Sequence-specific burden of oxidative DNA lesions was determined based on digest of mtDNA with the formamidopyrimidine-DNA glycolase (fpg), followed by quantitative real time PCR (qRT-PCR) amplification.
Although indel detection using high-throughput sequencing is burdened with high false-positive rates, 88.0% of the indels identified here validated favorably using orthogonal technologies.
For all demographic models and observed data, as more individuals are sequenced, the burden of private mutations decreases, because increasing sample size makes it more probable that a variant has already been discovered [ 9].
For example, for the NR data, when 492 individuals are sequenced, the estimated burden of mutation from the 493rd sequenced individual is about 0.76% (Table 1).
Therefore, several studies have performed large-scale targeted exome sequencing studies using genetic burden testing, a method that evaluates the combined effect of an accumulation of rare and low-frequency variants within a particular genomic segment such as a gene or exon.
Furthermore, given the rate with which NGS sequence data are currently being produced (Mardis, 2008), the additional burden of sequence preprocessing must be kept relatively modest so as to avoid adding undue overhead to the bioinformatics pipeline.
We present an extensive assessment of mutation burden through sequencing analysis of >81,000 tumors from pediatric and adult patients, including tumors with hypermutation caused by chemotherapy, carcinogens, or germline alterations.
This technique, referred to as high resolution melting (HRM), can distinguish single base variation and then has the potential to identify SNPs without the burden of sequencing [13], [14].
