Abstract: A method for analyzing a sequence comprising a SNP site is provide. In general terms, the method comprises: a) contacting a first DNA sample with a first restriction enzyme to provide DNA fragments, wherein: i) the first restriction enzyme cleaves the sequence only if a first allele of a SNP is present at the SNP site; b) end-labeling the DNA fragments to produce an end-labeled sample; c) hybridizing the end-labeled sample to an array comprising a probe sequence; and d) comparing the amount of hybridization between the digested sample and the probe sequence to a reference signal.

Abstract: A compact ultrasound needle guidance system and method of use is described. The needle guidance system has components to adjustably target a needle's destination in the plane of a two-dimensional ultrasound image before insertion of a needle into a patient. Needle movement is tracked using a position detector that provides a visual display of the needle path on the ultrasonic image.

Abstract: A method for analyzing a sequence comprising a SNP site is provide.

Abstract: A method for partitioning a genome is provided. In certain embodiments, the method comprises: a) nicking a region of the genome using a sequence-specific nicking endonuclease to produce a nicked double-stranded genomic region; b) hybridizing the nicked double-stranded genomic region with an oligonucleotide comprising: i. an affinity tag; and ii. a nucleotide sequence that is complementary to the nucleotide sequence that is immediately adjacent to the nick site, to produce a duplex in which a terminal nucleotide of the oligonucleotide lies immediately adjacent to said a nucleotide of the nick site; c) ligating the terminal nucleotide of the oligonucleotide to the nucleotide of the nick site to produce a ligation product; and d) separating the ligation product from unligated products using the affinity tag. Compositions and kits for practicing the method are provided.

Abstract: A method of genome analysis is provided. In certain embodiments, the method may comprise: labeling the test genome using a first site-specific methyltransferase to produce a labeled test genome comprising a label; and analyzing the labeled test genome to determine if the test genome comprises a sequence alteration relative to a reference sequence. In certain embodiments, the method may comprise: evaluating binding of the labeled test genome to an array of probes, or observing a pattern of labeling along the labeled test genome.

Abstract: A method for partitioning a genome is provided. In certain embodiments, the method comprises: a) nicking a region of the genome using a sequence-specific nicking endonuclease to produce a nicked double-stranded genomic region; b) hybridizing the nicked double-stranded genomic region with an oligonucleotide comprising: i. an affinity tag; and ii. a nucleotide sequence that is complementary to the nucleotide sequence that is immediately adjacent to the nick site, to produce a duplex in which a terminal nucleotide of the oligonucleotide lies immediately adjacent to said a nucleotide of the nick site; c) ligating the terminal nucleotide of the oligonucleotide to the nucleotide of the nick site to produce a ligation product; and d) separating the ligation product from unligated products using the affinity tag. Compositions and kits for practicing the method are provided.

Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting a plurality of Q probes with a nucleic acid sample comprising a target polynucleotide under hybridization conditions to form a plurality of flap endonuclease substrates each comprising a Q probe and a site in the target polynucleotide; b) contacting the plurality of flap endonuclease substrates with a flap endonuclease under cleavage conditions to produce cleavage products, in which each of the Q probes of the flap endonuclease substrates is cleaved to produce cleavage products that include at least a first fragment that is hybridized with a site in the target polynucleotide and a second fragment that is linear and free in solution; and c) detecting at least one of the cleavage products.

Abstract: An array-based method for performing genomic analysis is provided. In certain embodiments, the method may comprise: a) contacting a sample comprising genomic DNA with a Type IIB restriction enzyme to produce Type IIB fragments; b) directly labeling the Type IIB fragments with a fluorescent label to produce labeled fragments; c) contacting the labeled fragments with an array to produce a contacted array; and d) reading the contacted array to produce data. In certain instances, the data may be analyzed to determine the copy number of a genomic region in the sample. Also provided are arrays and kits useful to practice the method.

Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting a surface-tethered oligonucleotide with a sample comprising a barcode oligonucleotide to produce an oligonucleotide duplex comprising a double-stranded surface-proximal region and a single-stranded surface-distal overhang; b) extending the barcode oligonucleotide using the overhang as a template to produce an extended duplex; c) subjecting the extended duplex to a wash that separates the oligonucleotide duplex but does not separate said extended duplex; and d) detecting the extended duplex.