SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: Analysis of cancer metabolism with high-throughput technologies. Newsbot! Literature Watch 0 12-23-2011 03:00 AM
PubMed: Targeted deep resequencing of the human cancer genome using next-generation t Newsbot! Literature Watch 0 04-09-2011 01:16 AM
PubMed: Combining target enrichment with barcode multiplexing for high throughput SNP Newsbot! Literature Watch 0 11-19-2010 03:40 AM
PubMed: High-throughput SNP discovery through deep resequencing of a reduced represen Newsbot! Literature Watch 0 05-09-2010 08:00 PM
High-throughput genotyping by whole-genome resequencing lry198010 Literature Watch 1 06-15-2009 05:55 AM

Reply
 
Thread Tools
Old 09-22-2011, 12:30 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,439
Default PubMed: High-throughput resequencing of target-captured cDNAs in cancer cells.

Syndicated from PubMed RSS Feeds

High-throughput resequencing of target-captured cDNAs in cancer cells.

Cancer Sci. 2011 Sep 20;

Authors: Ueno T, Yama****a Y, Soda M, Fukumura K, Ando M, Yamato A, Kawazu M, Choi YL, Mano H

Abstract
The recent advent of whole exon (exome)-capture technology coupled with second-generation sequencers has made it possible to readily detect genomic alterations that affect encoded proteins in cancer cells. Such target resequencing of the cancer genome, however, fails to detect most clinically relevant gene fusions, given that such oncogenic fusion genes are often generated through intron-to-intron ligation. To develop a resequencing platform that simultaneously captures point mutations, insertions-deletions (indels), and gene fusions in the cancer genome, we chose cDNAs as the input for target-capture and extensive resequencing, and we now describe the versatility of such a cDNA-capture system. As a test case, we constructed a custom target-capture system for 913 cancer-related genes, and we purified cDNA fragments for the target gene set from five cell lines of chronic myeloid leukemia. Whereas our target gene set included ABL1, it did not include BCR; however, the sequence output faithfully detected reads spanning the fusion points of these two genes in all cell lines, confirming the ability of cDNA-capture to detect gene fusions. Furthermore, computational analysis of the sequence data set successfully identified nonsynonymous mutations and indels, including those of TP53. Our data may thus support the feasibility of a cDNA-capture system coupled with massively parallel sequencing as a simple platform for the detection of a variety of anomalies in protein-coding genes among hundreds of cancer specimens.


PMID: 21929543 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:55 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO