Objective: To compare whole genome sequencing (WGS) results in the 100K Genome Project with the results of routine molecular diagnostics in the treatment precision.
Materials and Methods: We analyzed 374 cancer include a high tumor burden mutation (TMB-high) subgroup, defined as> 10 non-synonymous single nucleotide variation per megabase. colon cancer were evaluated for microsatellite instability (MSI), mismatch repair (MMR) genes and NRAS, KRAS and BRAF mutations using molecular diagnostic routine. Fluorescence in situ hybridization / immunohistochemistry were used to evaluate Her2Neu status in breast cancer.
Results: There was a high correlation between the WGS and routine diagnostic test results regardless of the status of TMB in colon cancer. Her2Neu status was discordant in 3 of 5 TMB-high breast cancer (p = 0.049). The presence of ductal carcinoma in-situ correlated significantly with irregularities (p = 0.04). There are 3 (5%) cases of colorectal discordant, all in the KRAS gene, two of which came from non-invasive adenomatous component (p = 0.0058). Of the 374 cases we have identified 24 tumors with TMB> 10; comprising (colorectal carcinoma (CRC) n = 16, n = 5 breast carcinoma, bladder urothelial cell cancer n = 3). Of the 16 high-TMB colorectal adenocarcinoma, 13 have the status of MSI-high. Same 13 has broken MMR protein expression. TMB-high colorectal cancer have 100% results in line between the WGS and NGS testing for KRAS, BRAF and NRAS (16/16).
Conclusion: The microsatellite and colorectal cancer mutation status was evaluated by WGS seems to correlate well with routine diagnostic tests if it’s determined that the invasive component sequencing. WGS evaluation results need to be carefully correlated with histomorphology, such as tumor heterogeneity / contamination with pre-malignant components that need to be taken into account.
Comparative Genome Sequence Analysis of samples of Aspergillus fumigatus Geographic-Relevance to Amphotericin B Resistance
Amphotericin B (AMB) is the main fungicide polyene agent has a broad spectrum of action against invasive fungal infections. AMB is usually used as a last-line drug against serious and life-threatening infections when other drugs have failed to eliminate pathogenic fungi. More recently, resistance in Aspergillus fumigatus AMB has become more evident. For example, high levels of resistance AMB (96%) was recorded in populations of A. fumigatus in Hamilton, Ontario, Canada. AMB resistant strains have also been found in other countries. However, AMB resistance mechanisms are still largely unknown.
Here, we investigated the potential genes and mutations associated with resistance to AMB using whole genome sequences and examined the distribution of AMB resistance between genetic population. A total of 196 sequences representing the entire genome of a strain of the 11 countries examined. Analysis of single nucleotide polymorphisms (SNPs) at the level of the entire genome revealed that this strain belongs to three different genetic groups, with the majority (90%) of AMB resistant strains is situated in one of the three clusters, cluster 2. Our analysis identified more than 60 SNP AMB significantly associated with resistance. Together, these SNPs represent promising candidates from which to investigate the molecular mechanism of resistance is suspected AMB and for their potential use in developing rapid diagnostic marker for clinical screening AMB resistance in A. fumigatus.
Validity of whole genomes sequencing results in neoplasms in precision medicine
Rate Campylobacter fetus subsp. venerealis molecular diagnosis using clinical samples of bull
Background: Campylobacter fetus subsp. venerealis (CFV) is the pathogen responsible for Bovine Genital Campylobacteriosis (BGC), a venereal disease of cattle that is associated with impaired reproductive performance. Although some developed PCR tests to identify pathogens, most of them still lack evaluated in clinical samples. This study evaluated the real-time PCR tests for detection bull CFV in preputial samples (n = 308).
Results: The detection at the subspecies level (CFV) compared four tests: two targeting ISCfe1 and two PARA gene targeting. Detection at the level of species (C. fetus) is regarded as a test of gene targeting Nahe and commercial kits for the identification of C. fetus. At the subspecies level, tests directed either to a different target (Para and ISCfe1), or for the same target (ISCfe1 or PARA), showed a high percentage of the results agree. All samples were positive at the subspecies level (n = 169) detection tests negative in C. fetus, a strong showing horizontal gene transfer ISCfe1 and PARA to other bacterial species.
NATtrol Human Parvovirus B19 (10,000 IU/mL) (1 mL)
This was confirmed by microbiological isolation of three strains of Campylobacter portucalensis responsible for false positive results. The sequence with a high degree of identity with ISCfe1 and PARA from CFV genes identified in C. portucalensis genome.
Conclusion: Overall, the study revealed that the PCR test is directed solely to the subspecies derived targeting high level of false positive results, due to the presence of homologous sequences ISCfe1 and in other bacterial species, namely from the genus Campylobacter. Although the specificity of these methods may be higher if applied steers from the herd with clinical features BGC or in other geographical areas, PCR diagnosis at this time should be several subspecies and target species, and further research should be considered to identify specific molecular targets CFV.
