[Tutorial] Adding a new target gene to PyPGx

[sbslee]

The post describes how to add a new target gene to PyPGx using the ACYP2 gene as an example.

Step 1. Define the target region

We can use UCSC Table Browser to find the target region for ACYP2:

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38) or Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: NCBI RefSeq
table: RefSeq All (ncbiRefSeq)

Below is the output for assembly: Dec. 2013 (GRCh38/hg38):

#bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
124	NM_001320586.2	chr2	+	53971112	54305300	53973748	54304802	7	53971112,53973712,54050957,54057238,54135452,54138638,54304687,	53971321,53973810,54051050,54057360,54135469,54138748,54305300,	0	ACYP2	cmpl	cmpl	-1,0,2,2,1,0,2,
124	NM_001320587.2	chr2	+	53971112	54305300	53973748	54304802	6	53971112,53973712,54057238,54135452,54138638,54304687,	53971321,53973810,54057360,54135469,54138748,54305300,	0	ACYP2	cmpl	cmpl	-1,0,2,1,0,2,
124	NM_001320588.2	chr2	+	54123282	54305300	54135466	54304802	4	54123282,54135452,54138638,54304687,	54123410,54135469,54138748,54305300,	0	ACYP2	cmpl	cmpl	-1,0,0,2,
124	NM_001320589.2	chr2	+	54115614	54305300	54115698	54267323	5	54115614,54135452,54138638,54267295,54304687,	54115756,54135469,54138748,54267365,54305300,	0	ACYP2	cmpl	cmpl	0,1,0,2,-1,
124	NM_001320590.2	chr2	+	54115614	54143316	54115698	54141907	4	54115614,54135452,54138638,54141882,	54115756,54135469,54138748,54143316,	0	ACYP2	cmpl	cmpl	0,1,0,2,
124	NM_138448.4	chr2	+	54115614	54305300	54115698	54304802	4	54115614,54135452,54138638,54304687,	54115756,54135469,54138748,54305300,	0	ACYP2	cmpl	cmpl	0,1,0,2,

We will use the NM_138448.4 transcript, but for the final region, we need to add +/- 3 kb (i.e., chr2:54112614-54308300).

Step 2. Download 1KGP reference panels

PyPGx uses 1KGP Phase 3 data for GRCh37 (The 1000 Genomes Project Consortium, 2015, Nature) and 1KGP NYGC 30x WGS data for GRCh38 (Byrska-Bishop et al., 2021, Cell).

Since ACYP2 is located on chromosome 2, we need to download a chr2 panel for each genome assembly:

(GRCh37) chr2.1kg.phase3.v5a.vcf.gz
(GRCh37) chr2.1kg.phase3.v5a.vcf.gz.tbi
(GRCh38) 1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz
(GRCh38) 1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.tbi

Step 3. Update pypgx-bundle

Next, we should slice each VCF file to create a mini-VCF file and upload it to pypgx-bundle:

$ fuc vcf-slice chr2.1kg.phase3.v5a.vcf.gz chr2:54339751-54535437 > ~/pypgx-bundle/1kgp/GRCh37/ACYP2.vcf
$ fuc vcf-slice 1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz chr2:54112614-54308300 > ~/pypgx-bundle/1kgp/GRCh38/ACYP2.vcf
$ fuc vcf-index ~/pypgx-bundle/1kgp/GRCh37/ACYP2.vcf
$ fuc vcf-index ~/pypgx-bundle/1kgp/GRCh38/ACYP2.vcf

Step 4. Update CSV files

First, we need to update the gene-table.csv file:

Gene	Target	Control	Paralog	Variants	SV	PhenotypeMethod	RefAllele	GRCh37Default	GRCh38Default	Strand	GRCh37Region	GRCh38Region	GRCh37ExonStarts	GRCh37ExonEnds	GRCh38ExonStarts	GRCh38ExonEnds
ACYP2	TRUE	FALSE	N/A	TRUE	FALSE	N/A	Reference	Reference	Reference	+	chr2:54339751-54535437	chr2:54112614-54308300	54342751,54362589,54365775,54531824,	54342893,54362606,54365885,54532437,	54115614,54135452,54138638,54304687,	54115756,54135469,54138748,54305300,

Then, we update the variant-table.csv file:

Gene	GRCh37Name	GRCh38Name	rsID	Chromosome	GRCh37Position	GRCh38Position	GRCh37Allele	GRCh38Allele	Variant	Impact	GRCh37Synonym	GRCh38Synonym
ACYP2	2-54395259-G-A	2-54168122-G-A	rs1872328	2	54395259	54168122	G	G	A	N/A	N/A	N/A

Finally, we need to update the allele-table.csv file:

Gene	StarAllele	ActivityScore	Function	GRCh37Core	GRCh37Tag	GRCh38Core	GRCh38Tag	SV
ACYP2	Reference	N/A	Normal Function	N/A	N/A	N/A	N/A	FALSE
ACYP2	rs1872328	N/A	Unknown Function	2-54395259-G-A	2-54168122-G-A	N/A	N/A	FALSE

Step 5. Update the docs

The following files need to be updated:

docs/genes.rst
docs/create.py