understanding chromosomal variantions

lre1234 · 01-07-2014, 05:30 AM

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

rboettcher · 01-08-2014, 12:58 AM

Hi lre1234,

If you are looking at a pool of samples this might actually be a true thing, but I would check for repetitive or very similar sequences on the other side of the fusion to check if you are looking at a mapping artifact. It could be that mate 1 is mapping uniquely and mate 2 has multiple hits.

lre1234 · 01-08-2014, 05:27 AM

Thanks you for the reply, but unfortunately we are only doing this 1 sample, so I wouldn't be able to check with multiple samples. Also, we are using only unique mappings so I don't think that one of the mates could be at a repeat region.

I was thinking of trying another program such as breakdancer, but have been having trouble getting it to run.

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01-07-2014, 05:30 AM	#1
lre1234 Senior Member Location: US Join Date: Aug 2011 Posts: 106	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

01-08-2014, 12:58 AM	#2
rboettcher Member Location: Berlin Join Date: Oct 2010 Posts: 71	Hi lre1234, If you are looking at a pool of samples this might actually be a true thing, but I would check for repetitive or very similar sequences on the other side of the fusion to check if you are looking at a mapping artifact. It could be that mate 1 is mapping uniquely and mate 2 has multiple hits.

01-08-2014, 05:27 AM	#3
lre1234 Senior Member Location: US Join Date: Aug 2011 Posts: 106	Thanks you for the reply, but unfortunately we are only doing this 1 sample, so I wouldn't be able to check with multiple samples. Also, we are using only unique mappings so I don't think that one of the mates could be at a repeat region. I was thinking of trying another program such as breakdancer, but have been having trouble getting it to run.