Premium
Comparison of three whole genome amplification methods for detection of genomic aberrations in single cells
Author(s) -
Normand Elizabeth,
Qdaisat Sadeem,
Bi Weimin,
Shaw Chad,
Van den Veyver Ignatia,
Beaudet Arthur,
Breman Amy
Publication year - 2016
Publication title -
prenatal diagnosis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.956
H-Index - 97
eISSN - 1097-0223
pISSN - 0197-3851
DOI - 10.1002/pd.4866
Subject(s) - comparative genomic hybridization , biology , gene duplication , genotyping , trisomy , copy number variation , digeorge syndrome , microbiology and biotechnology , genetics , gene dosage , multiple displacement amplification , molecular inversion probe , genomic dna , chromosome , aneuploidy , genome , dna , genotype , gene , polymerase chain reaction , gene expression , dna extraction
Objective Detection of genomic copy number abnormalities in a single cell using array comparative genomic hybridization (CGH) offers a promising non‐invasive alternative for prenatal diagnosis. Our objective was to compare three commercially available whole‐genome amplification (WGA) kits for their capacity to produce high quality DNA from single cells that is suitable for both molecular genotyping and array CGH. Methods We examined kit performance on unfixed, fixed and fixed/permeabilized lymphoblastoid cells. Molecular genotyping methods were used to evaluate the fidelity of amplified DNA for genomic profiling, while array CGH was used to assess copy number from single cells harboring trisomy 21, a DiGeorge syndrome deletion, a CMT1A duplication or a MECP2 duplication. Results Molecular genotyping was achieved from single cells but performance varied between WGA kits. Furthermore, we consistently detected a dosage difference in sex chromosomes for gender mismatched hybridizations and for chromosome 21 in trisomy 21 cells. The 2.5 Mb DiGeorge syndrome deletion was also detected using all three WGA platforms, whereas the 1.3 Mb CMT1A and the 0.6 Mb MECP2 duplications were not consistently detected. Conclusion These data suggest that single cell molecular genotyping and copy number analysis can be accomplished when WGA conditions are optimized. © 2016 John Wiley & Sons, Ltd.