Abstract: An array of inter-Alu gene-enriched amplicons produced by a polymerase chain reaction (“PCR”) process. The PCR process comprises combining one or a plurality of Head-type/Tail-type Alu- or AluY- or any other Alu-subfamily-consensus sequence-based primer; a genomic DNA template isolated from cells; and a PCR-extension mix. The combination of primers, DNA template; and PCR extension mix comprises an inter-Alu-PCR-mixture. After making the inter-Alu-PCR mixture, an inter-Alu PCR cycle program is used in connection with a PCR machine for a period of time to produce the array of inter-Alu gene-enriched amplicons that are sequenced by massively parallel sequencing to allow genome wide scanning of sequence and structure variations in the human genome.

Abstract: A method of genotyping single nucleotide polymorphisms (“SNP”) and point mutations in nucleic acid based on chain extension by polymerase. This invention is based on the fact that the nucleoside immediately 5? adjacent to any SNP/point mutation site is known, and the neighboring sequence immediately 3? adjacent to the site is also known. A primer complementary to the sequence directly adjacent to the SNP on the 3? side in a target polynucleotide is used for chain elongation. The polymerase reaction mixture contains one chain-terminating nucleotide having a base complementary to the nucleotide directly adjacent to the SNP on the 5? side in the target polynucleotide. An additional dNTP may be added to produce a primer with the maximum of a two-base extension. The resultant elongation/termination reaction products are analyzed for the length of chain extension of the primer, or for the amount of label incorporation from a labeled form of the terminator nucleotide.

Abstract: A method of genotyping single nucleotide polymorphisms (“SNP”) and point mutations in nucleic acid based on chain extension by polymerase. This invention is based on the fact that the nucleoside immediately 5′ adjacent to any SNP/point mutation site is known, and the neighboring sequence immediately 3′ adjacent to the site is also known. A primer complementary to the sequence directly adjacent to the SNP on the 3′ side in a target polynucleotide is used for chain elongation. The polymerase reaction mixture contains one chain-terminating nucleotide having a base complementary to the nucleotide directly adjacent to the SNP on the 5′ side in the target polynucleotide. An additional dNTP may be added to produce a primer with the maximum of a two-base extension. The resultant elongation/termination reaction products are analyzed for the length of chain extension of the primer, or for the amount of label incorporation from a labeled form of the terminator nucleotide.