Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples.

Next generation sequencing (NGS) is an emerging technology becoming relevant for genotyping of clinical samples. Here, we assessed the stability of amplicon sequencing from formalin-fixed paraffin-embedded (FFPE) and paired frozen samples from colorectal cancer metastases with different analysis pipelines. 212 amplicon regions in 48 cancer related genes were sequenced with Illumina MiSeq using DNA isolated from resection specimens from 17 patients with colorectal cancer liver metastases. From ten of these patients, paired fresh frozen and routinely processed FFPE tissue was available for comparative study. Sample quality of FFPE tissues was determined by the amount of amplifiable DNA using qPCR, sequencing libraries were evaluated using Bioanalyzer. Three bioinformatic pipelines were compared for analysis of amplicon sequencing data. Selected hot spot mutations were reviewed using Sanger sequencing. In the sequenced samples from 16 patients, 29 non-synonymous coding mutations were identified in eleven genes. Most frequent were mutations in TP53 (10), APC (7), PIK3CA (3) and KRAS (2). A high concordance of FFPE and paired frozen tissue samples was observed in ten matched samples, revealing 21 identical mutation calls and only two mutations differing. Comparison of these results with two other commonly used variant calling tools, however, showed high discrepancies. Hence, amplicon sequencing can potentially be used to identify hot spot mutations in colorectal cancer metastases in frozen and FFPE tissue. However, remarkable differences exist among results of different variant calling tools, which are not only related to DNA sample quality. Our study highlights the need for standardization and benchmarking of variant calling pipelines, which will be required for translational and clinical applications.

Abdominopelvic actinomycosis in three different locations with invasion of the abdominal wall and ureteric obstruction: An uncommon presentation.

INTRODUCTION: Actinomycosis is a rare chronic infectious disease caused by Gram-positive anaerobic bacteria that normally colonize the bronchial system and gastrointestinal tract in humans. The most common diseases associated with actinomycosis are orocervicofacial, thoracic and abdominal infections involving Actinomyces israelii. Due to its rarity, its various clinical presentations and often-infiltrative characteristics in radiological imaging, it can easily be mistaken for other clinical conditions, including malignancy. PRESENTATION OF CASE: We present an uncommon case of extended abdominopelvic actinomycosis with infiltrative lesions in multiple locations, including an abscess in the abdominal wall and ureteric obstruction, which underwent successful surgical and subsequent long-term antibiotic therapy. DISCUSSION: To our knowledge, such a combination of different sites of manifestation has not yet been reported for actinomycosis in the presence of an IUD. Possible differential diagnoses included diverticulitis with covered perforation, pelvic inflammatory disease, tuberculosis and inflammatory bowel disease. The possibility of a malignant process required radical resection. As in most cases of actinomycosis, diagnosis could not be established with certainty until postoperative pathology investigation. CONCLUSION: A rare actinomyceal infection should be considered in patients with a non-specific pelvic mass and atypical abdominal presentations, especially if a previous history of IUD usage is known.

Limb shortening osteotomy in a patient with achondroplasia and leg length difference after total hip arthroplasty.

INTRODUCTION: Achondroplasia is the most common reason for disproportionate short stature. Normally, orthopedic limb lengthening procedures must be discussed in the course of this genetic disorder and have been successful in numerous achondroplastic patients in the past. In some cases, the disease may lead to leg length differences with need for surgical correction. CASE REPORT: We report a case of achondroplastic dysplastic coxarthrosis with symptomatic leg length difference after bilateral total hip arthroplasty in a 52-year-old female patient, in which a distal femoral shortening osteotomy was successfully performed. CONCLUSION: Femoral shortening osteotomy is very uncommon in patients with achondroplasia. We conclude, however, that in rare cases it can be indicated and provide the advantage of shorter operation time, less perioperative complications and faster recovery compared to leg lengthening procedures.

Thoracoscopic resection of a giant midesophageal diverticulum.

A giant midesophageal true diverticulum is a medical rarity. We report a case of successful minimally invasive resection of a giant midesophageal diverticulum masquerading as a malignancy in a young patient.