A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

Background

Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies.

Objective

The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now.

Results

The proposed study, based on previous studies and manufacturers' descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position.

Conclusion

The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.

Compound Homozygous Rare Mutations in PLCE1 and HPS1 Genes Associated with Autosomal Recessive Retinitis Pigmentosa in Pakistani Families

Background

Retinitis pigmentosa (RP) belongs to pigmentary retinopathies, a generic name for all retinal dystrophies with a major phenotypical and genotypical variation, characterized by progressive reduction of photo-receptor functionality of the rod and cone. Global prevalence of RP is ~ 1/4000 and it can be inherited as autosomal dominant (adRP), autosomal recessive (arRP) or X- linked (xlRP). We designed this study to identify causative mutations in Pakistani families affected with arRP.

Methods

In 2019, we recruited two unrelated Pakistani consanguineous families affected with progressive vision loss and night blindness from Punjab region. Clinical diagnosis confirmed the; bone spicule pigmentation of the retina, and an altered electroretinogram (EGR) response. Proband and healthy individual from each family were subjected for whole-exome sequencing (WES). Various computational tools were used to analyze the Next Generation Sequencing (NGS) data and to predict the pathogenicity of the identified mutations.

Results

WES data analysis highlighted two missense homozygous variants at position c.T1405A (p.S469T) in PLCE1 and c.T11C (p.V4A) in HPS1 genes in proband of both families. Healthy individuals of two families were tested negative for p.S469T and p.V4A mutations. The variant analysis study including molecular dynamic simulations predicted mutations as disease causing.

Conclusion

Compound effect of mutations in rarely linked PLCE1 and HPS1 genes could also cause RP. This study highlights the potential application of WES for a rapid and precise molecular diagnosis for heterogeneous genetic diseases such as RP.

A 58-Year-Old Woman with Gallstones, Chronic Pancreatitis, and Pancreatic Pseudocyst Presenting with Pleural Effusion Due to a Pancreaticopleural Fistula

BACKGROUND Pancreaticopleural fistula (PPF) is a rare complication of acute and chronic pancreatitis. PPF results from the release of pancreatic enzymes, either from a damaged pancreatic duct or pancreatic pseudocyst. This report is of a 58-year-old woman with a history of chronic pancreatitis associated with gallstones who had a known pancreatic pseudocyst that was being managed conservatively and who presented to the Emergency Department with pleural effusion due to a PPF. CASE REPORT A 58-year-old woman with past medical history of gallstone pancreatitis with subsequent development of pancreatic pseudocyst (being managed conservatively) presented with a 2-week history of progressive exertional shortness of breath. Physical examination indicated decreased breath sounds on the right lower lung fields. A chest X-ray revealed possible subphrenic free air. Laboratory test results were unremarkable except for elevated D-dimer levels. Computed tomography angiography revealed a large right-sided pleural effusion, which led to thoracentesis and the results illustrated elevated amylase levels. Magnetic resonance cholangiopancreatography was done, which showed pancreatic pseudocyst and possibly a fistula. Pancreatic enzymes were not checked in pleural fluid, as diagnosis was established with the presence of amylase and imaging findings. The patient felt better clinically after thoracentesis with volume removal and was discharged. She later underwent endoscopic ultrasound, which revealed a pancreatic duct leak requiring stent placement. CONCLUSIONS Pleural effusions rarely occur secondary to PPF. Physicians must be wary of the presentation, especially in patients with a history of a conservatively managed pancreatitis pseudocyst. Early diagnosis and management can lead to prevention of long-term morbidity and mortality.

Hypercalcaemia Caused by Sunflower Seeds and Calcium Carbonate Supplements

Introduction

Hypercalcaemia is commonly associated with malignancy or endocrinological disorders. However, sometimes it can occur due to increased oral intake of calcium. We present an interesting case of hypercalcaemia due to ingestion of sunflower seeds and calcium carbonate supplements.

Case Description

We present the case of a 53-year-old man with history of T-cell lymphoma and gastroesophageal reflux disease who was brought to the emergency room due to altered mental status, nausea, vomiting and abdominal pain. His calcium level was 3.30 mmol/l (normal value 2.23-2.58 mmol/l). Imaging studies were unremarkable. The patient was hydrated with normal saline and calcium levels improved. Once he was more coherent, he disclosed that he had consumed significant amounts of sunflower seeds and calcium carbonate supplements, which were considered to be the cause of his hypercalcaemia.

Conclusion

Hypercalcaemia is common and can lead to critical illness. Although hypercalcaemia is frequently associated with endocrinological disorders, sometimes the presentation is secondary to increased intake. The consumption of sunflower seeds and antacids containing calcium carbonate can cause symptomatic hypercalcaemia. It is important to recognize rare causes of hypercalcaemia in order to treat it in a timely manner and prevent recurrence.

LEARNING POINTS

Hypercalcaemia can occur due to excessive intake of sunflower seeds and calcium carbonate supplements.Hydration and cessation of oral supplements can result in rapid reversal of hypercalcaemia.It is important to obtain a complete history in order to determine the aetiology of hypercalcaemia.

A Case of Evans Syndrome and Unstable Angina

Evans syndrome (ES) is characterized by autoimmune hemolytic anemia (AIHA) and immune-mediated thrombocytopenia. It is more common in the pediatric population than in adults. ES has been reported to be associated with thrombotic events and rarely can lead to acute coronary syndrome (ACS). There have been only a few reported cases of ACS secondary to ES. We present an interesting case of ES with unstable angina (UA) which had a limited response to oral and intravenous (IV) steroids requiring rituximab. A 64-year-old male with past medical history significant for hypertension, hyperlipidemia, diabetes mellitus and coronary artery disease, presented to the emergency room complaining of a 2-week history of chest pain, shortness of breath and hematuria. Physical examination indicated splenomegaly but was otherwise unremarkable with no petechiae or rash. Labs showed hemoglobin of 9.6 g/dL, platelet count 58 × 10³/µL, troponin < 0.03 ng/mL, lactic acid 2.5 mmol/L and with parameters indicative of hemolysis, evidenced by elevated lactate dehydrogenase, low haptoglobin and elevated bilirubin levels. Electrocardiography (EKG) demonstrated ST depression in leads I, aVL, V5 - V6 and T wave inversions in lead III and aVL, which were new compared to previous EKG. Peripheral blood smear indicated spherocytes. Direct antiglobulin test was positive for immunoglobulin G (IgG). Patient was admitted for ES and initially treated with oral prednisone 80 mg daily. He was also diagnosed with UA thought to be possibly secondary to ES. He then underwent cardiac stress test which showed mild reversible inferior apical ischemia. Cardiac catheterization revealed 95% stenosis of proximal left circumflex artery requiring single drug eluding stent placement and dual antiplatelet therapy. Patient continued to have anemia despite blood transfusions, although platelet count improved. Prednisone was transitioned to high-dose IV dexamethasone, and patient was also started on rituximab which resulted in stabilization of anemia. The presentation of ES with ACS is a rare occurrence. ACS can be challenging to manage as stent placement may be required followed by dual antiplatelet therapy. Treatment of ES involves steroids followed by rituximab, IV immunoglobulin (IVIG) or splenectomy for non-responsive cases. Early intervention and management can prevent mortality and morbidity.

Hypercalcaemia Caused by Sunflower Seeds and Calcium Carbonate Supplements

Introduction: Hypercalcaemia is commonly associated with malignancy or endocrinological disorders. However, sometimes it can occur due to increased oral intake of calcium. We present an interesting case of hypercalcaemia due to ingestion of sunflower seeds and calcium carbonate supplements. Case Description: We present the case of a 53-year-old man with history of T-cell lymphoma and gastroesophageal reflux disease who was brought to the emergency room due to altered mental status, nausea, vomiting and abdominal pain. His calcium level was 3.30 mmol/l (normal value 2.23–2.58 mmol/l). Imaging studies were unremarkable. The patient was hydrated with normal saline and calcium levels improved. Once he was more coherent, he disclosed that he had consumed significant amounts of sunflower seeds and calcium carbonate supplements, which were considered to be the cause of his hypercalcaemia. Conclusion: Hypercalcaemia is common and can lead to critical illness. Although hypercalcaemia is frequently associated with endocrinological disorders, sometimes the presentation is secondary to increased intake. The consumption of sunflower seeds and antacids containing calcium carbonate can cause symptomatic hypercalcaemia. It is important to recognize rare causes of hypercalcaemia in order to treat it in a timely manner and prevent recurrence.

Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene

Single Nucleotide Polymorphisms (SNPs) are the most common candidate mutations in human beings that play a vital role in the genetic basis of certain diseases. Previous studies revealed that Solute Carrier Family 26 Member 4 (SLC26A4) being an essential gene of the multi-faceted transporter family SLC26 facilitates reflexive movement of Iodide into follicular lumen through apical membrane of thyrocyte. SLC26A4 gene encodes Pendred protein, a membrane glycoprotein, highly hydrophobic in nature, present at the apical membrane of thyrocyte functioning as transporter of iodide for thyroid cells. A minor genetic variation in SLC26A4 can cause Pendred syndrome, a syndrome associated with thyroid glands and deafness. In this study, we performed in-silico analysis of 674 missense SNPs of SLC26A4 using different computational platforms. The bunch of tools including SNPNEXUS, SNAP-2, PhD-SNP, SNPs&GO, I-Mutant, ConSurf, and ModPred were used to predict 23 highly confident damaging and disease causing nsSNPs (G209V, G197R, L458P, S427P, Q101P, W472R, N392Y, V359E, R409C, Q235R, R409P, G139V, G497S, H723R, D87G, Y127H, F667C, G334A, G95R, S427C, R291W, Q383H and E384G) that could potentially alter the SLC26A4 gene. Moreover, protein structure prediction, protein-ligand docking and Molecular Dynamics simulation were performed to confirm the impact of two evident alterations (Y127H and G334A) on the protein structure and function.

Antral Helicobacter pylori in patients with chronic renal failure

Patients with chronic renal failure who were undergoing dialysis were recently shown to have a low prevalence of duodenal Helicobacter (Campylobacter) pylori colonisation in spite of a high incidence of gastric metaplasia. The prevalence of the organism in the gastric antrum of 50 similar patients was estimated and compared with that in a control group comprising 120 consecutive patients with no renal failure who were being investigated for a variety of symptoms and signs related to the upper alimentary tract. Seventeen of the patients with renal disease had upper gastrointestinal symptoms. The prevalence of antral H pylori was significantly less in patients with renal disease (12, 24%) than in the control group (51, 42%), but was associated with a similar active chronic inflammatory reaction with prominent lymphoid follicles. The prevalence of the bacteria in patients with renal disease was similar to that reported in normal volunteers, and was the same whether the patients had upper gastrointestinal symptoms or not. This low prevalence may be related to the wide variety of medication, including antibiotics, which these patients are prescribed during the course of their illness.

Helicobacter pylori is not identified in areas of gastric metaplasia of gall bladder

Sections from 200 cholecystectomy specimens were searched microscopically for areas of gastric metaplasia and Helicobacter (Campylobacter) pylori colonization. The presence of gastric metaplasia was confirmed in 31 cases by the presence of tall columnar cells with abundant apical neutral mucin. Examination of haematoxylin and eosin and, in some cases, Warthin-Starry stained sections failed to demonstrate H. pylori in any of these 31 cases or in 29 other cases with 'bladder neck-type mucous gland metaplasia'. The failure of H. pylori to colonize areas of gastric metaplasia in the gall bladder confirms their intolerance to high concentrations of bile.