Centrillion Technology Holdings Corporation

Other

Centrillion Technologies Taiwan Co. Ltd.

Wei Zhou

Glenn H McGall

Rui Mei

Filip Crnogorac

Moti Jain

Jun Ye

Hong M Chen

Luoqi Chen

Hanying Feng

Hajime Matsuzaki

Xiaofeng Liu

Guochun Liao

Justin Costa

Julian Lucas

Jian Cao

Kendall Hoff

Jeremy Cheng

Jeremy Scott Edwards

Alivia Faye Zhou

Yao-Kuang Chung

Tzu-Kun Ku

Vijay Singh

Maurizio Righini

Michelle Halpain

Lin-Hsin Tu

Giancarlo Garbagnati

T Scott Pollom

Yaning Li

Thomas Scott Pollom, Jr

Suzy Chang

Xun Ding

Glenn Mcgall

The present disclosure provides methods of sequencing polynucleotides and compounds, compositions useful for sequencing of polynucleotides. The chemical compounds include nucleotides and their analogs which possess a sugar moiety comprising a cleavable chemical group capping the 3′-OH group and a base that is attached to a detectable label through a cleavable linker comprising a disulfide bond. In addition, the disulfide bond(s) can be cleavable by a reducing reagent. In addition, after the disulfide bond(s) is/are cleaved by the reducing reagent, there is no free thiol group linked to the nucleotides. Examples of chemical compounds according to the present disclosure are shown as Formulae (IV) and (V).

Disulfide-linked reversible terminators

The present disclosure provides methods, device, and system for a hybridization assay to detect nucleic acid targets. The assay may use a probe array format with addressable microwells. Each microwell may retain a plurality of copies of one probe which may be complementary to a portion of a specific nucleic acid target. The plurality of copies of probes may be produced from a pooled library of probe sequences by amplification techniques, including, rolling circle amplification and emulsion-PCR. Detection of hybridization may rely on methods using ion-sensitive field effect transistor (ISFET) and optical detectors to detect signals indicating the presence of the nucleic acid targets.

Oligonucleotide probe array with electronic detection system

An anchor head mounted to or incorporated into the shaft of conventional tie down stakes and earth anchors. The anchor head eliminates the need to manually drive the earth anchor into the ground and allows the anchor to be placed and removed using conventional powered drill/drivers and hex sockets or wrenches. The anchor head has a hexagonal top section and a hexagonal bottom sectional separated by an integral, central annular shoulder. The top and bottom sections are each configured to have six equilateral side walls and dimensioned to receive two different sizes of wrench or hex socket. The bottom section of the anchor head has a threaded axial bore for receiving the threaded end of the anchor shaft. The bottom section also has a lateral 'swage' bore through which a punch is inserted to swage or deform the threads of the shaft to permanently secure the anchor head to the shaft.

Tie down ground anchor head

The present disclosure relates to methods, processes and systems for enzymatic synthesis of oligonucleotide from a single-stranded, immobilized primer in the presence of a polymerase. Using the disclosed methods single-stranded oligonucleotides can be synthesized enzymatically from a single-stranded, immobilized primer in the presence of deoxyribonucleotide triphosphates or ribonucleotide triphosphates. Dideoxyribonucleotide triphosphates, deoxyribonucleotide triphosphates with reversible terminators, or ribonucleotide triphosphates with reversible terminators can be added enzymatically to the end of the primer or its extension products. According to the disclosed method, a single-stranded primer can bind to a template such that the thus-formed double-stranded structure can allow the polymerase to extend the primer at 3' end.

Method and system for enzymatic synthesis of oligonucleotides

The present disclosure relates to processes for suspending stretched nucleic acids over surface features. These processes can be used to prepare stretched nucleic acids that are more active in enzymatic reactions and other reactions than those laid down on a flat surface. These processes can be achieved by using a photoresist layer on top of a substrate, stretch a nucleic acid on top of the surface, and then remove part of the photoresist to form surface features that suspend the stretched nucleic acid. Furthermore, the formation of a hydrogel layer over the stretched nucleic acid and the surface features can transfer the stretched nucleic acid to the hydrogel for further reactions, including enzymatic reactions.

DNA bridge methods for capturing DNA molecules

The present disclosure provides methods of sequencing polynucleotides and compounds, compositions useful for sequencing of polynucleotides. The chemical compounds include nucleotides and their analogs which possess a sugar moiety comprising a cleavable chemical group capping the 3'-OH group and a base that is attached to a label through a cleavable linker comprising a disulfide bond. In addition, both the disulfide bond and the cleavable chemical group are cleavable by a chemical reagent. Furthermore, after the disulfide bond is cleaved by the chemical reagent, there is no free thiol group linked to the base of the nucleotides according to the fragmentation reaction shown below as an example. Example compounds according to the present disclosure are shown as Formula (I):  

Provided herein are methods and compositions for the sequencing of long nucleic acids, such as DNA. The methods and compositions are suited for the spatial labeling and sequencing of long nucleic acid molecules.

Methods for sequencing nucleic acids

A microarray carrier assembly including a scan tray and a plurality of microarray blocks detachably disposed on the scan tray is provided. The scan tray includes a frame including an opening and a slot, and a transparent substrate covering the opening of the frame. Each of the microarray blocks includes a main body, a probe array distributed on the main body and facing towards the transparent substrate of the scan tray, and a plurality of guiding pins disposed on the main body and surrounding the probe array, wherein a top surface area of the guiding pin opposite to the main body is less than a bottom surface area of the guiding pin connected to the main body, and the guiding pins are detachably inserted into the slot of the frame of the scan tray.

Microarray carrier assembly

The present invention provides methods and systems for sequencing long nucleic acid fragments. In one aspect of the invention, methods, systems and reagent kits are provided for sequencing nucleic acid target sequences. Some embodiments of the methods, systems and reagent kits are particularly suitable for sequencing a large number of fragments, particularly long fragments.

Methods and systems for sequencing long nucleic acids

The present disclosure relates to processes for inverting oligonucleotide probes in an in situ synthesized array. These processes can be used to reverse the orientation of probes with respect to the substrate from 3'-bound to 5&#x2032;-bound. These processes can also be used to reduce or eliminate the presence of truncated probe sequences from an in situ synthesized array.

Probe inversion process for in situ synthesized probe arrays

The methods, systems, kits and reagents provided herein relate to the synchronization of dephased/prephased nucleic acid molecules during sequencing reactions. The methods, systems, kits and reagents provided herein can be utilized to improve the efficiency and accuracy of sequencing technologies.

Methods for synchronizing nucleic acid molecules

Provided herein are methods and compositions for analyzing epigenetic modifications of genomes. The methods and compositions are suited for complete epigenome sequencing of any modification for which an antibody or an affinity binding agent has been developed. In one aspect, provided herein is a method for analyzing epigenetic modification of a genome. In some embodiments of aspects provided herein, the method further comprises sequencing a sequencing library to generate sequence reads, and assembling the sequence reads with aid of a positional barcode sequence information. In some embodiments of aspects provided herein, the method further comprises determining a location of at least two different epigenetic modifications of the nucleic acid. Another aspect of the present disclosure provides a kit for analyzing an epigenetic modification of a nucleic acid.

Methods for phrasing epigenetic modifications of genomes

The present disclosure provides a computer-implemented method for analyzing variants from a plurality of nucleic acid sequence reads using a computation pipeline, which comprises a module depending on a location-dependent parameter. The method comprises executing on a processor the steps of: receiving a plurality of nucleic acid sequence reads comprising at least a first nucleic acid sequence read and a second nucleic acid sequence read; mapping the first nucleic acid sequence read and the second nucleic acid sequence read to a first location and a second location in a genome, respectively; setting a first value and a second value for the location-dependent parameter on the basis of the first location and the second location in the genome, respectively; passing the first nucleic acid sequence read and the second nucleic acid sequence read through the module using the first value and the second value, respectively; and generating a variant call.

Computation pipeline of location-dependent variant calls

The present disclosure provides a computer-implemented method of analyzing variants from a plurality of nucleic acid sequence reads. The method uses a computation pipeline having at least one invariable module and at least one variable module, wherein the variable module depends on a variable parameter. The method includes executing on a processor the steps of receiving the plurality of nucleic acid sequence reads; setting a plurality of values for the variable parameter; passing the plurality of the nucleic acid sequence reads through the invariable module to generate an intermediate output; passing the intermediate output through the variable module for multiple rounds, each round using one of the variable values; and generating a plurality of variant calls.

Growing community of inventors

Saratoga, CA, United States of America

Wei Zhou