Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population

Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip

Primary Intracranial Squamous Cell Carcinoma in the Brain Stem with a Cerebellopontine Angle Epidermoid Cyst

Primary intracranial squamous cell carcinoma is extremely rare, with most cases arising from a preexisting benign epidermoid cyst. We report a rare case of primary intracranial squamous cell carcinoma in the brain stem with a cerebellopontine angle (CPA) epidermoid cyst. A 72-year-old female suffered from progressive left hemiparesis, difficulty in swallowing, and right hemifacial numbness. Diffusion-weighted magnetic resonance imaging revealed a high signal intensity (SI) lesion in the CPA region and an intra-axially ring-enhanced cystic mass in the right brain stem with low SI. Whole-body positron emission tomography showed no evidence of metastatic disease. The histological findings revealed a typical epidermoid cyst in the CPA region and a squamous cell carcinoma in the brain stem. We speculate that the squamous cell carcinoma may have been developed due to a chronic inflammatory response by the adjacent epidermoid cyst. The patient underwent a surgical resection and radiotherapy. After 12 months, she had no evidence of recurrence

Cerebellar Pilocytic Astrocytomas with Spontaneous Intratumoral Hemorrhage in Adult

Cerebellar pilocytic astrocytomas (PAs) are benign gliomas predominantly found in the pediatric population. Intracranial hemorrhages are extremely rare in initial presentations of cerebellar PAs. There are no reports in the medical literature of adult cerebellar PA cases presenting with intratumoral hemorrhage. We report 2 cases of adult cerebellar pilocytic astrocytomas with intratumoral hemorrhage. The first case is a 37-year-old woman presenting with severe headache, nausea, and vomitting. Computed tomography demonstrated an acute hemorrhage adjacent to the right cerebellar hemisphere and hydrocephalus. Magnetic resonance imaging (MRI) revealed a cerebellar vermian tumor with the hemorrhage as a mixed isointense area in the T2-weighted image, and as a mixed hyperintense area in the contrast-enhanced T1-weighted image. The second case is a 53-year-old man presenting with headache for 3 weeks. MRI revealed a cerebellar hemispheric tumor with the hemorrhage as a mixed hyperintense area. It had a cystic mass with a heterogeneous enhanced mural nodule in the gadolinium-enhanced T1-weighted image and a fluid-fluid level within the cyst in the T2-weighted image. Both of them underwent radical resections of their respective lesions. Histological examination of the specimens revealed typical astrocytoma, including a hemorrhagic portion. Both patients recovered postoperatively and continue to do well at present. The medical literature on hemorrhagic cerebellar PAs is also reviewed