IDeRare: a lightweight and extensible open-source phenotype and exome analysis pipeline for germline rare disease diagnosis.

Objectives: Diagnosing rare diseases is an arduous and challenging process in clinical settings, resulting in the late discovery of novel variants and referral loops. To help clinicians, we built IDeRare pipelines to accelerate phenotype-genotype analysis for patients with suspected rare diseases. Materials and Methods: IDeRare pipeline is separated into phenotype and genotype parts. The phenotype utilizes our handmade Python library, while the genotype part utilizes command line (bash) and Python script to combine bioinformatics executable and Docker image. Results: We described various implementations of IDeRare phenotype and genotype parts with real-world clinical and exome data using IDeRare, accelerating the terminology conversion process and giving insight on the diagnostic pathway based on disease linkage analysis until exome analysis and HTML-based reporting for clinicians. Conclusion: IDeRare is freely available under the BSD-3 license, obtainable via GitHub. The portability of IDeRare pipeline could be easily implemented for semi-technical users and extensible for advanced users.

Determinants of prematurity in urban Indonesia: a meta-analysis.

OBJECTIVES: Indonesia is the fifth country with the highest number of preterm births worldwide. More than a third of neonatal deaths in Indonesia were attributed to preterm birth. Residential areas affected the occurrence of preterm birth due to differing socioeconomic and environmental conditions. Many studies have investigated the determinants of prematurity in Indonesia, however, most of them were performed in rural areas. This study is the first meta-analysis describing the determinants of preterm birth in urban Indonesia, which aimed to become the foundation upon implementing the most suitable preventative measure and policy to reduce the rate of preterm birth. METHODS: We collected all published papers investigating the determinants of preterm birth in urban Indonesia from PubMed MEDLINE and EMBASE, using keywords developed from the following key concepts: "preterm birth", "determinants", "risk factors", "Indonesia" and the risk factors, such as "high-risk pregnancy", "anemia", "pre-eclampsia", and "infections". Exclusion criteria were multicenter studies that did not perform a specific analysis on the Indonesian population or did not separate urban and rural populations in their analysis, and articles not available in English or Indonesian. The Newcastle Ottawa Scale was used to assess the risk of bias. This systematic review was registered in PROSPERO. RESULTS: Sixteen articles were included in the analysis and classified into five categories: genetic factors, nutrition, smoking, pregnancy characteristics or complications, and disease-related characteristics. CONCLUSIONS: Our meta-analysis revealed adolescent pregnancy, smoking, eclampsia, bacterial vaginosis, LC-PUFA, placental vitamin D, and several minerals as the significant determinants of preterm birth in urban Indonesia.

A Mixed Gonadal Dysgenesis in an 19 Year Old Girl with Ambigous Genitalia: A Case Report.

A 19-year-old girl was referred with delayed puberty and ambiguous genitalia. She had short stature with high blood pressure and Turner's stigmata with external genitalia Prader Score 4. Ultrasound revealed hypoplastic uterus with no gonad. Follicle stimulating hormone, luteinizing hormone and testosterone level were increased (51.29 mIU/mL, 23.66 mIU/mL and 742 ng/dl). Karyotyping revealed 46 XY with Fluorescence in situ hybridization cytogenetic study based on 300 cells showed mosaic chromosome, monosomy X (17%) and XY (83%). Laparascopic gonadectomy was done and showed that testes were only in the right inguinal canal. Then patient had external genitalia reconstruction and received estrogen replacement therapy.

Genetics and genomic medicine in Indonesia.

Genetics and genomic medicine in Indonesia.