cBioportal and oncoKB

[ramakrishnan krishnan]

Hi,

I am trying to map the cBioportal data of OV with the oncoKB. When I mapped it I am getting 0 mapped data 

Can you someone help me in this 

Thank you

Sincerely,

Ramakrishnan Krishnan   

[Kelsey Zhu]

Hi Ramakrishnan,

thank you for reaching out!

could you please give more details on what you were trying to do? for instance, which study you were looking at, which genes you were trying to query? 

Best!

Kelsey

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[Kelsey Zhu]

Hi Ramakrishnan,

please note protein changes (HGVSp or column 36) from mutation data you downloaded all have a prefix of "p.", while oncoKB does not use it. 

For instance, 

$ grep E17K msk_impact_2017/data_mutations_extended.txt |head -1

AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 0

$ grep E17K ~/Downloads/allAnnotatedVariants.txt |head -1
ENST00000349310 NM_001014431.1 207 AKT1 E17K E17K Oncogenic Gain-of-function 23134728, 20440266, 23741320, 18256540, 21793738, 17611497, 9843996

could that be the cause of mismatch?

Best!

Kelsey

On Tue, Aug 20, 2019 at 10:12 AM ramakrishnan krishnan <ramakrish...@gmail.com> wrote:

HI Kelsey,

Thank you for getting back to me so quickly

I am currently mapping the cbioportal data with oncoKB data which I downloaded from datahub. When I am trying to map these two datasets I find there is no match between them. So can you please help me

Thank you

Sincerely,

Ramakrishnan Krishnan