RETROFIT: Reference-free deconvolution of cell-type mixtures in spatial transcriptomics.

Spatial transcriptomics (ST) profiles gene expression in intact tissues. However, ST data measured at each spatial location may represent gene expression of multiple cell types, making it difficult to identify cell-type-specific transcriptional variation across spatial contexts. Existing cell-type deconvolutions of ST data often require single-cell transcriptomic references, which can be limited by availability, completeness and platform effect of such references. We present RETROFIT, a reference-free Bayesian method that produces sparse and interpretable solutions to deconvolve cell types underlying each location independent of single-cell transcriptomic references. Results from synthetic and real ST datasets acquired by Slide-seq and Visium platforms demonstrate that RETROFIT outperforms existing reference-based and reference-free methods in estimating cell-type composition and reconstructing gene expression. Applying RETROFIT to human intestinal development ST data reveals spatiotemporal patterns of cellular composition and transcriptional specificity. RETROFIT is available at https://bioconductor.org/packages/release/bioc/html/retrofit.html.

Assessing reproducibility of high-throughput experiments in the case of missing data.

High-throughput experiments are an essential part of modern biological and biomedical research. The outcomes of high-throughput biological experiments often have a lot of missing observations due to signals below detection levels. For example, most single-cell RNA-seq (scRNA-seq) protocols experience high levels of dropout due to the small amount of starting material, leading to a majority of reported expression levels being zero. Though missing data contain information about reproducibility, they are often excluded in the reproducibility assessment, potentially generating misleading assessments. In this article, we develop a regression model to assess how the reproducibility of high-throughput experiments is affected by the choices of operational factors (eg, platform or sequencing depth) when a large number of measurements are missing. Using a latent variable approach, we extend correspondence curve regression, a recently proposed method for assessing the effects of operational factors to reproducibility, to incorporate missing values. Using simulations, we show that our method is more accurate in detecting differences in reproducibility than existing measures of reproducibility. We illustrate the usefulness of our method using a single-cell RNA-seq dataset collected on HCT116 cells. We compare the reproducibility of different library preparation platforms and study the effect of sequencing depth on reproducibility, thereby determining the cost-effective sequencing depth that is required to achieve sufficient reproducibility.

The impact of primary open-angle glaucoma: Quality of life in Indian patients.

PURPOSE: Glaucoma significantly affects the quality of life (QoL) of a patient. Despite the huge number of glaucoma patients in India, not many, QoL studies have been carried out. The purpose of the present study was to evaluate the QoL in Indian patients with varying severity of glaucoma. METHODS: This was a hospital-based, cross-sectional, analytical study of 180 patients. The QoL was assessed using orally administered QoL instruments comprising of two glaucoma-specific instruments; Glaucoma Quality of Life-15 (GQL-15) and Viswanathan 10 instrument, and 1 vision-specific instrument; National Eye Institute Visual Function Questionnaire-25 (NEIVFQ25). RESULTS: Using NEIVFQ25, the difference between mean QoL scores among cases (88.34 ± 4.53) and controls (95.32 ± 5.76) was statistically significant. In GQL-15, there was a statistically significant difference between mean scores of cases (22.58 ± 5.23) and controls (16.52 ± 1.24). The difference in mean scores with Viswanathan 10 instrument in cases (7.92 ± 0.54) and controls (9.475 ± 0.505) was also statistically significant. QoL scores also showed moderate correlation with mean deviation, pattern standard deviation, and vertical cup-disc ratio. CONCLUSION: In our study, all the three instruments showed decrease in QoL in glaucoma patients compared to controls. With the increase in severity of glaucoma, corresponding decrease in QoL was observed. It is important for ophthalmologists to understand about the QoL in glaucoma patients so as to have a more holistic approach to patients and for effective delivery of treatment.

Enigmatic Weak D antigen: An Experience in a Tertiary Care Hospital of East Delhi.

INTRODUCTION: The Rh blood group system is one of the most polymorphic and immunogenic blood group systems in humans. The expression of Rh blood group antigen is complex, among that Rh-D antigen is the most important antigen because of its immunogenicity. It is easy to detect D antigen in most of the cases. Sometimes, variable expression of Rh-D antigen leads to presence of weak forms. Weak D reacts variably with anti D sera and poses a problem in blood banking. Molecular genetics of Rh-D revealed that weak D antigen is a Rh-D phenotype that possesses less numbers of complete D antigens on the surface of red blood cells. AIM: Present study was carried out to study weak D positivity in a tertiary neuropsychiatry hospital of East Delhi for compatibility testing in blood transfusion, to assess the implications and need of weak D testing and for population genetics study. This study tried to observe pattern of weak D antigen in four broadly classified religious communities also (Hindus, Muslims, Sikhs and Christians). MATERIALS AND METHODS: This was a two years prospective hospital based study including patients as well as donors. All patients were tested for Rh-D factor by commercially available monoclonal anti-D sera. The individuals who were found negative with anti-D were further investigated for weak D antigen by using indirect antiglobulin test (IAT) by tube as well as gel card technique. RESULTS: The results were compiled by using SPSS software version 21.0 and Microsoft excel. Among 3619 cases, 3502 (96.7%) were Rh-D factor positive while 117(3.2%) were Rh D factor negative. Among these 117 Rh-D negative cases, 9 (7.6% out of total Rh-D negatives and 0.25% out of total samples) were weak D positive and 108(2.98%) were actually D negative individuals after IAT. Weak D positivity showed a slight predominance in females (55.5%). As per broad religious communities, weak D antigen was found in Hindus only and not observed in Muslims, Sikhs and Christians. In weak D positive individuals, B phenotype (0.43%) was found to be most common followed by A (0.26%) and O (0.2%). CONCLUSION: Considerably high frequency of weak D antigen was noticed in study samples of this hospital. With this data based information, it is felt worthwhile to perform weak D testing routinely of those individuals who are negative with saline anti-D to prevent possibility of haemolysis and for efficient blood transfusion practices by making compatible blood available.