Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.

Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited.

Phytochemicals and bioactive compounds effective against acute myeloid leukemia: A systematic review.

This systematic review identified various bioactive compounds which have the potential to serve as novel drugs or leads against acute myeloid leukemia. Acute myeloid leukemia (AML) is a heterogeneous hematopoietic malignancy that arises from the dysregulation of cell differentiation, proliferation, and cell death. The risk factors associated with the onset of AML include long-term exposure to radiation and chemicals such as benzene, smoking, genetic disorders, blood disorders, advancement in age, and others.

Clinical Profile of Adult Bronchial Asthma Patients Presenting at a Tertiary Care Teaching Institute in Northern India.

Background: In the previous four decades there have been remarkable changes and development in the approach toward the diagnosis and management of asthma. There are wide variations in the clinical profile of asthma patients in different parts of a vast country like India due to significant variations in the geography, culture, ethnicity, and socioeconomic profile of the Indian population. In the present study, we have aimed to study the clinical profile of adult asthmatic patients in a tertiary care teaching institute in Northern India.

A Rare Case of Sternoclavicular Tuberculosis Diagnosed Using Microchip-Based Polymerase Chain Reaction in a Diabetic Female.

Osteoarticular tuberculosis (TB) accounts for almost 10% of all extrapulmonary TB cases. In the majority of cases, the spine, knee, hip, and large bones are involved; other sites like the sternoclavicular joint, elbow, wrist, and smaller joints are infrequently involved. Uncommon locations of extrapulmonary TB pose a challenge in diagnosis due to lack of clinical suspicion, non-availability of samples, and unavailability of suitable diagnostic modalities.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples.

Fluorescent carbon dots driven from ayurvedic medicinal plants for cancer cell imaging and phototherapy.

Ayurveda based nanomaterials are recently conceptualized phenomena for biomedical applications especially for imaging and treatment of in vitro cancer cell. Wide range florescent (blue to red emission) quantum dots are versatile materials for imaging and sensing applications. Various procedures and precursors of fluorescent carbon quantum dots (CQDs) are well established and documented in the literature.

Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia.

Background: Methylation changes are frequent in cancers, but understanding how hyper- and hypomethylated region changes coordinate, associate with genomic features, and affect gene expression is needed to better understand their biological significance. The functional significance of hypermethylation is well studied, but that of hypomethylation remains limited. Here, with paired expression and methylation samples gathered from a patient/control cohort, we attempt to better characterize the gene expression and methylation changes that take place in cancer from B cell chronic lymphocyte leukemia (B-CLL) samples.

A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data.

Backgroud: DNA methylation is an epigenetic modification that plays important roles on gene regulation. Study of whole-genome bisulfite sequencing and reduced representation bisulfite sequencing brings the availability of DNA methylation at single CpG resolution. The main interest of study on DNA methylation data is to test the methylation difference under two conditions of biological samples.

PRIMEGENSw3: a web-based tool for high-throughput primer and probe design.

Highly specific and efficient primer and probe design has been a major hurdle in many high-throughput techniques. Successful implementation of any PCR or probe hybridization technique depends on the quality of primers and probes used in terms of their specificity and cross-hybridization. Here we describe PRIMEGENSw3, a set of web-based utilities for high-throughput primer and probe design.

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.

We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21,408 CGIs and more than 15,946 transcriptional regulatory regions. Of the CpGs analyzed, 77-84% fell on or near capture probe sequences; 69-75% fell within CGIs.

Homolog-specific PCR primer design for profiling splice variants.

To study functional diversity of proteins encoded from a single gene, it is important to distinguish the expression levels among the alternatively spliced variants. A variant-specific primer pair is required to amplify each alternatively spliced variant individually. For this purpose, we developed a new feature, homolog-specific primer design (HSPD), in our high-throughput primer and probe design software tool, PRIMEGENS-v2.