Journal: Biomedicines

Article Title: An Integrated Approach Including CRISPR/Cas9-Mediated Nanopore Sequencing, Mate Pair Sequencing, and Cytogenomic Methods to Characterize Complex Structural Rearrangements in Acute Myeloid Leukemia

doi: 10.3390/biomedicines12030598

Figure Lengend Snippet: Structural variants by CRISPR/Cas9-mediated nanopore sequencing.

Article Snippet: Using this method, thirty crRNAs were designed to detect twenty-nine chromosomal abnormalities in chromosomes 3 and 7 ( ). crRNA #28 and #29 were targeted for the same genomic region. crRNAs were designed using Custom Alt-R CRISPR-Cas9 guide RNA ( https://www.idtdna.com/site/order/designtool/index/CRISPR_CUSTOM , 15 February 2020) and Chopchop ( https://chopchop.cbu . uib.no/, 15 February 2020) with CRISPR-Cas9.

Techniques: CRISPR, Sequencing, Variant Assay, Amplification

Journal: Biomedicines

Article Title: An Integrated Approach Including CRISPR/Cas9-Mediated Nanopore Sequencing, Mate Pair Sequencing, and Cytogenomic Methods to Characterize Complex Structural Rearrangements in Acute Myeloid Leukemia

doi: 10.3390/biomedicines12030598

Figure Lengend Snippet: Summarization of various structural variant breakpoints revealed by CRISPR/Cas9-mediated nanopore sequencing, MPseq, and SNP microarray. From left to right, SNP microarray revealed three chromoanagenesis regions: two on chromosome 3q and one on 7q (shown by red circles). Mate pair sequencing data is in a solid red circle, CRISPR/Cas9 nanopore sequencing data is in green circles, and overlapped data of MPseq and CRISPR/cas9 are in brown circles. ( A , B ) Complex SVs in the IGV view. Reads of chromosome 7q11.22 genomic region (69,431,166–69,480,285, A ) and 3q21.3 genomic region (126,248,059–126,263,338, B ). ( C ) Copy number variants by nanopore sequencing and SNP microarray. Reads of chromosome 3q21.1 genomic region (121,889,250–122,611,342) show complex SVs including amplification, gain, and loss detected by nanopore sequencing, which were consistent with SNP microarray findings. Nanopore reads and SNP microarray data were analyzed by the VIA software to generate copy number variants. Chr: chromosome, CNVs: copy number variants, ROIs: regions of interest by CRISPR/cas9 guideRNAs, SVs: structural variants.

Article Snippet: Using this method, thirty crRNAs were designed to detect twenty-nine chromosomal abnormalities in chromosomes 3 and 7 ( ). crRNA #28 and #29 were targeted for the same genomic region. crRNAs were designed using Custom Alt-R CRISPR-Cas9 guide RNA ( https://www.idtdna.com/site/order/designtool/index/CRISPR_CUSTOM , 15 February 2020) and Chopchop ( https://chopchop.cbu . uib.no/, 15 February 2020) with CRISPR-Cas9.

Techniques: Variant Assay, CRISPR, Nanopore Sequencing, Microarray, Sequencing, Amplification, Software

Journal: Biomedicines

Article Title: An Integrated Approach Including CRISPR/Cas9-Mediated Nanopore Sequencing, Mate Pair Sequencing, and Cytogenomic Methods to Characterize Complex Structural Rearrangements in Acute Myeloid Leukemia

doi: 10.3390/biomedicines12030598

Figure Lengend Snippet: Comparison of data of SNP microarray, MPseq, and CRISPR/Cas9-mediated nanopore sequencing.

Article Snippet: Using this method, thirty crRNAs were designed to detect twenty-nine chromosomal abnormalities in chromosomes 3 and 7 ( ). crRNA #28 and #29 were targeted for the same genomic region. crRNAs were designed using Custom Alt-R CRISPR-Cas9 guide RNA ( https://www.idtdna.com/site/order/designtool/index/CRISPR_CUSTOM , 15 February 2020) and Chopchop ( https://chopchop.cbu . uib.no/, 15 February 2020) with CRISPR-Cas9.

Techniques: Comparison, Microarray, CRISPR, Sequencing, Variant Assay, Nanopore Sequencing, Amplification