Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • mamons
    replied
    Originally posted by hagir View Post
    hello every body, i'm a new member and hope that you help me
    i want to perform an exome sequencing on oral cancer cases using illumina. i need you to help me with a good protocol for doing so
    thanks

    Leave a comment:


  • gensdei
    replied
    [QUOTE=AJERYC;88920]
    Originally posted by gensdei View Post
    Cell lines have the benefit of being a relatively pure population of clonal cells and thus represent a particular snapshot of cancers. Is there anybody who have seen a paper using exome-seq with 100x coverage based on cell line? If there is not, does it means that we don't need perform that deep sequencing due to its purity?


    Theoretically a cell line is homozygous and that is more easy to resolve with NGS so you could go 10-30x.
    To be more specific, exome-seq from cell line have no variant sites, e.g, SNP? Theoretically is it true? If so, you are right, no need for deep sequencing. What about exome-seq from cancer cell line? Did anybody see a paper on 100x exome-seq data from cancer cell line? Thanks.
    Last edited by gensdei; 11-10-2012, 11:31 PM.

    Leave a comment:


  • AJERYC
    replied
    [QUOTE=gensdei;88907]Cell lines have the benefit of being a relatively pure population of clonal cells and thus represent a particular snapshot of cancers. Is there anybody who have seen a paper using exome-seq with 100x coverage based on cell line? If there is not, does it means that we don't need perform that deep sequencing due to its purity?


    Theoretically a cell line is homozygous and that is more easy to resolve with NGS so you could go 10-30x.

    Leave a comment:


  • gensdei
    replied
    Cell lines have the benefit of being a relatively pure population of clonal cells and thus represent a particular snapshot of cancers. Is there anybody who have seen a paper using exome-seq with 100x coverage based on cell line? If there is not, does it means that we don't need perform that deep sequencing due to its purity?

    Thanks in advance!

    Leave a comment:


  • ymc
    replied
    Originally posted by AJERYC View Post
    30x is definitely not enough, since it means 30x averge, so you will get a lot of regions with very few sequences, that will make impossible for you to resolve heterozygous mutations. Go 50x or 100x.
    How many x also depends on your enrichment kit. For example, according to the BGI paper, for 90% call sensitivity, Nimblegen SeqCap EZ v1 needs 50x, Agilent SureSelect All Exon needs 80x.

    Leave a comment:


  • AJERYC
    replied
    30x is definitely not enough, since it means 30x averge, so you will get a lot of regions with very few sequences, that will make impossible for you to resolve heterozygous mutations. Go 50x or 100x.

    Leave a comment:


  • hagir
    replied
    exome sequencing

    hello every body, i'm a new member and hope that you help me
    i want to perform an exome sequencing on oral cancer cases using illumina. i need you to help me with a good protocol for doing so
    thanks

    Leave a comment:


  • hagir
    replied
    hello every body, i'm a new member and hope that you help me
    i want to perform an exome sequencing on oral cancer cases using illumina. i need you to help me with a good protocol for doing so
    thanks

    Leave a comment:


  • arvi8689
    started a topic Exome sequencing

    Exome sequencing

    Hey I am trying to sequence the melanoma exome to find somatic mutation involved in the melanoma. I am very new to this technique and I have some questions regarding this:

    1)Generally how many exomes from different melanoma samples need to be done to get some satisfactory results?
    2)What coverage is essential for such a study? Initially I was thinking of around 30X but some papers have used nearly 100X. Will I be okay with 30X coverage of the exome?

    Your help is well appreciated.

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:58 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-12-2024, 02:20 PM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-07-2024, 06:58 AM
0 responses
182 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-06-2024, 08:18 AM
0 responses
231 views
0 likes
Last Post seqadmin  
Working...
X