Association of common genetic variants with breast cancer risk and clinicopathological characteristics in a Chinese population.

Genome-wide association studies (GWAS) have identified various genetic susceptibility loci for breast cancer based mainly on European-ancestry populations. Differing linkage disequilibrium patterns exist between European and Asian populations, and thus GWAS-identified single nucleotide polymorphisms (SNPs) in one population may not be of significance in another population. In order to explore the role of breast cancer susceptibility variants in a Chinese population of Southern Chinese descent, we analyzed 22 SNPs for 1,191 breast cancer cases and 1,534 female controls. Associations between the SNPs and clinicopathological features were also investigated. In addition, we evaluated the combined effects of associated SNPs by constructing risk models. Eight SNPs were associated with an elevated breast cancer risk. Rs2046210/6q25.1 increased breast cancer risk via an additive model [per-allele odds ratio (OR) = 1.43, 95 % confidence interval (CI) = 1.26-1.62], and was associated with estrogen receptor (ER)-positive (per-allele OR = 1.39, 95 % CI = 1.20-1.61) and ER-negative (per-allele OR = 1.55, 95 % CI = 1.28-1.89) disease. Rs2046210 was also associated with stage 1, stage 2, and stage 3 disease, with per-allele ORs of 1.38 (1.14-1.68), 1.48 (1.25-1.74), and 1.58 (1.28-1.94), respectively. Four SNPs mapped to 10q26.13/FGFR2 were associated with increased breast cancer risk via an additive model with per-allelic risks (95 % CI) of 1.26 (1.12-1.43) at rs1219648, 1.22 (1.07-1.38) at rs2981582, 1.21 (1.07-1.36) at rs2981579, and 1.18 (1.04-1.35) at rs11200014. Variants of rs7696175/TLR1, TLR6, rs13281615/8q24, and rs16886165/MAP3K1 were also associated with increased breast cancer risk, with per-allele ORs (95 % CI) of 1.16 (1.00-1.34), 1.15 (1.02-1.29), and 1.15 (1.01-1.29), respectively. Five SNPs associated with breast cancer risk predominantly among ER-positive tumors (rs2981582/FGFR2, rs4415084/MRPS30, rs1219648/FGFR2, rs2981579/FGFR2, and rs11200014/FGFR2). Among our Chinese population, the risk of developing breast cancer increased by 90 % for those with a combination of 6 or more risk alleles, compared to patients with ≤3 risk alleles.

Analysis of rpsL and rrs mutations in Beijing and non-Beijing streptomycin-resistant Mycobacterium tuberculosis isolates from Singapore.

The Beijing genotype of Mycobacterium tuberculosis has frequently been found to be associated with drug resistance. Mutation analysis of the genes encoding 16S rRNA (rrs) and ribosomal protein S12 (rpsL) revealed a high frequency (97/102; 95.1%) of alterations in streptomycin-resistant M. tuberculosis isolates from Singapore, with rpsL K43R being the most common rpsL mutation (82/92; 89%), which was significantly associated with Beijing strains compared to non-Beijing strains (odds ratio = 10.88, 95% confidence interval = 3.48-34.1). This is the first study to report the association of Beijing strains with the rpsL K43R mutation in STR-resistant M. tuberculosis isolates with de novo resistance, as determined by clustering analysis.

LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast and colorectal cancer.

Deletion of 11q23-q24 is frequent in a diverse variety of malignancies, including breast and colorectal carcinoma, implicating the presence of a tumor suppressor gene at that chromosomal region. We examined a 6-Mb region on 11q23 by high-resolution deletion mapping, using both loss of heterozygosity analysis and customized microarray comparative genomic hybridization. LARG (leukemia-associated Rho guanine-nucleotide exchange factor) (also called ARHGEF12), identified from the analysed region, is frequently underexpressed in breast and colorectal carcinomas with a reduced expression observed in all breast cancer cell lines (n=11), in 12 of 38 (32%) primary breast cancers, 5 of 10 (50%) colorectal cell lines and in 20 of 37 (54%) primary colorectal cancers. Underexpression of the LARG transcript was significantly associated with genomic loss (P=0.00334). Hypermethylation of the LARG promoter was not detected in either breast or colorectal cancer, and treatment of four breast and four colorectal cancer cell lines with 5-aza-2'-deoxycytidine and/or trichostatin A did not result in a reactivation of LARG. Enforced expression of LARG in breast and colorectal cancer cells by stable transfection resulted in reduced cell proliferation and colony formation, as well as in a markedly slower cell migration rate in colorectal cancer cells, providing functional evidence for LARG as a candidate tumor suppressor gene.

Analysis of the role of Mycobacterium tuberculosis kasA gene mutations in isoniazid resistance.

Previous studies have suggested that Mycobacterium tuberculosis kasA G312S and G269S gene mutations may represent sequence polymorphisms of the M. tuberculosis East-African-Indian (EAI) and T families, respectively, rather than relating to isoniazid resistance. The present study examined polymorphisms of these two codons in 98 drug-susceptible M. tuberculosis isolates (68 EAI and 30 T isolates). Twenty-eight isolates belonging to a sub-lineage of the EAI family had the kasA G312S mutation, but none of the 30 T isolates had the G269S mutation. The data suggest that the kasA G312S mutation is not related to isoniazid resistance, but represents a sequence polymorphism in a sub-lineage of the EAI family.

Genotype and phenotype relationships and transmission analysis of drug-resistant tuberculosis in Singapore.

SETTING: The small urban country of Singapore. OBJECTIVES: To investigate the relationships between Mycobacterium tuberculosis genotypes and drug-resistant phenotypes and to analyse the transmission of drug-resistant tuberculosis (DR-TB). DESIGN: A 29-month population-based study comparing drug-resistant and drug-susceptible M. tuberculosis isolates. RESULTS: We found that multidrug-resistant (MDR) isolates (n = 41, OR 2.66, 95%CI 1.28-5.50), rifampicin-resistant isolates (n = 48, OR 2.88, 95%CI 1.44-5.76), and streptomycin (SM) resistant isolates (n = 103, OR 3.35, 95%CI 1.99-5.62) were more common among Beijing genotype strains than among non-Beijing strains, while SM-resistant isolates were less common in East-African-Indian (EAI) genotype strains than in non-EAI strains (OR 0.30, 95%CI 0.14-0.64). Based on clustering analysis and drug-resistant patterns, 22 of 230 drug-resistant isolates were found to have likely resulted from recent transmission. The estimated transmission rate of DR-TB was 9.6% and that of MDR-TB was 7.7%. The transmission rate of DR-TB was significantly higher among Beijing genotype strains than non-Beijing strains (12.9% vs. 4.4%; P = 0.034). CONCLUSIONS: Compared to other genotypes, Beijing genotype strains are associated with a higher frequency of drug resistance, including multidrug resistance, and are more transmissible. However, the overall transmission rate of DR-TB in Singapore is low.

Association of Mycobacterium tuberculosis Beijing genotype with tuberculosis relapse in Singapore.

The relationship of Mycobacterium tuberculosis Beijing genotype with tuberculosis relapse was examined. Beijing strains were detected from 32 out of 45 (71%) relapsed cases and 148 out of 290 (51%) non-relapsed cases. Multivariate logistic regression analysis revealed that Beijing genotype was significantly associated with tuberculosis relapse (OR 2.64, 95% CI 1.30-5.34, P=0.005).

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia.

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia. Chronic myeloid leukemia (CML) is characterized by the Philadelphia translocation t(9;22)(q34;q11) resulting in the BCR/ABL fusion gene. Submicroscopic deletion of the derivative chromosome 9 occurs in a subset of these patients and is associated with poor prognosis. In the current study, we present two unusual cases of CML selected from a series of 54 consecutive cases. A detailed study using classical cytogenetics and fluorescence in situ hybridization (FISH) analysis was done using dual color extra signal FISH and whole chromosome paint in order to elucidate the mechanism of 9q deletion. One case had two clones on interphase FISH, one with and one without chromosome 9q deletion. The other case had two clones on both cytogenetic and FISH analyses, one with and one without a marker chromosome carrying chromosome 9q sequences. In this latter case, the clone with deletion of the derivative chromosome 9 comprised 21.1% at diagnosis, increasing to 36.8% after 11 months, suggesting a growth advantage. We report here evidence that deletions on 9q in CML may occur through breakage and rearrangement of chromosomes resulting in derivative chromosomes and either a marker chromosome or fragment/episome, followed by loss of chromosome material from the cell.

Prevalence of hepatitis G virus infection in patients with liver diseases in Singapore.

The prevalence of hepatitis G virus (HGV) infection in patients with liver diseases in Singapore and its pathogenic role in these patients was studied. One hundred and forty-eight patients who had chronic hepatitis or acute non A-E hepatitis were studied. Presence of HGV RNA was determined by nested polymerase chain reaction of the 5'non-coding region of the virus in all the patients. Hepatitis G IgG antibody to the envelope (E2) antigen was tested with an enzyme immunoassay (Boehringer Mannheim, Singapore) in 76 of them. Most patients (93%) were ethnically Chinese, predominantly males (74%) and chronic hepatitis B (72%) patients. Others had chronic hepatitis C (19%) or cryptogenic cirrhosis (6%). Four patients had acute non A-E hepatitis. HGV RNA and anti-HGenv were present in 3.5% and 8.3% of those with chronic liver disease. HGV infection did not account for any of the acute non A-E hepatitis and most of the cryptogenic cirrhosis.