Retrospective Analysis to Optimize the Detection of MET Exon 14 Skipping Mutations in Non-Small Cell Lung Cancer.

Our study optimized METex14 skipping mutation detection by analyzing 223 Oncomine™ Focus Assay-positive cases using Pan Lung Cancer PCR Panel and reverse transcription (RT)-PCR. Among the 11 METex14 skipping mutation-positive cases (average read counts: 1390), 2 with Oncomine™ Focus Assay read counts of 2540 and 10,177 were positive on all platforms. Those with Oncomine™ Focus Assay read counts ranging from 179 to 612 tested negative elsewhere. Specimens with low ratios (average ratio: 0.12% for nine cases) may yield false-positive results. Our results suggested that monitoring read counts and ratios and validating the results with RT-PCR are crucial to prevent false positives.

Screening of single nucleotide polymorphisms within HLA region related to hematopoietic stem cell transplantation using MassARRAY technology.

A growing number of studies showed that single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA)-related genes were associated with the outcome of hematopoietic stem cell transplantation (HSCT). Thus, other SNPs located nearby the classical HLA genes must be considered in HSCT. We evaluated the clinical feasibility of MassARRAY by comparing to Sanger sequencing. The PCR amplicons with each one of the 17 loci that were related to the outcomes of HSCT published by our previous study were transferred onto a SpectroCHIP Array for genotyping by mass spectrometry. The sensitivity of MassARRAY was 97.9% (614/627) and the specificity was 100% (1281/1281), where the positive predictive value (PPV) was 100% (614/614) and the negative predictive value (NPV) was 99.0% (1281/1294). MassARRAY is high-throughput, which can accurately analyze multiple SNPs at the same time. Based on these properties, we proposed that it could be an efficient method to match the genotype between the graft and the recipient before transplantation.

Transmission of Classical Swine Fever Virus in Cohabitating Piglets with Various Immune Statuses Following Attenuated Live Vaccine.

Classical swine fever (CSF) is a systemic hemorrhagic disease affecting domestic pigs and wild boars. The modified live vaccine (MLV) induces quick and solid protection against CSF virus (CSFV) infection. Maternally derived antibodies (MDAs) via colostrum could interfere with the MLV's efficacy, leading to incomplete protection against CSFV infection for pigs. This study investigated CSFV transmission among experimental piglets with various post-MLV immune statuses. Nineteen piglets, 18 with MDAs and 1 specific-pathogen-free piglet infected with CSFV that served as the CSFV donor, were cohabited with piglets that had or had not been administered the MLV. Five-sixths of the piglets with MDAs that had been administered one dose of MLV were fully protected from contact transmission from the CSFV donor and did not transmit CSFV to the piglets secondarily exposed through cohabitation. Cell-mediated immunity, represented by the anti-CSFV-specific interferon-γ-secreting cells, was key to viral clearance and recovery. After cohabitation with a CSFV donor, the unvaccinated piglets with low MDA levels exhibited CSFV infection and spread CSFV to other piglets through contact; those with high MDA levels recovered but acted as asymptomatic carriers. In conclusion, MLV still induces solid immunity in commercial herds under MDA interference and blocks CSFV transmission within these herds.

Deletion in the S1 Region of Porcine Epidemic Diarrhea Virus Reduces the Virulence and Influences the Virus-Neutralizing Activity of the Antibody Induced.

Porcine epidemic diarrhea virus (PEDV) causes severe diarrhea and a high rate of mortality in suckling pigs. The epidemic of PEDV that occurred after 2013 was caused by non-insertion and deletion of S gene (S-INDEL) PEDV strains. During this epidemic, a variant of the non-S-INDEL PEDV strain with a large deletion of 205 amino acids on the spike gene (5-17-V) was also found to co-exist with a non-S-INDEL PEDV without deletion (5-17-O). Herein, we describe the differences in the complete genome, distribution, virulence, and antigenicity between strain 5-17-O and variant strain 5-17-V. The deletion of 205 amino acids was primarily located in the S1O domain and was associated with milder clinical signs and lower mortality in suckling pigs than those of the 5-17-O strain. The 5-17-V strain-induced antibody did not completely cross-neutralize the 5-17-O strain. In conclusion, the deletion in the S1 region reduces the virulence of PEDV and influences the virus-neutralizing activities of the antibody it induces.

NRAS germline variant G138R and multiple rare somatic mutations on APC in colorectal cancer patients in Taiwan by next generation sequencing.

Colorectal cancer (CRC) arises from mutations in a subset of genes. We investigated the germline and somatic mutation spectrum of patients with CRC in Taiwan by using the AmpliSeq Cancer Hotspot Panel V2. Fifty paired freshly frozen stage 0-IV CRC tumors and adjacent normal tissue were collected. Blood DNA from 20 healthy donors were used for comparison of germline mutations. Variants were identified using an ion-torrent personal genomic machine and subsequently confirmed by Sanger sequencing or pyrosequencing. Five nonsynonymous germline variants on 4 cancer susceptible genes, CDH1, APC, MLH1, and NRAS, were observed in 6 patients with CRC (12%). Among them, oncogene NRAS G138R variant was identified as having a predicted damaging effect on protein function, which has never been reported by other laboratories. CDH1 T340A variants were presented in 3 patients. The germline variants in the cancer patients differed completely from those found in asymptomatic controls. Furthermore, a total of 56 COSMIC and 21 novel somatic variants distributed in 20 genes were detected in 44 (88%) of the CRC samples. High inter- and intra-tumor heterogeneity levels were observed. Nine rare variants located in the ß-catenin binding region of the APC gene were discovered, 7 of which could cause amino acid frameshift and might have a pathogenic effect. In conclusion, panel-based mutation detection by using a high-throughput sequencing platform can elucidate race-dependent cancer genomes. This approach facilitates identifying individuals at high risk and aiding the recognition of novel mutations as targets for drug development.

Real-time biallelic polymorphism-polymerase chain reaction for chimerism monitoring of hematopoietic stem cell transplantation relapsed patients.

BACKGROUND: An accurate analysis of chimerism kinetics permits early detection of hematopoietic stem cell transplantation (HSCT) in patients with high risks of graft-versus-host disease or those liable to relapse. Although short tandem repeats-PCR (STR-PCR) is the golden standard for quantitative chimerism analysis in most of the clinical laboratories, it has a relatively low sensitivity of 5% and the detection of low percentage in mixed chimerism is usually delayed. In this study, we developed a real-time PCR for chimerism analysis based on the informative biallelic polymorphisms (BP). METHODS: The allele frequencies of 19 selective biallelic polymorphic markers were analyzed using the genomic DNA from 100 healthy Taiwanese volunteers. The informative biallelic polymorphic markers with high discrimination power in the Taiwanese population were identified. The TaqMan probe-based real-time BP-PCR for amplification of the informative loci was designed and the detection sensitivity was determined. Clinical application of real-time BP-PCR in chimerism monitoring was evaluated and was compared with the conventional STR-PCR by analyzing the DNA samples obtained at different time points post-HSCT from 4 relapsed and 10 non-relapsed patients. RESULTS: Allele distribution analysis revealed that the loci of S01a, S03, S04a, S05b, S06, S07b, S08b, S09b, S10b and S11a had a relatively high discrimination power and were the informative BP for chimerism monitoring in the Taiwanese population. Real-time BP-PCRs for these 10 BP loci were set up with the detection sensitivity equivalent to 0.003-0.006%. Real-time BP-PCR of the 4 HSCT patients revealed the presence of recipient-specific DNA at early time point than STR-PCR for 3 of the patients, whereas real-time BP-PCR was as effective as STR-PCR in uncovering the sign of relapse for one of the patients. In addition, the baseline value for the patients with no sign of relapse was 0.127 ± 0.193% of recipient DNA. CONCLUSION: We conclude that real-time BP-PCR is a sensitive and reliable method for chimerism monitoring and is superior to the STR-PCR in identifying patients who are at high risk for relapse after transplantation.

[Perceived barriers to taking a Pap smear: predictors in immigrant women].

BACKGROUND: New immigrant women in Taiwan are believed to generally perceive that "no illness" infers good health. Because medical inspection induces feelings of discomfit and due to language barriers, limited/no insurance coverage and more limited access to medical resources, understanding better the motivation of immigrant women to take Pap smears, the actual examination rate and key factors that influence willingness is important. Coverage of this issue, however, is extremely limited in domestic research. PURPOSE: This study aimed to investigate: (i) The Pap smear screening rate amongst immigrant women; (ii) Immigrant women's perception of cervical cancer susceptibility and severity as well as cues to action and perceived barriers to taking a Pap smear; and (iii) Predictors of perceived barriers to taking Pap smears in this target population. METHODS: Using a cross-sectional descriptive correlation study design, 100 immigrant women were recruited from the outpatient clinic and inpatient wards of a regional teaching hospital in Kaohsiung. Structured questionnaires included a demographic survey, scales of susceptibility and cervical cancer severity, scales of cues to action and barriers to receiving a Pap smear. RESULTS: One-quarter (25%) of the surveyed population had never taken a Pap smear. Immigrant women perceived their knowledge somewhat insufficient with regard to cervical cancer susceptibility and severity. Level of education, previous Pap smear experience, and number of children represented significant predictors of perceived barriers in taking Pap smears, accounting collectively for 26.1% perceived variance. CONCLUSIONS/IMPLICATIONS FOR PRACTICE: Findings suggest that appropriate interventions should be targeted on the general healthcare population as well as tailored to specific immigrant national populations in order to improve Pap smear screening rates amongst immigrant women.

Use of X-linked short tandem repeats loci to confirm mutations in parentage caseworks.

BACKGROUND: Analysis of short tandem repeats (STRs) has become wide-spread in routine for parentage test. However, the accuracy of STR is sometimes interfered by the presence of microsatellite mutations. Analysis of other DNA markers such as the HV1 and HV2 hypervariable regions of mitochondrial DNA or the Y-STR becomes essential to settle the noncongruence. Owing to the time-consuming nature of these tests, we explored here the use of X-chromosome STR (X-STR) to resolve the paternity and maternity disputes. METHODS: At first, the autosomal STR mutation frequencies among 4758 Taiwanese were analyzed. Population data were obtained from randomly selected 99 females and 101 males to setup the X-STR database. Two families with a mismatch of one allele in autosomal STR analysis were subjected to the X-STR test to explore its clinical application. RESULTS: The STR mutations occurred in all 15 autosomal STR loci with the exception of TH01 and TPOX. The mutation rates could reach as high as 0.106% for the loci of D8S1179 and D18S51. As to the X-STR frequencies, the probability values of exact tests for Hardy-Weinberg equilibrium were 0.1471, 0.0019, 0.0025, 0.1427, and 0.1167 for the loci of DXS7132, DXS981, DXS6789, DXS101, and HPRTB, respectively. In addition, 33 and 34 different haplotypes were revealed for DXS101-DXS6789 and DXS7132-DXS981, respectively. Furthermore, two cases with one allele mismatch in routine parentage test were resolved by performing X-STR analysis. CONCLUSION: Typing of X-STR markers is recommended for parentage test when 1 or 2 alleles mismatch is present or when the samples are difficult to be analyzed.

Systematic analysis of stutters to enhance the accuracy of chimerism testing.

Post-transplantation chimerism testing is important to monitor the engraftment of donor stem cells and for the diagnosis of relapse. Detecting the presence of donor/recipient-specific short tandem repeats (STRs) is a frequently used method for engraftment study. Unfortunately, the interpretation of the STR-based chimerism tests is often subject to interference by the presence of a stutter peak, which is one 4-base repeat unit smaller than an authentic allele. The aim of this study was to systematically analyze and resolve the effect of stutter peaks on the interpretation of STR-based chimerism tests. The AmpFlSTR Identifiler Amplification kit (Applied Biosystems)was used to amplify 15 STR loci using genomic DNA from 30 randomly selected, healthy donors. We found that the stutter peaks had locus-specific characteristics. The stutter percentage was defined as the percentage of the stutter peak area/main STR peak area. Based on mean values for the 30 DNA samples, the stutter percentage varied from locus to locus and ranged from 3.12% to 10.71% for 15 STR loci. The locus-specific stutter effect can be eliminated through appropriately adjusted equations. The usefulness of these equations in the prediction of relapse was confirmed by the 5% sensitivity test. Hence, this report offers a valuable scheme to enhance the accuracy of chimerism testing.

Bone marrow transplant relapse with loss of an allele.

BACKGROUND: Detection of the extent of chimerism after transplantation is an important method for monitoring the engraftment of donor stem cells or diagnosing relapse. METHODS: The AmpFlSTR Identifiler amplification kit (Applied Biosystem, CA) was used to perform STR-PCR for the study of engraftment. RESULTS: At 6 months post-transplantation, the peripheral blood genotype shows a mixture of donor and recipient alleles, consistent with disease relapse. Interestingly, the D18S51 locus shows 2 donor alleles and only 1 recipient allele, the other recipient allele is missing. To further confirm chromosome loss, we used the D18S53 and D18S1129 in the ABI PRISM Linkage Mapping Sets. The D18S53 locus showed the recipient allele (179 bp) and shared allele (171 bp). Interestingly, the D18S1129 locus showed almost only 1 recipient allele (243 bp); the other recipient allele and shared allele (251 bp) is missing. CONCLUSION: The case illustrates that chromosome loss in tumor cells during the course of disease may cause corresponding loss of an STR locus. This circumstance is a potential source of error in the interpretation of engraftment analysis, especially if only one informative allele is used to monitor engraftment.

Assembly of hybrid oligonucleotide modified gold (Au) and alloy nanoparticles building blocks.

The alloy-based hybrid materials with macroscopic network arrays were developed by AuAg/Au and AuAgPd/Au nanoparticle composites through oligonucleotides hybridization. AuAg/Au and AuAgPd/Au exhibited distinct organization. The morphology of AuAg/Au conjugation assembled mainly as compact aggregates while AuAgPd/Au hybrid conjugated into the loosen network assemblies. The dehybridization temperatures were studied as a function of molar ratio of alloy/Au. It was found that higher alloy/gold molar ratio led to stronger hybridization for alloy/gold composite, accompanied with increased melting temperature. These results could be interpreted in terms of more alloy nanoparticles bound to a Au particle when the molar ratio of alloy/gold increased. The thermal analysis also showed that AuAg/Au exhibited higher dehybridization temperature. A modified model describing the dehybridization probability of an intact Au/alloy aggregate was performed to support the dehybridization temperature increased with increasing alloy/Au molar ratio. As to more oligonucleotides carried by AuAg (4.9 +/- 1.9 nm) than by AuAgPd (4.4 +/- 1.5 nm) due to larger size in AuAg, the efficient hybridization could result in higher dehybridization temperature in AuAg/Au.

Effect of hair and clothing on neck immobilization using a cervical collar.

An important step during spine immobilization is application of a cervical collar. Clothing or hair covering the neck may impinge on this process. The purpose of this study was to evaluate the effect of clothing and hair covering the neck on immobilization using a cervical collar. Study participants were 18 female volunteers with long hair aged 20 to 28 years. Cervical range of motion (ROM) was tested in 6 directions (flexion, extension, right and left lateral bending, right and left axial rotation) using a cervical ROM (CROM) device. After measuring unrestricted ROM (no cervical collar), a 1-piece rigid cervical collar was placed the neck (1) covered by hair and clothing; (2) covered by clothing; (3) covered by hair; or (4) uncovered. Range of motion was retested under all 4 conditions. Data were compared using crossover-design analysis of variance (P<.05 statistically significant). Range of motion in all directions was significantly restricted by cervical collar placement under all conditions. Unrestricted ROM in all directions ranged from 41.50 degrees (7.25 degrees) to 70.76 degrees (15.4 degrees). In contrast, ROM with a cervical collar under the 4 conditions in all directions ranged from 10.80 degrees (5.10 degrees) to 18.81 degrees (7.37 degrees). We were unable to detect any significant differences in ROM between the 4 conditions. Our data suggest that long hair and clothing, which cover the neck, do not alter the effectiveness of cervical collar immobilization as measured by the cervical ROM device.