Seroprevalence of SARS-CoV-2 in Pakistan: an update on epidemiological trends

The emergence of the pandemic in 2020 is a huge threat to global public health. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first reported in China in December 2019 and later spread to almost all parts of the world in four months and declared as a pandemic in March 2020. SARS-CoV-2 has infected 15.8 million people worldwide while 641,000 died of it. This study aims to report the seroprevalence of SARS-CoV-2 in Pakistan. Of total of 635 samples of symptomatic individuals processed at Genome Center for Molecular Based Diagnostics and Research Pakistan, 313 (49.3%) were found SARS-CoV-2 seropositive. The study also confirmed more seroprevalence in elderly patients (>80 years) and children less than 13 years.

A meta-analysis of Italian and Estonian individuals shows an effect of common variants in HMGCR on blood apoB levels

Aim: The aim of the study was to explore the effects of variants at HMGCR-KIF6loci on a range of cardio-metabolic phenotypes. Methods: We analyzed the range of variants within Genetics in Brisighella Health Study and KIF6 genes using an additive genetic model on 18 cardiometabolic phenotypes in a sample of 1645 individuals from the Genetics in Brisighella Health Study and replicated in 10,662 individuals from the Estonian Genome Center University of Tartu. Results: We defined directly the effects of rs3846662:C>A at HMGCR on apoB levels. The analysis also confirmed effects of on low-density lipoprotein-cholesterol and total cholesterol levels. Variants in KIF6 gene did not reveal any associations with cardiometabolic phenotypes. Conclusion: This study highlights effect of HMGCR locus on assay-determined apoB levels, an infrequent measure of blood lipids in large studies.

Cost-effective, high-throughput, single-haplotype iterative mapping and sequencing for complex genomic structures

Reference sequence of structurally complex regions can only be obtained through highly accurate clone-based approaches. We and others have successfully employed Single-Haplotype Iterative Mapping and Sequencing (SHIMS 1.0) to assemble structurally complex regions across the sex chromosomes of several vertebrate species and in targeted improvements to the reference sequences of human autosomes. However, SHIMS 1.0 was expensive and time consuming, requiring the resources that only a genome center could command. Here we introduce SHIMS 2.0, an improved SHIMS protocol to allow even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library preparation protocol, and taking advantage of high-throughput, inexpensive, short-read sequencing technologies, a small group can sequence and assemble hundreds of clones in a week. Relative to SHIMS 1.0, SHIMS 2.0 reduces the cost and time required by two orders of magnitude, while preserving high sequencing accuracy.

ARMS-PCR based diagnosis of APCB and KRAS genes in colorectal cancer patients in Iraqi Sulaimania province

Amplification Refractory Mutation System (ARMS) assay is achieved for 30 blood samples of colorectal cancer (CRC) patients including 17 male and 13 female in order to determine the mutations in APCB gene and a proto-oncogene KRAS. ARMS-PCR analysis shows that all 30 samples are negative for I1307K variant (APCB) and seven common mutations in codons 12 and 13 (APCB). In addition two CRC patient samples are randomly chosen and purified for sequencing at Genome Center/KOYA University, then the sequence of the samples were BLAST on NCBI Website. The sequence alignment showed that both samples were wild for I1307K (APCB) and (G12S, G12C, G12A, G12D, G12V, G13D) (KRAS). We believe that these variants might absent in CRC patients of Iraqi Sulaimania province.

Biobanking in Estonia

Estonia is a democratic, parliamentary republic with a health care system that is built on the principle of compulsory, solidarity-based insurance and the all-round availability of services of private service providers. Estonia has specific biobank legislation as well as oversight via data protection laws. Its population-based biobank, the Estonian Genome Center (EGCUT), established in 2001, is one of the largest biobanks in Europe, and its database may be used only for scientific research, public health research, and statistics. The EGCUT can issue data to a third party, but only in coded form. This comprehensive database of genotypic, phenotypic, health, and genealogical information represents about 5% of Estonia's adult population, and is the largest cohort ever gathered in Estonia. Government approval is required for international data sharing, and sharing can be further limited by the requirement of ethics approval and permission from Estonian government.