Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Mechanism and prevention method of drill string uplift during shut-in after overflow in an ultra-deep well

Drill string will sustain large uplift force during the shut-in period after gas overflow in an ultra-deep well, and in serious case, it will run out of the wellhead. A calculation model of uplift force was established to analyze dynamic change characteristics of the uplift force of drill string during the shut-in period, and then a management procedure for the uplift risk during the shut-in period after gas overflow in the ultra-deep well was formed. Cross section method and pressure area method were used to analyze the force on drill string after shut-in of well, it was found that the source of uplift force was the “fictitious force” caused by the hydrostatic pressure in the well. When the fictitious force is in the opposite direction to the gravity, it is the uplift force. By adopting the theory of annular multiphase flow, considering the effects of wellbore afterflow and gas slippage, the dynamic change of the pressure and fluid in the wellbore and the uplift force of drill string during the shut-in period were analyzed. The magnitude and direction of uplift force are related to the length of drill string in the wellbore and shut-in time, and there is the risk of uplift of drill string when the length of drill string in the wellbore is smaller than the critical drill string length or the shut in time exceeds the critical shut in time. A set of treatment method and process to prevent the uplift of drill string is advanced during the shut-in period after overflow in the ultra-deep well, which makes the risk management of the drill string uplift in the ultra-deep well more rigorous and scientific. Key words: ultra-deep well, drilling, overflow, shut-in, drill string, uplift force, axial loa