Abstract: The present invention provides methods for analyzing blocks of closely spaced SNPs, or haplotypes for use in identification of the origin of DNA in a sample. The methods comprise aligning common alleles of a gene of interest and identifying a region containing a plurality of SNPs which is flanked by non-polymorphic DNA which can be used for primer placement. Any sequencing method, including next generation sequencing methods can then be used to determine the haplotypes in the sample with a lower limit of detection of at least 0.01%. These inventive methods are useful, for example, for identification of hematopoietic stem cell transplantation patients destined to relapse, microchimerism associated with solid organ transplantation, detection of solid organ transplant rejection by detecting donor DNA in recipient plasma, forensic applications, and patient identification.

Abstract: The present invention provides methods for analyzing blocks of closely spaced SNPs, or haplotypes for use in identification of the origin of DNA in a sample. The methods comprise aligning common alleles of a gene of interest and identifying a region containing a plurality of SNPs which is flanked by non-polymorphic DNA which can be used for primer placement. Any sequencing method, including next generation sequencing methods can then be used to determine the haplotypes in the sample with a lower limit of detection of at least 0.01%. These inventive methods are useful, for example, for identification of hematopoietic stem cell transplantation patients destined to relapse, microchimerism associated with solid organ transplantation, detection of solid organ transplant rejection by detecting donor DNA in recipient plasma, forensic applications, and patient identification.

Abstract: The present invention provides a method for detecting mutations in the PALB2 gene in pancreatic cancer patients and in individuals having a family history of pancreatic cancer. Methods are also provided for diagnosing a predisposition to pancreatic cancer, for predicting a patient's response to pancreatic cancer therapies, and for treating pancreatic cancer, based on presence of a PALB2 mutation or abberant PALB2 gene expression in a patient.

Abstract: The present invention provides a method for detecting mutations in the PALB2 gene in pancreatic cancer patients and in individuals having a family history of pancreatic cancer. Methods are also provided for diagnosing a predisposition to pancreatic cancer, for predicting a patient's response to pancreatic cancer therapies, and for treating pancreatic cancer, based on presence of a PALB2 mutation or abberant PALB2 gene expression in a patient.

Abstract: The present invention provides a method for detecting mutations in the PALB2 gene in pancreatic cancer patients and in individuals having a family history of pancreatic cancer. Methods are also provided for diagnosing a predisposition to pancreatic cancer, for predicting a patient's response to pancreatic cancer therapies, and for treating pancreatic cancer, based on presence of a PALB2 mutation or abberant PALB2 gene expression in a patient.

Abstract: The invention provides methods permitting the detection of small amounts of different nucleic acids in the presence of an excess amount of wild-type nucleic acids. Also provided herein are method so detecting infectious disease minority variants, methods of forensic identification, methods of diagnosing cancer and monitoring disease progress.

Abstract: An oligonucleotide based therapeutic strategy, called anti-gene locks, is described which specifically kills cells based on their genotype. The strategy employs oligonucleotides with arms and a backbone that are complementary to both strands of the gene target. Anti-gene locks bind in vitro in a sequence dependent fashion and inhibit DNA synthesis. In bacterial cells containing an episome target, they cause elimination of the extra-chromosomal DNA structure. When the target is present in the bacterial or human genome, they selectively kill the majority of these cells.

Abstract: There are currently few therapeutic options for patients with pancreatic cancers and new insights into the pathogenesis of this lethal disease are urgently needed. To this end, we performed a comprehensive analysis of the genes altered in 24 pancreatic tumors. First, we determined the sequences of 23,781 transcripts, representing 20,583 protein-encoding genes, in DNA from these tumors. Second, we searched for homozygous deletions and amplifications using microarrays querying ˜one million single nucleotide polymorphisms in each sample. Third, we analyzed the transcriptomes of the same samples using SAGE and next-generation sequencing-by-synthesis technologies. We found that pancreatic cancers contain an average of 63 genetic alterations, of which 49 are point mutations, 8 are homozygous deletions, and 6 are amplifications. Further analyses revealed a core set of 12 regulatory processes or pathways that were each genetically altered in 70% to 100% of the samples.

Abstract: The present invention provides a method for detecting mutations in the PALB2 gene in pancreatic cancer patients and in individuals having a family history of pancreatic cancer. Methods are also provided for diagnosing a predisposition to pancreatic cancer, for predicting a patient's response to pancreatic cancer therapies, and for treating pancreatic cancer, based on presence of a PALB2 mutation or abberant PALB2 gene expression in a patient.

Abstract: Methods for the simultaneous sequencing of multiple nucleic acid molecules are provided. Preferred methods include simultaneous single-direction sequencing of multiple genes or forward and reverse sequencing from a single gene, within a single reaction vessel. Additional methods of the invention include combined amplification and sequencing of nucleic acids, from a variety of sources, within a single reaction and wherein nucleic acid products also can be simultaneously analyzed, and where the reaction can be either bidirectional or long unidirectional. Additional methods encompass combined amplification and sequencing of multiple nucleic acid molecules simultaneously.