Illumina Corporation

Clear Labs, Inc.

Prodermiq, Inc.

Sasan Amini

Frank J Steemers

Kevin L Gunderson

Michael Taylor

Ramin Khaksar

David Tran

Adam Forrest Allred

Hossein Namazi

Shadi Shokralla

Sima Mortazavi

Jeffrey S Fisher

Christian Gloeckner

Christopher Haney

Pavan Vaidyanathan

Julius Barsi

Dana Hosseini

Stephanie Pollard

Eveie Schwartz

Molly Min He

Jerome J Jendrisak

Min-Jui Richard Shen

Amirali Kia

Igor Yu Goryshin

Emrah Kostem

Kathryn M Stephens

Cydne Holt

Trina Faye Osothprarop

Natasha Pignatelli

Anne Jager

Carey Davis

Paulina Walichiewicz

Yonmee Han

Prasanna Thwar Krishnan

Shaokang Zhang

Kyle Rhoden

David Silva

Susan Jisoon Lee

Bryan Thomas Barney

Henrik Gehrmann

Frank Steemers

Fiona Kaper

Kaveh Milaninia

Nicholas Caruccio

Mark A Maffitt

Thomas Royce

Eugene Cannon Kane, Ii

Mahni Ghorashi

Eveie W Schwartz

Igor Goryshin

Casey Turk

Reza Kahlor

Kia Amirali

Reza Kalhor

Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.

Methods and compositions using one-sided transposition

Provided herein are fully-automated next-generation sequencing platforms and processes for detection of a target specimen (e.g., SARS-CoV-2) and for distinguishing infectious from non-infectious signals from the specimen. An analysis can provide simultaneous diagnosis and genomic surveillance of a multitude of distinct specimens in a sample information. The analysis can comprise distinguishing between infectious versus infectious specimens and provide a recommendation as to how infectious the sample can be. The information on can be used to better inform the status of a subject or a location with regards to infectivity from the specimen.

Systems and processes for distinguishing pathogenic and non-pathogenic sequences from specimens

Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.

Transposase compositions for reduction of insertion bias

Embodiments of the present invention relate to a combination of experimental and computational workflows that allow characterization of skin and subcutaneous tissue microbial flora and its associated metabolome, aiming to first evaluate an individual's skin and subcutaneous tissue to determine if any skin condition is as a result of an imbalance or absence of commensal or mutualistic microorganisms or their associated metabolites. In particular, embodiments of the methods and the associated computational platform provided herein relate to conducting a customized or personalized test and obtaining customized or personalized information regarding the skin and subcutaneous tissue flora and its associated metabolome there from. This may be accomplished by simultaneously identifying hundreds of microorganisms or metabolites on an individual's skin and subcutaneous tissue and comparing the resulting profile to a previously compiled healthy profile from our database of skin profiles. An individual's profile provides the basis of a proprietary probiotic skin care product and personal care products that either maintains a health profile or shifts the individual's skin and subcutaneous tissue flora or its associated metabolome close to a healthy profile, at the same time enhancing the synergies between the microbial flora and host's immune system.

Customized skin care products and personal care products based on the analysis of skin flora

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Automated nucleic acid library preparation and sequencing device

Provided herein are automated apparatus and methods for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by library preparation and sequencing.

Automated priming and library loading device

Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.

Methods and compositions for DNA profiling

Methods of determining a haplotype or partial haplotype of a DNA sample containing high molecular weight segments of genomic DNA are disclosed. Such methods may include sequencing DNA in an enriched DNA sample to produce a plurality of sequence reads, where some of the sequence reads contain a first allele of the first haplotype and other of the sequence reads contain a second allele of the first haplotype. Some methods align the sequence reads to a reference genome to produce aligned reads, where aligned reads from the first high molecular weight segment tend to cluster into islands on the reference genome. Some methods further determine distances separating adjacent aligned reads on the reference genome and select a first group of the aligned reads having separation distances to adjacent aligned reads that are smaller than a cutoff value. Using alleles from the first group of aligned reads, the method may define a first haplotype or first partial haplotype.

Haplotype resolved genome sequencing

Embodiments of the present invention relate to sequencing nucleic acids. In particular, embodiments of the methods and compositions provided herein relate to preparing nucleic acid templates and obtaining sequence data therefrom.

Methods and compositions for nucleic acid sequencing

Provided herein are fully-automated next-generation sequencing platforms and processes for detection of a target specimen (e.g., SARS-CoV-2) and for distinguishing infectious from non-infectious signals from the specimen. An analysis can provide simultaneous diagnosis and genomic surveillance of a multitude of distinct specimens in a sample information. The analysis can comprise distinguishing between infectious versus infectious specimens and provide a recommendation as to how infectious the sample can be. The information can be used to better inform the status of a subject or a location with regards to infectivity from the specimen.

The present invention relates to a combination of experimental and computational workflows that allow characterization of specific molecular mechanisms by which the microbiome contribute to skin health and skin age.

Predicting skin age based on the analysis of skin flora and lifestyle data

A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.

Preserving genomic connectivity information in fragmented genomic DNA samples

Present invention relate to a combination of experimental and computational workflows that allow characterization of skin and subcutaneous tissue microbial flora and its associated metabolome, aiming to first evaluate an individual's skin and subcutaneous tissue to determine if any skin condition is as a result of an imbalance or absence of commensal or mutualistic microorganisms or their associated metabolites. The methods and the associated computational platform provided herein relate to conducting a customized or personalized test and obtaining customized or personalized information regarding the skin and subcutaneous tissue flora and its associated metabolome there from also have been disclosed.

Growing community of inventors

Redwood City, CA, United States of America

Sasan Amini