Intra- and inter-individual differences in human sperm DNA methylation

There is growing evidence that sperm DNA methylation is important in maintaining proper sperm health and function. Previous studies have associated sperm DNA methylation levels with sperm quality and function, however, little is known regarding the intra- and inter-individual variability in sperm methylation levels. This study characterizes this variation. Sperm epigenetic differences between successive semen samples from 12 patients were examined to identify the intra- and inter-individual differences globally across the genome, and in specifically defined genomic regions using the Illumina Infinium HumanMethylation450 BeadChips. Methylation analysis identified a bimodal distribution in the methylation levels that were non-uniformly distributed across the different genomic regions. The methylation levels were highly correlated in both the intra- and inter-individual comparisons. The intra-individual methylation levels were more highly correlated than the inter-individual comparison both globally and across the defined genomic regions, demonstrating that sperm DNA methylation levels are relatively stable between semen sample collections.

Estimation of the 6-digit level allele and haplotype frequencies of HLA-A, -B, and -C in Koreans using ambiguity-solving DNA typing

Because Korean society is fast becoming multi-ethnic, the determination of ambiguous human leukocyte antigen (HLA) types using HLA allele frequencies is becoming less applicable. In this study, we focused on the development of new technical methods to directly resolve the ambiguities arising from HLA genotyping. One hundred and fifty unrelated healthy Korean adults were included in this study. All alleles from each HLA locus were first divided into 2-4 groups, with each group amplified in a single PCR tube (multi-group-specific amplification, MGSA). To resolve phase ambiguities, some allele groups were also amplified separately in small group-specific amplification (SGSA) tubes. In order to then resolve incomplete sequence ambiguities, primers for MGSA and SGSA were initially designed to cover additional exons. If needed, a heterozygous ambiguity resolving primer (HARP) or sequence specific primer (SSP) was also used. When MGSA and SGSA methods were applied, the rate of phase ambiguity was greatly reduced to an average of 6% (1.3% in HLA-A, 15.7% in -B, and 2.0% in -C). Additional HARP and SSP methods could resolve all the phase ambiguities. Using our proposed method, we also detected three alleles that have not been previously reported in Korea, C*04:82, C*07:18, and C*08:22, and report 6-digit level HLA allele and haplotype frequencies among Koreans. In conclusion, the use of MGSA/SGSA for the initial amplification step is a cost-effective method facilitating timely and accurate reporting, given the continuing increase in the ethnic diversity of the Korean population. The MGSA described here can be applicable to various populations and thus could be shared by the majority of HLA typing laboratories. However, efforts to solve HLA ambiguity should continue, because SGSA, HARPs and SSPs would be specific to a particular population.

WE-G-217A-06: Spatial Accuracy Quantification of an MR System

PURPOSE

To develop a phantom and measurement protocol for quantifying spatial accuracy of an MR imaging system over its entire imaging volume.

METHODS

The measurement protocol is comprised of a phantom, a set of MR sequence parameters for imaging the phantom, and analysis software for calculating spatial errors in the acquired phantom images. The phantom covers the entire imaging volume of the scanner above the patient table. It consists of layers of tooling foam which does not produce any detectable signal on conventional MR images, embedded with a matrix of oil capsules to serve as markers. To account for possible spatial errors in the construction of the phantom, the phantom was imaged with CT to create a gold standard data set. On MR scanners, the phantom is acquired with a 3D FGRE sequence that covers an extended FOV of 61.44 mm and with bandwidth = ±62.5 kHz. Error measurements are performed by detecting markers in the image sets and identifying them based on their known locations on the phantom. The spatial error of a marker is defined as the difference between its locations on the MR and CT image sets.

RESULTS

The phantom was constructed and the measurement protocol was executed on two different MR scanners. Some markers were located in areas of severe field inhomogeneity or gradient nonlinearity, and could not be adequately detected for analysis. Maximum errors over concentric spherical regions were observed by plotting the error of each marker as a function of their distance from isocenter.

CONCLUSION

The proposed phantom and protocol can be an effective tool for verifying the spatial accuracy of an MR system, which in turn can improve the accuracy and confidence of MR guided therapies. Data from this protocol may also be used in the development of advanced distortion correction algorithms. Employed by General Electric Healthcare.

WE-G-217A-07: Increased MR Spatial Accuracy with Improved Gradient Nonlinearity and Magnet Inhomogeneity Correction

PURPOSE

To develop improved distortion correction of MR images based on higher degree spherical harmonic models of the gradient system and the main magnetic field.

METHODS

The induced field gradient along all three axes can be modeled by first order spherical harmonics. These models provide a true encoding of the physical location of a spin to the frequency at which it is detected. Currently on many commercial systems, only the lower 5 degrees of the model are used for gradient nonlinearity correction. While this provides sufficient accuracy for diagnostic imaging, the gradient nonlinearity correction was extended to include all first order harmonics up to the 9th degree to improve the spatial accuracy of the images. Using zeroth degree spherical harmonics up to the 20th order, a model of the main magnetic field was also incorporated into the correction algorithm. Shifts caused by field inhomogeneity were calculated using knowledge of the receiver bandwidth, frequency encode direction, and the magnetic field at any given point. These corrections were applied to images of a 50 cm diameter phantom, acquired with an extended FOV 3D FGRE sequence. Any improvements in spatial accuracy were measured in the resulting images.

RESULTS

Visual improvements in spatial accuracy were observed with both corrections. With standard gradient nonlinearity correction, edges of the phantom were distorted in a wave-like fashion. With accurate models, almost all of the errors at the edges of the phantom were corrected when both gradient and field homogeneity corrections were applied.

CONCLUSION

With accurate models of the gradient and magnetic field, the two greatest system-induced spatial errors can be corrected. This improved spatial accuracy enables the use of widebore MR scanners for therapy planning on large FOV images and guidance of percutaneous devices. Further applications include extended FOV imaging for combined PET-MR systems. All authors are employed by General Electric Healthcare.