keyword
MENU ▼
Read by QxMD icon Read
search

exome hierarchical clustering

keyword
https://www.readbyqxmd.com/read/27363029/genomic-similarity-between-gastroesophageal-junction-and-esophageal-barrett-s-adenocarcinomas
#1
Daysha Ferrer-Torres, Derek J Nancarrow, Rork Kuick, Dafydd G Thomas, Ernest Nadal, Jules Lin, Andrew C Chang, Rishindra M Reddy, Mark B Orringer, Jeremy M G Taylor, Thomas D Wang, David G Beer
The current high mortality rate of esophageal adenocarcinoma (EAC) reflects frequent presentation at an advanced stage. Recent efforts utilizing fluorescent peptides have identified overexpressed cell surface targets for endoscopic detection of early stage Barrett's-derived EAC. Unfortunately, 30% of EAC patients present with gastroesophageal junction adenocarcinomas (GEJAC) and lack premalignant Barrett's metaplasia, limiting this early detection strategy. We compared mRNA profiles from 52 EACs (tubular EAC; tEAC) collected above the gastroesophageal junction with 70 GEJACs, 8 normal esophageal and 5 normal gastric mucosa samples...
June 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27095580/thin-and-thick-primary-cutaneous-melanomas-reveal-distinct-patterns-of-somatic-copy-number-alterations
#2
Valentina Montagnani, Matteo Benelli, Alessandro Apollo, Chiara Pescucci, Danilo Licastro, Carmelo Urso, Gianni Gerlini, Lorenzo Borgognoni, Lucio Luzzatto, Barbara Stecca
Cutaneous melanoma is one of the most aggressive type of skin tumor. Early stage melanoma can be often cured by surgery; therefore current management guidelines dictate a different approach for thin (<1mm) versus thick (>4mm) melanomas. We have carried out whole-exome sequencing in 5 thin and 5 thick fresh-frozen primary cutaneous melanomas. Unsupervised hierarchical clustering analysis of somatic copy number alterations (SCNAs) identified two groups corresponding to thin and thick melanomas. The most striking difference between them was the much greater abundance of SCNAs in thick melanomas, whereas mutation frequency did not significantly change between the two groups...
May 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27060170/whole-exome-sequencing-to-identify-genetic-risk-variants-underlying-inhibitor-development-in-severe-hemophilia-a-patients
#3
Marcin M Gorski, Kevin Blighe, Luca A Lotta, Emanuela Pappalardo, Isabella Garagiola, Ilaria Mancini, Maria Elisa Mancuso, Maria Rosaria Fasulo, Elena Santagostino, Flora Peyvandi
The development of neutralizing antibodies (inhibitors) against coagulation factor VIII (FVIII) is the most problematic and costly complication of FVIII replacement therapy that affects up to 30% of previously untreated patients with severe hemophilia A. The development of inhibitors is a multifactorial complication involving environmental and genetic factors. Among the latter, F8 gene mutations, ethnicity, family history of inhibitors, and polymorphisms affecting genes involved in the immune response have been previously investigated...
June 9, 2016: Blood
https://www.readbyqxmd.com/read/26433572/balanced-translocations-disrupting-smarcb1-are-hallmark-recurrent-genetic-alterations-in-renal-medullary-carcinomas
#4
Julien Calderaro, Julien Masliah-Planchon, Wilfrid Richer, Laetitia Maillot, Pascale Maille, Ludovic Mansuy, Claire Bastien, Alexandre de la Taille, Hélène Boussion, Cécile Charpy, Anne Jourdain, Claire Bléchet, Gaelle Pierron, David Gentien, Laurence Choudat, Christophe Tournigand, Olivier Delattre, Yves Allory, Franck Bourdeaut
BACKGROUND: Renal medullary carcinoma (RMC) is a rare and highly aggressive neoplasm that most often occurs in the setting of sickle cell trait or sickle cell disease (SCD). Most patients present with metastatic disease resistant to conventional chemotherapy, and therefore there is an urgent need for molecular insight to propose new therapies. OBJECTIVE: To determine the molecular alterations and oncogenic pathways that drive RMC development. DESIGN, SETTING, AND PARTICIPANTS: A series of five frozen samples of patients with RMC was investigated by means of gene expression profiling, array comparative genomic hybridization, and RNA and whole exome sequencing (WES)...
June 2016: European Urology
https://www.readbyqxmd.com/read/25162009/improved-variant-calling-accuracy-by-merging-replicates-in-whole-exome-sequencing-studies
#5
Yanfeng Zhang, Bingshan Li, Chun Li, Qiuyin Cai, Wei Zheng, Jirong Long
In large scale population-based whole-exome sequencing (WES) studies, there are some samples occasionally sequenced two or more times due to a variety of reasons. To investigate how to efficiently utilize these duplicated sequencing data, we conducted comprehensive evaluation of variant calling strategies. 92 samples subjected to WES twice were selected from a large population study. These 92 duplicated samples were divided into two groups: group H consisting of the higher sequencing depth for each subject and group L consisting of the lower depth for each subject...
2014: BioMed Research International
https://www.readbyqxmd.com/read/24599305/comparative-genomic-analysis-of-primary-and-synchronous-metastatic-colorectal-cancers
#6
COMPARATIVE STUDY
Sun Young Lee, Farhan Haq, Deokhoon Kim, Cui Jun, Hui-Jong Jo, Sung-Min Ahn, Won-Suk Lee
Approximately 50% of patients with primary colorectal carcinoma develop liver metastases. Understanding the genetic differences between primary colon cancer and their metastases to the liver is essential for devising a better therapeutic approach for this disease. We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss...
2014: PloS One
1
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"