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Single-cell copy number varation detection


ABSTRACT: Detection of genomic rearrangements from a single cell instead of a population of cells is an emerging research technique with important applications in the study of human fertility, constitutional chromosomal disorders, and tumor progression. Here, we develop a method to improve the detection of single-cell genome-wide copy number variation. At this study, 7 amplified single cell DNA samples derived from EBV-line [47,XY,+21], [46,XY,der(20),t(18;20)(p11.21;p13)], [46,XX,del(18)(p11.21->pter)], [46,X,der(X),t(X;14)(q21.1;q12.2)] were analyzed by Agilent 244K array CGH. For these single cell Agilent 244K array CGH analyses: non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample. As a validation, the corresponding non-amplified genomic DNA samples were analyzed by 250K Nsp I SNP arrays (platform GPL3718). Non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample for BAC array CGH

ORGANISM(S): Homo sapiens

SUBMITTER: Jiqiu Cheng 

PROVIDER: E-GEOD-27892 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single-cell copy number variation detection.

Cheng Jiqiu J   Vanneste Evelyne E   Konings Peter P   Voet Thierry T   Vermeesch Joris R JR   Moreau Yves Y  

Genome biology 20110829 8


Detection of chromosomal aberrations from a single cell by array comparative genomic hybridization (single-cell array CGH), instead of from a population of cells, is an emerging technique. However, such detection is challenging because of the genome artifacts and the DNA amplification process inherent to the single cell approach. Current normalization algorithms result in inaccurate aberration detection for single-cell data. We propose a normalization method based on channel, genome composition  ...[more]

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