TABLE 3.
Rare variants (aMAF =< 1%) in 499 cancer related genes in NF+BrCa samples
| Found in NF+BrCa samples | Nucleotide in UCSC browser | Somatic variant in COSMIC | Variants (described as Reference SNP Cluster ID or coordinates from Human GRCh37/hg19 Assembly) |
|---|---|---|---|
| N = 1 (found in one sample); bp is not significant | cHighly Conserved | – – –-> | APC rs150973053; ATG16L1 rs149927020; AXIN2 rs755990979;eEGFR rs121913418; ERCC2 rs149818919; ERCC6 rs142580756; FANCI chr15:89807202(T>C); MSH2 rs34136999; NELL1 rs144555978; PIGF rs367591899; PIK3C2A rs138982128; SOS1 rs56219475 |
| dLess Conserved | Observed | eAPC rs747362422;eMET rs56391007; | |
| N = 2 (found in two samples); bp=<0.02 | cHighly Conserved | – – –-> | MSH3 rs766742870; fUVRAG rs75431002 |
| dLess Conserved | – – –-> | fBUB1B rs56079734; PIK3C2A rs61755370; PLCG rs75472618; PLCG rs187956469; PMS2 rs63750668; fRECQL4 rs35842750; |
MAF: Minimal Allele Frequency in 1000 Genomes.
p-value of allele frequency (AF) in NF+BrCa compared with control group or with population AF in UCSC genomic browser.
Highly Conserved: PhyloP value is greater than 4.0.
Less Conserved: PhyloP value is less than 4.0.
Variants observed in COSMIC.
APC rs747362422 was observed in 3 samples of different type of cancers, all confirmed somatic.
EGFR rs121913418 was observed in 6 samples, 2 were confirmed somatic.
MET rs56391007 was observed in 23 samples, 8 were confirmed somatic.
Discordant population allele frequencies between ancestries.
RECQL4 rs35842750 and BUB1B rs56079734: Both alleles were observed in 2 non-European samples of NF+BrCa. MAF of non-Europeans in 1000 Genomes, such as Africans, is higher than 1%.
UVRAG rs75431002: This allele was observed in one European and one non-European NF+BrCa samples. Its population MAF is rare in Europeans, but is slightly higher in non-Europeans. MAF is 3% in Sierra Leon.