Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers

Current human leukocyte antigen (HLA) DNA typing methods such as the sequence-based typing (SBT) and sequence-specific oligonucleotide (SSO) methods generally yield ambiguous typing results because of oligonucleotide probe design limitations or phase ambiguity for HLA allele assignment. Here we describe the development and application of the super high-resolution single-molecule sequence-based typing (SS-SBT) of HLA loci at the 8-digit level using next generation sequencing (NGS). NGS which can determine an HLA allele sequence derived from a single DNA molecule is expected to solve the phase ambiguity problem. Eight classical HLA loci-specific polymerase chain reaction (PCR) primers were designed to amplify the entire gene sequences from the enhancer-promoter region to the 3' untranslated region. Phase ambiguities of HLA-A, -B, -C, -DRB1 and -DQB1 were completely resolved and unequivocally assigned without ambiguity to single HLA alleles. Therefore, the SS-SBT method described here is a superior and effective HLA DNA typing method to efficiently detect new HLA alleles and null alleles without ambiguity.

Factors associated with lobar vs. non-lobar intracerebral hemorrhage

OBJECTIVES

The relationship between body mass index (BMI) and stroke subtypes has received more research attention than that between BMI and location of intracerebral hemorrhage (ICH). Lobar hemorrhage (LH) differs from non-LH primarily in terms of etiology, i.e. cerebral amyloid angiopathy is the main cause of LH. This study aimed to determine the relationship between BMI and ICH.

MATERIALS AND METHODS

In this retrospective study involving 460 consecutive patients with ICH, BMI was significantly lower in LH than for other ICH locations. BMI categories were underweight (BMI < 18.5 kg/m(2)), normal weight (18.5-23.0 kg/m(2)), overweight (23.0-27.5 kg/m(2)), or obesity (≥27.5 kg/m(2)). Outcome at 1 year was evaluated by the modified Rankin Scale (mRS). We investigated the relationship of BMI and other clinical characteristics with LH and non-LH.

RESULTS

LH was associated with age (>70 years), underweight, unfavorable outcome (mRS ≥3), and daily alcohol consumption. Hypertension and intraventricular bleeding were significantly less common in patients with LH than those with non-LH.

CONCLUSIONS

Alongside risk factors conventionally thought to be related to LH, underweight may also be a LH-related factor, specifically in the elderly.

Optimal prostate-specific antigen screening interval for prostate cancer

BACKGROUND

To identify the optimal interval for repeat prostate-specific antigen (PSA) testing to screen for prostate cancer in healthy adults.

PATIENTS AND METHODS

A retrospective cohort study was conducted on 7332 healthy males without prostate cancer at baseline from 2005 to 2008. Participants underwent annual health checkups including PSA testing at the Center for Preventive Medicine in Japan. Participants with high PSA (≥ 4.0 ng/ml) underwent further examination for prostate cancer. A subgroup analysis was conducted age group (<50 years, ≥ 50 years).

RESULTS

Mean age was 50 years. Mean PSA at baseline was 1.2 ng/ml. In over 50-year group, for those with initial PSA of <1.0, 1.0-1.9, 2.0-2.9, and 3.0-3.9 ng/ml at baseline, the 3-year cumulative incidence of prostate cancer was 0%, 0.1%, 0.3%, and 5.7%, respectively. No prostate cancer was identified in those <50 years, regardless of PSA level.

CONCLUSIONS

If PSA screening is recommended, males >50 years with PSA of 3.0-3.9 ng/ml at baseline should undergo rescreening at 2 years. For men with PSA <3.0 ng/ml, PSA rescreening at intervals of ≥ 3 years is appropriate. PSA screening may not be indicated in males of <50 years of age.

P4-20-05: Inflammatory Breast Cancer: Comparison of Epidemiology, Biology, and Prognosis between Japan and the United States, a Hospital-Based Study

Background: Inflammatory breast cancer (IBC) is a challenging disease characterized by low incidence, rapid progression, and poor survival. The epidemiology of IBC has been slow to emerge, given that the rarity of IBC makes large prospective clinical trials difficult. Compared to non-IBC, well-established features of IBC include a younger age of onset and lower frequency of hormone receptor positivity. Higher body mass index (BMI) is a purported risk factor. Previous reports also suggest that IBC is associated with more racial disparities, including incidence and age at diagnosis. The epidemiology of IBC in East Asia, however, has not been investigated. We performed a comparative study of IBC in Japan versus the United States to determine its epidemiologic and clinical features and to evaluate the differences in epidemiological factors between the two countries.

Patients and Method: Patients who visited St. Luke's International hospital (SLIH) in Tokyo, Japan and The University of Texas MD Anderson Cancer Center (MDA) in Texas, USA between 2003 and 2009 were identified. Epidemiological and biological data were collected from electronic medical records. Patient and tumor characteristics were tabulated and stratified by hospital. Kaplan-Meier curves were created for survival estimates and log-rank test was used for cross-group comparisons. Cox proportional-hazard analysis was used to identify a subset of significant prognostic variables that related to overall survival.

Result: 34 patients at SLIH and 531 patients at MDA were identified. Mean age at diagnosis was 52 years old (range, 32–81, SD, 10.8) and 50 years old (range, 22–87, SD, 11.6), respectively (P=0.476). Mean BMI was 22.9 kg/m2 (range, 17.3−30.5, SD 3.3 ) and 31.0 kg/m2 (range, 13.6−88.9, SD, 7.8) respectively (P&lt;0.01). Clinical Staging was not significantly different; Stage IIIB 38.2%, Stage IIIC 26.5%, and Stage IV 32.4% at SLIH versus 48.6%, 23.7%, and 27.3% at MDA (P= 0.167). Estrogen receptor (ER) and progesterone receptor (PR) negative cases were, respectively, 50.0% and 64.7% at SLIH and 50.5% and 64.2% at MDA (ER, P= 0.935; PR, P=0.908). Her-2 over-expression cases were 38.2% at SLIH and 28.6% at MDA (P=0.174). A significant difference in nuclear grade was seen between SLIH and MDA: 20.6% at SLIH were Grade 3 versus 68.7% at MDA (P&lt;0.01). Median overall survival at SLIH was 3.6 years versus 2.3 years at MDA (P=0.570). No prognostic factors were associated with overall survival.

Conclusion: Though IBC at SLIH differed significantly from IBC at MDA by several epidemiologic and biologic factors, there was no significant difference in survival. To define the epidemiological, prognostic, and risk factors of IBC in Japan, as well as in the world, further studies are needed.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-20-05.

Projection of Si 1s photoexcited orbitals into resonant Auger electron spectra in KLL decays of Si(CH3)4 and SiF4

Spectator resonant KL(23)L(23) Auger electron spectra have been measured in the Si 1s photoexcitation region of Si(CH(3))(4) using monochromatized undulator radiation combined with a hemispherical electron spectrometer. The broad peak with high intensity in a total ion yield spectrum, coming mainly from excitation of a 1s electron into the 6t(2) vacant orbital, induces a spectator Auger decay in which the excited electron remains in its excited orbital. The component on the higher energy side of this peak through 1s excitation into a Rydberg orbital produces resonant Auger decays in which the excited Rydberg electron moves into a slightly higher Rydberg orbital, or is partly shaken up to a significantly higher Rydberg orbital. These findings of Si(CH(3))(4) indicate a clear contrast to those for SiF(4), in which the 1s excitation into a Rydberg orbital induces a shake-down phenomenon as well as a shake-up one. The results of these molecules exhibit a clear splitting effect among excited orbitals which are smeared out by overlapping due to lifetime widths and due to densely populated levels in the 1s electron excitation spectrum. This is consistent with the calculation on photoexcitation within the framework of density functional theory.

Theory of docking scores and its application to a customizable scoring function

In general, the docking scoring tends to have a size dependence related to the ranking of compounds. In this paper, we describe a novel method of parameter optimization for docking scores which reduce the size dependence and can efficiently discriminate active compounds from chemical databases. This method is based on a simplified theoretical model of docking scores which enables us to utilize large amounts of data of known active and inactive compounds for a particular target without requiring large computational resources or a complicated procedure. This method is useful for making scoring functions for the identification of novel scaffolds using the knowledge of active compounds for a particular target or a customized scoring function for an interesting family of drug targets.

Site-specific behavior in de-excitation spectra of F(3)SiCH(2)CH(2)Si(CH(3))(3) in the Si 1s excitation region

Excitation (total ion yield) and de-excitation (resonant photoemission) spectra have been measured in the Si 1s photoexcitation region of the F(3)SiCH(2)CH(2)Si(CH(3))(3) molecule using monochromatized undulator radiation. Theoretical calculations within the framework of density functional theory have reproduced the observed total ion yield spectrum very well. The first peak at the lowest photon energy, coming from Si 1s excitation at the trimethyl side into a vacant orbital, induces spectator Auger decays in which the excited electron remains in its valence orbital. The second peak produced through excitation of Si 1s electron at the trifluoride side generates resonant Auger decays in which the excited valence electron remains predominantly also in the valence orbital or is partly shaken up into higher Rydberg orbitals. The third peak generated through Si 1s excitation at the trifluoride side produces resonant Auger decays in which the excited Rydberg electron remains or is partly shaken down to a lower lying valence molecular orbital. These findings exhibit a clear distinction between resonant Auger decays following photoexcitation of Si 1s electrons under different chemical environments.

The inhomogeneous structure of water at ambient conditions

Small-angle X-ray scattering (SAXS) is used to demonstrate the presence of density fluctuations in ambient water on a physical length-scale of approximately 1 nm; this is retained with decreasing temperature while the magnitude is enhanced. In contrast, the magnitude of fluctuations in a normal liquid, such as CCl(4), exhibits no enhancement with decreasing temperature, as is also the case for water from molecular dynamics simulations under ambient conditions. Based on X-ray emission spectroscopy and X-ray Raman scattering data we propose that the density difference contrast in SAXS is due to fluctuations between tetrahedral-like and hydrogen-bond distorted structures related to, respectively, low and high density water. We combine our experimental observations to propose a model of water as a temperature-dependent, fluctuating equilibrium between the two types of local structures driven by incommensurate requirements for minimizing enthalpy (strong near-tetrahedral hydrogen-bonds) and maximizing entropy (nondirectional H-bonds and disorder). The present results provide experimental evidence that the extreme differences anticipated in the hydrogen-bonding environment in the deeply supercooled regime surprisingly remain in bulk water even at conditions ranging from ambient up to close to the boiling point.

PDA usage by Japanese resident physicians is low: a cross-sectional survey

OBJECTIVES

Personal digital assistants (PDAs) are in widespread use by resident physicians in many countries, reaching as high as 95% in some reports. Uses are varied and include clinical decision support and support of evidence-based practice. Utilization by resident doctors in Japan has not been characterized. This study was conducted to determine practice patterns of PDA use by Japanese resident physicians.

METHODS

A nationwide cohort survey study was distributed to all 1070 residency teaching programs in Japan. The survey included questions pertaining to use of PDAs in clinical practice.

RESULTS

1124 surveys were returned (response rate of approximately 75%). 297 (30.7%) respondents reported currently using PDAs, while 971 (86.4%) reported having used a PDA in the past. PDA users were more likely to be male (p <0.05), but no other significant differences were found when examining the following variables: age, training site (university hospital versus community teaching hospital), satisfaction with existing information technology access.

CONCLUSIONS

Use of PDAs among Japanese resident physicians is much lower than their counterparts in other countries. In light of this, further research on patient outcomes in Japan and the impact of PDA usage on patient outcomes is urgently needed. If demonstrated to improve outcomes, barriers to adoption need to be identified and overcome.

Recognition site for the side chain of 2-ketoacid substrate in d-lactate dehydrogenase

Replacement of Tyr52 with Val or Ala in Lactobacillus pentosus d-lactate dehydrogenase induced high activity and preference for large aliphatic 2-ketoacids and phenylpyruvate. On the other hand, replacements with Arg, Thr or Asp severely reduced the enzyme activity, and the Tyr52Arg enzyme, the only one that exhibited significant enzyme activity, showed a similar substrate preference to the Tyr52Val and Tyr52Ala enzymes. Replacement of Phe299 with Gly or Ser greatly reduced the enzyme activity with less marked change in the substrate preference. Except for the Phe299Ser enzyme, these mutant enzymes with low catalytic activity consistently stimulated NADH oxidation in the absence of 2-ketoacid substrates. However, the double mutant enzymes, Tyr52Arg/Phe299Gly and Tyr52Thr/Phe299Ser, did not exhibit synergically decreased enzyme activity or the substrate-independent NADH oxidation, but rather increased activities toward certain 2-ketoacid substrates. These results indicate that the coordinative combination of amino acid residues at two positions is pivotal in both the functional recognition of the 2-ketoacid side chain and the protection of the bound NADH molecule from the solvent. Multiplicity in such combinations appears to provide d-LDH-related 2-hydroxyacid dehydrogenases with a great variety of catalytic and physiological functions.