Accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing

#The present invention is directed to accelerating identification of single nucleotide polymorphisms and an alignment of clone in genomic sequencing.

#Introduction to Applications of SNPS

#Accumulation of genetic changes affecting cell cycle control, cell differentiation, apoptosis, and DNA replication and repair lead to carcinogenesis (Bishop, J. M., “Molecular Themes In Oncogenesis,” Cell, 64(2):235-48 (1991)). DNA alterations include large deletions which inactivate tumor supressor genes, amplification to increase expression of oncogenes, and most commonly single nucleotide mutations or polymorphisms which impair gene expression or gene function or predispose an individual to further genomic instability (Table 1). 1 TABLE 1 Genetic Alterations Commonly Found in the Human Genome Type of Alteration Possible Causes of Alteration Possible Consequences of Alteration Detection of Alteration Single nucleotide Inherited variation Silent does not alter function DNA sequencing polymorphism Methylation Missense: alters gene function SSCP, DGGE, CDGE (SNP) Carcinogens Nonsense: truncates gene Protein truncation Defective repair genes Mismatch cleavage Microsatellite Defective DNA repair genes Frameshift truncates gene Microsatellite Analysis instability (MIN) Carcinogens Large deletions Defective DNA repair genes Loss of gene function Loss of heterozygosity Defective DNA replication genes CGH Illegitimate recombination SNP analysis Double strand break DNA amplifications Defective DNA repair genes Overexpression of gene Competitive PCR Defective DNA replication genes CGH Illegitimate recombination SNP analysis Others: Defective methylase genes Gene silencing or overexpression, Endonuclease digestion Methylation, Double strand break creation of chimeric protein PCR, FISH Translocation

#FIG. 1 is a schematic drawing showing the sequencing of DrdI islands in random plasmid or cosmid clones in accordance with the present invention.

#FIG. 2 is a schematic drawing of a first embodiment for sequencing restriction enzyme generated representations.

#FIG. 3 is a schematic drawing of a second embodiment for sequencing restriction enzyme generated representations.

#The present invention is directed to a method of assembling genomic maps of an organism's DNA or portions thereof. A library of an organism's DNA is provided where the individual genomic segments or sequences are found on more than one clone in the library. Representations of the genome are created, and nucleic acid sequence information is generated from the representations. The sequence information is analyzed to determine clone overlap from a representation. The clone overlap and sequence information from different representations is combined to assemble a genomic map of the organism.

#Summary of DrdI Island Approach to Accelerate Alignment of Clones.

#The DrdI island approach obtains a representation of the sequence in a genome which may be used to complete the map of the genome, to find mapped SNPs, and to evaluate genome differences and their association with diseases.