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Cell-free RNA (cfRNA) is a promising analyte for cancer diagnosis. Here, the authors determine the baseline cell-free transcriptome in the absence of cancer and identify tissue- and subtype-specific cfRNA biomarkers in breast and lung cancer patients.

Mediastinal tuberculous lymphadenitis rarely mimics esophageal submucosal tumor, particularly in the case of multidrug-resistant tuberculosis (MDR-TB). Herein, we report the case of a 61-year-old woman who visited a local hospital complaining of odynophagia. An initial esophagogastroduodenoscopy revealed an esophageal submucosal tumor, and subsequent chest computed tomography showed subcarinal lymphadenopathy with an esophagomediastinal fistula. The patient was then referred to Samsung Medical Center, and a second esophagogastroduodenoscopy showed deep central ulceration, as well as a suspicious fistula in the esophageal submucosal tumor-like lesion. A biopsy examination of the ulcerative lesion confirmed focal inflammation only. Next, an endobronchial, ultrasound-guided lymph node biopsy was performed, and TB was confirmed. The patient initially began a course of isoniazid, rifampicin, ethambutol, and pyrazinamide. However, after a drug sensitivity test, she was diagnosed with MDR-TB, and second-line anti-TB medications were prescribed. She recovered well subsequently.

Correctly matching the HLA haplotypes of donor and recipient is essential to the success of allogenic hematopoietic stem cell transplantation. Current HLA typing methods rely on targeted testing of recognized antigens or sequences. Despite advances in Next Generation Sequencing, general high throughput transcriptome sequencing is currently underutilized for HLA haplotyping due to the central difficulty in aligning sequences within this highly variable region. Here we present the method, HLAforest, that can accurately predict HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest correctly predicts >99% of allele group level (2 digit) haplotypes and 93% of peptide-level (4 digit) haplotypes of the most diverse HLA genes in simulations with read lengths and error rates modeling currently available sequencing technology. The method is very robust to sequencing error and can predict 99% of allele-group level haplotypes with substitution rates as high as 8.8%. When applied to data generated from a trio of cell lines, HLAforest corroborated PCR-based HLA haplotyping methods and accurately predicted 16/18 (89%) major class I genes for a daughter-father-mother trio at the peptide level. Major class II genes were predicted with 100% concordance between the daughter-father-mother trio. In fifty HapMap samples with paired end reads just 37 nucleotides long, HLAforest predicted 96.5% of allele group level HLA haplotypes correctly and 83% of peptide level haplotypes correctly. In sixteen RNAseq samples with limited coverage across HLA genes, HLAforest predicted 97.7% of allele group level haplotypes and 85% of peptide level haplotypes correctly.