. A repeat expansion was called when the repeat tract length for one allele of the tumour sample was greater than 100 bp and exceeded the repeat tract length of both normal alleles. A locus was considered validated if at least ten cancer genomes had a repeat expansion.Twelve pairs of matching normal and tumour samples from patients with clear cell RCC were obtained with the patients’ informed consent ex vivo upon surgical tumour resection and analysed.
We benchmarked the local read depth filter in silico by observing its behaviour with simulated reads. First, we created a reference genome containing artificially expanded repeats. We randomly selected ten TRs located on chromosome 1 that were shorter than the sequencing read length of 100 bp. We artificially expanded these TRs on chromosome 1 of GRCh37 with the BioPython Python package .
To simulate copy number amplification, the read simulation process was repeated using reference files that contained only the artificially expanded repeats and their surrounding 1,000-bp flanking regions. We created ten pairs of fastq files, each with an increasing copy number. We specified the copy number by multiplying the number of reads to generate by the required number.
The base fastq file with a copy number of 2, in addition to the eight copy number-amplified fastq files, was aligned to chromosome 1 of GRCh37 with bwa-mem with the default options. The resulting SAM files were converted to BAM format with samtools using the default options. Finally, we ran the EHdn profile command with the minimum anchor mapping quality set to 50 and maximum IRR mapping quality set to 40.
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