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Abstract

BACKGROUND:

Human embryonic stem cells have two different X chromosome inactivation patterns: skewed X chromosome inactivation and random X chromosome inactivation. Whether there is any difference in copy number variation between those cells is not clear.

OBJECTIVE:

To analyze the copy number variation in human embryonic stem cells with skewed X chromosome inactivation at whole genome level, and to analyze the effect of copy number variation on the function of human embryonic stem cells with skewed X chromosome inactivation.

METHODS:

Three skewed X chromosome inactivation cell strains were included in the research group, and two random skewed X chromosome inactivation cell strains were included in the control group. The copy number variation was analyzed with Cytogenetics Whole-Genome 2.7M array produced by Affymetrix, USA. The data were analyzed using ChAS software and OMIM software. The same copy number variation regions and genes were found in the three skewed X chromosome inactivation cell strains.

RESULTS AND CONCLUSION:

More than 130 copy number variation (> 50 kb) were found in the research group, which was higher than that of 36 copy number variation in the control group, the changes of copy number variation in the two groups were mainly repeated (> 70%). Nine gain copy number variation regions were found in the research group, distributed on 1q22, 1p34.1, 6q16.3, 7q31.32, 11q13.1, 16q12.2, 19p13.12, Xp22.33 and Xq26.2, respectively, all were repeated for three copy number variation. Nineteen genes were found within those copy number variation. All of those above copy number variation regions and genes in the control group were normal two copies. Genes within the copy number variation were closely related to the function of binding of DNA and nucleotide. GPC3 gene mutation on the Xq26.2 was found to be correlated with the skewed X chromosome inactivation. Micro-genomic variation in human embryonic stem cells with skewed X chromosome inactivation was higher than that in the random skewed X chromosome inactivation human embryonic stem cells. Key genes within copy number variation may have disadvantage to the function of human embryonic stem cells.

RESULTS AND CONCLUSION:

Liu WQ, He WZ, Cao DY, Li JL, Guo LY, Li Q, Sun XF. Copy number variation in human embryonic stem cells with skewed X chromosome inactivation. Zhongguo Zuzhi Gongcheng Yanjiu. 2013;17(10):1748-1752.

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