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The present disclosure provides systems and methods to detect somatic or germline variants by providing a predetermined genomic DNA (gDNA) to an assay mixture, and capturing a sample of a subjects genetic information using a DNA sequencer and detecting genetic variants from the genetic information. A mutation may then be classified as being from a germline source if gDNA derived molecules have lengths inconsistent with those expected from cell-free DNA (cfDNA) derived molecules.


Systems and methods are disclosed to detect single-nucleotide variations (SNVs) from somatic sources in a cell-free biological sample of a subject by generating training data with class labels; in computer memory, generating a machine learning unit comprising one output for each of adenine (A), cytosine (C), guanine (G), and thymine (T) calls; training the machine learning unit; and applying the machine learning unit to detect the SNVs from somatic sources in the cell-free biological sample of the subject, wherein the cell-free biological sample comprises a mixture of nucleic acid molecules from somatic and germline sources.


News Article | February 16, 2017
Site: www.businesswire.com

DUARTE, Calif.--(BUSINESS WIRE)--City of Hope researchers and scientists strive to find less invasive ways to help treat patients diagnosed with kidney cancer. Despite a wave of new targeted therapies being approved to treat the disease, many of those therapies have been challenging to use because of the difficulty in obtaining cancer tissue for genomic testing. Now, researchers may have found a way to combat this problem: the liquid biopsy. The liquid biopsy, using cell-free cancer DNA that is circulating in the patient’s blood, is an easy and less invasive method of accessing the important genomic information in solid tumors, but had not yet been tested in patients with kidney tumors. In a study led by City of Hope’s Sumanta K. Pal, M.D., assistant professor in the Department of Medical Oncology & Therapeutics Research and co-director of the Kidney Cancer Program at City of Hope, he and his team identified cancer-related DNA in about 80 percent of patients who had a liquid biopsy performed. A majority of the patients were found to have clinically relevant genomic alterations, including alterations in the TP53, VHL, EGFR, NF1 and ARID1A genes. The results, based on data from Guardant Health, will be presented on Saturday, Feb. 18, at the 2017 Genitourinary Cancers Symposium, which is sponsored by the American Society of Clinical Oncology and the American Society for Radiation Oncology. The analysis of 224 patients diagnosed with metastatic renal cell carcinoma (mRCC) and tested with Guardant360 is the largest assessment of circulating tumor DNA in patients to date. Analysis of this large cohort demonstrated significant changes in circulating tumor DNA (ctDNA) profiles across patients’ clinical courses, which may have therapeutic implications. “Until now, the only means of assessing kidney tumor DNA has been through biopsies of cancer tissue, a procedure which can be associated with risk of infection and bleeding,” said Pal. “The liquid biopsy circumvents this completely.” Guardant360 has been used by more than 3,000 oncologists to identify somatic genomic alterations associated with targeted therapies in the tumor DNA of more than 30,000 patients with advanced cancer. Many doctors rely on biopsies to create an individual treatment plan that is directed toward specific genomic changes in the patient’s tumor. Because tumors evolve and develop resistance in response to treatment, the changes in ctDNA might provide key insights into how resistance to treatments for kidney cancer occurs. Pal and colleagues now aim to replicate this work in a larger study of patients to confirm the results. This study also represents an example of City of Hope’s ongoing commitment to developing personalized medicine and targeted therapies. Personalized medicine, which offers physicians the ability to better diagnose, treat, cure and prevent diseases, depends on three factors: discovering the genetic causes of diseases, understanding why individuals respond to different therapies and translating this understanding into new diagnostic tests and therapies. City of Hope is an independent research and treatment center for cancer, diabetes and other life-threatening diseases. Designated as one of only 47 comprehensive cancer centers, the highest recognition bestowed by the National Cancer Institute, City of Hope is also a founding member of the National Comprehensive Cancer Network, with research and treatment protocols that advance care throughout the world. City of Hope is located in Duarte, California, just northeast of Los Angeles, with community clinics throughout Southern California. It is ranked as one of "America's Best Hospitals" in cancer by U.S. News & World Report. Founded in 1913, City of Hope is a pioneer in the fields of bone marrow transplantation, diabetes and numerous breakthrough cancer drugs based on technology developed at the institution. For more information about City of Hope, follow us on Facebook, Twitter, YouTube or Instagram.


Mortimer S.A.,University of California at Berkeley | Mortimer S.A.,Guardant Health | Kidwell M.A.,University of California at Berkeley | Doudna J.A.,University of California at Berkeley | And 2 more authors.
Nature Reviews Genetics | Year: 2014

A comprehensive understanding of RNA structure will provide fundamental insights into the cellular function of both coding and non-coding RNAs. Although many RNA structures have been analysed by traditional biophysical and biochemical methods, the low-throughput nature of these approaches has prevented investigation of the vast majority of cellular transcripts. Triggered by advances in sequencing technology, genome-wide approaches for probing the transcriptome are beginning to reveal how RNA structure affects each step of protein expression and RNA stability. In this Review, we discuss the emerging relationships between RNA structure and the regulation of gene expression. © 2014 Macmillan Publishers Limited. All rights reserved.


The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.


The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.


The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.


Patent
Guardant Health | Date: 2015-09-22

Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.


The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.


The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

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