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A new method to accurately identify single nucleotide variants using small FFPE breast samples [article]

Angelo Fortunato, Diego Mallo Adan, Shawn M Rupp, Lorraine King, Timothy Hardman, Joseph Lo, Allison Hall, Jeffrey R Marks, E Shelley Hwang, Carlo C Maley
2020 bioRxiv   pre-print
It provides a significant improvement in detecting somatic single nucleotide variants in FFPE samples that can be used to accurately profile the genomes of neoplasms.  ...  We developed a new bioinformatic algorithm to robustly identify somatic mutations using small amounts of DNA extracted from archival FFPE samples of breast ductal carcinoma in situ, a preinvasive form  ...  Acknowledgments This work was supported primarily by a CDMRP Breast Cancer Research Program  ... 
doi:10.1101/2020.10.22.350983 fatcat:zbr3d6st6bcq3lgorqohqb2aia

A new method to accurately identify single nucleotide variants using small FFPE breast samples

Angelo Fortunato, Diego Mallo, Shawn M Rupp, Lorraine M King, Timothy Hardman, Joseph Y Lo, Allison Hall, Jeffrey R Marks, E Shelley Hwang, Carlo C Maley
2021 Briefings in Bioinformatics  
We developed and validated a new bioinformatic pipeline to use existing variant-calling strategies to robustly identify somatic single nucleotide variants (SNVs) from whole exome sequencing using small  ...  Our method provides a significant improvement in detecting SNVs in FFPE samples over previous approaches.  ...  . • We developed and validated a new bioinformatic algorithm to robustly identify somatic single nucleotide variants using small amounts of DNA extracted from archival FFPE samples of breast cancers. •  ... 
doi:10.1093/bib/bbab221 pmid:34117742 pmcid:PMC8574974 fatcat:q5gjb22l7fexbhqqdsk6uoghzu

Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples

Márton Zsolt Enyedi, Gábor Jaksa, Lajos Pintér, Farkas Sükösd, Zoltán Gyuris, Adrienn Hajdu, Erika Határvölgyi, Katalin Priskin, Lajos Haracska
2016 OncoTarget  
Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples.  ...  (FFPE) tumor samples.  ...  ACKNOWLEDGMENTS We are grateful to Imre Boros and László Bodai at the University of Szeged, Dept.  ... 
doi:10.18632/oncotarget.11259 pmid:27533253 pmcid:PMC5308695 fatcat:anjetn5z5vdrzbutdeoa27k7nq

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens

Shawn E. Yost, Erin N. Smith, Richard B. Schwab, Lei Bao, HyunChul Jung, Xiaoyun Wang, Emile Voest, John P. Pierce, Karen Messer, Barbara A. Parker, Olivier Harismendy, Kelly A. Frazer
2012 Nucleic Acids Research  
By applying innovative quality filters incorporating global nucleotide mismatch rates and local mismatch rates, we present a method to identify high-confidence somatic mutations even in the presence of  ...  The tumor samples show differing amounts of FFPE damaged DNA sequencing reads revealed as relatively high alignment mismatch rates enriched for C · G > T · A substitutions compared to germline samples.  ...  ACKNOWLEDGEMENTS We would like to thank Kersi Pestonjamasp, Ph.D., Manager of the UCSD Cancer Center Microscopy Core, who helped isolate cell nuclei from stained FFPE slides for cell counting.  ... 
doi:10.1093/nar/gks299 pmid:22492626 pmcid:PMC3413110 fatcat:boflcbwuafhephq64vwyij7z3y

New challenges for BRCA testing: a view from the diagnostic laboratory

Andrew J Wallace
2016 European Journal of Human Genetics  
An efficient, costeffective accurate mutation detection strategy and a standardised, systematic approach to the reporting of BRCA test results is imperative for diagnostic laboratories.  ...  However, migration to NGS introduces complexities arising from choice of components of the BRCA testing workflow, such as NGS platform, enrichment method and bioinformatics analysis process.  ...  A small number of variants were identified as potential artefacts common to FFPE-extracted DNA; however, the majority of these were in the poor-quality low-input DNA samples with lower coverage depth and  ... 
doi:10.1038/ejhg.2016.94 pmid:27514839 pmcid:PMC5141576 fatcat:67fwrs4a5jecdngaauoidohdea

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue

Alejandro Quiroz-Zárate, Benjamin J. Harshfield, Rong Hu, Nick Knoblauch, Andrew H. Beck, Susan E. Hankinson, Vincent Carey, Rulla M. Tamimi, David J. Hunter, John Quackenbush, Aditi Hazra, Kwong-Kwok Wong
2017 PLoS ONE  
We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic  ...  Using a new a procedure for testing hypotheses relating SNP content to expression patterns in gene sets, defined as molecular function pathways, we find that loci on 6q14 and 6q25 affect various gene sets  ...  Statistical analysis To identify regulatory variants, we investigated the association of 71 breast cancer risk alleles (each entered as a single continuous dosage variable as counts of the minor allele  ... 
doi:10.1371/journal.pone.0170181 pmid:28152060 pmcid:PMC5289428 fatcat:ev6egood4rdevhyaakpnxjg4ya

Validation of a NGS panel, with automated analysis, designed for detection of medically actionable tumor biomarkers for Latin America [article]

Mauricio Salvo, Evelin Feliu, Jessica Toro, Ivan Gallegos, Ignacio Maureira, Nicolas Miranda, Olga Barajas, Eva Bustamante, Monica Ahumada, Alicia Colombo, Ricardo Armisen, Camilo Villaman (+13 others)
2021 medRxiv   pre-print
The workflow was validated in 265 clinical samples, including breast, colorectal, gastric, ovarian, and gallbladder tumors and blood, leading to identifying 131 actionable variants.  ...  Our panel detects small insertions and deletions and single nucleotide variants (SNVs) with 100% sensitivity and specificity down to allelic frequencies of 0.05, and with 100% between-run and within-run  ...  We validated this workflow locally using breast, colorectal, gastric, ovarian, pancreatic, and gallbladder tumor tissue samples and report the ability to detect single nucleotide variants (SNVs) and small  ... 
doi:10.1101/2021.03.19.21253988 fatcat:ighefhulnfeu5cp3fbacbojpju

A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer

Pushpinder Kaur, Daniel Campo, Tania B. Porras, Alexander Ring, Janice Lu, Yvonne Chairez, Yunyun Su, Irene Kang, Julie E. Lang
2020 International Journal of Molecular Sciences  
In clinical samples, a significant fraction of somatic variants had low VAFs in CTCs compared to metastases.  ...  Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing  ...  Acknowledgments: We would like to thank all patients that participated in this study. We thank ANGLE plc for generously providing separation and cleaning cassettes for use in this project.  ... 
doi:10.3390/ijms21144826 pmid:32650480 fatcat:kaj25tsxnjej5dhbix4pzz4efq

Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing

Stephen Q Wong, Jason Li, Angela Y-C Tan, Ravikiran Vedururu, Jia-Min B Pang, Hongdo Do, Jason Ellul, Ken Doig, Anthony Bell, Grant A McArthur, Stephen B Fox, David M Thomas (+3 others)
2014 BMC Medical Genomics  
Methods: The Cancer 2015 study is a population-based cancer cohort used to assess the feasibility of mutational screening using MPS in cancer patients from Victoria, Australia.  ...  Results: Consistent with the signature of DNA damage due to formalin fixation, many formalin-fixed samples displayed disproportionate levels of C>T/G>A changes in the 1-10% allele frequency range.  ...  NRAS mutation testing To confirm the NRAS negative result in sample Ca97, a second MPS method using deep sequencing was also used to assess exon 3 of the NRAS gene.  ... 
doi:10.1186/1755-8794-7-23 pmid:24885028 pmcid:PMC4032349 fatcat:andff3csnfhdtfyk452bd5vqlm

Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples

Chunxiao Fu, Michal Marczyk, Michael Samuels, Alexander J. Trevarton, Jiaxin Qu, Rosanna Lau, Lili Du, Todd Pappas, Bruno V. Sinn, Rebekah E. Gould, Lajos Pusztai, Christos Hatzis (+1 others)
2021 BMC Cancer  
SET4 assay to the original (OLD) SET4 assay and to whole transcriptome RNAseq using RNA from matched fresh frozen (FF) and FFPE samples from 12 primary breast cancers.  ...  Results The modified (NEW) SET4 assay measured single transcripts (p< 0.001) and SETER/PR (p=0.002) more reproducibly in technical replicates from FFPE samples.  ...  Acknowledgments The RainDance Source instrument was provided to the research laboratory of WFS as a gift from the Toomim Family Fund. this study: WFS owns shares of IONIS Pharmaceuticals.  ... 
doi:10.1186/s12885-021-07814-8 pmid:33541297 fatcat:e23zfij23rf7zmppraesf5qavq

Currently Applied Molecular Assays for Identifying ESR1 Mutations in Patients with Advanced Breast Cancer

Nuri Lee, Min-Jeong Park, Wonkeun Song, Kibum Jeon, Seri Jeong
2020 International Journal of Molecular Sciences  
Regarding the sample type, tissue (50.0%) was more frequently used than plasma (27.3%). However, plasma (46.2%) became the most used method in 2016–2019, in contrast to 2012–2015 (22.2%).  ...  However, ER positivity is reduced and ESR1 mutations play an important role in resistance to endocrine therapy, leading to advanced breast cancer.  ...  [82] used both multiplex and single ddPCR assays to identify the seven most common ESR1 mutations from the SoFEA and PALOMA-3 samples.  ... 
doi:10.3390/ijms21228807 pmid:33233830 fatcat:oqbe7iugsza4fkcakldv5vjobu

Concordance of metabolic enzyme genotypes assayed from paraffin-embedded, formalin-fixed breast tumors and normal lymphatic tissue

Thomas Ahern
2010 Clinical Epidemiology  
Methods: We assayed paired DNA samples extracted from archived tumor and normal lymph node tissues from 106 breast cancer patients.  ...  We used TaqMan assays to determine the genotypes of three enzyme variants hypothesized to modify tamoxifen effectiveness, ie, CYP2D6*4, UGT2B15*2, and UGT1A8*2.  ...  Mr Ahern's effort on this study was supported by a CDMRP predoctoral training award (BC073012).  ... 
doi:10.2147/clep.s13811 pmid:21152250 pmcid:PMC2998813 fatcat:operpjng55hphleqyjvv6kd3s4

Next-generation sequencing in the clinic: Promises and challenges

Jiekun Xuan, Ying Yu, Tao Qing, Lei Guo, Leming Shi
2013 Cancer Letters  
A recent crop of discoveries have highlighted the medical impact of NGS technologies on Mendelian and complex diseases, particularly cancer.  ...  Over the past years, rapid technological advances led by academic institutions and companies have continued to broaden NGS applications from research to the clinic.  ...  Undoubtedly, the use of FFPE material could provide a rich sample source for molecular studies of cancer.  ... 
doi:10.1016/j.canlet.2012.11.025 pmid:23174106 pmcid:PMC5739311 fatcat:2dih6lqq75ampn6vq26jjxw6fi

Pan-genomic/Pan-proteomic Approaches to Diseases

2013 Laboratory Investigation  
We next performed a modeling experiment of ulcerative colitis using image analysis to predict cellular ratio changes (Fig. 1B) .  ...  MicroRNAs as Diagnostic Markers Background: Since the discovery of small non-coding RNAs, the analysis of microRNA (miRNA) expression patterns in human cancer have provided new insights into cancer biology  ...  FFPE tissue cores yielded a median of 2.7 µg DNA (interquartile range, 1.19-5.55 µg). Sequencing identified a mean of 4.6 non-synonymous variants per case (single-nucleotide variants and indels).  ... 
doi:10.1038/labinvest.2013.32 fatcat:rfx7n7yfync3rbiqdd4mb5dvze

Detection of Circulating Tumor DNA with a Single-Molecule Sequencing Analysis Validated for Targeted and Immunotherapy Selection

Alexander Atkins, Pratyush Gupta, Bing Melody Zhang, Wen-Sy Tsai, Julian Lucas, Manana Javey, Anagh Vora, Rui Mei
2019 Molecular Diagnosis & Therapy  
We have developed the single-molecule sequencing (SMSEQ) platform to address these challenges.  ...  Comprehensive genetic cancer profiling using circulating tumor DNA has enabled the detection of National Comprehensive Cancer Network (NCCN) guideline-recommended somatic alterations from a single, non-invasive  ...  Fig. 1 1 Single-nucleotide variants detection performance using singlemolecule sequencing (SMSEQ).  ... 
doi:10.1007/s40291-019-00406-0 pmid:31209714 pmcid:PMC6675782 fatcat:o5d3dvwchvgjlmcbs7fymr6l3u
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