A 316MP, 120FPS, High Dynamic Range CMOS Image Sensor for Next Generation Immersive Displays.

We present a 2D-stitched, 316MP, 120FPS, high dynamic range CMOS image sensor with 92 CML output ports operating at a cumulative date rate of 515 Gbit/s. The total die size is 9.92 cm × 8.31 cm and the chip is fabricated in a 65 nm, 4 metal BSI process with an overall power consumption of 23 W. A 4.3 µm dual-gain pixel has a high and low conversion gain full well of 6600e- and 41,000e-, respectively, with a total high gain temporal noise of 1.8e- achieving a composite dynamic range of 87 dB.

Identification of individuals by trait prediction using whole-genome sequencing data.

Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and demographic information is limited. However, we have developed a maximum entropy algorithm that integrates multiple predictions to determine which genomic samples and phenotype measurements originate from the same person. Using this algorithm, we have reidentified an average of >8 of 10 held-out individuals in an ethnically mixed cohort and an average of 5 of either 10 African Americans or 10 Europeans. This work challenges current conceptions of personal privacy and may have far-reaching ethical and legal implications.

A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease.

With an overall prevalence of 10-20%, gallstone disease (cholelithiasis) represents one of the most frequent and economically relevant health problems of industrialized countries. We performed an association scan of >500,000 SNPs in 280 individuals with gallstones and 360 controls. A follow-up study of the 235 most significant SNPs in 1,105 affected individuals and 873 controls replicated the disease association of SNP A-1791411 in ABCG8 (allelic P value P(CCA) = 4.1 x 10(-9)), which was subsequently attributed to coding variant rs11887534 (D19H). Additional replication was achieved in 728 German (P = 2.8 x 10(-7)) and 167 Chilean subjects (P = 0.02). The overall odds ratio for D19H carriership was 2.2 (95% confidence interval: 1.8-2.6, P = 1.4 x 10(-14)) in the full German sample. Association was stronger in subjects with cholesterol gallstones (odds ratio = 3.3), suggesting that His19 might be associated with a more efficient transport of cholesterol into the bile.

Temporal arteritis presenting with facial swelling and a negative temporal artery biopsy.

A man in his 60s presented to the emergency department with marked bilateral preauricular swelling, associated with jaw claudication, temporal tenderness and blurred vision. He was immediately treated for temporal arteritis by commencing systemic corticosteroids. A temporal artery biopsy showed no evidence of vasculitis. However, positron emission tomography-CT demonstrated increased uptake in the medium-large vessels, including the left superficial temporal artery and aorta. This case illustrates that facial swelling may be an under-recognised presenting feature of temporal arteritis, and that a negative temporal artery biopsy does not always rule out a diagnosis of temporal arteritis, and should not delay treatment.

GeneSigDB--a curated database of gene expression signatures.

The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst thousands of experimentally derived gene signatures are published, their potential value to the community is limited by their computational inaccessibility. Gene signatures are embedded in published article figures, tables or in supplementary materials, and are frequently presented using non-standard gene or probeset nomenclature. We present GeneSigDB (http://compbio.dfci.harvard.edu/genesigdb) a manually curated database of gene expression signatures. GeneSigDB release 1.0 focuses on cancer and stem cells gene signatures and was constructed from more than 850 publications from which we manually transcribed 575 gene signatures. Most gene signatures (n = 560) were successfully mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats.

The efficacy of repeated treatment with B-cell depletion therapy in systemic lupus erythematosus: an evaluation.

OBJECTIVE: Since 2000, we have given B-cell depletion therapy (BCDT) with rituximab to 76 patients with active SLE refractory to standard immunosuppression. Twenty-four of these patients have now received repeated cycles of BCDT. The aims of the study were to: (i) assess the efficacy and safety of repeated cycles of BCDT in treating refractory SLE; and (ii) assess whether retreatment produced a more sustained clinical response. METHODS: BCDT was administered using CYC 750 mg, methylprednisolone 125-250 mg and rituximab 1 g given intravenously on two occasions, 2 weeks apart. Patients were reviewed at 1-2 monthly intervals and disease activity assessed using the BILAG activity index and serological markers. Clinical response was categorized as complete or partial remission, or no response, based on the change in BILAG scores. RESULTS: Eighteen patients had sufficient data for detailed analysis. All were female; mean age 29.9 years; mean duration of follow-up 58.7 months. Two patients died during follow-up and there were two infusion reactions. Disease activity was significantly reduced after both cycles of BCDT at 6 months. More patients achieved disease remission after the second cycle (82 vs 61% first cycle), which was maintained in 65% at 12 months (vs 39% first cycle). The time to disease flare was significantly longer after the second cycle (P < 0.001) and 33% of our patients have still not flared to date following retreatment (mean follow-up 24.5 months). CONCLUSION: Repeated cycles of BCDT with rituximab are effective in treating refractory SLE and has a favourable safety profile. Retreatment may produce a more sustained clinical response.

Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting.

OBJECTIVE: We sought to evaluate a multiplexed massively parallel shotgun sequencing assay for noninvasive trisomy 21 detection using circulating cell-free fetal DNA. STUDY DESIGN: Sample multiplexing and cost-optimized reagents were evaluated as improvements to a noninvasive fetal trisomy 21 detection assay. A total of 480 plasma samples from high-risk pregnant women were employed. RESULTS: In all, 480 prospectively collected samples were obtained from our third-party storage site; 13 of these were removed due to insufficient quantity or quality. Eighteen samples failed prespecified assay quality control parameters. In all, 449 samples remained: 39 trisomy 21 samples were correctly classified; 1 sample was misclassified as trisomy 21. The overall classification showed 100% sensitivity (95% confidence interval, 89-100%) and 99.7% specificity (95% confidence interval, 98.5-99.9%). CONCLUSION: Extending the scope of previous reports, this study demonstrates that plasma DNA sequencing is a viable method for noninvasive detection of fetal trisomy 21 and warrants clinical validation in a larger multicenter study.

Clinical improvements in proliferative vs membranous lupus nephritis following B-cell depletion: pooled data from two cohorts.

OBJECTIVE: To compare the clinical results after treatment with B-cell depleting therapy in patients with membranous (WHO Class V) vs proliferative (WHO Class III or IV) lupus nephritis (LN). METHODS: Data were compiled from two European centres on all patients with LN who were treated with i.v. rituximab (RTX) in a combination protocol with i.v. cyclophosphamide and steroids. Laboratory and serological evaluations were performed at 3, 6 and 12 months of follow-up. No immunosuppressive drugs were given before B-cell repopulation. RESULTS: Forty-three patients, 28 with proliferate and 15 with membranous LN by renal biopsy, were evaluated. Six months after treatment with RTX, both the membranous and the proliferative LN patients had a significant reduction in proteinuria and an increase in serum albumin. The main improvements were observed during the first 6 months and only minor non-significant changes in albumin and proteinuria were observed thereafter. As expected, the patients with membranous nephritis had lower anti-dsDNA titres and higher complement C3 levels at baseline, but in both groups a significant reduction in anti-dsDNA titre and improvements in complement C3 levels were seen during the first 6 months after treatment; the kinetics of improvement were similar in both groups. CONCLUSION: The clinical course following B-cell depleting therapy is strikingly similar between patients with membranous and those with proliferative LN. These observational data suggest that, if controlled studies confirm the efficacy of B-cell depleting therapy in proliferative nephritis, clinicians may reasonably consider such therapy in membranous LN.

Long-term improvement of lipid profile in patients with refractory systemic lupus erythematosus treated with B-cell depletion therapy: a retrospective observational study.

OBJECTIVE: Lipid abnormalities contribute to the increased risk of premature atherosclerosis in patients with SLE. This study was undertaken to investigate changes in lipid profile after B-cell depletion therapy (BCDT) in patients with active SLE who had failed standard immunosuppressive therapy. METHODS: Twelve patients with refractory SLE treated with BCDT based on rituximab (two biweekly infusions of 1 g) were examined. Lipid profile and lupus activity were measured before the infusions and 1 year later. The control group consisted of 26 age- and sex-matched lupus patients not treated with BCDT. RESULTS: In the study group, the mean levels of total, high-density lipoprotein (HDL) and low-density lipoprotein cholesterols were 4.6, 1.4 and 2.4 mmol/l at baseline and changed to 4.1, 1.6 and 2.0 mmol/l (P = NS, P = 0.04 and P = NS) at 1 year, respectively. The atherogenic index was 3.8 at baseline and decreased to 2.7 (P = 0.02). The triglyceride (TG) level was 2.1 mmol/l at baseline and decreased to 1.3 mmol/l (P = 0.04). BCDT was followed by a significant decrease in global BILAG scores and a drop in the mean dose of prednisolone at 1 year (P = 0.01). Reduction in disease activity was significantly associated with a reduction in total cholesterol and TG levels and an increase in HDL cholesterol levels. In the control group, there were no differences in any of the lipid determinations over a 1-year period. CONCLUSION. This provisional observational study suggests a favourable long-term effect of BCDT on the lipid profile of patients with refractory SLE, which correlated with decreasing activity of the disease.

Urinary neutrophil gelatinase-associated lipocalin as a novel biomarker for disease activity in lupus nephritis.

OBJECTIVES: Clinical and laboratory markers in current use have limited specificity and sensitivity for predicting the development of renal disease in lupus patients. In this longitudinal study, we investigated whether urinary neutrophil gelatinase-associated lipocalin (uNGAL) predicts active nephritis and renal flares in lupus patients with and without a history of biopsy-proven lupus nephritis. METHODS: Renal disease activity and flare status was determined by SLEDAI and BILAG scores. Random effects models were used to determine whether uNGAL was a significant predictor for renal disease activity in SLE patients, and for renal flares in patients with established nephritis. To assess the predictive performance of uNGAL, receiver operating characteristic (ROC) curves were constructed using the previous visit's uNGAL level. These curves were then compared with curves constructed with currently used biomarkers. Cut-offs determined by ROC curves were tested in an independent validation cohort. RESULTS: uNGAL was found to be a significant predictor of renal disease activity in all SLE patients, and a significant predictor for flare in patients with a history of biopsy-proven nephritis, in multivariate models adjusting for age, race, sex and anti-double-stranded (ds)DNA antibody titres. As a predictor of renal flare in patients with biopsy-proven nephritis, uNGAL outperformed anti-dsDNA antibody titres. These results were confirmed in an independent validation cohort. CONCLUSIONS: uNGAL predicts renal flare in patients with a history of biopsy-proven nephritis with high sensitivity and specificity. Furthermore, uNGAL is a more sensitive and specific forecaster of renal flare in patients with a history of lupus nephritis than anti-dsDNA antibody titres.

Genome-wide association analysis in sarcoidosis and Crohn's disease unravels a common susceptibility locus on 10p12.2.

BACKGROUND & AIMS: Crohn's disease (CD) and sarcoidosis (SA) are chronic inflammatory barrier diseases that share several clinical and immunological features, including the occurrence of granulomas. METHODS: A 100k genome-wide association study with 83,360 single-nucleotide polymorphisms (SNPs) was performed on 382 CD patients, 398 SA patients, and 394 control individuals. The 24 SNPs that were most strongly associated in the combined CD/SA phenotype were selected for verification in an independent sample of 1,317 patients (660 CD and 657 SA) and 1,091 controls. RESULTS: The most significant association (Bonferroni corrected P = .036) was obtained at SNP rs1398024 on chromosome 10p12.2, with an odds ratio (OR) for both diseases of 0.81 (95% confidence interval [CI], 0.69-0.96) for carriership of the rarer allele A. The P value in the overall combined sample was 4.24 x 10(-6). During further follow-up, a moderate association (OR, 0.83; 95% CI, 0.72-0.96; P = .015) was observed between rs1398024 and ulcerative colitis (1,080 patients vs 1,091 controls), the second main subphenotype of inflammatory bowel disease in addition to CD. Extensive fine mapping of the 10p12.2 locus points to yet unidentified variants in the C10ORF67 gene region as the most likely underlying risk factors. CONCLUSION: Our study demonstrates that the combined analysis of different, albeit clinically related, phenotypes can lead to the identification of common susceptibility loci.

Inflammatory muscle disease assessment.

In recent years, idiopathic inflammatory muscle disease assessment has advanced significantly with the development of an international consensus on outcome measurement indices. The International Myositis Assessment and Clinical Studies Group continues to evaluate the validity and reliability of various disease activity and disease damage tools, which will facilitate adequately controlled randomized trials of recently developed therapeutic agents.

GENOMIZER: an integrated analysis system for genome-wide association data.

Genome-wide association analysis appears to be a promising way to identify heritable susceptibility factors for complex human disorders. However, the feasibility of large-scale genotyping experiments is currently limited by an incomplete marker coverage of the genome, a restricted understanding of the functional role of given genomic regions, and the small sample sizes used. Thus, genome-wide association analysis will be a screening tool to facilitate subsequent gene discovery rather than a means to completely resolve individual genetic risk profiles. The validation of association findings will continue to rely upon the replication of "leads" in independent samples from either the same or different populations. Even under such pragmatic conditions, the timely analysis of the large data sets in question poses serious technical challenges. We have therefore developed public-domain software, GENOMIZER, that implements the workflow of an association experiment, including data management, single-point and haplotype analysis, "lead" definition, and data visualization. GENOMIZER (www.ikmb.uni-kiel.de/genomizer) comes with a complete user manual, and is open-source software licensed under the GNU Lesser General Public License. We suggest that the use of this software will facilitate the handling and interpretation of the currently emerging genome-wide association data.

WOFIE stimulates regulatory T cells: a 2-year follow-up of renal transplant recipients.

BACKGROUND: Initial interruption of immunosuppression for 72 hr was analyzed in renal transplant recipients according to Calne et al.'s "window of opportunity for immunologic engagement" (WOFIE) concept. METHODS: This pilot study was designed as a randomized, open-label, prospective trial of 40 recipients (20 in the WOFIE group, 20 in the control group) of cadaveric kidney transplants who were followed up for 2 years. Immunosuppression comprised tacrolimus (trough levels 5-8 ng/mL), daclizumab (1 mg per kilogram of body weight on day 0 and after 2, 4, 6, and 8 weeks), mycophenolate mofetil (1-2 g/day), and prednisolone (maintenance dose of 10 mg/day). After induction with daclizumab, prednisolone, and mycophenolate mofetil, immunosuppression was interrupted for 72 hr in the WOFIE group. Steroid withdrawal followed in both groups within 12 to 16 weeks posttransplant. RESULTS: Patient and graft survival did not differ significantly between the two cohorts. However, the WOFIE group experienced less acute rejection episodes and developed better graft function. Although all but one of the patients in the WOFIE group successfully discontinued steroid treatment, permanent steroid withdrawal was achieved in only 76.4% of the control group. After daclizumab discontinuation, the WOFIE group demonstrated an increase of CD4CD25 T cells in peripheral blood (P<0.05 vs. control group), which was stable over time and strongly correlated with a significantly higher expression level of Foxp3-mRNA. CONCLUSIONS: Initial interruption of immunosuppression for 72 hr correlates with the induction of regulatory immunologic mechanisms and allows early and reliable minimization of immunosuppressive treatment.

Geographical heterogeneity of Y-chromosomal lineages in Norway.

Y-chromosomal variation at five biallelic markers (Tat, YAP, 12f2, SRY(10831) and 92R7) and nine multiallelic short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II and DYS388) in a Norwegian population sample are presented. The material consists of 1766 unrelated males of Norwegian origin. The geographical distribution of the population sample reflects fairly well the population distribution around the year 1942, which is the median birth year of the index persons. Seven hundred and twenty-one different Y-STR haplotypes but 726 different lineages (Y-STRs plus biallelic markers) were encountered. We observed six known (P*(xR1a), BR(xDE, J, N3, P), R1a, N3, DE, J), and one previously undescribed haplogroup (probably a subgroup within haplogroup P*(xR1a)). Four of the haplogroups (P*(xR1a), BR(xDE, J, N3, P), R1a and N3) represented about 98% of the population sample. The analysis of population pairwise differences indicates that the Norwegian Y-chromosome distribution most closely resembles those observed in Iceland, Germany, the Netherlands and Denmark. Within Norway, geographical substructuring was observed between regions and counties. The substructuring reflects to some extent the European Y-chromosome gradients, with higher frequency of P*(xR1a) in the south-west and of R1a in the east. Heterogeneity in major founder groups, geographical isolation, severe epidemics, historical trading links and population movements may have led to population stratification and have most probably contributed to the observed regional differences in distribution of haplotypes within two of the major haplogroups.

Can Zipf's law be adapted to normalize microarrays?

BACKGROUND: Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented. RESULTS: Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques. CONCLUSION: Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays).

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.

BACKGROUND: The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially understood. cDNA microarrays can be used to decipher gene regulation events at a genome-wide level and to identify novel unknown genes that might be involved in perpetuating inflammatory disease progression. METHODS AND FINDINGS: High-density cDNA microarrays representing 33,792 UniGene clusters were prepared. Biopsies were taken from the sigmoid colon of normal controls (n = 11), CD patients (n = 10) and UC patients (n = 10). 33P-radiolabeled cDNA from purified poly(A)+ RNA extracted from biopsies (unpooled) was hybridized to the arrays. We identified 500 and 272 transcripts differentially regulated in CD and UC, respectively. Interesting hits were independently verified by real-time PCR in a second sample of 100 individuals, and immunohistochemistry was used for exemplary localization. The main findings point to novel molecules important in abnormal immune regulation and the highly disturbed cell biology of colonic epithelial cells in IBD pathogenesis, e.g., CYLD (cylindromatosis, turban tumor syndrome) and CDH11 (cadherin 11, type 2). By the nature of the array setup, many of the genes identified were to our knowledge previously uncharacterized, and prediction of the putative function of a subsection of these genes indicate that some could be involved in early events in disease pathophysiology. CONCLUSION: A comprehensive set of candidate genes not previously associated with IBD was revealed, which underlines the polygenic and complex nature of the disease. It points out substantial differences in pathophysiology between CD and UC. The multiple unknown genes identified may stimulate new research in the fields of barrier mechanisms and cell signalling in the context of IBD, and ultimately new therapeutic approaches.

Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains.

BACKGROUND: Circulating cell-free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the maternal and fetal DNA. Testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA; however, this depends on knowledge of the methylomes of circulating cell-free DNA and its cellular contributors. RESULTS: We perform whole genome bisulfite sequencing on a set of unmatched samples including circulating cell-free DNA from non-pregnant and pregnant female donors and genomic DNA from maternal buffy coat and placenta samples. We find CpG cytosines within longer fragments are more likely to be methylated. Comparison of the methylomes of placenta and non-pregnant circulating cell-free DNA reveal many of the 51,259 identified differentially methylated regions are located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases. We find these placenta hypomethylated domains are consistently located within regions exhibiting low CpG and gene density. Differentially methylated regions identified when comparing placenta to non-pregnant circulating cell-free DNA are recapitulated in pregnant circulating cell-free DNA, confirming the ability to detect differential methylation in circulating cell-free DNA mixtures. CONCLUSIONS: We generate methylome maps for four sample types at single-base resolution, identify a link between DNA methylation and fragment length in circulating cell-free DNA, identify differentially methylated regions between sample groups, and uncover the presence of megabase-size placenta hypomethylated domains.

A comparison of oligonucleotide and cDNA-based microarray systems.

Large-scale public data mining will become more common as public release of microarray data sets becomes a corequisite for publication. Therefore, there is an urgent need to clarify whether data from different microarray platforms are comparable. To assess the compatibility of microarray data, results were compared from the two main types of high-throughput microarray expression technologies, namely, an oligonucleotide-based and a cDNA-based platform, using RNA obtained from complex tissue (human colonic mucosa) of five individuals. From 715 sequence-verified genes represented on both platforms, 64% of the genes matched in "present" or "absent" calls made by both platforms. Calls were influenced by spurious signals caused by Alu repeats in cDNA clones, clone annotation errors, or matched probes that were designed to different regions of the gene; however, these factors could not completely account for the level of call discordance observed. Expression levels in sequence-verified, platform-overlapping genes were not related, as demonstrated by weakly positive rank order correlation. This study demonstrates that there is only moderate overlap in the results from the two array systems. This fact should be carefully considered when performing large-scale analyses on data originating from different microarray platforms.