Sentences with phrase «in tumor genomes»

Genome - wide detection of SVs and copy number alterations, which are often pervasive (and clinically relevant) in tumor genomes

Unlike previous studies, which tracked lymphoma progression by monitoring the sequence of just one cancer - associated protein, CAPP - Seq can identify a much larger range of mutations in the tumor genome.

In tumor genome processing, we identify discrete coverage levels based on the distribution of the observed normalized coverage levels in the tumor genome.

Not exact matches

To determine how the cells switch from one type to another, they took three human uterine carcinosarcoma samples and sequenced the genomes of cells in two parts of each tumor: the carcinoma and sarcoma components.

«Cancer cells disguise themselves by switching off genes, new research reveals: A genome - wide map of the genes switched off in aggressive tumors reveals a «signature».»

In a study published in Neoplasia, researchers at the Washington University School of Medicine created a map showing which genes were switched on and off in different parts of the tumor, providing a «signature» of these switches throughout the genomIn a study published in Neoplasia, researchers at the Washington University School of Medicine created a map showing which genes were switched on and off in different parts of the tumor, providing a «signature» of these switches throughout the genomin Neoplasia, researchers at the Washington University School of Medicine created a map showing which genes were switched on and off in different parts of the tumor, providing a «signature» of these switches throughout the genomin different parts of the tumor, providing a «signature» of these switches throughout the genome.

«This model was trained on genetic data from human tumors in The Cancer Genome Atlas and was able to predict response to certain inhibitors that affect cancers with overactive Ras signaling in an encyclopedia of cancer cell lines,» Greene said.

«Machine learning finds tumor gene variants and sensitivity to drugs in The Cancer Genome Atlas.»

«Just as normal cells with the same genome differentiate into many different cell types, a single tumor characterized by specific genetic mutations can contain many different types of cells — stem - like and more differentiated cells — with the difference being rooted in their epigenetic information.

With a grant from the Morris Animal Foundation, Antczak, his collaborators Samantha Brooks and Ann Staiger from the University of Florida, and the rest of the team applied a genomewide association study to compare the genetic makeup of horses with and without sarcoid tumors at more than 50,000 sites in the equine genome.

The genome - wide epigenetic changes clustered in certain chromatin domains and controlled «gene expression changes that specify different malignant traits, including the ability to form tumors,» McDonald said.

«Studies like the current one involving rhabdomyosarcoma are giving us a close - up look at the way cancer evolves in response to treatment,» said study co-author Richard K. Wilson, Ph.D., director of The Genome Institute at Washington University School of Medicine in St. Louis, where scientists have extensive expertise analyzing tumor recurrence using whole - genome sequeGenome Institute at Washington University School of Medicine in St. Louis, where scientists have extensive expertise analyzing tumor recurrence using whole - genome sequegenome sequencing.

«Based on mutations we found in the genome, there is evidence of high levels of oxidative stress in the tumors,» Dyer said.

Most of the mutations that drive recurrent tumors when they pop up elsewhere in the body were present in the original tumor, geneticist Elaine Mardis reported May 9 at the Biology of Genomes meeting.

This stress, which is notably induced in pre-cancerous lesions, is characterised by an increased DNA replication rate, which provokes DNA damage and genome instability, major drivers of tumor formation.

«One of the major and immediate downstream effects of myc activation is a dramatic increase in the capacity of affected cells to make protein,» Ruggero said «This, in turn, leads to increased cell survival and proliferation, and to unstable genomes that foster additional mutations that turn these abnormal cells into tumor cells.»

The 15 AACR scientists, who were already in Washington, D.C., to meet with the U.S. Food and Drug Administration on genetic testing for cancer patients, tossed around ideas including expanding NCI's tumor genome - sequencing efforts and getting the government to cover the costs of genomic tumor profiling.

The team integrated three, complementary gene sequencing approaches to look for mutations in tumor cells from SS patients: whole - genome sequencing in six subjects, sequencing of all protein - coding regions (exomes) in 66 subjects, and comparing variation in the number of copies of all genes across the genome in 80 subjects.

His laboratory develops and deploys new biochemical and computational methods in functional genomics, to elucidate the genetic basis of human disease and human physiology, and to create and deploy novel techniques in next - generation sequencing and algorithms for tumor evolution, genome evolution, DNA and RNA modifications, and genome / epigenome engineering.

Rather, tumors arise from the complex interplay between any number of mutually exclusive abnormal changes in the genome, the combinations of which can be unique to each individual patient.

New research led by Li Ding, Ph.D., of Washington University School of Medicine in St. Louis, shows that current approaches to genome analysis systematically miss detecting a certain type of complex mutation in cancer patients» tumors.

«This development has the potential to enable earlier detection of solid tumors through a simple blood draw by substantially improving our ability to detect very low quantities of circulating DNA derived from tumor cells,» says corresponding author Hunter Underhill, M.D., Ph.D., who initiated the research while in the lab of senior author Jay Shendure, M.D., Ph.D., a professor in genome sciences at the University of Washington.

But tumors from patients with distant metastases to the lung and liver showed massive epigenetic changes that mapped to large, blocklike segments of the genome, both in the distant metastases themselves and in the section, or «subclone,» of the primary tumors they came from.

«The idea of not catching a targetable mutation in a patient's tumor is devastating,» said senior author Li Ding, PhD, associate professor of medicine and assistant director of the McDonnell Genome Institute at Washington University.

Just as no two people possess the same genetic makeup, a recent study has shown that no two single tumor cells in breast cancer patients have an identical genome.

The tumors» genomes were then analyzed for genetic mutations, or alterations in their DNA, by her team and that of Bert Vogelstein, M.D., professor of oncology at the Johns Hopkins University School of Medicine and the co-director of the Ludwig Center at the Johns Hopkins Kimmel Cancer Center.

Hoping to cash in on personalized cancer therapy, a new company called Foundation Medicine — founded in part by genome guru Eric Lander of the Broad Institute — plans to develop tests for genetic glitches in tumors that make them vulnerable to specific drugs, reports the United Kingdom's Times Online.

By performing a genome - wide screen in breast cancer cells, Dr. Oesterreich and her colleagues identified a gene called HOXC10 as one that the cancer seems to modify to allow continued tumor growth in patients whose cancer becomes resistant to traditional therapies.

During the last three years the Spanish Consortium for the Study of the Genome of the Chronic Lymphatic Leukemia, where the researchers of the present study already collaborate, has sequenced the genome of hundreds of patients with the more common leukemia in our society, identifying new mechanisms of tumor progression and new therapeutic taGenome of the Chronic Lymphatic Leukemia, where the researchers of the present study already collaborate, has sequenced the genome of hundreds of patients with the more common leukemia in our society, identifying new mechanisms of tumor progression and new therapeutic tagenome of hundreds of patients with the more common leukemia in our society, identifying new mechanisms of tumor progression and new therapeutic targets.

Until now, scientists have failed to establish a link between the properties of pancreatic cancer, such as its aggressiveness, and changes, i.e. mutations, in the tumor's genome.

This phenomenon could result in breakage in the human genome, and when a breakage impacts important genes, such as tumor suppressors, it could lead to cancer development.

«It was hard to find a single microRNA in the human genome that wasn't differentially turned on or off across different tumor types in different tissues,» Golub says.

The new study, a comprehensive analysis of the genomes of 178 primary cervical cancers, found that over 70 percent of the tumors had genomic alterations in either one or both of two important cell signaling pathways.

The National Institutes of Health today announced in Nature that it has reached an understanding with the family of the late Henrietta Lacks to allow biomedical researchers controlled access to the whole genome data of cells derived from her tumor, commonly known as HeLa cells.

The researchers were able to replicate this finding by comparing the healthy thyroid tissues in GTEx to 500 samples taken from thyroid tumors, compiled by The Cancer Genome Atlas, and giving support to the extensive impact of FOXE1 on cellular state.

In particular, he wanted to study the genomes of marbled crayfish to uncover basic mechanisms underlying epigenetics, the binding of molecules to DNA that can drive tumor growth and help cancer spread.

They used the gene - editing CRISPR / Cas9 technique to sift the genomes of melanoma cells for changes that made tumors resistant to being killed by immune T cells, which are the main actors in the immune system response against infections and cancer cells.

As the cost of DNA sequencing continues to plummet, the lab will move ever closer to a once - elusive goal: economically processing every patient's complete genome in both tumors and healthy cells.

This approach allows us to detect, with high confidence, changes in circulating tumor DNA across a large part of the genome without information from tumor tissue,» said Dr. Razavi.

Sequencing RNA, not just DNA, could help doctors predict how prostate cancer tumors will respond to treatment, according to research published in the open access journal Genome Biology.

Scientists have discovered a new «mastermind fusion gene» may be associated with a rare cancer - causing tumor — pheochromocytomas («pheo») and paragangliomas, according to a study published Feb. 13 in Cancer Cell, by researchers at the Uniformed Services University (USU) and the National Cancer Institutes» The Cancer Genome Atlas.

The Yale - led study performed whole exome sequencing ¬ — a technique for sequencing all the expressed genes in a genome ¬ — on TNBC tumors to identify mutations in specific genes or pathways that may indicate response or resistance to the standard of care, which is anthracycline / taxane (ACT) chemotherapy.

Next year, NCI will wind up The Cancer Genome Atlas (TCGA), a huge project piloted in 2006 that is systematically searching tumors for genetic changes involved in cancer.

Possible successor to The Cancer Genome Atlas would scale up the search for rare mutations in tumors

His group uses genome - wide and gene - specific DNA methylation analysis to identify aberrantly silenced tumor suppressor genes in B cell leukemias and lymphomas.

Sequencing the whole genome of a prostate tumor, says co-author Levi Garraway, a physician and biologist at Harvard Medical School in Boston, allowed the researchers to see «biology that would have been invisible with any other method.»

In these experiments, Berger and colleagues show that somatic PREX2 mutations identified through whole - genome sequencing of human melanoma can contribute to enhanced lethality of tumor xenografts in nude mice (Figure 3B, S6B, and S6C; Berger et al., 2012In these experiments, Berger and colleagues show that somatic PREX2 mutations identified through whole - genome sequencing of human melanoma can contribute to enhanced lethality of tumor xenografts in nude mice (Figure 3B, S6B, and S6C; Berger et al., 2012in nude mice (Figure 3B, S6B, and S6C; Berger et al., 2012).

This analysis discovered an average of 97 structural rearrangements of the genome per tumor, and some 9,653 mutations of various types in 5,712 genes.

In addition, the study, led by investigators in The Cancer Genome Atlas (TCGA) Research Network, revealed four novel tumor subtypes, while also identifying genomic similarities between endometrial and other cancer types, including breast, ovarian, and colorectal cancerIn addition, the study, led by investigators in The Cancer Genome Atlas (TCGA) Research Network, revealed four novel tumor subtypes, while also identifying genomic similarities between endometrial and other cancer types, including breast, ovarian, and colorectal cancerin The Cancer Genome Atlas (TCGA) Research Network, revealed four novel tumor subtypes, while also identifying genomic similarities between endometrial and other cancer types, including breast, ovarian, and colorectal cancers.

We developed SomaticSniper to detect somatic mutations in whole - genome sequencing data while allowing for tumor contamination of normal cells that occurs in some types of leukemia.