I'm working on cancer exome and transcriptome sequencing project. Sequencing data on tumor samples are derived from a mixed population of cells. Is there any good way to handle this issue?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
MuTect (and many others) published to deal with this
-
For SNV calling, I would also highly recommend VarScan2 (http://www.ncbi.nlm.nih.gov/pubmed/22300766). Others include SomaticSniper (http://www.ncbi.nlm.nih.gov/pubmed/22155872) and Strelka (http://www.ncbi.nlm.nih.gov/pubmed/22581179). In all cases, a matched reference tissue is required.
It is also important to be aware of/accomodate varying sources of contamination. For example, contamination levels (normal sample in the tumour sample and vice-versa) vary significantly between liquid and solid tumours, and the sampling schema. Unfortunately though there is no magic bullet, yet.
Comment
-
Magic bullet might be single cell sequencing. The results of edge tumor vs. core samples would be interesting as would, of course, differences between adjacent malignant cells. After talking with leukemia researchers, I'm under the impression that they do , somehow, sort the cells into "evil" vs. (presumably) "not so evil" and harvest the evil ones.
Comment
-
Yes, with leukemias that might actually be feasible. For solid tumors, really challenging -- the "good" and "evil" are so intertwined it is hard to pick them apart. Probably will need single-cell sequencing that is cheap enough that you can just sequence many & then decide downstream which are "good" and "evil".
If you look closely at the original Mardis lab publication on leukemia WGS (if not first, one of the early ones), they actually encountered the converse problem -- because the patient had a very severe blast crisis, the normal samples were significantly contaminated with leukemic cells!
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
34 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
||
Started by seqadmin, 04-04-2024, 08:48 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 08:48 AM
|
||
Started by seqadmin, 04-01-2024, 06:45 AM
|
0 responses
45 views
0 likes
|
Last Post
by seqadmin
04-01-2024, 06:45 AM
|
||
Started by seqadmin, 03-27-2024, 06:37 PM
|
0 responses
32 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:37 PM
|
Comment