mutations have been reportedly to be involved in certain genetic heritable diseases and/or syndromes. Their relationships were analyzed using Pathway Studio 7.1 software to demonstrate key pathways concerning prenatal genetic defects. Respective components including protein kinases and phosphatases, transcription factors, hormones and receptors were participated in our analyzed pathway. Gathering together, our detailed CNVs and CNVR via aCGH of amniotic cells might be meaningful database to improve strategy in genetic disease-specific researches and follow-up after medication during pregnancy.