pwilmart/PrecisionProDB_references

PrecisionProDB_reference

PrecisionProDB is a Python package for proteogenomics, which can generate a customized protein database for peptide search in mass spectrometry.

The Genome Aggregation Database (gnomAD) project provides variant allele frequencies in different human opulations based on genomes and exomes of hundreds of thousands of individuals. The population-specific common allele information can be integrated into a protein database. We applied PrecisionProDB to alleles from different populations from the gnomAD (v3.1) data and provided the pre-calculated protein databases here.

• PrecisionProDB_reference
• gnomAD3.1
  • Summary of population common alleles based on gnomAD 3.1
  • Common alleles in different populations
• GENCODE
  • GENCODE_gnomAD_common.protein_all.fa.gz
  • GENCODE_POPULATION_ABREVIATION.pergeno.aa_mutations.csv.gz
  • GENCODE_gnomAD_all.protein_changed.fa.gz
  • Summary of GENCODE variation
• RefSeq
  • RefSeq_gnomAD_common.protein_all.fa.gz
  • RefSeq_POPULATION_ABREVIATION.pergeno.aa_mutations.csv.gz
  • RefSeq_gnomAD_all.protein_changed.fa.gz
  • Summary of RefSeq variation
• Ensembl
  • Ensembl_gnomAD_common.protein_all.fa.gz
  • Ensembl_POPULATION_ABREVIATION.pergeno.aa_mutations.csv.gz
  • Ensembl_gnomAD_all.protein_changed.fa.gz
  • Summary of Ensembl variation
• UniProt
  • UniProt_gnomAD_common.protein_all.fa.gz
  • UniProt_gnomAD_all.protein_changed.fa.gz
  • Summary of UniProt variation

gnomAD3.1

Summary of population common alleles based on gnomAD 3.1

Several population go

population	abreviation	genomes	# alt > ref
African/African American	adj_afr	20,744	2,334,582
Amish	adj_ami	456	2,435,528
Latino/Admixed American	adj_amr	7,647	2,343063
Ashkenazi Jewish	adj_asj	1,736	2,375,907
East Asian	adj_eas	2,604	2,579,504
Finnish	adj_fin	5,316	2,364,824
Middle Eastern	adj_mid	158	2,346,917
Non-Finnish European	adj_nfe	34,029	2,369,937
South Asian	adj_sas	2,419	2,367,008
Other	adj_oth	1,047	-
Total	adj	76,156	2,274,088

weblink: https://gnomad.broadinstitute.org/faq

# alt > ref: count of alleles that the alternative allele have a higher allele frequency (AF) than the allele in the reference genome.

Common alleles in different populations

Variants from gnomAD 3.1. Only include sites which is "PASS" in quality-control and the allele frequency of alt is higher than ref.

file names: POPULATION_ABREVIATION.csv.gz

files are in csv format (with \t as separator), which looks like:

chr	pos	ref	alt	alt_AF	ref_AF
1	10146	AC	A	0.6328	0.3672
1	15274	A	G	0.6311	0.0635
1	28563	A	G	0.6842	0.3158
1	49298	T	C	0.5852	0.4148
1	52238	T	G	0.9013	0.0987

GENCODE

GENCODE Release 35 (GRCh38.p13)

https://www.gencodegenes.org/human/release_35.html

GENCODE_gnomAD_common.protein_all.fa.gz

GENCODE gene models with alleles from gnomAD 3.1 most common alleles from all indiviudals (adj).

GENCODE_POPULATION_ABREVIATION.pergeno.aa_mutations.csv.gz

Amino acid change mutations for different populations. For explanations of the columns, visit the wiki page of PREFIX.pergeno.aa_mutations.csv.

GENCODE_gnomAD_all.protein_changed.fa.gz

Combine changed proteins from 10 populations and keep only unique ones.

This file could be added to current offical protein models to improve protein database search of mass spectrometry.

Proteins are the original names + '__' + populations. For example: ENSP00000390334.1|ENST00000453855.5|ENSG00000101019.22|OTTHUMG00000032335.13|OTTHUMT00000078865.3|UQCC1-213|UQCC1|126__adj|nfe_adj|fin_adj|mid_adj|ami_adj|asj_adj|eas_adj|amr_adj, where ENSP00000390334.1|ENST00000453855.5|ENSG00000101019.22|OTTHUMG00000032335.13|OTTHUMT00000078865.3|UQCC1-213|UQCC1|126 is the original protein_id in GENCODE, adj|nfe_adj|fin_adj|mid_adj|ami_adj|asj_adj|eas_adj|amr_adj are the populations with this altered protein.

If the population annotation is ALLSHARE, it means that altered protein exists in all ten populations.

Summary of GENCODE variation

Total number of proteins: 101486, total number of AA: 38549462

	stopGain_Pr	stopLoss_Pr	frameChange_Pr	variant_AA	variant_Pr	indel_pr
adj	90	44	156	14768	10728	404
afr_adj	78	51	131	15697	11402	480
ami_adj	101	50	157	15441	10993	432
amr_adj	95	52	141	14769	10705	442
asj_adj	90	44	158	15181	10830	419
eas_adj	94	41	154	16524	11570	500
fin_adj	92	47	151	15291	10881	439
mid_adj	103	44	166	15215	10800	425
nfe_adj	94	48	154	15134	10747	429
sas_adj	84	46	147	15172	10917	419

• stopGain_Pr: count of proteins with stop-gain
• stopLoss_Pr: count of proteins with stop-loss
• frameChange_Pr: count of proteins with frame change
• variant_AA: total AA substitutions
• variant_Pr: count of proteins with AA substitutions
• indel_pr: count of proteins with insertion or deletion of AAs

RefSeq

RefSeq GCF_000001405.39

ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/current

Release version: 109.20200815

RefSeq_gnomAD_common.protein_all.fa.gz

RefSeq gene models with alleles from gnomAD 3.1 most common alleles from all indiviudals (adj).

RefSeq_POPULATION_ABREVIATION.pergeno.aa_mutations.csv.gz

Amino acid change mutations for different populations.

RefSeq_gnomAD_all.protein_changed.fa.gz

Combine changed proteins from 10 populations and keep only unique ones.

Summary of RefSeq variation

Total number of proteins: 114963, total number of AA: 76187452

	stopGain_Pr	stopLoss_Pr	frameChange_Pr	variant_AA	variant_Pr	indel_pr
adj	104	0	174	28723	19298	632
afr_adj	95	0	214	29885	20389	773
ami_adj	134	15	224	29865	19645	697
amr_adj	125	14	184	28724	19241	722
asj_adj	117	0	176	29147	19083	681
eas_adj	127	0	201	31791	20630	805
fin_adj	113	0	186	29453	19233	692
mid_adj	125	0	179	29496	19332	692
nfe_adj	113	0	185	29291	19020	684
sas_adj	112	0	165	29040	19428	659

Ensembl

Ensembl Homo_sapiens.GRCh38.101

Ensembl_gnomAD_common.protein_all.fa.gz

Ensembl gene models with alleles from gnomAD 3.1 most common alleles from all indiviudals (adj).

Ensembl_POPULATION_ABREVIATION.pergeno.aa_mutations.csv.gz

Amino acid change mutations for different populations.

Ensembl_gnomAD_all.protein_changed.fa.gz

Combine changed proteins from 10 populations and keep only unique ones.

Summary of Ensembl variation

Total number of proteins: 112012, total number of AA: 42584212

	stopGain_Pr	stopLoss_Pr	frameChange_Pr	variant_AA	variant_Pr	indel_pr
adj	102	1	147	15136	10750	401
afr_adj	89	1	126	16096	11426	476
ami_adj	112	4	151	15844	11013	429
amr_adj	109	5	133	15131	10724	441
asj_adj	103	0	144	15664	10851	415
eas_adj	111	1	143	16953	11587	499
fin_adj	102	1	140	15706	10898	436
mid_adj	115	0	154	15692	10820	421
nfe_adj	107	0	144	15558	10767	425
sas_adj	98	0	137	15398	10940	417

UniProt

UniProt reference proteins for proteome, human (12/02/2020).

ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640_9606.fasta.gz ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640_9606_additional.fasta.gz

UniProt_gnomAD_common.protein_all.fa.gz

UniProt gene models with alleles from gnomAD 3.1 most common alleles from all indiviudals (adj).

UniProt_gnomAD_all.protein_changed.fa.gz

Combine changed proteins from 10 populations and keep only unique ones.

Summary of UniProt variation

The percentage of changed proteins will be similar to Ensembl, as UniProt information were mostly extracted from Ensembl gene models.

UP000005640_9606: 20609 proteins, 11395683 AA.
UP000005640_9606_additional: 77157 proteins, 27708325 AA.
Total: 97766 proteins, 39104008 AA.