Digital karyotyping

Detection of copy number variation in the human genome is important for identifying naturally occurring copy number polymorphisms as well as alterations that underlie various human diseases, including cancer. Digital karyotyping uses short sequence tags derived from specific genomic loci to provide a quantitative and high-resolution view of copy number changes on a genome-wide scale. Genomic tags are obtained using a combination of enzymatic digests and isolation of short DNA sequences. Individual tags are linked into ditags, concatenated, cloned and sequenced. Tags are matched to reference genome sequences and digital enumeration of groups of neighboring tags provides quantitative copy number information along each chromosome. Digital karyotyping libraries can be generated in about a week, and library sequencing and data analysis require several additional weeks.

[1]  D. Pinkel,et al.  Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors , 2022 .

[2]  K. Gunderson,et al.  High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. , 2006, Genome research.

[3]  R. McLendon,et al.  Identification of OTX2 as a medulloblastoma oncogene whose product can be targeted by all-trans retinoic acid. , 2005, Cancer research.

[4]  K. Kinzler,et al.  The Genetic Basis of Human Cancer , 1997 .

[5]  G. Parmigiani,et al.  Digital karyotyping identifies thymidylate synthase amplification as a mechanism of resistance to 5-fluorouracil in metastatic colorectal cancer patients. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Jun Yao,et al.  Distinct epigenetic changes in the stromal cells of breast cancers , 2005, Nature Genetics.

[7]  J. Shendure,et al.  Advanced sequencing technologies: methods and goals , 2004, Nature Reviews Genetics.

[8]  Jun Yao,et al.  Methylation-specific digital karyotyping , 2006, Nature Protocols.

[9]  A. Sparks,et al.  Using the transcriptome to annotate the genome , 2002, Nature Biotechnology.

[10]  J. Sebat,et al.  Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. , 2003, Genome research.

[11]  D. Ledbetter,et al.  Multicolor Spectral Karyotyping of Human Chromosomes , 1996, Science.

[12]  Y. Rogers,et al.  Genomics: Massively parallel sequencing , 2005, Nature.

[13]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[14]  W. Kuo,et al.  High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays , 1998, Nature Genetics.