Journal: Journal of Korean Medical Science

Article Title: Clinical Significance of Previously Cryptic Copy Number Alterations and Loss of Heterozygosity in Pediatric Acute Myeloid Leukemia and Myelodysplastic Syndrome Determined Using Combined Array Comparative Genomic Hybridization plus Single-Nucleotide Polymorphism Microarray Analyses

doi: 10.3346/jkms.2014.29.7.926

Figure Lengend Snippet: Genetic aberrations detected using CGH+SNP microarray analysis. ( A ) Copy loss at 12p13.33-p12.3 in patient 6. ( B ) Large terminal LOH in 9p in patient 15. ( C ) Homozygous acquisition of chromosome 6 in patient 12. CGH, comparative genomic hybridization; SNP, single-nucleotide polymorphism; LOH, loss of heterozygosity.

Article Snippet: Genomic DNA (gDNA) was isolated from frozen BM (n=17) or PB samples (n=1) using the QiagenDNeasy Blood & Tissue Kit (P/N 69504;Qiagen Inc., Valencia, CA, USA) and processed according to the manufacturer's protocol for the Agilent SurePrint G3 Cancer CGH+SNP 4×180K microarray (P/N G4869A; Agilent Technologies, Santa Clara, CA, USA).

Techniques: Microarray, Hybridization

Journal: Nature neuroscience

Article Title: Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR

doi: 10.1038/nn.4235

Figure Lengend Snippet: ( a ) Overview and design of the experimental procedures. ( b ) Illustration of targeted 16p11.2 rMDS segment and/or SDs. For simplicity, only protein coding genes are shown from the Ensembl GRCh37 V.71 annotation . The targeted unique genomic segment for the dual-guide 575 kb deletion is indicated in yellow, and the single-guide RNA targeting the SDs to promote a model of NAHR-mediated CNV is indicated in red (Target sequence: 5′-ACATGCCTATATCGCATAG -3′, chromosome 16: 29,487,572–29,487,590 and 30,226,917–30,226,935). ( c ) Efficiency of CRISPR/Cas9 generation of the 740 kb rMDS using the single-guide SCORE method that targets the SDs is shown, as determined by copy number screening assay for six genes. Further characterization by microarray and RNAseq was performed for a subset of microdeletion clones (6), and all microduplication clones (5). ( d ) Microarray analyses showing deletion (CRISPR Del) and duplication (CRISPR Dup) of the 16p11.2 region in CRISPR-treated lines is shown. Gains or losses of 16p11.2 region were determined by normalized log2 ratios. No off-target CNVs were observed in CRISPR-generated clones.

Article Snippet: Array-based comparative genomic hybridization (aCGH) was performed on the Agilent 4×180K SurePrint G3 Human CGH Microarray (Design #022060) according to the protocol provided by the manufacturer.

Techniques: Sequencing, CRISPR, Screening Assay, Microarray, Clone Assay, Generated

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Neomorphic effects of recurrent somatic mutations in Yin Yang 1 in insulin-producing adenomas

doi: 10.1073/pnas.1503696112

Figure Lengend Snippet: Altered YY1T372R DNA-binding motif imparts a unique expression signature. (A) Motifs enriched by ChIP-seq following expression of YY1WT and YY1T372R in HEK293T cells compared with the published YY1WT motif. Sites at which R371 and H373 of YY1WT contact the DNA backbone between bases of the recognition motif are indicated by blue and orange arrows, respectively. (B) Expression profiles of YY1T372R-harboring tumors (red) are distinct from those with YY1WT (blue). Expression of all probes on the microarray for each tumor was used as input for unsupervised clustering by PCA.

Article Snippet: Five insulinomas with somatic YY1 T372R mutation and six with YY1 WT underwent RNA expression analysis using the SurePrint G3 Human Exon 4 × 180K Microarray (Agilent Technologies).

Techniques: Binding Assay, Expressing, ChIP-sequencing, Microarray