esophageal squamous cell carcinoma (ICD10: C15): 20 cases

          cancer tissues: 20 samples

          paired non-cancer tissues: 20 samples

Data with bad base quality and high %GC content were removed.

Aligment:

Data matched for the following condition were removed.

- Low mapping rate

- Different insert size

- Gender information mismatch between meta-data and genotype data

- Suspected sex chromosome aberration

Genotyping:

GATK’s best practices includes a variant filtering step following Variant Quality Score Recalibration (VQSR)

- DP/GP (DP < 5, GQ < 20, DP > 60, GQ < 95 )

- Heterozygosity (F>=0.05)

- Hardy-Weinberg equilibrium (p < 10^-6)

- Repeat & Low Complexity

Principal Component Analysis (PCA):

PCA was performed with individuals included in the 1000 genomes project and outliers from Japanese cluster were removed.

After these filtering steps, variants located in the regions listed as the HighConfidenceRegion (Genome-In-A-Bottle project) were flagged.

76,768,387 (Autosomal Chromosomes)

2,898,518 (X Chromosome)

10,202,908 (Autosomal Chromosomes)

410,435 (X Chromosome)

JGAD000233 (fastq)

JGAD000405 (bam, vcf): Whole genome sequencing analyzed data included in the JGAD000117 were mapped to the GRCh37 reference genome sequence, and variant detection was carried out using the GATK (Genome Analysis Toolkit) standards. This project is an initiative of the GEnome Medical alliance Japan (GEM Japan, GEM-J). Lean more..