MR1 encompasses at least six allele groups with coding region alterations.

Unlike classical HLA class I genes, MR1 is assumed to have limited polymorphic positions. We developed a MR1 specific PCR assay and sequenced 56 DNA samples from cells with a diverse set of HLA genotypes. In this relatively small panel we found six allele groups encoding for different MR1 proteins. The two most frequent allele groups found in this panel had a frequency of 71% (MR1*01) and 25% (MR1*02), respectively. Moreover, the panel contained many intronic SNPs and silent variants, with individual samples containing up to 15 heterozygous positions. The data presented here is consistent with marked variation in MR1.

Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing.

The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and software developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information - message annotation, reference context, full genotype, consensus sequence and novel polymorphism - and references to three categories of accessory information - NGS platform documentation, read processing documentation and primary data. These eight categories of information ensure the long-term portability and broad application of this NGS data for all current histocompatibility and immunogenetics use cases. In addition, MIRING can be extended to allow the reporting of genotype data generated using pre-NGS technologies. Because genotyping results reported using MIRING are easily updated in accordance with reference and nomenclature databases, MIRING represents a bold departure from previous methods of reporting HLA and KIR genotyping results, which have provided static and less-portable data. More information about MIRING can be found online at miring.immunogenomics.org.

Analytical sensitivity and stability of DNA methylation testing in stool samples for colorectal cancer detection.

BACKGROUND: Stool-based molecular tests hold large potential for improving colorectal cancer screening. Here, we investigated the analytical sensitivity of a DNA methylation assay on partial stool samples, and estimated the DNA degradation in stool over time. In addition, we explored the detection of DNA methylation in fecal immunochemical test (FIT) fluid. MATERIALS AND METHODS: Partial stool samples of colonoscopy-negative individuals were homogenized with stool homogenization buffer, spiked with different numbers of HCT116 colon cancer cells and kept at room temperature for 0, 24, 48, 72 and 144 h before DNA isolation. Analytical sensitivity was determined by the lowest number of cells that yielded positive test results by DNA methylation or mutation analysis. DNA methylation in FIT fluid was measured in 11 CRC patients and 20 control subjects. RESULTS: The analytical sensitivity for detecting DNA methylation was 3000 cells per gram stool, compared to 60000 cells per gram stool for detection of DNA mutations in the same stool samples. No degradation up to 72 h was noted when a conservation buffer was used. DNA methylation was detected in 4/11 CRC FIT samples and in none of the 20 control FIT samples. CONCLUSIONS: Methylation based stool DNA testing showed a high analytical sensitivity for tumor DNA in partial stool samples, which was hardly influenced by DNA degradation over time, provided an adequate buffer was used. The feasibility of detecting DNA methylation in FIT fluid demonstrates the opportunity to combine testing for occult blood with DNA methylation in the same collection device.

Circulating mitochondrial nucleic acids have prognostic value for survival in patients with advanced prostate cancer.

PURPOSE: Advanced prostate cancer represents a heterogeneous disease entity with differences in clinical behavior, response to therapy, and survival. We assessed whether we could distinguish poor from good prognosis patients at presentation in our clinic by means of quantifying circulating cell-free mitochondrial and genomic nucleic acids in plasma. EXPERIMENTAL DESIGN: We collected plasma from 75 prostate cancer patients and from 14 subjects with benign disease. Nucleic acids were isolated, and mitochondrial DNA (mtDNA; 16S rRNA), mitochondrial RNA (mtRNA; cytochrome c oxidase subunit 1), and genomic DNA (U1A DNA) transcripts were quantified by real-time amplification. An association between cell-free nucleic acids and metastasis, prostate-specific antigen doubling time, and hemoglobin levels was determined. Multivariate Cox proportional hazard and survival estimation studies were done. RESULTS: We show that elevated mtDNA and mtRNA levels are present in plasma of prostate cancer patients with a poor 2-year survival (P = 0.02 and 0.003, respectively). Cancer patients with high plasma mitochondrial nucleic acids, using a calculated optimal cutoff point, show a decreased survival compared with patients with low levels (35% versus 73% cumulative survival for mtDNA and 21% versus 73% for mtRNA). Multivariate analysis indicates that mtRNA is an independent predictor of 2-year survival. CONCLUSIONS: Quantification of plasma mitochondrial nucleic acids may be used to recognize patients with a poor prognosis. In advanced prostate cancer patients, mtRNA seemed the strongest predictor of overall survival and an independent prognostic factor for cancer-related death. Amplification of mitochondrial nucleic acids shows increased sensitivity and specificity over genomic DNA as diagnostic and prognostic marker in prostate cancer patients.

Progenitor marker CD133 mRNA is elevated in peripheral blood of cancer patients with bone metastases.

PURPOSE: We examined whether RNA expression of CD133, a surface molecule expressed on progenitors from hematopoietic and endothelial lineages, and CD146, a pan-endothelial marker, are increased in the blood of cancer patients and whether these factors correlate with patient characteristics and are predictive factors of survival. EXPERIMENTAL DESIGN: We developed a real-time quantification method (nuclear acid sequence-based amplification) to determine expression of CD146 and CD133 mRNA in the peripheral blood mononuclear cells of 131 progressive cancer patients, 37 healthy volunteers, and 5 patients who received granulocyte colony-stimulating factor. Overall survival and other clinicopathologic variables were obtained. Cox proportional hazards studies were done. RESULTS: We show that patients with metastatic disease have a significant increase in CD133 mRNA (P = 0.03), specifically patients with bone metastasis (P < 0.001). Cancer patients with high CD133 mRNA expression, using a defined cutoff value, show a decreased survival compared with patients with low or undetectable CD133 expression (21% versus 45% cumulative survival, respectively, after 20 months; P = 0.01). Among patients with metastasis to the bone, cumulative survival was 22%, compared with 61% for patients with high or low CD133 levels (P = 0.004). Multivariate analysis showed that CD133 expression is an independent predictor for overall survival in patients with bone metastases. CD146 mRNA was not increased in patients with cancer, nor did it correlate with clinical variables or survival. CONCLUSION: CD133, but not CD146, mRNA expression is increased in cancer patients with metastatic disease, specifically with bone metastasis. In addition, CD133 mRNA expression seems to be an independent prognostic factor for overall survival.