Using HapMap data: a cautionary note

The HapMap data are being widely used in human genetic studies. We show by direct resequencing of a 6-kb region of chromosome 1 that the HapMap data are unreliable for this region. This region contains a recent mitochondrial (mt) DNA insertion. The HapMap data report the corresponding mtDNA variation and not the nuclear DNA variation. In view of mtDNA insertions of varying lengths throughout the human genome and considerable segmental duplications, it is necessary to use the HapMap data cautiously

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

Abstract: The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era

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

A large, systematic molecular-genetic study of G6PD in Indian populations identifies a new non-synonymous variant and supports recent positive selection

Malaria has been endemic in India. G6PD deficiency is known to confer resistance to malaria. Many G6PD deficiency variants, some of which are India-specific, are known to occur in high frequencies in India. This is the first systematic molecular-genetic study in multiple populations from India drawn from diverse ethnic, socio-cultural and geographical backgrounds. Resequencing of the G6PD gene was carried out in 80 males and then the polymorphic variants were genotyped in 400 individuals of both genders, drawn from 10 ethnic groups of India. Our study has identified one new exonic variant (M159I; exon-5), occurring in multiple populations, that is predicted to result in G6PD deficiency. A strong geographical sub-structuring of known G6PD variants has also been established. We have compared all available data from public-domain resources with those generated in this study to identify the nature and extent of natural selection. Our results (a) provide indication of weak negative selection, and (b) reveal signals of recent positive selection for the G6PD Orissa and G6PD Coimbra mutation bearing haplotypes. These inferences have been interpreted in the light of malarial protection to the populations that have been long exposed to plasmodium infection

Study of Caspase 8 mutation in oral cancer and adjacent precancer tissues and implication in progression.

It is hypothesized that same driver gene mutations should be present in both oral leukoplakia and cancer tissues. So, we attempted to find out mutations at one of the driver genes, CASP8, in cancer and adjacent leukoplakia tissues. Patients (n = 27), affected by both of cancer and adjacent leukoplakia, were recruited for the study. Blood and tissue DNA samples were used to identify somatic mutations at CASP8 by next generation sequencing method. In total, 56% (15 out of 27) cancer and 30% (8 out of 27) leukoplakia tissues had CASP8 somatic mutations. In 8 patients, both cancer and adjacent leukoplakia tissues, located within 2-5 cm of tumor sites, had identical somatic mutations. But, in 7 patients, cancer samples had somatic mutations but none of the leukoplakia tissues, located beyond 5cm of tumor sites, had somatic mutations. Mutated allele frequencies at CASP8 were found to be more in cancer compared to adjacent leukoplakia tissues. This study provides mutational evidence that oral cancer might have progressed from previously grown leukoplakia lesion. Leukoplakia tissues, located beyond 5cm of cancer sites, were free from mutation. The study implies that CASP8 mutation could be one of the signatures for some of the leukoplakia to progress to oral cancer

Analysis of the whole transcriptome from gingivo-buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy

<div><p>Background</p><p>Gingivo-buccal squamous cell carcinoma (GBSCC) is one of the most common oral cavity cancers in India with less than 50% patients surviving past 5 years. Here, we report a whole transcriptome profile on a batch of GBSCC tumours with diverse tobacco usage habits. The study provides an entire landscape of altered expression with an emphasis on searching for targets with therapeutic potential.</p><p>Methods</p><p>Whole transcriptomes of 12 GBSCC tumours and adjacent normal tissues were sequenced and analysed to explore differential expression of genes. Expression changes were further compared with those in TCGA head and neck cohort (n = 263) data base and validated in an independent set of 10GBSCC samples.</p><p>Results</p><p>Differentially expressed genes (n = 2176) were used to cluster the patients based on their tobacco habits, resulting in 3 subgroups. Immune response was observed to be significantly aberrant, along with cell adhesion and lipid metabolism processes. Different modes of immune evasion were seen across 12 tumours with up-regulation or consistent expression of <i>CD47</i>, unlike other immune evasion genes such as <i>PDL1</i>, <i>FUT4</i>, <i>CTLA4</i> and <i>BTLA</i> which were downregulated in a few samples. Variation in infiltrating immune cell signatures across tumours also indicates heterogeneity in immune evasion strategies. A few actionable genes such as <i>ITGA4</i>, <i>TGFB1</i> and <i>PTGS1/COX1</i> were over expressed in most samples.</p><p>Conclusion</p><p>This study found expression deregulation of key immune evasion genes, such as <i>CD47</i> and <i>PDL1</i>, and reasserts their potential as effective immunotherapeutic targets for GBSCC, which requires further clinical studies. Present findings reiterate the idea of using transcriptome profiling to guide precision therapeutic strategies.</p></div

Schematic view of fusion events.

<p>(A) ANO1-PLA2G16 fusion gene which retains exon 16 along with upstream exons of ANO1 and exon 3 along with downstream exons of PLA2G16 in tumour tissue (i.e. 23D) of the tumour-normal paired S23 sample. (B) S100A9-KRT17 fusion gene deduced from coding regions up to exon 3 of S100A9 and exon 1 to all other downstream exons of KRT17 in tumour tissue (i.e. 2D) of the tumour-normal paired S2 sample.</p

Expression deregulation of miRNA and target mRNAs.

<p>(A) Bar plots show log₂fold change in expression of miRNAs (hsa-miR-18b, hsa-miR-1293and hsa-miR-21) and their target, TIMP3. Scatter plots show negative correlation of TIMP3 expression with hsa-miR-18b and hsa-miR-21expression. Negative correlation was not observed between TIMP3 and hsa-miR-1293. Negative values of log₂fold change indicate upregulated expression whereas positive log₂fold change values indicate downregulation. (B) Bar plot showslog₂fold change of expression of miRNAs (hsa-miR-126 and hsa-miR-7) and their target, IRS1. Scatter plot shows negative correlation of IRS1 expression with hsa-miR-126 and hsa-miR-7expression. Negative values of log₂fold change indicate upregulated expression whereas positive fold change values indicate downregulation.</p

Immune response alterations in tumor compared to normal tissues.

<p>(A) Heatmap shows diverse expression levels (log fold change of FPKM values) of immune evasion genes. Orange values in color bar shows up regulation while values in blue show down regulation. The panel below shows proliferation scores per samples with green color intensity indicating higher proliferation score and numbers indicates % CCP score. The right-side panel indicates fold change values (FPKM) in TCGA HNSCC cohort (n = 263) for each gene. In case of TCGA HNCC tissues, Green color denotes downregulation while red color shows upregulation in the right-side panel. (B) The barplot shows how relative composition of immune cells is altered across 12 pairs of tumor compared to its control tissues. Plot was derived from the <i>CIBERSORT</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183606#pone.0183606.ref009" target="_blank">9</a>] estimated data output from FPKM normalized expression data. Every color stands for a type of immune cell and height of each colored bar represents relative frequency of an immune cell type. In the plot, 2N and 2D indicate normal and tumour tissues of tumour-normal paired S2sample, respectively. Similar nomenclature was used for tumour and normal tissues of other samples.</p

Hierarchical clustering of GBSCC tumours by 2176 deregulated gene expressions.

<p>Hierarchical clusters were constructed based on log2 transformed expression values of 1002 upregulated (represented by colours of negative values in heatmap) and 1174 downregulated genes (represented by colours of positive values in heatmap). Across all 12 tumours there is a gross similarity in deregulation pattern, with some exceptions. As a result, 3 distinct sample clusters were noticed. The coloured panel below, represent subject's smoking (orange) and/or chewing tobacco (red) and/or alcohol abuse (green)status.</p