New insights into the performance of human whole-exome capture platforms.

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.

Is the JAK2 V617F mutation a hallmark for different forms of thrombosis?

BACKGROUND/AIMS: The association between venous thrombosis outside the splanchnic area as well arterial thromboembolism and the JAK2 V617F mutation, an important marker for chronic myeloproliferative neoplasms (MPN), is not completely clear. METHODS: Four hundred forty-four patients with venous thrombosis of the lower/upper limbs and/or pulmonary embolism and 60 patients with ischemic stroke were screened for the JAK2 V617F mutation, factor V Leiden, and factor II G20210A. RESULTS: The JAK2 V617F mutation was detected in 1.4% of patients with venous thrombosis and in 3.3% of patients with ischemic stroke. Because 6 out of 2,430 control individuals with no medical history of venous thrombosis, stroke, or MPN were positive for the JAK2 V617F mutation, a significant association was observed (OR 5.53, CI 1.77-17.2, p = 0.0053 for venous thrombosis; OR 13.9, CI 2.75-70.5, p = 0.0145 for stroke). CONCLUSION: We provide evidence of the association between the JAK2 V617F mutation and different forms of thrombosis. This association is comparable with the association between inherited risk factors (factor V Leiden and factor II G20210A) and thrombotic events, but with a much lower prevalence of the mutation. Finally, the JAK2 V617F mutation is not absent from the general population despite being considered somatic and an acquired genetic variation.

The association of the JAK2 46/1 haplotype with non-splanchnic venous thrombosis.

BACKGROUND: The inherited JAK2 46/1 haplotype is strongly associated with the development of myeloproliferative neoplasms (MPNs), and its increased frequency has also been reported in splanchnic venous thrombosis (SVT). In the present study, the role of the JAK2 46/1 haplotype in non-splanchnic venous thrombosis (non-SVT) was investigated. METHODS AND RESULTS: We genotyped 438 patients with non-SVT, 226 patients with MPNs and 459 healthy controls for three single nucleotide polymorphisms (SNPs) which tag the JAK2 46/1 haplotype (rs12342421 G>C, rs12343867 T>C and rs10974944 C>G). We found statistically significant association of the rs12342421 GC+CC genotypes (OR=1.40; p=0.023) and the rs12343867 TC+CC genotypes (OR=1.83; p=7.02 x 10(-5)) with non-SVT. We also found that the CC haplotype of these two SNPs was associated with an increased risk of the disease (OR=1.68; p=0.009). Stratification analysis indicated that the observed association of the JAK2 46/1 haplotype with non-SVT was probably largely free of confounding effect of thrombophilic risk factors. In addition, we established a strong association of SNPs rs12342421 and rs10974944 and their CG haplotype with MPNs and with JAK2 V617F-positive MPNs. CONCLUSIONS: This study provides statistical evidence that SNPs rs12342421 and rs12343867 are associated with an increased risk of non-SVT. Consistently, haplotypes of the SNPs were also associated with non-SVT risk, suggesting that inherited genetic variation in the JAK2 gene may play a role in the pathogenesis of non-SVT. Furthermore, the reported associations of the JAK2 46/1 haplotype with MPNs as well as with the occurrence of the JAK2 V617F mutation in MPNs were confirmed.

Emergence of the quinolone resistance-mediating gene aac(6')-Ib-cr in extended-spectrum-beta-lactamase-producing Klebsiella isolates collected in Slovenia between 2000 and 2005.

Seventy-four nonrepetitive uropathogenic fluoroquinolone-resistant or -intermediate extended-spectrum-beta-lactamase-producing Klebsiella isolates from Slovenia were screened for the presence of plasmid-mediated quinolone resistance genes. None of the known qnr genes were detected. The aac(6')-Ib-cr allele was detected on plasmids from 25 transconjugants for which the ciprofloxacin MIC was higher than for the recipient Escherichia coli strain.