View Single Post
Old 01-07-2014, 05:30 AM   #1
lre1234
Senior Member
 
Location: US

Join Date: Aug 2011
Posts: 106
Default understanding chromosomal variantions

Hi all,
I am in the process of doing a WGS on tumor samples and looking at chromosomal translocations. For this, I have been using SVdetect. In doing this I got a result which I don't really understand. Here is a snipet of the output:

[FONT="Times New Roman"]chr_type SV_type BAL_type chromosome1 start1-end1 average_dist chromosome2 start2-end2 nb_pairs score_strand_filtering score_order_filtering score_insert_size_filtering final_score breakpoint1_start1-end1 breakpoint2_start2-end2
INTER INV_TRANSLOC UNBAL chr1 91852776-91853152 - chr5 71146729-71146961 445 100% 100% - 1 91849380-91852776 71143189-71146729
INTER INV_TRANSLOC UNBAL chr1 91852777-91853144 - chr19 36066496-36066772 316 100% 100% - 1 91849372-91852777 36063000-36066496
INTER INV_TRANSLOC UNBAL chr1 91852779-91853119 - chr6 119558555-119558738 1476 100% 100% - 1 91853119-91856551 119558738-119562327
INTER TRANSLOC UNBAL chr1 91852777-91853127 - chr4 70296616-70296753 282 100% 100% - 1 91849355-91852777 70296753-70300388
INTER TRANSLOC UNBAL chr1 91852778-91853176 - chr19 24183636-24185006 511 100% 100% - 1 91849404-91852778 24185006-24187408
INTER TRANSLOC UNBAL chr1 91852779-91853128 - chr2 230045479-230045721 483 100% 100% - 1 91849356-91852779 230045721-230049251
INTER TRANSLOC UNBAL chr1 91852803-91853152 - chr2 133037525-133039167 543 100% 99% - 0.996 91849380-91852803 133039167-133041297
[/FONT]

As you can see from this, all of these have locations on chr1 at around the same positions, but go to different chromosomes. My question is, would you believe this results? Can this kind of situation actually happen? Or has anyone seen this event before?

Any insights would be appreciated.
Thanks

Last edited by lre1234; 01-07-2014 at 05:33 AM. Reason: didn't mean to post without finishing
lre1234 is offline   Reply With Quote