MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies.

The Infinium DNA Methylation BeadChips have significantly contributed to population-scale epigenetics research by enabling epigenome-wide trait association discoveries. Here, we design, describe, and experimentally verify a new iteration of this technology, the Methylation Screening Array (MSA), to focus on human trait screening and discovery. This array utilizes extensive data from previous Infinium platform-based epigenome-wide association studies (EWAS). It incorporates knowledge from the latest single-cell and cell type-resolution whole genome methylome profiles. The MSA is engineered to achieve scalable screening of epigenetics-trait association in an ultra-high sample throughput. Our design encompassed diverse human trait associations, including those with genetic, cellular, environmental, and demographical variables and human diseases such as genetic, neurodegenerative, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity for cell-type deconvolution and supporting 5-hydroxymethylation profiling in diverse human tissues. Our first atlas data using this platform uncovered the complex chromatin and tissue contexts of DNA modification variations and genetic variants linked to human phenotypes.

A genome-wide association study for colorectal cancer identifies a risk locus in 14q23.1.

Over 50 loci associated with colorectal cancer (CRC) have been uncovered by genome-wide association studies (GWAS). Identifying additional loci has the potential to help elucidate aspects of the underlying biological processes leading to better understanding of the pathogenesis of the disease. We re-evaluated a GWAS by excluding controls that have family history of CRC or personal history of colorectal polyps, as we hypothesized that their inclusion reduces power to detect associations. This is supported empirically and through simulations. Two-phase GWAS analysis was performed in a total of 16,517 cases and 14,487 controls. We identified rs17094983, a SNP associated with risk of CRC [p = 2.5 × 10(-10); odds ratio estimated by re-including all controls (OR) = 0.87, 95% confidence interval (CI) 0.83-0.91; minor allele frequency (MAF) = 13%]. Results were replicated in samples of African descent (1894 cases and 4703 controls; p = 0.01; OR = 0.86, 95% CI 0.77-0.97; MAF = 16 %). Gene expression data in 195 colon adenocarcinomas and 59 normal colon tissues from two different studies revealed that this locus has genotypes that are associated with RTN1 (Reticulon 1) expression (p = 0.001), a protein-coding gene involved in survival and proliferation of cancer cells which is highly expressed in normal colon tissues but has significantly reduced expression in tumor cells (p = 1.3 × 10(-8)).

Successfully treated calcific uremic arteriolopathy: two cases of a high anion gap metabolic acidosis with intravenous sodium thiosulfate.

Calcific uremic arteriolopathy (CUA) is a rare and potentially fatal disorder of calcification involving subcutaneous small vessels and fat in patients with renal insufficiency. We describe the successful use of intravenous sodium thiosulfate (STS) for the treatment of CUA in two patients. The first case was complicated by the development of a severe anion gap metabolic acidosis, which was accompanied by a seizure. Both patients had complete wound healing within five months. Although STS should be considered in the treatment of CUA, little is known about pharmacokinetics and additional studies are required to determine dosing strategies to minimize severe potential side effects.

Compact cryogenic self-aligning fiber-to-detector coupling with losses below one percent.

We present a compact packaging technique for coupling light from a single-mode telecommunication fiber to cryogenic single-photon sensitive devices. Our single-photon detectors are superconducting transition-edge sensors (TESs) with a collection area only a factor of a few larger than the area of the fiber core which presents significant challenges to low-loss fiber-to-detector coupling. The coupling method presented here has low loss, cryogenic compatibility, easy and reproducible assembly and low component cost. The system efficiency of the packaged single-photon counting detectors is verified by the "triplet method" of power-source calibration along with the "multiple attenuator" method that produces a calibrated single-photon flux. These calibration techniques, when used in combination with through-wafer imaging and fiber back-reflection measurements, give us confidence that we have achieved coupling losses below 1% for all devices packaged according to the self-alignment method presented in this paper.

Single photon source characterization with a superconducting single photon detector.

Superconducting single photon detectors (SSPD) based on nanopatterned niobium nitride wires offer single photon counting at fast rates, low jitter, and low dark counts, from visible wavelengths well into the infrared. We demonstrate the first use of an SSPD, packaged in a commercial cryocooler, for single photon source characterization. The source is an optically pumped, microcavity-coupled InGaAs quantum dot, emitting single photons at 902 nm. The SSPD replaces the second silicon Avalanche Photodiode (APD) in a Hanbury-Brown Twiss interferometer measurement of the source second-order correlation function, g(2)( ?). The detection efficiency of the superconducting detector system is >2 % (coupling losses included). The SSPD system electronics jitter is 170 ps, versus 550 ps for the APD unit, allowing the source spontaneous emission lifetime to be measured with improved resolution.