Evaluation of a Commercial Point-of-Care RT-LAMP Assay for Rapid Detection of SARS-CoV-2

The goal of this study was to evaluate the performance of a commercial reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay (Detect COVID-19 Test) in the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A total of 202 human respiratory and viral culture specimens were tested retrospectively. The performance of the Detect COVID-19 Test was comparable to that of commercial real-time polymerase chain reaction assays (sensitivity: 93.42%; specificity: 100%), and better than that of the rapid antigen test (sensitivity: 48.00%; specificity: 100%) for specimens with threshold cycle (Ct) values of less than 30. The Beta, Delta, and Omicron variants of concern were successfully detected. With their simplicity of use and good assay sensitivity, point-of-care RT-LAMP assays may be a viable option for SARS-CoV-2 testing at home, or in regions without sophisticated laboratory facilities.

Molecular characteristics of Asian male BRCA-related cancers

PURPOSE

Germline mutations of BRCA1 or BRCA2 predispose men to develop various cancers, including breast cancers and prostate cancers. Male breast cancer (MBC) is a rare disease while prostate cancer (PRC) is uncommon in young men at the age of less than 40. The prevalence of BRCA genes in Asian male patients has to be elevated.

METHODS

Germline mutations screening was performed in 98 high-risk Chinese MBC and PRC patients.

RESULT

We have identified 16 pathogenic BRCA2 mutation carriers, 12 were MBC patients, 2 were PRC patients and 2 were patients with both MBC and PRC. The mutation percentages were 18.8%, 6.7% and 50% for MBC, PRC and both MBC and PRC patients, respectively. BRCA2 gene mutations confer a significantly higher risk of breast/prostate cancers in men than those with BRCA1 mutations. BRCA mutated MBC patients had a younger age of diagnosis and strong family histories of breast cancers while BRCA mutated PRC patients had strong family histories of ovarian cancers.

CONCLUSION

Male BRCA carriers with breast cancers or prostate cancers showed distinct clinical and molecular characteristics, a male-specific genetic screening model would be useful to identify male cancer patients who have a high risk of BRCA mutation.

Genomic characteristics and viral load dynamics of a SARS-CoV-2 Omicron BA.2.2 variant from a hospitalized patient treated with molnupiravir

We sequenced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from nasal and throat swabs of a hospitalized patient during the fifth wave of coronavirus disease 2019 (COVID-19) pandemic in Hong Kong. Genomic characteristics and viral load dynamics of an Omicron BA.2.2 variant before and after molnupiravir treatment were presented.

How does re-classification of variants of unknown significance (VUS) impact the management of patients at risk for hereditary breast cancer?

Background

The popularity of multigene testing increases the probability of identifying variants of uncertain significance (VUS). While accurate variant interpretation enables clinicians to be better informed of the genetic risk of their patients, currently, there is a lack of consensus management guidelines for clinicians on VUS.

Methods

Among the BRCA1 and BRCA2 mutations screening in 3,544 subjects, 236 unique variants (BRCA1: 86; BRCA2: 150) identified in 459 patients were being reviewed. These variants consist of 231 VUS and 5 likely benign variants at the initial classification.

Results

The variants in 31.8% (146/459) patients were reclassified during the review, which involved 26 unique variants (11.0%). Also, 31 probands (6.8%) and their family members were offered high-risk surveillance and related management after these variants were reclassified to pathogenic or likely pathogenic. At the same time, 69 probands (15%) had their VUS downgraded to cancer risk equivalent to the general population level.

Conclusion

A review of archival variants from BRCA1 and BRCA2 genetic testing changed the management for 31.8% of the families due to increased or reduced risk. We encourage regular updates of variant databases, reference to normal population and collaboration between research laboratories on functional studies to define the clinical significances of VUS better.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01270-4.

Germline mutations in Chinese ovarian cancer with or without breast cancer

BACKGROUND

Ovarian and breast cancers are known to have significant genetic components. Considering the differences in the mutation spectrum across ethnicity, it is important to identify hereditary breast and ovarian cancer (HBOC) genes mutation in Chinese for clinical management.

METHODS

Two cohorts of 451 patients with ovarian cancer only (OV) and 93 patients with both breast and ovarian (BROV) cancers were initially screened for BRCA1, BRCA2, TP53, and PTEN. 109 OV and 43 BROV patients with extensive clinical risk and were being tested negative, were then further characterized by 30-gene panel analysis.

RESULTS

Pathogenic BRCA1/2 variants were identified in 45 OV patients and 33 BROV patients, giving a prevalence of 10% and 35.5%, respectively. After the extended screening, mutations in other HBOC genes were identified in an additional 12.8% (14/109) of the OV cohort and 14% (6/43) in the BROV cohort. The most commonly mutated genes in the OV cohort were MSH2 (4.6%) while in the BROV cohort were MSH2 (4.7%) and PALB2 (4.7%). With this extended multigene testing strategy, pathogenic mutations were detected in 12.8% of OV patients (BRCAs: 10%; additional genes: 12.8%) and 40.9% (BRCAs: 35.5%; additional genes: 14%) of BROV patients.

CONCLUSION

Extended characterization of the contributions of HBOC genes to OV and BROV patients has significant impacts on further management in patients and their families, expanding the screening net for more asymptomatic individuals.

Rapid antigen test during a COVID-19 outbreak in a private hospital in Hong Kong

INTRODUCTION

In response to two nosocomial clusters of coronavirus disease 2019 (COVID-19) in our hospital, we adopted a series of strict infection control measures, including regular rapid antigen test (RAT) screening for high-risk patients, visitors, and healthcare workers. We evaluated the diagnostic performance of a locally developed RAT, the INDICAID COVID-19 Rapid Antigen Test (Phase Scientific, Hong Kong), using respiratory samples from both symptomatic and asymptomatic individuals.

METHODS

Real-time reverse-transcription polymerase chain reaction (rRT-PCR)-confirmed deep throat saliva (DTS) and pooled nasopharyngeal swab and throat swab (NPS/TS) samples collected from 1 November to 30 November 2020 were tested by INDICAID. Screening RATs were performed on asymptomatic healthcare workers during a 16-week period (1 December 2020 to 22 March 2021).

RESULTS

In total, 20 rRT-PCR-confirmed samples (16 DTS, four pooled NPS/TS) were available for RAT. Using the original sample, RAT results were positive in 17/20 samples, indicating 85% sensitivity (95% confidence interval [CI]=62.11%-96.79%). Negative RAT results were associated with higher cycle threshold (Ct) values. For samples with Ct values <25, the sensitivity was 100%. Of the 49 801 RATs collected from healthcare workers, 33 false positives and one rRT-PCR-confirmed case were detected. The overall specificity was 99.93% (95% CI=99.91%-99.95%). The positive and negative predictive values were 2.94% (95% CI=2.11%-4.09%) and 100%, respectively.

CONCLUSION

The INDICAID COVID-19 RAT demonstrated good sensitivity for specimens with high viral loads and satisfactory specificity for low-risk, asymptomatic healthcare workers.

Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2

Coronavirus disease 2019 (COVID-19) pandemic has been a catastrophic burden to global healthcare systems. The fast spread of the etiologic agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need to identify unknown coronaviruses rapidly for prompt clinical and public health decision making. Moreover, owing to the high mutation rate of RNA viruses, periodic surveillance on emerging variants of key virus components is essential for evaluating the efficacy of antiviral drugs, diagnostic assays and vaccines. These 2 knowledge gaps formed the basis of this study. In the first place, we evaluated the feasibility of characterizing coronaviruses directly from respiratory specimens. We amplified partial RdRP gene, a stable genetic marker of coronaviruses, from a collection of 57 clinical specimens positive for SARS-CoV-2 or other human coronaviruses, and sequenced the amplicons with Nanopore Flongle and MinION, the fastest and the most scalable massively-parallel sequencing platforms to-date. Partial RdRP sequences were successfully amplified and sequenced from 82.46% (47/57) of specimens, ranging from 75 to 100% by virus type, with consensus accuracy of 100% compared with Sanger sequences available (n = 40). In the second part, we further compared 19 SARS-CoV-2 RdRP sequences collected from the first to third waves of COVID-19 outbreak in Hong Kong with 22,173 genomes from GISAID EpiCoV™ database. No single nucleotide variants (SNVs) were found in our sequences, and 125 SNVs were observed from global data, with 56.8% being low-frequency (n = 1-47) missense mutations affecting the rear part of RNA polymerase. Among the 9 SNVs found on 4 conserved domains, the frequency of 15438G > T was highest (n = 34) and was predominantly found in Europe. Our data provided a glimpse into the sequence diversity of a primary antiviral drug and diagnostic target. Further studies are warranted to investigate the significance of these mutations.

Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis

Objective

We designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden.

Results

At least 8 loci were successfully amplified from the majority for predicting first- and second-line drug resistance (14/23, 60.87%), and the 12 specimens yielding all 10 targets were sequenced with Nanopore MinION and Illumina MiSeq. MinION sequencing data was corrected by Nanopolish and recurrent variants were filtered. A total of 67,082 bases across all consensus sequences were analyzed, with 67,019 bases called by both MinION and MiSeq as wildtype. For the 41 single nucleotide variants (SNVs) called by MiSeq with 100% variant allelic frequency (VAF), 39 (95.1%) were called by MinION. For the 22 mixed bases called by MiSeq, a SNV with the highest VAF (70%) was called by MinION. With short assay time, reasonable reagent cost as well as continuously improving sequencing chemistry and signal correction pipelines, this Nanopore method can be a viable option for direct tuberculosis drug resistance profiling in the near future.

An economical Nanopore sequencing assay for human papillomavirus (HPV) genotyping

Background

Human papillomavirus (HPV) testing has been employed by several European countries to augment cytology-based cervical screening programs. A number of research groups have demonstrated potential utility of next-generation sequencing (NGS) for HPV genotyping, with comparable performance and broader detection spectrum than current gold standards. Nevertheless, most of these NGS platforms may not be the best choice for medium sample throughput and laboratories with less resources and space. In light of this, we developed a Nanopore sequencing assay for HPV genotyping and compared its performance with cobas HPV Test and Roche Linear Array HPV Genotyping Test (LA).

Methods

Two hundred and one cervicovaginal swabs were routinely tested for Papanicolaou smear, cobas HPV Test and LA. Residual DNA was used for Nanopore protocol after routine testing. Briefly, HPV L1 region was amplified using PGMY and MGP primers, and PCR-positive specimens were sequenced on MinION flow cells (R9.4.1). Data generated in first 2 h were aligned with reference sequences from Papillomavirus Episteme database for genotyping.

Results

Nanopore detected 96 HPV-positive (47.76%) and 95 HPV-negative (47.26%) specimens, with 10 lacking β-globin band and not further analyzed (4.98%). Substantial agreement was achieved with cobas HPV Test and LA (κ: 0.83–0.93). In particular, Nanopore appeared to be more sensitive than cobas HPV Test for HPV 52 (n = 7). For LA, Nanopore revealed higher concordance for high-risk (κ: 0.93) than non-high risk types (κ: 0.83), and with similar high-risk positivity in each cytology grading. Nanopore also provided better resolution for HPV 52 in 3 specimens co-infected with HPV 33 or 58, and for HPV 87 which was identified as HPV 84 by LA. Interestingly, Nanopore identified 5 additional HPV types, with an unexpected high incidence of HPV 90 (n = 12) which was reported in North America and Belgium but not in Hong Kong.

Conclusions

We developed a Nanopore workflow for HPV genotyping which was economical (about USD 50.77 per patient specimen for 24-plex runs), and with comparable or better performance than 2 reference methods in the market. Future prospective study with larger sample size is warranted to further evaluate test performance and streamline the protocol.

Potential utility of targeted Nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection

Background

Diversified etiology of lower respiratory tract infection renders diagnosis challenging. The mainstay microbial culture is time-consuming and constrained by variable growth requirements. In this study, we explored the use of Nanopore sequencing as a supplementary tool to alleviate this diagnostic bottleneck.

Methods

We developed a targeted Nanopore method based on amplification of bacterial 16S rRNA gene and fungal internal transcribed spacer region. The performance was compared with routine infectious disease workups on 43 respiratory specimens.

Results

Nanopore successfully identified majority of microbes (47/54, 87.04%) and 7 possible pathogens not detected by routine workups, which were attributable to the content of microbiological investigations (n = 5) and negative culture (n = 2). The average sequencing time for first target reads was 7 min (1–43 min) plus 5 h of pre-sequencing preparation.

Conclusions

The Nanopore method described here was rapid, economical and hypothesis-free, which might provide valuable hints to further microbiological follow-up for opportunistic pathogens missed or not detectable by conventional tests.

Frequent functional activation of RAS signalling not explained by RAS/RAF mutations in relapsed/refractory multiple myeloma

RAS mutations are frequent in relapsed/refractory multiple myeloma (RRMM) but functional study in primary samples is scanty. Herein, in primary myeloma plasma cells of 17 suspected RRMM, functional activation of RAS signalling was studied by Western blot of phosphorylated ERK1/2 (phospho-ERK1/2). Moreover, activating mutations in KRAS, NRAS, BRAF, and ALK were studied by PCR and bidirectional direct sequencing. Furthermore, methylation of negative RAS signalling regulator genes, RASSF1A and RASD1, were analyzed by methylation-specific PCR. As evidenced by phospho-ERK1/2 over-expression, functional RAS activation was detected in 12 (75.0%) RRMM. Of patients with functional RAS activation, sequencing data showed only seven (58.3%) patients with one each had NRAS Q61H, NRAS Q61K, KRAS G12D, KRAS G12V, KRAS G13D, KRAS Q61P, or BRAF V600E mutation, whereas five (41.7%) patients had no RAS/RAF mutation. Conversely, patients without functional RAS activation had no RAS/RAF mutation. Moreover, none of the patients with functional RAS activation had ALK mutations, or methylation of RASSF1A and RASD1. Collectively, functional activation of RAS signalling was present in majority of RRMM but only about half (58.3%) accountable by RAS/RAF mutations. If verified in larger studies, clinical investigations of MEK inhibitors are warranted regardless of RAS/RAF mutations.

Next-generation sequencing with a myeloid gene panel in core-binding factor AML showed KIT activation loop and TET2 mutations predictive of outcome

Clinical outcome and mutations of 96 core-binding factor acute myeloid leukemia (AML) patients 18–60 years old were examined. Complete remission (CR) after induction was 94.6%. There was no significant difference in CR, leukemia-free-survival (LFS) and overall survival (OS) between t(8;21) (N=67) and inv(16) patients (N=29). Univariate analysis showed hematopoietic stem cell transplantation at CR1 as the only clinical parameter associated with superior LFS. Next-generation sequencing based on a myeloid gene panel was performed in 72 patients. Mutations in genes involved in cell signaling were associated with inferior LFS and OS, whereas those in genes involved in DNA methylation were associated with inferior LFS. KIT activation loop (AL) mutations occurred in 25 patients, and were associated with inferior LFS (P=0.003) and OS (P=0.001). TET2 mutations occurred in 8 patients, and were associated with significantly shorter LFS (P=0.015) but not OS. Patients negative for KIT-AL and TET2 mutations (N=41) had significantly better LFS (P<0.001) and OS (P=0.012) than those positive for both or either mutation. Multivariate analysis showed that KIT-AL and TET2 mutations were associated with inferior LFS, whereas age ⩾40 years and marrow blast ⩾70% were associated with inferior OS. These observations provide new insights that may guide better treatment for this AML subtype.

Hong Kong domestic health spending: financial years 1989/90 to 2011/12

This report presents the latest estimates of Hong Kong domestic health spending for financial years 1989/90 to 2011/12, cross-stratified and categorized by financing source, provider, and function. Total expenditure on health (TEH) was HK$101 985 million in financial year 2011/12, which represents an increase of HK$8580 million or 9.2% over the preceding year. TEH grew faster relative to gross domestic product (GDP) leading to a rise in TEH as a percentage of GDP from 5.1% in 2010/11 to 5.2% in 2011/12. During the period 1989/90 to 2011/12, total health spending per capita (at constant 2012 prices) grew at an average annual rate of 4.8%, which was faster than the average annual growth rate of per capita GDP by 1.8 percentage points. In 2011/12, public and private expenditure on health increased by 8.3% and 10.0% when compared with 2010/11, reaching HK$49,262 million and HK$52,723 million respectively. Consequently, public share of total health expenditure dropped slightly from 48.7% to 48.3% over the year. Of private spending, the most important source of health financing was out-of-pocket payments by households (34.9% of TEH), followed by employer-provided group medical benefits (7.5%) and private insurance (7.4%). It is worth noting that private insurance will likely take over employers as the second largest private payer if the insurance market continues to expand at the current rate. Of the HK$101,985 million total health expenditure in 2011/12, current expenditure comprised HK$96,572 million (94.7%), whereas HK$5413 million (5.3%) was for capital expenses (ie investment in medical facilities). Analysed by health care function, services of curative care accounted for the largest share of total health spending (65.2%), which was made up of ambulatory services (33.6%), in-patient curative care (26.9%), day patient hospital services (4.1%), and home care (0.5%). Notwithstanding its small share, the total spending for day patient hospital services shows an increasing trend over the period 1989/90 to 2011/12, likely as a result of policy directives to shift the emphasis from in-patient to day patient care. Hospitals accounted for an increasing share of total spending, from 28.2% in 1989/90 to 46.8% in 2002/03 and then dropped slightly to 42% to 44% during the period 2005/06 to 2011/12, which was primarily driven by reduced expenditure of Hospital Authority. As a result of the epidemics which are of public health importance (eg avian flu, SARS, swine flu) and the expansion of private health insurance market in the last two decades, spending on provision and administration of public health programmes, and general health administration and insurance accounted for increasing, though less significant, shares of total health spending over the period. Without taking into account capital expenses (ie investment in medical facilities), public current expenditure on health amounted to HK$45,321 million (46.9% of total current expenditure) in 2011/12 with the remaining HK$51,251 million made up of private sources of funds. Public current expenditure was mostly incurred at hospitals (74.1%), whereas private current expenditure was mostly incurred at providers of ambulatory health care (51.2%). Although both public and private spending were mostly expended on personal health care services and goods (91.1% of total current spending), the distributional patterns among functional categories differed. Public expenditure was targeted at in-patient care (47.3%) and substantially less on out-patient care (27.4%). In comparison, private spending was mostly concentrated on out-patient care (42.7%), whereas in-patient care (24.7%) and medical goods outside the patient care setting (19.9%) comprised the majority of the remaining share. Compared to the Organisation for Economic Co-operation and Development countries, Hong Kong has devoted a relatively low percentage of GDP to health care in the last decade. As a share of total spending, public funding (either general government revenue or social security funds) was also lower than those in most economies with comparable economic development and public revenue collection base. Nonetheless, Hong Kong health care system achieved service quality and health outcome that fared well by global standards, indicating cost efficiency and effectiveness.

Evaluation of the new red cell parameters on Beckman Coulter DxH800 in distinguishing iron deficiency anaemia from thalassaemia trait

INTRODUCTION

The new red blood cell (RBC) parameters such as reticulocyte haemoglobin content and percentage of hypochromic red cells or equivalent, although useful in the laboratory assessment of iron deficiency anaemia (IDA), are confounded by thalassaemia trait (TT). We aim to evaluate the new red cell parameters on the Beckman Coulter DxH800 in distinguishing between IDA and TT.

METHODS

A total of 246 normal subjects, 102 patients with IDA and 115 subjects with TT were accrued for the study. The parameters studied were red blood cell size factor (RSF), low haemoglobin density (LHD%), microcytic anaemia factor (MAF), standard deviation of conductivity of the nonreticulocyte population (SD-C-NRET) and unghosted cell (UGC). Comparison between groups was performed by Student's t-test, and the diagnostic performance was determined by receiver operating characteristic (ROC) curve analysis.

RESULTS

Both the LHD% and RSF were significantly higher in IDA than TT, whereas MAF and SD-C-NRET were significantly lower. The SD-C-NRET showed the best diagnostic performance as a single parameter. A formula, [(RBC + Hb) × (HCT + SD-C-NRET)]/RDW-SD, was devised to distinguish between IDA and TT. With a cut-off value of 23, the area under the curve (AUC) was 0.995 (95% CI of 0.99-1.00), the sensitivity was 97%, and the specificity was 99.1%.

CONCLUSIONS

The new RBC parameters on Beckman Coulter DxH800 provide useful information in distinguishing between IDA and TT, which is important for clinical decision-making and for streamlining laboratory testing. A new formula is devised that performs better than other discriminant functions in the literature.

Abstract P4-11-02: Novel BRCA1 and BRCA2 genomic rearrangements in Southern Chinese breast/ovarian cancer patients

Background and Aims: Germline mutations in the two breast cancer susceptibility genes, BRCA1 and BRCA2 account for a significant portion of hereditary breast/ovarian cancer. Most of the BRCA mutations reported in Southern Chinese patients were point mutations, small deletions, and insertions. The spectrum of large genomic rearrangement (LGR) is largely unknown. Here we perform the first study on the LGR of BRCA genes in a Hong Kong Chinese population. We aimed to determine the spectrum of BRCA LGRs in Southern Chinese patients with breast cancer.

Methods: A total of 555 clinically high-risk breast and/or ovarian cancer patients were recruited from the Hong Kong Hereditary Breast Cancer Family Registry, diagnosed from March 2007 to November 2011. Multiplex ligation-dependent probe amplification (MLPA) for detecting BRCA LGRs together with comprehensive BRCA1 and BRCA2 gene sequencing of all coding exons were performed. cDNA sequencing of the LGRs was performed to locate the breakpoint of the deletions.

Results: Overall BRCA1/2 mutation prevalence among this cohort was 12.4% (69/555). Among the 69 mutations identified, 4 novel LGRs (2 in BRCA1 and 2 in BRCA2) were detected only by MLPA but not full gene sequencing. Overall the LGR genes accounted for 5.8% (4/69) of all BRCA mutations in our cohort, 6.9% (2/29) of all BRCA1 mutations and 5% (2/40) of all BRCA2 mutations.

Conclusions: These findings highlight the LGR spectrum of BRCA1 and BRCA2 genes in Southern Chinese breast cancer patients. LGR testing together with BRCA1/2 full gene sequencing is superior to other methods for comprehensive BRCA1/2 analysis in clinical settings.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-11-02.

Abstract P3-11-02: Male breast cancer: A comparison between BRCA mutation carriers and non-carriers in Hong Kong, Southern China

Background: Male breast cancer is suggested to be biologically different from female breast cancer. The differences in clinicopathology between male and female breast cancer raise the issues of establishing specific strategies and treatment regime for male breast cancer patients. The single most significant risk factor for male breast cancer is a mutation in the BRCA2 gene. The lack of information on hereditary breast cancer in male, particularly in Asians, leaves great but forgiven research area on epidemiological studies for this group of patients.

Methods: All male breast cancer patients and their family members, from a Hong Kong Hereditary and High Risk Breast Cancer Program since year 2007, were recruited in this study. All received genetic counseling and BRCA mutation testing using DNA extracted from blood samples. A questionnaire was administered at their first visit which included questions on their demographics and socioeconomic status. Other information including family history of breast cancer or other kinds of cancer, method of diagnosis, surgical strategies, pathological results, treatment regime, relapse, metastasis, and outcomes were obtained from their medical records. Descriptive analysis was performed describing the background characteristics. Chi-square test and Student's t-test were applied to calculate the associations between BRCA mutation and risk factors. Survival analysis was performed to look for their survival patterns.

Results: Thirty-six male breast cancer patients were recruited between year 2007 and 2012, while 21 were diagnosed before year 2007 (range: 1996 to 2012). Mean, standard deviation, and median follow-up time were 5.75±4.31 and 5.25 years. Seven were found to carry the BRCA mutation. All were BRCA2 mutation and the mutation rate was 19.4% (N = 7). Family history of cancer was found in 52.8% (N = 19). Male BRCA mutation carriers were found to have higher risk of secondary cancer, and their first and second degree family members had higher risk of either breast cancer or other kinds of cancers. T stage in BRCA patients was significantly higher than non-BRCA patients (p = 0.028). All BRCA mutation carriers had ER positive cancers compared with 96.2% who were non-carriers. Half of the male BRCA patients were PR positive compared with higher percentage in non-BRCA patients (50% vs. 80.8%, p = 0.117). Both groups had similar overall (p = 0.962) and disease-free survivals (p = 0.919). The means and standard deviations of 5-year overall survival between BRCA and non-BRCA patients were 2.08±0.25 and 4.24±0.12 years respectively, and 2.08±3.03 and 4.41±1.46 years for disease-free survival.

Conclusions: The prevalence of male breast cancer patients with BRCA2 mutation in Hong Kong is comparable with other similar studies. Male breast cancer patients with BRCA2 mutation are suspected to have higher chance of secondary cancer and familial cancer. Although percentage of ER positive cancers are similar to the two groups, BRCA2 mutation carriers tend to have less PR positive cancers which may suggest a poorer prognosis although due to a small sample size this cannot be shown in this cohort. Further collaborative studies to better understand male breast cancer patients carrying the BRCA mutation is warranted.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-11-02.

A spuriously ‘normal’ haemoglobin A1c result

We report a case of spuriously ‘normal’ haemoglobin A1c (HbA1c) result due to misidentification of HbG Taipei as HbAo by the Variant II built-in retention time algorithm. The defect was circumvented effectively by the implementation of a chromatographic system specific internal quality control mechanism for peak identity verification. HbA1c and estimated average glucose results were corrected from 4.7% to 8.2%, and 4.9 to 10.5 mmol/L, respectively. The results were consistent with the patient's concurrent and previous fasting blood glucose concentrations and existence of diabetes mellitus dermopathy, indicating poor glycaemic control. A review of currently available analytical systems showed that other than mass spectrometry, HbA1c measurements by these systems were generally affected by the presence of haemoglobin variants. The same haemoglobin variant may affect different analytical systems differently, resulting in the deviation of HbA1c results from the true value to different extents. Including the analytical principle of HbA1c measurement in the laboratory report can avoid inappropriate comparison of results obtained by different analytical systems. Moreover, since individual haemoglobinopathy may affect the degree of glucose binding to haemoglobin in a different way, this uncertainty limits the general application of same decision cut-off of established guidelines for glycaemic control monitoring. Adoption of an individualized monitoring system based on the critical difference or reference change value of HbA1c can be considered.

Seroprevalence of antibody to pandemic influenza A (H1N1) 2009 among healthcare workers after the first wave in Hong Kong

During the first wave of an influenza pandemic prior to the availability of an effective vaccine, healthcare workers (HCWs) may be at particular risk of infection with the novel influenza strain. We conducted a cross-sectional study of the prevalence of antibody to pandemic influenza A (H1N1) 2009 (pH1N1) among HCWs in Hong Kong in February–March 2010 following the first pandemic wave. Sera collected from HCWs were tested for antibody to pH1N1 influenza virus by viral neutralisation (VN). We assessed factors associated with higher antibody titres, and we compared antibody titres in HCWs with those in a separate community study. In total we enrolled 703 HCWs. Among 599 HCWs who did not report receipt of pH1N1 vaccine, 12% had antibody titre ≥1:40 by VN. There were no significant differences in the age-specific proportions of unvaccinated HCWs with antibody titre ≥1:40 compared with the general community following the first wave of pH1N1. Under good adherence to infection control guidelines, potential occupational exposures in the hospital setting did not appear to be associated with any substantial excess risk of pH1N1 infection in HCWs. Most HCWs had low antibody titres following the first pandemic wave.

Abstract P3-01-02: Quantitative Analysis and Diagnostic Significance of Methylated SLC19A3 DNA in the Plasma of Breast Cancer Patients

Background: Previously, we have examined the methylation status of SLC19A3 (solute carrier family 19, member 3) promoter and found that SLC19A3 was epigenetically down-regulated in gastric cancer. Here, we aim to develop a new biomarker for cancer diagnosis using methylated SLC19A3 DNA in plasma.

Methods: SLC19A3 gene expression was examined by RT-qPCR. Methylation status of SLC19A3 promoter was evaluated by methylation-specific qPCR. A robust and simple methylation-sensitive restriction enzyme digestion and real-time quantitative PCR assay was developed to quantify SLC19A3 DNA methylation in plasma. Results: Expression of SLC19A3 was significantly down-regulated in 80% (12/15) of breast tumors (P &lt; 0.005). Breast tumors had significant increase in methylation percentage when compared to adjacent non-tumor tissues (P &lt; 0.05). A total of 155 independent plasma samples from participants including 60 breast cancer, 45 gastric cancer patients and 60 healthy subjects were analyzed. Plasma methylated SLC19A3 DNA yielded a ROC curve area of 77%, sensitivity of 82% and specificity of 60% in discriminating breast cancer from control subjects. This marker yielded a ROC curve area of 87%, sensitivity of 90.0% and specificity of 62% in discriminating gastric cancer from control subjects. Elevated level in plasma has been detected not only in advanced stages but also early stages of tumors. Intriguingly, of all DCIS cases from breast cancer patients this plasma marker generated a ROC value of 92%, sensitivity of 100% and specificity of 78% in discriminating DCIS cases from controls. Conclusions: These results suggested that aberrant SLC19A3 promoter hypermethylation in plasma may be a novel biomarker for early breast cancer diagnosis.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-01-02.

Abstract P2-10-01: The Accuracy of BRCA1/2 Mutation Prediction Models in Different Ethnicity and Gender: Experience in a Chinese Cohort

Background: Risk models (BRCAPRO, Myriad, Couch and Shattuck-Eidens, BOADICEA) are well established in Caucasian and African American cohorts to estimate the probability of BRCA1/2 mutation. Few studies have suggested its performance limitation in Asian cohorts. Most studies did not account for gender specific prediction. The aim of the study is to evaluate the performance of these models in a Chinese cohort who have breast/ovarian cancer at a pre-genetic test setting. Methods: Four risk assessment models, Boadicea, BRCAPRO, Myriad, Couch and Shattuck-Eidens, were used to perform risk calculations to 217 non-BRCA carriers (198 females and 19 males) and 32 BRCA carriers (28 females and 4 males. Sensitivity, specificity and area under the receiver operator characteristic (ROC) curve were calculated for each model to evaluate for calibration, discrimination and accuracy in BRCA mutation prediction stratified by gender.

Results: The mean in prediction score in all models were statistically significantly higher in female BRCA mutation carriers. However, there were no statistically difference in mean prediction score between BRCA carriers and non-carriers in all models for male patients. BRCAPRO slightly over-estimated the total numbers of BRCA1 and BRCA2 female carriers (13 vs. 11 and 20 vs.17), but underestimated the number of BRCA2 male carriers (2.8 vs. 4). While Myriad underestimated both the total numbers of BRCA1/2 male (3.1 vs. 4) and female (25.6 vs. 28) carriers. Boadicea did the closest estimation for both male (3.2 vs. 4) and female (1.5 vs. 11 for BRCA1 and 16.3 vs. 17 in BRCA2). BRCAPRO showed the greatest ROC area for BRCA1 (93%), BRCA2 (73%) and BRCA1/2 (79%) combination mutation prediction and highest sensitivity at conventional thresholds of 10% and 20% in female patients (71.4% vs.60.7%). Boadicea had the greatest ROC area for BRCA2 and BRCA1/2 combination mutation prediction and the same sensitivity at conventional thresholds of 10% and 20% in male patients (92% vs. 93%).

Conclusion: All 4 models could perform reasonably well in female patients, but not in male patients. Boadicea has the best performance in male and female Chinese cohort overall. Whereas when comparing females alone, BRCAPRO is most accurate.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-10-01.

Detection of KRAS mutations in colorectal cancer by high-resolution melting analysis

AIMS

Mutation of the KRAS gene predicts the clinical response to the monoclonal antibody cetuximab in patients with advanced colorectal cancer (CRC). This study aimed to perform KRAS mutation detection on formalin-fixed paraffin-embedded (FFPE) tumour tissue by two different methods for comparison.

METHODS

The FFPE sample was microdissected to enrich for tumour cells. KRAS exon 2 mutations were performed on 100 Chinese patients with CRC by direct nucleotide sequencing and high-resolution melting (HRM) analysis.

RESULTS

KRAS exon 2 mutations were detected in a total of 62 patients with the two methods combined, comprising 11 different mutant alleles. Three common mutations p.Gly12Asp, p.Gly12Val and p.Gly13Asp accounted for approximately 70% of all cases. The concordant rate between the two methods was 95%. Four mutations not initially detected by direct sequencing were identified by HRM and confirmed by sequencing of the HRM amplicons. One mutation detected by direct sequencing was inadvertently grouped as a wild-type allele by HRM software, but this was readily rectified through manual review.

CONCLUSION

HRM analysis is a sensitive method of detecting KRAS mutation on FFPE tumour tissue to guide cetuximab treatment and is applicable to routine molecular diagnostic service. Utilisation of HRM to screen for mutations upfront economises the resource used in the sequencing reaction.

Characterization of the pathogenic mechanism of a novel BRCA2 variant in a Chinese family

INTRODUCTION

Germline mutations of BRCA1 and BRCA2 account for the majority of hereditary breast cancers, many of which are classified as variants of unknown significance (VUS). We report the identification of a novel BRCA2 variant (c.7806-9T > G) in a Chinese family with multiple breast cancers and document it as a pathogenic mutation.

METHODS

The proband in this family was diagnosed with breast cancer at age 50 with a strong family history of breast cancer. DNA and RNA were extracted from the blood of the proband and her family, and was used for BRCA gene mutation/deletion screening and RNA splicing analysis.

RESULTS

BRCA2 c.7806-9T > G was identified in the proband, which was suggestive of a variant. This change was also found in two sisters of the proband with a history of breast cancer, as well as from the proband's maternal gastric cancer. The only sibling free of breast cancer did not carry the BRCA2 variant, thus demonstrating that the mutation segregates with the clinical phenotype in this family. RNA analysis on the proband blood sample revealed three aberrant splicing variants: c.7806_7874del, c.7806_7976del, and c.7806-8_7806-1ins. The latter causes a frameshift and creates a truncated protein, whilst the other two splicing variants resulted in shorter forms of the protein.

CONCLUSIONS

The identified BRCA2 c.7806-9T > G [Genbank: DQ889340] was found to be pathogenic, based on aberrant splicing events resulting in the formation of truncated protein products. Thus, better understanding and classification of BRCA variants as neutral or disease causing has important implications for genetic counseling so that appropriate management can be given.

The study of sequence configuration and functional impact of the (AC)n(AT)xTy motif in human beta-globin gene promoter

In this report we examine the (AC)n(AT)xTy motif residing -530 bp 5' upstream of the beta-globin gene in Chinese thalassaemic patients. This motif is a putative binding site for a repressor protein, termed beta protein 1 (BP1) (Berg et al., Nucleic Acids Res 1989;17:8833-8852). Variations in the (AC)n(AT)xTy repeats affect the binding affinity of BP1, thereby altering the expression of the beta-globin gene. Eight different configurations of this repeat motif are identified in our population of Chinese beta-thalassaemia patients. A (AC)3(AT)7T5 motif was identified among these thalassaemia patients and its influence in beta-globin gene expression was studied using stable transfection assay in murine erythroleukemia (MEL) cells. Our data demonstrated that the (AC)3(AT)7T5 motif has a moderately strong repressor effect on the expression of the cis-linked beta-globin gene. The high affinity of BP1 for this motif may result in the suppression of the transcription of the beta-globin gene (Berg et al., Am J Hematol 1991;36:42-47). We postulate that silencer elements in the beta-globin promoter play an important role in modifying the clinical presentation of the disease.

Preclinical evaluation of pharmacokinetics and safety of melatonin in propylene glycol for intravenous administration

Melatonin is a highly effective treatment in different animal models of excitotoxicity or ischemia/reperfusion injury. Due to a lack of patentability, commercial sponsors are not interested in funding clinical evaluations of melatonin. Investigators may initiate small-scale clinical evaluation, and intravenous (i.v.) administration is appropriate in acute stroke patients. Institutional Review Boards may require proper preclinical evaluation of the preparation. In this pharmacokinetic and safety study, melatonin in propylene glycol was evaluated in adult male Sprague-Dawley rats. Following a single i.v. injection at 5 or 15 mg/kg, plasma concentrations of melatonin increased to 39 and 199 million pg/mL at 2 min and 128,000 and 772,000 pg/mL at 120 min. Within 60 min of injection, the blood pressure, heart rate and body temperature remained unaffected. Melatonin at 5 mg/kg did not influence the complete blood counts at 60 min, but melatonin at 15 mg/kg had some effects on the differential white cell and platelet counts. Melatonin at 5 or 15 mg/kg slightly elevated some liver enzymes at 60 min of injection, and melatonin at higher dose also elevated plasma creatinine and lactate dehydrogenase levels. At 24 hr after completion of six daily injections of melatonin, there was a 5.5% reduction in body weight. Gross postmortem examination and histological examination of the brain, kidney, liver and spleen did not reveal any evidence of toxicity. In conclusion, melatonin in propylene glycol markedly elevates plasma levels of melatonin with no serious toxicity. This preparation should be further evaluated in human patients.

Pernicious anemia in Chinese: a study of 181 patients in a Hong Kong hospital

To study the clinical and hematologic features of pernicious anemia in Chinese, we describe 181 Chinese with megaloblastic anemia and low serum cobalamin, in association with either classic Schilling test results (82 patients) or the presence of serum antibody to intrinsic factor (99 patients), encountered in a regional hospital in Hong Kong from May 1994 to May 2005. The median age was 75 years (range, 32-95 yr) and the male to female ratio was 1:1.5. The chief presenting feature was anemia, and fewer than 10% of patients presented predominantly with neurologic deficit. Gastric biopsies of 109 patients showed glandular atrophy in 73, endocrine cell hyperplasia in 5, polyps in 14, adenocarcinoma in 1, and chronic gastritis in the rest. Gastric adenocarcinoma occurred in 1.7% of patients after a median follow-up of 35 months (range, 0.5-132 mo). Diabetes mellitus occurred in 24% of patients and thyroid disease in 7%. No specific ABO blood group was associated with pernicious anemia. Serum antibody to intrinsic factor (73%) occurred more frequently than serum antibody to gastric parietal cell (65%) (p=0.353). The frequency of serum antibody to gastric parietal cell was higher in male (78%) than in female patients (53%) (p=0.018). Pernicious anemia is a major cause of megaloblastic anemia in Chinese.

Ethnic differences in coagulation factor abnormalities after the Fontan procedure

We tested the hypothesis that Chinese patients have a coagulation profile that is less prothrombotic than that of Caucasian counterparts after the Fontan procedure by determining the type and prevalence of anticoagulant and procoagulant deficiencies in Chinese patients and comparing the findings to those previously reported in Caucasian series. The liver function and coagulation factors were assessed in 21 ethnic Chinese patients, aged 17.0 +/- 5.6 years, at 10.7 +/- 4.0 years after the Fontan procedure. The results were compared to those of 21 age-matched Chinese controls with minor congenital heart disease. The prevalence of coagulation factor deficiencies in our patients was further compared to that reported in Caucasian patients. When compared with controls, patients had significantly lower protein C (p = 0.014), factors II (p = 0.024), V (p < 0.001), VII (p < 0.001), IX (p = 0.036), and X (p < 0.001), and higher bilirubin (p = 0.001) levels. The prevalence of protein C deficiency was 9.5%, whereas those of factor II, V, VII, IX, and X deficiencies were 0, 66.7, 9.5, 0, and 57.1%, respectively. When compared with Caucasian data, our data showed a significantly lower prevalence of protein C, total protein S, antithorombin III, factor II, and factor VII deficiencies. Furthermore, the previously reported increase in factor VIII levels was not found. In contrast, the prevalence of factor X deficiency was higher in our patients. This study provides the first evidence of ethnic differences in coagulation factor abnormalities after the Fontan procedure. The imbalance between procoagulant and anticoagulant pathways in Chinese patients favors a bleeding, rather than a thrombotic, tendency.

Increased alpha 7 nicotinic acetylcholine receptor protein levels in Alzheimer's disease patients

We compared the intact alpha7 nicotinic acetylcholine receptor (alpha7nAChR) protein levels in the peripheral blood leukocytes in 15 Alzheimer's disease (AD) patients and 13 normal elderly control subjects. Demographic data and Mini-Mental State Examination (MMSE) scores were obtained. Western blot analysis for alpha7nAChR protein levels in peripheral blood leukocytes was performed. There were no significant differences in sex and age between the AD and control groups. The mean MMSE score of the AD subjects was significantly lower than that of the normal control subjects (15.4 +/- 5.5 vs. 28.5 +/- 1.9 respectively; p < 0.001). The median value of normalized alpha7nAChR protein levels (optical density, arbitrary unit) of the AD group was significantly higher than that of the normal control group (0.6923 vs. 0.4803 respectively; p = 0.045, Mann-Whitney U test). The normalized alpha7nAChR protein levels showed a significant inverse correlation with the MMSE scores (Spearman rho = -0.45; p = 0.016; n = 28). Receiver Operating Characteristic curve analyses showed that the area under curve was 0.72 (95% CI 0.52- 0.87). If the cut-off of the alpha7nAChR protein level was >0.312, the sensitivity, specificity, positive predictive value and negative predictive value would be 80, 39, 60 and 63%, respectively. These findings showed that the alpha7nAChR protein levels would be a potentially useful diagnostic marker for AD.

Diagnostic cues for natural killer cell lymphoma: primary nodal presentation and the role of in situ hybridisation for Epstein-Barr virus encoded early small RNA in detecting occult bone marrow involvement

Natural killer (NK) cell lymphomas are rare, and atypical features might lead to diagnostic pitfalls. This report describes an unusual patient in whom lymphoma occurred initially as isolated lymph node involvement, an exceptional presentation of an almost exclusively extranodal disease. Furthermore, during the terminal haemophagocytosis in the bone marrow, lymphoma cells lost the expression of the NK cell marker, CD56, making the histopathological diagnosis of bone marrow involvement difficult. This was resolved by in situ hybridisation for Epstein-Barr virus encoded small RNA, which detected occult bone marrow infiltration.

Cost-effectiveness of prenatal screening for thalassaemia in Hong Kong

OBJECTIVES

To determine the cost effectiveness of a universal prenatal screening program for alpha- and beta-thalassaemia.

METHODS

We retrospectively reviewed our program from 1998 to 2002, and calculated the direct and indirect costs of various components.

RESULTS

18,936 women were screened at our prenatal clinic and 153 couples were subsequently referred to our Prenatal Diagnostic Centre for counselling and further investigations. In addition, there were 238 tertiary referrals and 157 self-referrals. After investigations, 84 fetuses were at risk of beta-thalassaemia major/beta-E thalassaemia, 19 of them were affected and 18 were aborted. The total expenditure on our program (HK 10.0 million dollars) would be less than the postnatal service costs (HK 40.4 million dollars) for 18beta-thalassaemia major fetuses if they were born. Of 361 women at risk of carrying a homozygous alpha0-thalassaemia fetus, 311 (86.2%) opted for the indirect approach (using serial ultrasound examinations to exclude Hb Bart's disease), and 76 (24.5%) subsequently underwent an invasive test for a definitive diagnosis. The sensitivity and false positive rate of this indirect approach was 100.0% and 2.9% respectively.

CONCLUSION

It is cost effective to run a universal prenatal screening program in an area where both beta-thalassaemia and alpha-thalassaemia are prevalent. The indirect approach can effectively avoid an invasive test in unaffected pregnancies.

A case of severe haemolytic disease of the newborn due to anti-Di(a) antibody

Red cell allo-antibodies directed against the Diego (Di) blood group antigen have rarely been reported to cause a haemolytic reaction against transfusion or haemolytic disease of the newborn. The frequency of the Di(a+) phenotype among the Hong Kong Chinese population is estimated to be 4.4%. We report on a case of severe haemolytic disease of the newborn due to anti-Di(a) antibody--the first local case to the best of our knowledge. Rare but clinically significant antibodies targeting red blood cells have to be considered in the investigation of haemolytic disease of the newborn when common underlying factors have been eliminated.