Copy number analysis

YK Yasuo Kubota
MS Masafumi Seki
TK Tomoko Kawai
TI Tomoya Isobe
MY Misa Yoshida
MS Masahiro Sekiguchi
SK Shunsuke Kimura
KW Kentaro Watanabe
AS Aiko Sato-Otsubo
KY Kenichi Yoshida
HS Hiromichi Suzuki
KK Keisuke Kataoka
YF Yoichi Fujii
YS Yuichi Shiraishi
KC Kenichi Chiba
HT Hiroko Tanaka
MH Mitsuteru Hiwatari
AO Akira Oka
YH Yasuhide Hayashi
SM Satoru Miyano
SO Seishi Ogawa
KH Kenichiro Hata
YT Yukichi Tanaka
JT Junko Takita
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DNA samples were processed via SNP array analysis using the Affymetrix GeneChip 250K Nsp or CytoScan HD (Affymetrix, Santa Clara, CA, USA) according to the protocol provided by the manufacturer. Informatics analysis of the SNP array data was conducted using the CNAG/AsCNAR software, which enables the accurate detection of allelic status without paired normal DNA, even in the presence of up to 70–80% normal cell contamination50. Isochromosome 12p was confirmed when a sample had two more copies of 12p than of 12q. To confirm the copy number abnormalities detected using the SNP array, NGS-based copy number analyses were also performed in all samples using the in-house pipeline, CNACS51, which enable digital karyotyping.

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