mutation mapper in cbioportal

[pushpinder kaur]

Hi,

I want to use mutation mapper to visualize my own data which is having the information of mutations and other description. But when I upload the files into mutation mapper tool. It is showing that there is no mutation in this data.  Below here is the input. This data has been annotated to GRCH38.p7. I do not know why I am not seeing the mutations in the plot. Please help me in fixing this issue.

Thanks

Pushpinder

Hugo_Symbol	Protein change	Sample_ID	Cancer_Type	Chromosome	Start_Position	End_Position	Reference_allele	Variant_allele	Mutation_status	Impact	Biotype
TNR	Leu91fs	19065	Breast cancer	chr1	175396686	175396686	G	GC	Inframe	HIGH	protein_coding
PAPPA2	Ser1686fs	19065	Breast cancer	chr1	176793587	176793587	T	TC	Inframe	HIGH	protein_coding
C4BPA	Thr6fs	19065	Breast cancer	chr1	207113030	207113030	A	AC	Inframe	HIGH	protein_coding
PTPN14		19065	Breast cancer	chr1	214391023	214391023	T	TG	Inframe	HIGH	protein_coding
ESRRG		19065	Breast cancer	chr1	216506963	216506963	C	CA	Inframe	HIGH	protein_coding
SIPA1L2		19065	Breast cancer	chr1	232514891	232514891	T	TG	Inframe	HIGH	protein_coding
RGS7		19065	Breast cancer	chr1	241098724	241098724	A	AT	Inframe	HIGH	protein_coding
XDH		19065	Breast cancer	chr2	31403104	31403104	G	GC	Inframe	HIGH	protein_coding
KCMF1		19065	Breast cancer	chr2	85053284	85053284	C	CG	Inframe	HIGH	protein_coding
AFF3		19065	Breast cancer	chr2	99601451	99601451	T	TG	Inframe	HIGH	protein_coding

[Kelsey Zhu]

Hi Pushpinder, 

thank you for contacting us!

Currently, MutationMapper can only interpret mutations with protein annotations based on genome build GRCh37 (hg19).

Best!

Kelsey

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[Breno Osvaldo]

Hi,

I'm not part of the group, but I have a certain familiarity with this tool, but I will try to help you by directing.
I noticed the formatting sent up, not sure about all the points, however, some of the errors are due to formatting employed by you.
For example, in the above presentation you did not give the column nesting, moreover the chromosome needs to be noticed only by the indicative, i.e. 7.   
The attached file contains an example similar to yours, however, with the correct notation. Test it and observe the syntax.

I hope I've been able to help.

Att Breno Osvaldo.

[Kelsey Zhu]

Hi Pushpinder,

looks like your coordinates are still in hg38 (please see attached). I checked a few genes on your list.

please ensure you are using hg19.

Thanks!

Kelsey

On Thu, Jun 27, 2019 at 12:41 PM pushpinder kaur <pushpinde...@gmail.com> wrote:

Hi Kelsey,

I change the coordinates to hg19 also. But the mutation plot is not showing any mutations. However, the data shows that the sample is having mutation. How to fix this problem?

Thanks

Pushpinder

Hugo_Symbol

Protein change

Sample_ID

Cancer_Type

Chromosome

Start_Position

End_Position

Reference_allele

Variant_allele

Mutation_status

Impact

Biotype

TNR

Leu91fs

19065

Breast cancer

1

175365822

175365822

G

GC

Inframe

HIGH

protein_coding

PAPPA2

Ser1686fs

19065

Breast cancer

1

176762723

176762723

T

TC

Inframe

HIGH

protein_coding

C4BPA

Thr6fs

19065

Breast cancer

1

207286375

207286375

A

AC

Inframe

HIGH

protein_coding

PTPN14		19065	Breast cancer	1	214564366	214564366

T

TG

Inframe

HIGH

protein_coding

ESRRG		19065	Breast cancer	1	216680305	216680305

C

CA

Inframe

HIGH

protein_coding

SIPA1L2		19065	Breast cancer	1	232650637	232650637

T

TG

Inframe

HIGH

protein_coding

RGS7		19065	Breast cancer	1	241262024	241262024

A

AT

Inframe

HIGH

protein_coding

On Wed, Jun 26, 2019 at 9:48 PM Kelsey Zhu <kelse...@gmail.com> wrote:

you might want to go to the UCSC Genome Browser, from the homepage, click the "Downloads" link on the left column and then navigate to each assembly and find the appropriate liftOver directory. for instance,

http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/

Best!

Kelsey

On Thu, Jun 27, 2019 at 12:32 AM pushpinder kaur <pushpinde...@gmail.com> wrote:

Ok. But how I can convert those? Is there any program for the conversion?

Thanks.

On Wed, Jun 26, 2019, 9:30 PM Kelsey Zhu <kelse...@gmail.com> wrote:

Hi Pushpinder,

please convert those hg38 coordinates to hg19 if possible. Please also check MutationMapper page and ensure the required data format is used.

Best!

Kelsey

On Wed, Jun 26, 2019 at 10:52 PM pushpinder kaur <pushpinde...@gmail.com> wrote:

Hi Kelsey,

Thanks for the quick reply. Is it possible if I can convert GRCH38.p7 to hg19?

Thanks

Pushpinder