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

Band gap engineering in Cu2ZnGexSn1-xS4 thin film solar cells

Photovoltaics based on kesterite Cu2ZnSnS4 (CZTS) has attracted interest as a sustainable alternative to other thin film technologies due to their tunable material properties and earth-abundance. However, the efficiency is limited to 12.6 % for selenium-containing CZTS, with a large voltage-deficit due to tail states, deep defects, secondary phases etc. In this thesis, Ge incorporation in kesterite solar cells was utilized to reduce Sn-related deep defects and tune the band gap. CZTS, Cu2ZnGeS4 (CZGS), and mixed Cu2ZnGexSn1-xS4 (CZGTS) films, and solar cells were investigated. CZGS showed wurtzite-like phases when sputter-deposited in a sulfur-rich atmosphere using GeS target. The mixture of phases could not recrystallize to kesterite phase after annealing, so, metallic Ge target was utilized for CZGTS absorber fabrication. From varying the Ge content in CZGTS, it could be concluded that CZTS grain growth increased at a low concentration of Ge. Sulfurization of CZTS layers deposited on top of CZGS was done to achieve band gap grading. Glow Discharge Optical Emission Spectroscopy showed smooth grading while Scanning Tunneling Microscopy/Energy Dispersive Spectroscopy showed a separation between larger Sn-rich grains at the front and smaller Ge-rich grains at the back. For longer annealing times, recrystallization of the complete film was seen together with a smeared-out grading. Germanium-rich absorbers often delaminated during the etching of the annealed samples. Adhesive TiN interlayer was used on the Mo-coated Soda-Lime Glass substrate to avoid delamination with partial success. Ge-containing samples showed oxygen-rich grain boundaries and voids. Oxide removal during etching has a possible connection to the issues with adhesion. Solar cell performance was not improved for graded absorbers compared to CZTS. An increasing cliff-like band alignment with the buffer layer could negate the benefit of a band gap gradient since Ge diffused to the front. CZGS solar cells with alternative buffer layer were fabricated to investigate front interface improvement. Zn1-xSnxOy (ZTO) buffer layers were deposited at various temperatures and thicknesses. The open-circuit voltage (Voc) increased to 1.1 V for CZGS/ZTO solar cells; however, Voc was relatively insensitive to ZTO band gap variations. The current was generally low but improved with KCN-etching of the CZGS absorber before deposition of the ZTO buffer layer. A possible explanation for the device behavior is the presence of an oxide interlayer for non-etched devices. The backside interface recombination can be reduced using band gap grading as well with passivation layers. Therefore, ultrathin CZTS with oxide passivation layers of AlxOy or SiOx on the back contact was investigated. The solar cell parameters improved with the addition of a thin oxide layer, but blocking behavior increased with passivation layer thickness

Comparison of micro column technology with conventional tube methods for antibody detection

BACKGROUND AND OBJECTIVES: Conventional tube technique (CTT) has been the mainstay for antibody detection in pretransfusion testing. There have been rapid technological advances in blood banking and methodology of crossmatch has been modified to improve the sensitivity of these tests and to enable automation. This study was done to compare the efficacy of three crossmatch techniques: CTT, tube low-ionic-strength-saline indirect antiglobulin test (tube LISS-IAT), and micro column technology (MCT) used in the blood bank serology laboratory. MATERIALS AND METHODS: In this prospective study, 150 samples from patients who had received two or more transfusions on two different occasions (with at least 72 h between two transfusions) were subjected to cross match by three different techniques – CTT, LISS-IAT, and MCT. RESULTS: A total of 16 cases with antibodies were identified in 150 patients. Out of 16 cases, 14 were clinically significant (anti-c = 5, anti-K = 4, anti-E = 2, anti-S = 2, anti-Jka = 1) and 2 nonclinically significant antibody cases (anti-Lea). MCT detected all the 14 clinically significant antibody cases and no case of nonclinically significant antibody. Tube LISS-IAT detected 14 antibody cases including 2 cases of non-clinically significant antibody but failed to detect 1 case of anti-c and the only case of anti-Jka. CTT detected only 10 antibody cases including 2 cases of non-clinically significant antibody and but failed to detect 3 cases of anti-c, 1 case of anti-K, 1 case of anti-E, and the only case of anti-Jka. CONCLUSION: MCT was found to be most efficacious when compared to CTT and tube LISS-IAT in detecting clinically significant red cell antibodies; although MCT missed 2 cases of Lea antibody which were detected by CTT and LISS-IAT

Methamphetamine: symptoms under the bridge

This case report discusses the abuse of methamphetamine in North East India

Vertebrobasilar dolichoectasia presenting as symptomatic obstructive hydrocephalus: A case report with review of literature

Vertebrobasilar dolichoectasia (VBD) is a common, but usually asymptomatic condition characterized by marked elongation, dilatation, and tortousity of the vertebral and basilar arteries. VBD can sometimes present with symptoms related to mass effect like cranial nerve palsies, or with ischemia or hemorrhage. Hydrocephalus is an extremely uncommon presentation of VBD. We describe here a patient with VBD who presented with symptomatic hydrocephalus due to third ventricular obstruction, which was relieved by ventriculoperitoneal shunt

Properties of the Interface Between the Atomic Layer Grown Zinc-Tin-Oxide and Cu2ZnGeS4 Relevant for Kesterite Thin-Film Solar Cells

Recently, a record open-circuit voltage (1.1 V) is obtained for wide-bandgap Cu2ZnGeS4 (CZGS) thin-film solar cells with a Zn1-xSnxOy (ZTO) buffer grown by atomic layer deposition (ALD) (N. Saini et al. Sol. RRL 2021, 2100837). However, a low short-circuit current and a small variation in device performance with ZTO properties are observed, suggesting similar interface properties. Since the CZGS absorber cannot be etched due to peeling, it is suggested that the presence of an oxide interlayer can influence the device performance. Here, the chemical and electronic properties of the near-surface region of CZGS absorber and its interface with ZTO buffers with varying properties (bandgap and thickness) are studied nondestructively by employing excitation-dependent X-ray photoelectron spectroscopy. The formation of Ge oxide species is indicated at the absorber surface during device fabrication, which is preserved during ALD. Further, it is shown that the ZTO/CZGS interface properties are similar and not influenced by variations in ZTO properties, which can explain the small variation in device performance. Thus, attention shall be given to possible absorber surface cleaning treatment typically applied before the buffer deposition for Ge-containing CZGS, and an optimization of the ALD ZTO buffer layer growth shall be considered for a non-etched absorber

Bandgap engineered Cu2ZnGexSn1−xS4 solar cells using an adhesive TiN back contact layer

Kesterite-based solar cells are mainly restricted by their lower than expected open-circuit voltage (V ) due to non-radiative recombination. Therefore, an approach to reduce bulk and interface recombination through band gap grading to induce a back surface field is attempted. This contribution presents the challenges in the formation of compositional grading of the wide bandgap material Cu ZnGe Sn S (CZGTS) and successful fabrication of solar cells with an additional adhesive TiN interlayer. It is observed that the TiN interlayer improves adhesion between CZGTS and the back contact. The microstructure of the Cu ZnSnS (CZTS) film is significantly affected by the concentration of Ge, and the existence of a Ge concentration gradient is strongly correlated to the formation of smaller Ge-rich and larger Sn-rich grains. The bandgap grading is exploited with a moderate Ge concentration of up to (Ge/(Ge+Sn) = 0.25) in CZTS. As the Ge profile stretched all the way to the front interface, the cliff-like band alignment at the front interface of the absorber could negate the beneficial effect of Ge inclusion in the bulk and back interface of the absorber. Ordering the absorber can introduce an additional downward shift in the valence band. In one of the samples, the increased ordering and high concentration of Ge in CZTS are suggested to enhance the hole barrier at the back interface. It is concluded that the effect of the bandgap grading with Ge can only be realized with optimization of interface band alignment and back contact formation. oc 2 x 1−x 4 2