VEP specific celltype defining regulatory variants

Question

[c.clarido]

Hello biostar community,

I was just wondering if it is possible to have VEP report regulatory region in melanoma or melanocyte specific cell line? I tried to list the avaialble celltypes in vep96, however none of above mentioned celllines were there

PC_3
PC_9
Pancreas
Placenta
Psoas_Muscle
Right_Atrium
SK_N_SH
Small_Intestine
Spleen
T_cells_(PB)_Roadmap
T_helper_17_cell
Thymus
astrocyte
bipolar_neuron
brain
cardiac_muscle_cell
common_myeloid_progenitor_CD34_positive
common_myeloid_progenitor_CD34_positive_ENCSR337XXD_1
common_myeloid_progenitor_CD34_positive_ENCSR722JRY
effector_memory_CD4_positive_alpha_beta_T_cell
endodermal_cell
endothelial_cell_of_umbilical_vein
eosinophil_(VB)
erythroblast_(CB)
esophagus
fibroblast_of_dermis
fibroblast_of_lung
heart
heart_right_ventricle
hepatocyte
iPS-20b
iPS_15b
iPS_DF_19.11
iPS_DF_6.9
keratinocyte
kidney
lung_ENCSR465WKM
mammary_epithelial_cell
myotube
naive_B_cell_(To)
naive_B_cell_(VB)
naive_thymus_derived_CD4_positive_alpha_beta_T_cell
neural_progenitor_cell
neural_stem_progenitor_cell
neuron
neutrophil
neutrophil_(CB)
neutrophil_(VB)
neutrophil_myelocyte_(BM)
sigmoid_colon
skeletal_muscle_myoblast

Answer 1

[Emily]

Those are the cell types Ensembl has regulatory data for, so those are the only ones you will get information about in VEP.

Answer 2

[c.clarido]

Thank you for the reply,

I am not very familiar with the regulatory Ensembl build, however here they list the sources they used in the build, which includes melanocyte cell line (foreskin melanocyte) from Roadmap epigenomics. How come this is not on the list? How is the --regulatory flag connected to the regulatory build?

Thank you very much in advance!

[Emily]

Are you using GRCh37 or GRCh38?

[c.clarido]

Hello Emily, We are using GRCh38

[Emily]

How did you get that list? When I run the VEP with --cell_type list I get:

A549,A673,B,B_(PB),CD14+_monocyte_(PB),CD14+_monocyte_1,CD4+_CD25+_ab_Treg_(PB),CD4+_ab_T,CD4+_ab_T_(PB)_1,CD4+_ab_T_(PB)_2,CD4+_ab_T_(Th),CD4+_ab_T_(VB),CD8+_ab_T_(CB),CD8+_ab_T_(PB),CMP_CD4+_1,CMP_CD4+_2,CMP_CD4+_3,CM_CD4+_ab_T_(VB),DND-41,EB_(CB),EM_CD4+_ab_T_(PB),EM_CD8+_ab_T_(VB),EPC_(VB),GM12878,H1-hESC_2,H1-hESC_3,H9_1,HCT116,HSMM,HUES48,HUES6,HUES64,HUVEC,HUVEC-prol_(CB),HeLa-S3,HepG2,K562,M0_(CB),M0_(VB),M1_(CB),M1_(VB),M2_(CB),M2_(VB),MCF-7,MM.1S,MSC,MSC_(VB),NHLF,NK_(PB),NPC_1,NPC_2,NPC_3,PC-3,PC-9,SK-N.,T_(PB),Th17,UCSF-4,adrenal_gland,aorta,astrocyte,bipolar_neuron,brain_1,cardiac_muscle,dermal_fibroblast,endodermal,eosinophil_(VB),esophagus,foreskin_fibroblast_2,foreskin_keratinocyte_1,foreskin_keratinocyte_2,foreskin_melanocyte_1,foreskin_melanocyte_2,germinal_matrix,heart,hepatocyte,iPS-15b,iPS-20b,iPS_DF_19.11,iPS_DF_6.9,keratinocyte,kidney,large_intestine,left_ventricle,leg_muscle,lung_1,lung_2,mammary_epithelial_1,mammary_epithelial_2,mammary_myoepithelial,monocyte_(CB),monocyte_(VB),mononuclear_(PB),myotube,naive_B_(VB),neuron,neurosphere_(C),neurosphere_(GE),neutro_myelocyte,neutrophil_(CB),neutrophil_(VB),osteoblast,ovary,pancreas,placenta,psoas_muscle,right_atrium,right_ventricle,sigmoid_colon,small_intestine_1,small_intestine_2,spleen,stomach_1,stomach_2,thymus_1,thymus_2,trophoblast,trunk_muscle

As you can see, a number of "melanocyte" cells are in there.

[c.clarido]

I am using vep96 and it's not there, probably this is from the newer version. I will try to update my cache file. Thank you very much for the help!