Sequencing analysis of tumor dna sequence analysis dna. Medical search. Frequent questions

When bulk tumor tissues are profiled for somatic copy number alterations (sCNA) and point mutations, it may be difficult to estimate their cellular fractions when a mutation falls within a sCNA. (biomedcentral.com)
We present the Clonal Heterogeneity Analysis Tool, which estimates cellular fractions for both sCNAs and mutations, and uses their distributions to inform macroscopic clonal architecture. (biomedcentral.com)
Cancer cells acquire genetic heterogeneity to escape from immune surveillance during tumor evolution, but a systematic approach to distinguish driver from passenger mutations is lacking. (nature.com)
PJS is autosomal-dominant condition caused by mutations of STK11, characterized by gastrointestinal polyposis, mucocutaneous pigmentation, and predisposition to a range of epithelial cancers: including colorectal, gastric, pancreatic, breast, ovarian cancers and sex cord tumors with annular tubules). (cancerindex.org)
Genetic testing is "the analysis of chromosomes (DNA), proteins, and certain metabolites in order to detect heritable disease-related genotypes, mutations, phenotypes, or karyotypes for clinical purposes. (wikipedia.org)
Detection of each mutation depends on the test used, and panel gene sequencing using next-generation sequencing may result in a higher incidence of simultaneous mutations. (medscape.com)
The therascreen KRAS RGQ (Rotor-Gene Q) PCR (polymerase chain reaction) Kit tests for 7 mutations in codons 12 or 13 of the KRAS gene on formalin-fixed, paraffin-embedded tissue from the primary tumor or a metastasis. (medscape.com)
We developed a first-of-its-kind method, called UNCeqR, that detects somatic mutations by integrating patient-matched RNA-seq and DNA-WES. (usuhs.edu)
RNA provided greater mutation signal than DNA in expressed mutations. (usuhs.edu)
Both clear cell ovarian carcinomas (CCC) and ovarian endometrioid carcinomas (EC) may arise from endometriosis and frequently harbor mutations in the ARID1A tumor suppressor gene. (biomedcentral.com)
ARID1A mutations were identified by exome sequencing, and PIK3CA mutations were characterized by MALDI-TOF mass spectrometry. (biomedcentral.com)
For instance, NGS-based comprehensive analysis of certain cancers has already helped to uncover specific mutations that contribute to the malignant process, identify new therapeutic targets, and improve opportunities for choosing the best treatment for an individual patient. (biomedcentral.com)
Mutations in transcript isoforms of the neurofibromatosis 2 gene in multiple human tumour types. (nih.gov)
In a study of 450 CRC diagnosed under 50 years via the Ohio Colorectal Cancer Prevention Initiative, germline DNA analysis for mutations in 25 cancer susceptibility genes was done in addition to assessing microsatellite instability and/or immunohistochemistry for MMR deficiency. (cdc.gov)

This gene, which encodes a member of the serine/threonine kinase family, regulates cell polarity and functions as a tumor suppressor. (cancerindex.org)

However, in vitro screens are limited to a lack of tumor microenvironment, and the gRNA library coverage or selection often limits the pathological relevance of targets unraveled by in vivo screens. (nature.com)
It is therefore imperative to uncover novel immune evasion mechanisms in the dynamic tumor-immune microenvironment by untangling the genetic heterogeneity of cancer cells. (nature.com)

DNA hypermethylation and loss of expression of the P16 tumor suppressor gene in cadmium transformed BALB/C-3T3 cells. (cdc.gov)
DNA sequencing and sequence similarity analysis identified one of the aberrantlyl methylated DNA fragments as the p16 tumor suppressor gene. (cdc.gov)
Further studies have shown that the expression of p16 tumor suppressor gene was significantly lower in the transformed cells compared wiht the non-transformed cells. (cdc.gov)

In addition to analyzing whole chromosomes (cytogenetics), genetic testing has expanded to include the fields of molecular genetics and genomics which can identify changes at the level of individual genes, parts of genes, or even single nucleotide "letters" of DNA sequence. (wikipedia.org)
NEW YORK - Irvine, California-based Genomic Testing Cooperative (GTC) said on Tuesday it is collaborating with C2i Genomics to develop liquid biopsy tests for solid tumor staging and monitoring. (genomeweb.com)
Genome-wide mutational analysis of breast and lung cancer cohorts (n = 871) revealed remarkable tumor genomics properties. (usuhs.edu)

Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. (mit.edu)
RNA sequencing (RNA-seq) covers the expressed exome with depth proportional to expression. (usuhs.edu)
In a whole-genome sequencing in 17 Esophageal Squamous Cell Carcinoma cases and whole-exome sequencing in 71 cases, Song (2014), reported ASH1L alterations. (cancerindex.org)
A suite of custom software tools have been developed to rapidly integrate, explore, discover and validate molecular profiling data from the NGS modalities of Whole Exome Sequencing (WES) and RNA-seq with each other, as well as with historical microarray and salient clinical datasets. (biomedcentral.com)

Intra-tumor heterogeneity reflects cancer genome evolution and provides key information for diagnosis and treatment. (biomedcentral.com)
Further, heterogeneity in cancer could manifest on other levels: not just among different patients, but also among tumors of different grades or organ sites in the same patient, as well as among different cells within a tumor [ 10 ],[ 11 ]. (biomedcentral.com)
However, these studies are not designed to adequately investigate intra-tumor heterogeneity. (biomedcentral.com)
Ultimately, cancer genome evolution takes place at the single-cell level, and it is the cellular complexity and its dynamics that give rise to both intra- and inter-tumor heterogeneity. (biomedcentral.com)
Under such constraints, many groups have surveyed intra-tumor heterogeneity by comparing multiple specimens from the same patient by longitudinal sampling or spatial sampling (mainly for solid tumors). (biomedcentral.com)

METHODS: Sequence data of tumour specimens and clinicopathological information of 913 patients with advanced gastric cancer who were enrolled between April 2015 and March 2017 were obtained from the GI-SCREEN database. (bvsalud.org)
Only 3 benign breast tumour tissues (12.5%) and none of the healthy breast tissue specimens were HPV-DNA-positive. (who.int)

The study, led by scientists at the Broad Institute and Dana-Farber Cancer Institute, involved whole genome sequencing of normal and tumor DNA from 38 multiple myeloma patients to assess tumor-specific changes across the entire 3-billion-letter human genome, yielding new and unexpected insights into the events that lead to this form of cancer. (tgen.org)
But first, TGen provided an initial analysis of 250 multiple myeloma tumor samples. (tgen.org)

It is also approved for any solid tumor that has tested positive for MSI-H or MMR deficiency in patients who have had prior treatment and have no satisfactory alternative treatment options. (medscape.com)

Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. (biomedcentral.com)
However, the challenge of obtaining sufficient quantity and quality of DNA from formalin-fixed paraffin-embedded (FFPE) tissue has severely limited adoption of this approach. (biomedcentral.com)
PCR amplification and DNA sequence analysis or allele-specific PCR for BRAF V600E mutation status are performed on formalin-fixed, paraffin-embedded tissue from the primary tumor or a metastasis. (medscape.com)

These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. (mit.edu)

Knockdown of BAF250a by siRNA in three CCC cell lines wild type for ARID1A showed no increase in either pAKT-Thr 308 or pAKT-S 473 suggesting that pAKT in tumor tissues is indirectly regulated by BAF250a expression. (biomedcentral.com)
A further 20 blocks from The ISH results were given percentage vanced stages with a likely prevalence samples from normal breast tissues scores based on positive signals and of more aggressive tumour forms were labelled as a control group (i.e. number of cells that gave these signals. (who.int)

AKT phosphorylation is associated with ARID1A /BAF250a deficient tumors, however in ovarian cancers the mechanism remains to be elucidated. (biomedcentral.com)

These data confirm the presence of tumor-specific TCR within the cancer tissue and suggest the existence of shared epitopes among different patients that might be used as targets for tumor immunotherapy. (oncotarget.com)
He is working on a "battle map" that describes complex concepts such as immunotherapy, molecular signaling pathways and the tumor microenvironments, "and then how the measurements of a patient lay over that map and where and how it makes the most sense to intervene," he said. (tgen.org)
The test can identify CRC patients with MSI-high tumors who may respond well to PD1 blockade immunotherapy , recently approved by the Food and Drug Administration. (cdc.gov)

As part of the multicenter, population-based Ohio Colorectal Cancer Prevention Initiative, tumor DNA was sequenced for 419 consecutive CRC cases undergoing standard universal tumor screening and germline genetic testing, and 46 patients with CRC known to have LS due to a germline mutation in a mismatch repair gene. (cdc.gov)

Collectively, our results suggest that RUNX3-mediated CCL5 repression is critical for modulating anti-tumor immunity. (nature.com)

The REPLI-g Screening kit is intended for rapid screening using a range of genotyping, PCR, sequencing or microarray assays. (qiagen.com)
Microarray transcriptome analyses have resulted in important advances in both the scientific and clinical domains of biomedicine. (biomedcentral.com)

Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. (wikipedia.org)
Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, or through biochemical analysis to measure specific protein output. (wikipedia.org)
Genetic testing can also be used to determine biological relatives, such as a child's biological parentage (genetic mother and father) through DNA paternity testing, or be used to broadly predict an individual's ancestry. (wikipedia.org)
In the 1970s, a method to stain specific regions of chromosomes, called chromosome banding, was developed that allowed more detailed analysis of chromosome structure and diagnosis of genetic disorders that involved large structural rearrangements. (wikipedia.org)
Pangenome graphs in infectious disease: A comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads. (otago.ac.nz)
Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer. (cancerindex.org)
Obtaining uniform DNA yields from varying template concentrations is always important, but particularly essential for high-throughput applications, which require subsequent genetic analyses to be possible without additional measurement or adjustment of DNA concentration. (qiagen.com)
It reveals the genetic information carried by a particular DNA segment. (mdpi.com)

CNAs reflect the underlying biology of a tumor [ 2 ] and, given suitable detection methods, could be used in research and potentially in clinical settings to predict patients' response to treatment and prognosis. (biomedcentral.com)
Although the high success rate of CNA by MIP assays in FFPE-derived DNA makes it arguably the best currently used method, its application remains limited since in many research and clinical settings, obtaining 100 ng of input DNA is often unachievable, particularly for small biopsy samples and pre-cancerous lesions. (biomedcentral.com)
In addition, an independent cohort of 55 clinical samples was analyzed by quantitative real-time PCR analysis. (cancerindex.org)
The results were validated both by gene expression analysis and immunohistochemistry study in an independent 55 clinical samples from Fudan University Shanghai Cancer Center. (cancerindex.org)
Furthermore, a recent clinical trial for a CCR5 inhibitor treatment to patients suffering from liver metastasis of colorectal cancer showed its effect on reducing tumor mass with better prognosis, suggesting CCL5-CCR5 axis might also provide a procancer activity 22 . (nature.com)
GTC will sequence samples and help with technical and clinical validation, while C2I will be responsible for artificial intelligence-based analysis of data, recruitment of samples, and various clinical trial activities. (genomeweb.com)
GTC will adapt and distribute New York-based C2i's tools, which uses AI-based pattern recognition of whole-genome sequencing of cell-free DNA, to its Co-op members after the partners complete technical and clinical validation. (genomeweb.com)
Various clinical and non-clinical research samples can be used with REPLI-g Mini and Midi Kits, including genomic DNA, fresh or dried blood, fresh or frozen tissue and cells. (qiagen.com)
Thus, for cancer scenarios where the standard-of-care options are poor (e.g., drug resistance, metastasis), drug assignments based on the mutational landscape of a patient's tumor can sometimes provide significant benefit, and are a very active research topic in clinical trials and translational medicine [ 4 ]. (biomedcentral.com)
In the meantime, new genomic research could be changing clinical and public health approaches to reducing the burden of colorectal cancer from LS and in general, by shifting the laboratory testing approach toward tumor next generation sequencing. (cdc.gov)

Next Generation Sequencing (NGS) methods are rapidly providing remarkable advances in our ability to study the molecular profiles of human cancers. (biomedcentral.com)

We investigated methods of reducing DNA input and improving performance, including WGA, pre-treatment with a DNA repair procedure, and a low-input WGS library preparation method. (biomedcentral.com)
Professor Black is a member of the Centre for Translational Cancer Research, and his research focuses on the development of methods for the analysis of genomic data, with a strong emphasis on cancer and other human diseases. (otago.ac.nz)

By contrast, increased CCL5 expression resulting from RUNX3 mutation is associated with more tumor metastasis in the lung. (nature.com)

These studies analyze hundreds of tumors per cancer type, relying on bulk tissue samples, usually for one sample per patient. (biomedcentral.com)
The TGen researchers work directly with Stanton to devise strategies to organize, present and analyze his personal tumor data in ways that could broaden the possibilities for his future treatment. (tgen.org)
Next-generation sequencing has the great potential and promise to allow us to comprehensively analyze the cancer genome at extremely high resolution and see all of the events that happen in cancer," said Getz. (tgen.org)

SAM (Significance Analysis of Microarrays) was performed to determine differential protein expression by histological subtype and ARID1A mutation status. (biomedcentral.com)

Here we investigate the impact of different immune pressure on tumor clonal dynamics and immune evasion mechanism, by combining massive parallel sequencing of immune edited tumors and CRISPR library screens in syngeneic mouse tumor model and co-culture system. (nature.com)

Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations. (biomedcentral.com)
One of the most reliable approaches available to date is molecular inversion probe (MIP) technology, which can obtain high-quality CNA and genotype data from FFPE samples with less than 100 ng of input DNA [ 4 ]. (biomedcentral.com)
In an attempt to evaluate the immune response of renal cell carcinoma (RCC) patients, tumor lesions and / or blood samples from 12 RCC patients underwent deep T cell receptor (TCR) sequencing. (oncotarget.com)
Comparison among the tumor samples revealed also "patient-shared" TCR patterns. (oncotarget.com)
PHOENIX, Ariz. - May 18, 2022 - For cancer patients nearing the end of standard of care treatment, data gleaned from their tumor genome and tissue samples can be an invaluable resource for seeking out future care. (tgen.org)
Whole tumor lysates were prepared from frozen banked tumor samples and profiled by RPPA using 116 antibodies. (biomedcentral.com)
The average DNA yield from the REPLI-g UltraFast Mini Kit is 7-10 µg per 20 µl reaction in 90 minutes with standard quality samples. (qiagen.com)
In 112 patients, plasma samples were evaluable for dynamic analysis (57 and 55 from the BEV and aEGFR groups, respectively). (bvsalud.org)

Genomic DNA isolated from BALB/c-3T3 cells morphologically transformed with Cd was restriction digested with Mse1 (methylation non-sensitive) alone or with MSe1 and BstU1 (methylation sensitive). (cdc.gov)
Limitations on the number and type of genomic analyses that can be performed due to insufficient quantities of genomic DNA can be overcome by global amplification of all DNA within a sample (whole genome amplification). (qiagen.com)
REPLI‑g Kits provide DNA polymerase, buffers and reagents for highly uniform whole genome amplification with minimal sequence bias and can be used with various starting materials, including genomic DNA, fresh or dried blood, buccal swabs, fresh or frozen tissue and cells. (qiagen.com)

The other approach is to screen CRISPR-Cas9-based guide RNA (gRNA) libraries that target either the whole genome using cancer cell and immune cell co-culture systems 9 , 10 , or focused gene sets using immunocompetent murine tumors 11 , 12 . (nature.com)

Most of the RCC patients presented "patient-specific" TCR sequences, and those clonotypes were present at higher frequency in tumor lesions suggesting a specific extravasation from the blood. (oncotarget.com)

Approximately 30-50% of colorectal tumors are known to have a mutated (abnormal) KRAS gene, indicating that up to 50% of patients with colorectal cancer (CRC) might respond to anti-epidermal growth factor receptor (EGFR) antibody therapy. (medscape.com)
Universal Screening for Lynch Syndrome: Can Tumor Sequencing Have a Larger Public Health Impact on Treatment and Prevention of Colorectal Cancer? (cdc.gov)

A method often used to overcome the challenge of a limiting amount of DNA is whole genome amplification (WGA) to increase the amount of starting template DNA [ 9 ]. (biomedcentral.com)
The REPLI-g Mini and Midi Kits offer a single tube workflow with higher yields of amplified DNA, while the REPLI-g UltraFast Kit enables highly uniform and accurate whole genome amplification in just 60-90 minutes. (qiagen.com)

This task is potentially further complicated when a multitude of molecular profiling modalities are available, with the goal of a more integrative and comprehensive analysis of the cancer biology. (biomedcentral.com)

Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. (mit.edu)

In a set of approximately 700 breast tumors, more than half appear to contain multiple recognizable aneuploid tumor clones, and many show subtype-specific differences in clonality for known cancer genes. (biomedcentral.com)
We have undertaken studies investigation aberrant DNA methylation resulting in changes in the expression of cancer-related genes as a possible epigenetic mechanism for Cd carcinogenesis. (cdc.gov)
The protocol, led by TGen's Nicholas Schork, Ph.D. , along with Laura Goetz, M.D., M.P.H. and Edward Kalpas, M.D., M.P.H. , is designed to help Stanton aggregate his personal cancer assay data and perform subsequent analyses that could lead to a treatment that will save his life. (tgen.org)
A team of researchers led by co-senior author Gad Getz, director of Cancer Genome Analysis at the Broad Institute, has developed computational tools to address this. (tgen.org)
Next generation sequencing (NGS) is a new frontier in cancer and biomedical research, and these approaches are rapidly becoming the preferred method for human disease-based analysis due to vastly improved genome coverage and resolution [ 1 ]. (biomedcentral.com)
By enhancing a DNA examination with transcriptome data, a multi-modality study of a particular patient's cancer is formed, yielding increased scientific/analytical rigor and potential insights. (biomedcentral.com)
L'étude menée en Iraq a utilisé la méthode d'hybridation in situ pour déterminer la fréquence du papillomavirus humain et pour son génotypage dans les échantillons de tissus prélevés auprès de 129 patientes ayant reçu un diagnostic de cancer du sein malin, de 24 patientes porteuses d'une tumeur du sein bénigne et de 20 femmes témoins en bonne santé. (who.int)

Insights into H 2 O 2 -induced signaling in Jurkat cells from analysis of gene expression. (otago.ac.nz)

MiRNAs are generated by stepwise cleavage via double-stranded ribonuclease III enzymes DROSHA and DICER1 and loaded onto Argonaute (AGO) proteins to pair with target sequences on mRNAs 20 . (nature.com)
A recent study compared the performance of tumor next-generation sequencing to the current multistep approach (using microsatellite instability (MSI) testing and/or immunohistochemistry (IHC) for MMR proteins). (cdc.gov)

Localization of the ornithine aminotransferase gene and related sequences on two human chromosomes. (nih.gov)
Mapping of ornithine aminotransferase gene sequences to mouse chromosomes 7, X, and 3. (nih.gov)

however, this yields low sensitivity in low purity tumors. (usuhs.edu)

In 31 CCC cases, pAKT was similarly significantly increased in tumors with BAF250a loss on IHC. (biomedcentral.com)

DNA diagnosis of neurofibromatosis 2. (nih.gov)
Nucleic acid sequencing expresses the evolutionary changes among organisms and revolutionizes disease diagnosis in animals. (mdpi.com)

Whole genome sequencing (WGS) at 30× coverage can also be used for CNA and LOH detection, but requires at least 100 ng of high quality input DNA and has challenges associated with cost, bioinformatics processing time, and storage of large datasets. (biomedcentral.com)

CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. (biomedcentral.com)
Sequencing tends to focus on a few molecular targets already known to respond to drugs, "but are there other things in that sequence data that could identify things to focus on now? (tgen.org)

Each method has both common and unique issues related to the required starting DNA amount, specificity, sensitivity, genome coverage, and accuracy as well as cost. (biomedcentral.com)

In June 2017, the FDA approved the PRAXIS Extended RAS Panel, next-generation sequencing (NGS) kit. (medscape.com)
The information in this article contains billing, coding or other guidelines that complement the Local Coverage Determination (LCD) for MolDX: Next Generation Sequencing for Solid Tumors L38045. (cms.gov)
Over the last six years, "next-generation" sequencing technologies - machines that can sequence DNA at a rapid pace and deliver massive amounts of data in a short period of time - have surged. (tgen.org)

However, 40-60% of patients with wild-type KRAS tumors do not respond to such therapy. (medscape.com)
[ 1 ] In these patients, data suggest that the mutated BRAF gene, which is present in 5-10% of tumors, can affect response to these agents. (medscape.com)
Indeed, a central core of 16 different TCRs were shared by 3 patients, whereas other 6 patients shared between 4 and 6 TCR sequences, with two sub-groups sharing 12 to 17 different clonotypes. (oncotarget.com)
But how do patients safely access these data and obtain analyses to guide future personalized care? (tgen.org)
A universal tumor sequencing test can identify LS patients as well as guide treatment of CRC patients who do not have LS. (cdc.gov)

The data were primarily interpreted by regarding each tumor as a single population of cells with uniform character. (biomedcentral.com)
Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data. (otago.ac.nz)
The protocol seeks to find ways to handle the immense amounts of raw data generated by analyses such as tumor DNA sequencing. (tgen.org)

We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. (biomedcentral.com)
We hypothesized that integrating DNA-WES and RNA-seq would enable superior mutation detection versus DNA-WES alone. (usuhs.edu)
Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES. (usuhs.edu)
In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors. (usuhs.edu)

Altered coding sequence of the merlin tumor suppressor in an extended pedigree. (nih.gov)

The resulting DNA was analyzed for differential methylation using a PCR-based technique - Methylation Sensitive Restriction Fingerprinting (MSRF). (cdc.gov)

Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. (mit.edu)

Anatomy7

Organisms13

Diseases26

Chemicals and Drugs59

Analytical, Diagnostic and Therapeutic Techniques and Equipment43

Phenomena and Processes112

Disciplines and Occupations4

Information Science8

Health Care5

Geographicals3

Mutations14

Functions as a tumor1

Microenvironment2

Suppressor gene3

Genomics3

Exome4

Heterogeneity5

Specimens2

Multiple myeloma2

Solid tumor1

Formalin-fixed3

Somatic mutation1

Tissues2

Ovarian cancers1

Immunotherapy3

Germline1

Immunity1

Microarray2

Genetic8

Clinical10

Cancers1

Methods2

Metastasis1

Analyze3

ARID1A1

Clonal1

Samples8

Genomic DNA3

Immune1

Lesions1

Colorectal Cancer2

Whole genome amplif2

Biology1

Mutation signatures1

Cancer7

Gene expression1

Proteins2

Chromosomes2

Yields1

Significantly1

Diagnosis2

Bioinformatics1

Molecular2

Sensitivity1

Next-generation3

Patients5

Data3

Detection4

Pedigree1

Methylation1

Alterations1