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Genotyping of human cell lines with amplification of single cell vs. non amplied products to examime the effect of allele bias during amplification


ABSTRACT: Single-cell human genome analysis using whole-genome amplified product is hampered by allele bias during amplification. Using an oligonucleotide SNP array, we examined the nature of the allele bias and its effect on the chromosomal copy number analysis. Experiment Overall Design: TB106, lymphoblastoid cell line; CMK11-5 and CMK86, cell line; WGA, whole-genome amplified from bulk DNA; SC, whole-genome amplified product from single cell. Genotype and copy number status were compared between non-amplified products and their single cell products.

ORGANISM(S): Homo sapiens

SUBMITTER: Kazuya Iwamoto 

PROVIDER: E-GEOD-8567 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

Iwamoto Kazuya K   Bundo Miki M   Ueda Junko J   Nakano Yoko Y   Ukai Wataru W   Hashimoto Eri E   Saito Toshikazu T   Kato Tadafumi T  

PloS one 20071212 12


<h4>Background</h4>In single-cell human genome analysis using whole-genome amplified product, a strong amplification bias involving allele dropout and preferential amplification hampers the quality of results. Using an oligonucleotide single nucleotide polymorphism (SNP) array, we systematically examined the nature of this amplification bias, including frequency, degree, and preference for genomic location, and we assessed the effects of this amplification bias on subsequent genotype and chromos  ...[more]

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