Clinical exome sequencing reveals a novel pathogenic variant in KIF12 underlying cholestasis with highly variable phenotypes.

Four affected individuals from a large consanguineous family were diagnosed with variable phenotypes of cholestasis based on their clinical laboratory and biopsy findings. Cholestasis is a condition when there is not enough bile flow between liver and small intestine. Two of the affected individuals (IV-1, IV-4) died of cholestatic liver at an early age, while the other two patients are alive with chronic liver disease. Clinical exome and Sanger sequencing identified a novel homozygous pathogenic variant (c.482-7_500del) in the patients.

Mutational spectrum of CFTR in cystic fibrosis patients with gastrointestinal and hepatobiliary manifestations.

BACKGROUND: Cystic fibrosis (CF) is a rare and debilitating autosomal recessive disorder. It hampers the normal function of various organs and causes severe damage to the lungs, and digestive system leading to recurring pneumonia. Cf also affects reproductive health eventually may cause infertility. The disease manifests due to genetic aberrations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This study aimed to screen for CFTR gene variants in Pakistani CF patients representing variable phenotypes. METHODS: Clinical exome and Sanger sequencing were performed after clinical characterization of 25 suspected cases of CF (CF1-CF25). ACMG guidelines were followed to interpret the clinical significance of the identified variants. RESULTS: Clinical investigations revealed common phenotypes such as pancreatic insufficiency, chest infections, chronic liver and lung diseases. Some patients also displayed symptoms like gastroesophageal reflux disease (GERD), neonatal cholestasis, acrodermatitis, diabetes mellitus, and abnormal malabsorptive stools. Genetic analysis of the 25 CF patients identified deleterious variants in the CFTR gene. Notably, 12% of patients showed compound heterozygous variants, while 88% had homozygous variants. The most prevalent variant was p. (Met1Thr or Met1?) at 24%, previously not reported in the Pakistani population. The second most common variant was p. (Phe508del) at 16%. Other variants, including p. (Leu218*), p. (Tyr569Asp), p. (Glu585Ter), and p. (Arg1162*) were also identified in the present study. Genetic analysis of one of the present patients showed a pathogenic variant in G6PD in addition to CFTR. CONCLUSION: The study reports novel and reported variants in the CFTR gene in CF patients in Pakistani population having distinct phenotypes. It also emphasizes screening suspected Pakistani CF patients for the p. (Met1Thr) variant because of its increased observance and prevalence in the study. Moreover, the findings also signify searching for additional pathogenic variants in the genome of CF patients, which may modify the phenotypes. The findings contribute valuable information for the diagnosis, genetic counseling, and potential therapeutic strategies for CF patients in Pakistan.

Frequency of vitamin D deficiency in children with iron deficiency anaemia and factors associated with vitamin D deficiency.

Objective: To evaluate vitamin D deficiency in children with iron-deficiency anaemia, and to identify the risk factors for such deficiency. METHODS: The cross-sectional study was conducted at the Children's Hospital, Pakistan Institute of Medical Sciences, Islamabad, Pakistan, from October 2021 to March 2022, and comprised children aged 1-5 years who had been diagnosed with iron-deficiency anaemia. Quantitative variables, like age, height, weight, gender, socioeconomic status and sibling status, were controlled by stratification. Data was compared to assess the risk factors of vitamin D deficiency among the subjects. Data was analysed using SPSS 22. RESULTS: Of the 236 children with iron-deficiency anaemia, 159(67.5%) also had vitamin D deficiency; 95(59%) girls and 65(41%) boys. Overall, 104(65.4%) subjects were aged 4-5 years and 55(34.6%) were aged 1-3 years. Vitamin D deficiency had significant association with female gender, older age, height and weight <5th centiles, educated parents, low to middle socioeconomic status, urban residence and higher number of siblings (p<0.05). CONCLUSIONS: The prevalence of vitamin D deficiency among children with iron-deficiency anaemia was found to be high.

Whole exome sequencing identified a novel splice donor site variant in interleukin 2 receptor alpha chain.

Interleukin 2 receptor alpha chain (IL-2Rα or CD25) deficiency (OMIM #606367) is an immune dysregulation disorder segregating in autosomal recessive form. The disease is caused by biallelic variants in the IL-2Rα gene encoding IL-2Rα also known as CD25 protein. IL-2Rα combines with γ and ß chains of interleukin 2 receptor to form a functional interleukin 2 receptor (IL-2R). In the present study, we identified a Pakistani family presenting a unique presentation of IL-2Rα deficiency. Clinical whole exome sequencing revealed a novel splice donor site variant (NM_001378789.1 (NP_001365718); c.64 + 1G > A) in the IL-2Rα gene. American College of Medical Genetics (ACMG) guidelines interpreted the identified variant as likely pathogenic. The IL-2Rα gene mutation usually presents with autoimmunity and immunodeficiency but in our patient, it presents with congenital diarrhea, metabolic crisis, and strong family history of death in infancy due to the similar complications. Her congenital diarrhea is attributed to autoimmunity in the form of autoimmune enteropathy and eczema. The laboratory findings revealed severe metabolic acidosis hypokalemia and elevated lactate and ammonia levels. This is a new presentation of IL-2Rα gene mutation. The present study highlights the importance of clinical whole exome sequencing in the correct diagnosis of congenital disorders. The study will also help clinical geneticists for genetic counseling and prevention of the disease in the affected family.

ADLAuth: Passive Authentication Based on Activity of Daily Living Using Heterogeneous Sensing in Smart Cities.

The Internet of Things is a rapidly growing paradigm for smart cities that provides a way of communication, identification, and sensing capabilities among physically distributed devices. With the evolution of the Internet of Things (IoTs), user dependence on smart systems and services, such as smart appliances, smartphone, security, and healthcare applications, has been increased. This demands secure authentication mechanisms to preserve the users' privacy when interacting with smart devices. This paper proposes a heterogeneous framework "ADLAuth" for passive and implicit authentication of the user using either a smartphone's built-in sensor or wearable sensors by analyzing the physical activity patterns of the users. Multiclass machine learning algorithms are applied to users' identity verification. Analyses are performed on three different datasets of heterogeneous sensors for a diverse number of activities. A series of experiments have been performed to test the effectiveness of the proposed framework. The results demonstrate the better performance of the proposed scheme compared to existing work for user authentication.

Primary Antibiotic Resistance And Effectiveness Of Clarithromycin Vs Metronidazole Based Therapy For Helicobacter Pylori Infection In Children.

BACKGROUND: NASPGHAN guidelines recommend regional antibiotic susceptibility profiling for H. pylori eradication treatment. Profiling local antibiotic resistance patterns is mandatory for successful H. pylori eradication in children. The aim of our study was to determine primary resistance to Clarithromycin and Metronidazole, most commonly used in the eradication regimens in children presenting with symptomatic H. pylori infection. This study was conducted at Children Hospital PIMS Islamabad from June 2020 to August 2021. METHODS: The children of either gender age 2-14 years having symptomatic H. pylori infection (hematemesis, chronic abdominal pain) underwent stool for H. pylori Antigen. Children requiring urgent diagnostic endoscopy underwent rapid urease tests. Biopsies were taken from children having positive stool H. pylori Ag and rapid urease test for histological examination. The biopsy specimens were cultured and subsequently tested for antibiotic sensitivity. RESULTS: Out of 54 children having H. pylori infection 40/54 (74.074%) children had strains susceptible to antimicrobials and 14/54 (25.92%) were having resistance to antimicrobials. According to the pattern of antimicrobial sensitivity, they were further grouped into three (a) Clarithromycin and Metronidazole sensitive group (18/40, 45%) (b) Clarithromycin sensitive and Metronidazole resistant group (12/40, 30%) (c) Metronidazole sensitive group (10/40 25%). CONCLUSIONS: Clarithromycin and Metronidazole cannot be used as1stline treatment for H. pylori eradication in children and can only be used with known antimicrobial susceptibility.