Sample | Chrom | Position | Ref | Variant | Allele Call | Frequency | Quality | Type | Coverage |
|---|
Blood | chr1 | 241667244 | G | T | Homozygous | 100 | 3825.7 | SNP | 399 |
chr1 | 241669249 | C | T | Homozygous | 100 | 3797.23 | SNP | 398 |
chr1 | 241671938 | G | A | Heterozygous | 63.5 | 1405.16 | SNP | 400 |
chr1 | 241675240 | A | – | Homozygous | 100 | 2791.44 | DEL | 387 |
chr1 | 241682820 | G | T | Homozygous | 100 | 3806.12 | SNP | 397 |
Cancer tissue | chr1 | 241667244 | G | T | Homozygous | 100 | 3853.67 | SNP | 400 |
chr1 | 241669249 | C | T | Homozygous | 100 | 3853.67 | SNP | 400 |
chr1 | 241671938 | G | A | Heterozygous | 45 | 669.28 | SNP | 400 |
chr1 | 241675240 | A | – | Homozygous | 100 | 2733.7 | DEL | 383 |
chr1 | 241682820 | G | T | Homozygous | 100 | 3796.5 | SNP | 396 |
Positive Ctrla | chr1 | 241667233 | C | T | Heterozygous | 55.5 | 1058.17 | SNP | 400 |
chr1 | 241667244 | G | T | Heterozygous | 51.3 | 888.08 | SNP | 398 |
chr1 | 241675240 | A | – | Homozygous | 100 | 2622.8 | DEL | 385 |
- Positive Ctrla : Centre d'Étude du Polymorphisme Human, http://www.cephb.fr/ (for chromosome 2 linkage map and DNA from individual 1347–02)
- The average Ion PGM™ sequencing output per sample was 150 mega bases with 0.9 million sequencing reads. Of the 16 amplicons in the FH-gene, 100 % achieved a minimum average sequencing depth of 500X and mean depth were 28,419X-34,591X. In samples, the Ion PGM™ detected single-nucleotide Polymorphisms (SNPs) and deletions, details of results are shown in Table 1. In blood sample and cancer tissue sample of the current case, SNPs same as the past report [7], hetero on FH-gene exon5, was detected, and new alleles were detected at intron regions
- SNPs of chr1:241,667,244 bp and chr1:241,675,240 were common between blood, cancer samples and normal human cell (CEPH individuals 1347–02 control DNA, Lifetechnologies). This result indicates these SNPs have low association with cancer. Other variants were located at intron; such mutations may cause a proportion of mature messenger RNA with improperly spliced intron sequences. So we will try gene expression profiling, RNA-seq, for these samples including fusion-gene analysis
