Exploring the Neandertal legacy of pancreatic ductal adenocarcinoma risk in Eurasians

Biological Research

Table 1 Candidate aSNPs for each ancestry group

Panel A. Association studies results
Population	aSNP	Position (GRCh37)	Alleles (M/m)	Gene^a	MAF^b	OR (95%C.I.)	P
PanScan + PanC4^c	rs12998719	2:67583252	G/A	–	29%	1.11 (1.05–1.16)	5.51 × 10^–5
PANDoRA^c	rs12998719	2:67583252	G/A	–	28%	1.05 (0.95–1.15)	0.38
FinnGen	rs113955626	3:23107748	C/T	–	7%	1.35 (1.17–1.55)	4.79 × 10^–5
JaPAN	rs117585753	10:25190572	C/T	PRTFDC1	10%	1.35 (1.19–1.54)	3.59 × 10^–6

Panel B. Top SNP population-based frequency
Population	aSNP	Position (GRCh37)	Alleles (M/m)	1000G MAF			gnomAD MAF			HGDP^d
Population	aSNP	Position (GRCh37)	Alleles (M/m)	EUR	FIN	EAS (%)	EUR (%)	FIN	EAS (%)	EUR (%)	EAS
PanScan + PanC4^c	rs12998719	2:67583252	G/A	27%	30%	43	36	29%	42	25	35%
FinnGen	rs113955626	3:23107748	C/T	4%	4%	13	5	8%	14	8	18%
JaPAN	rs117585753	10:25190572	C/T	8‰	5‰	10	1	3‰	9	1	8%

Panel A shows the summary statistics of aSNPs with the lowest association P-value, panel B shows the minor allele frequency of SNPs with the lowest P-value of associations across several datasets
aSNP Neandertal introgressed SNP; M major allele; m, minor allele; MAF minor allele frequency; OR Odds Ratio; 95%C.I. 95% Confidence Interval; PRTFDC1 phosphoribosyl transferase domain containing 1; 1000G 1000 Genomes project phase 3 [43]; gnomAD Genome Aggregation Database [44]; HGDP Human Genome Diversity Project [45] EUR Europeans; FIN Finns; EAS East Asians
^aGene in which aSNP lies
^bMAF of the SNP of interest in the analysed datasets. Since allele frequencies are not freely available in JaPAN dataset, the MAF in East Asians from 1000G is reported
^cPanScan + PanC4 (discovery phase), PANDoRA (replication phase)
^dIn HGDP, SNP frequency in Finns is not available. Frequency in all European populations is displayed

ISSN: 0717-6287