Leland Stanford Junior University

Grail, Inc.

Maneesh Jain

Ronald W Davis

Mostafa Ronaghi

Thomas Willis

Paul Hardenbol

Viktor Stolc

Eugeni A Namsaraev

Robert L White

Stephen E Harris

Guang-Yu Yin

Lester A Roberts

Provided herein are methods for enriching a biological sample for a target nucleic acid, and analyzing the nucleic acid. In some cases, a biological sample is enriched for target nucleic acids associated with a cancer or tumor. In some cases, a biological sample is enriched for target nucleic acids, and the target nucleic acids vary in length. In some cases, one or more probes are used to enrich the biological sample for the target nucleic acid. In some cases, one or more probes hybridize to one or more ends of a target nucleic acid.

Methods of analyzing nucleic acid fragments

The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

Precircle probe nucleic acid amplification methods

Method for detecting and amplifying target DNA

The invention includes devices and methods for forming random arrays of magnetic particles, arrays formed using these devices and methods, and to methods of using the arrays. The invention provides an assembly (chip) with magnetic domains that produce localized magnetic fields capable of immobilizing magnetic particles such as commercially available magnetic beads. Probe or sensor molecules can be coupled to the beads, which are then dispersed on the assembly, forming a random order array. The arrays can be used for analyzing samples, targets, and/or the interaction between samples and targets. The invention finds particular use in processes such as high-throughput genotyping and other nucleic acid hybridization-based assays.

Devices and methods to form a randomly ordered array of magnetic beads and uses thereof

Direct multiplex characterization of genomic DNA

Efficient nonlinear processes in a nonlinear optical medium are achieved by combining the concept of electromagnetically induced transparency (EIT) and a strongly-driven atomic local oscillator. The present method uses a nonlinear optical medium having elementary entities, such as atoms or molecules, in which a ground state .vertline.1&gt; and a second state .vertline.2&gt; are selected such that the transition between the ground state .vertline.1&gt; and the second state .vertline.2&gt; is a dipole forbidden transition. An upper state .vertline.3&gt; selected from among the energy states .vertline.i&gt; above the ground state .vertline.1&gt; such that a two-photon transition between the ground state .vertline.1&gt; and the second state .vertline.2&gt; via the upper state .vertline.3&gt; is allowed. A strongly-driven coherent superposition state which gives rise to the strongly-driven local oscillator is produced by applying two pumping beams, P1 and P2, at frequencies corresponding to transitions between states .vertline.2&gt; and .vertline.3&gt; and between states .vertline.1&gt; and .vertline.3&gt;. The nonlinear optical medium prepared in this way is used for efficient sum-and-difference and parametric generation in .LAMBDA. and ladder systems.

Method and apparatus for nonlinear frequency generation using a

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Menlo Park, CA, United States of America

Maneesh Jain