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Investigation on the association between serum lipid levels and periodontitis: a bidirectional Mendelian randomization analysis

Chen Z, Song J, Tang L

BMC Oral Health, 2023 Nov 02;23(1):827.
PMID: 37919698 DOI: 10.1186/s12903-023-03575-x

OBJECTIVE: Several research has considered the potential correlation between periodontitis and serum lipids. However, serum lipid profiles correlation with periodontitis remains largely unknown. The investigation objective was to examine periodontitis correlation with serum lipid levels using a bidirectional Mendelian randomization (MR) analysis.
METHODS: The study employed a bidirectional MR analysis with two samples, utilizing a freely accessible genome-wide association study (GWAS). Furthermore, the primary analysis employed the inverse variance weighted (IVW) method. To determine whether the lipid profiles were associated with periodontitis, a variety of sensitivity analyses (including MR-Egger regression, MR-PRESSO, and weighted median), as well as multivariable MR, were employed.
RESULTS: MR analysis performed by IVW did not reveal any relationship between periodontitis and low-density lipoprotein (LDL), high-density lipoprotein (HDL), triglycerides (TG), or total cholesterol (TC). It was also found that LDL, HDL, TG, and TC were not associated to periodontitis. Furthermore, the MR estimations exhibited consistency with other MR sensitivity and multivariate MR (MVMR) analyses. These results show that the correlation between serum lipid levels and periodontitis could not be established.
CONCLUSION: The finding indicates a negligible link between periodontitis and serum lipid levels were identified, despite previous observational studies reporting a link between periodontitis and serum lipid levels.

Matched MeSH terms: Polymorphism, Single Nucleotide
Fulltext Positive selection footprints and haplotype distribution in the genome of dromedary camels

Bahbahani H, Alfoudari A, Al-Ateeqi A, Al Abri M, Almathen F

Animal, 2024 Mar;18(3):101098.
PMID: 38377812 DOI: 10.1016/j.animal.2024.101098

Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries' adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima's D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries' adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome.

Matched MeSH terms: Polymorphism, Single Nucleotide
Evaluation of SNPs associated with mammographic density in European women with mammographic density in Asian women from South-East Asia

Mariapun S, Ho WK, Eriksson M, Tai MC, Mohd Taib NA, Yip CH, et al.

Breast Cancer Res Treat, 2023 Sep;201(2):237-245.
PMID: 37338730 DOI: 10.1007/s10549-023-06984-2

PURPOSE: Mammographic density (MD), after accounting for age and body mass index (BMI), is a strong heritable risk factor for breast cancer. Genome-wide association studies (GWAS) have identified 64 SNPs in 55 independent loci associated with MD in women of European ancestry. Their associations with MD in Asian women, however, are largely unknown.
METHOD: Using linear regression adjusting for age, BMI, and ancestry-informative principal components, we evaluated the associations of previously reported MD-associated SNPs with MD in a multi-ethnic cohort of Asian ancestry. Area and volumetric mammographic densities were determined using STRATUS (N = 2450) and Volpara™ (N = 2257). We also assessed the associations of these SNPs with breast cancer risk in an Asian population of 14,570 cases and 80,870 controls.
RESULTS: Of the 61 SNPs available in our data, 21 were associated with MD at a nominal threshold of P value 0.05, 29 variants showed consistent directions of association as those previously reported. We found that nine of the 21 MD-associated SNPs in this study were also associated with breast cancer risk in Asian women (P

Matched MeSH terms: Polymorphism, Single Nucleotide
Relationship between ABCB1 polymorphisms and serum methadone concentration in patients undergoing methadone maintenance therapy (MMT)

Zahari Z, Lee CS, Ibrahim MA, Musa N, Mohd Yasin MA, Lee YY, et al.

Am J Drug Alcohol Abuse, 2016 09;42(5):587-596.
PMID: 27284701 DOI: 10.3109/00952990.2016.1172078

BACKGROUND: Methadone is a substrate of the permeability glycoprotein (P-gp) efflux transporter, which is encoded by the ABCB1 (MDR1) gene. Large interindividual variability in serum methadone levels for therapeutic response has been reported. Genetic variations in ABCB1 gene may be responsible for the variability in observed methadone concentrations.
OBJECTIVE: This study investigated the associations of ABCB1 polymorphisms and serum methadone concentration over the 24-hour dosing interval in opioid-dependent patients on methadone maintenance therapy (MMT).
METHODS: One hundred and forty-eight male opioid-dependent patients receiving MMT were recruited. Genomic deoxyribonucleic acid (DNA) was extracted from whole blood and genotyped for ABCB1 polymorphisms [i.e. 1236C>T (dbSNP rs1128503), 2677G>T/A (dbSNP rs2032582), and 3435C>T (dbSNP rs1045642)] using the allelic discrimination real-time polymerase chain reaction (PCR). Blood samples were collected at 0, 0.5, 1, 2, 4, 8, 12, and 24 hours after the dose. Serum methadone concentrations were measured using the Methadone ELISA Kit.
RESULTS: Our results revealed an association of CGC/TTT diplotype (1236C>T, 2677G>T/A, and 3435C>T) with dose-adjusted serum methadone concentration over the 24-hour dosing interval. Patients with CGC/TTT diplotype had 32.9% higher dose-adjusted serum methadone concentration over the 24-hour dosing interval when compared with those without the diplotype [mean (SD) = 8.12 (0.84) and 6.11 (0.41) ng ml-1mg-1, respectively; p = 0.033].
CONCLUSION: There was an association between the CGC/TTT diplotype of ABCB1 polymorphisms and serum methadone concentration over the 24-hour dosing interval among patients on MMT. Genotyping of ABCB1 among opioid-dependent patients on MMT may help individualize and optimize methadone substitution treatment.
Study site: Psychiatric Clinic, Hospital Universiti Sains Malaysia (HUSM), and other MMT clinics in Kelantan,
Malaysia

Matched MeSH terms: Polymorphism, Single Nucleotide/genetics*
Fulltext The Influence of OLR1 and PCSK9 Gene Polymorphisms on Ischemic Stroke: Evidence from a Meta-Analysis

Au A, Griffiths LR, Cheng KK, Wee Kooi C, Irene L, Keat Wei L

Sci Rep, 2015 Dec 15;5:18224.
PMID: 26666837 DOI: 10.1038/srep18224

Both OLR1 and PCSK9 genes are associated with atherosclerosis, cardiovascular disease and ischemic stroke. The overall prevalence of PCSK9 rs505151 and OLR1 rs11053646 variants in ischemic stroke were 0.005 and 0.116, respectively. However, to date, association between these polymorphisms and ischemic stroke remains inconclusive. Therefore, this first meta-analysis was carried out to clarify the presumed influence of these polymorphisms on ischemic stroke. All eligible case-control and cohort studies that met the search terms were retrieved in multiple databases. Demographic and genotyping data were extracted from each study, and the meta-analysis was performed using RevMan 5.3 and Metafor R 3.2.1. The pooled odd ratios (ORs) and 95% confidence intervals (CIs) were calculated using both fixed- and random-effect models. Seven case-control studies encompassing 1897 cases and 2119 controls were critically evaluated. Pooled results from the genetic models indicated that OLR1 rs11053646 dominant (OR = 1.33, 95% CI:1.11-1.58) and co-dominant models (OR = 1.24, 95% CI:1.02-1.51) were significantly associated with ischemic stroke. For the PCSK9 rs505151 polymorphism, the OR of co-dominant model (OR = 1.36, 95% CI:1.01-1.58) was found to be higher among ischemic stroke patients. In conclusion, the current meta-analysis highlighted that variant allele of OLR1 rs11053646 G > C and PCSK9 rs505151 A > G may contribute to the susceptibility risk of ischemic stroke.

Matched MeSH terms: Polymorphism, Single Nucleotide*
Patterns of linkage disequilibrium at PARK16 may explain variances in genetic association studies

Li H, Teo YY, Tan EK

Mov Disord, 2015 Sep;30(10):1335-42.
PMID: 25758099 DOI: 10.1002/mds.26176

Reproducing genomewide association studies findings in different populations is challenging, because the reproducibility fundamentally relies on the similar patterns of linkage disequilibrium between the unknown causal variants and the genotyped single-nucleotide polymorphisms (SNPs).

Matched MeSH terms: Polymorphism, Single Nucleotide/genetics*
Haplotype data of mitochondrial DNA coding region encompassing nucleotide positions 11,719-12,184 and evaluate the importance of these positions for forensic genetic purposes in Iraq

Hameed IH, Jebor MA, Ommer AJ, Abdulzahra AI, Yoke C

Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1324-7.
PMID: 25090379 DOI: 10.3109/19401736.2014.945576

Samples of 100 random healthy unrelated Iraqi male persons from the Arab ethnic group of Iraqi population were collected for mtDNA coding region sequencing by using the Sanger technique and to establish the degree of variation characteristic of a fragment. Portion of coding region encompassing positions 11,719-12,184 was amplified in accordance with the Anderson reference sequence. PCR products were purified by EZ-10 spin column then sequenced and detected by using the ABI 3130xL DNA Analyzer. This is to intend the detection of polymorphisms of mtDNA. Four new polymorphic positions 11,741, 11,756, 11,878, and 12,133 are described which may be suitable in the future to be the sources for human identification purpose in Iraq. The obtained data can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants. The calculated value GD = 0.95 and RMP = 0.048 of the genetic diversity should be understood as high in the context of coding function of the analysed DNA fragment. The relatively high gene diversity and a relatively low random match probability were observed in this study.

Matched MeSH terms: Polymorphism, Single Nucleotide*
Fulltext A genome-wide pleiotropy scan for prostate cancer risk

Panagiotou OA, Travis RC, Campa D, Berndt SI, Lindstrom S, Kraft P, et al.

Eur Urol, 2015 Apr;67(4):649-57.
PMID: 25277271 DOI: 10.1016/j.eururo.2014.09.020

BACKGROUND: No single-nucleotide polymorphisms (SNPs) specific for aggressive prostate cancer have been identified in genome-wide association studies (GWAS).
OBJECTIVE: To test if SNPs associated with other traits may also affect the risk of aggressive prostate cancer.
DESIGN, SETTING, AND PARTICIPANTS: SNPs implicated in any phenotype other than prostate cancer (p≤10(-7)) were identified through the catalog of published GWAS and tested in 2891 aggressive prostate cancer cases and 4592 controls from the Breast and Prostate Cancer Cohort Consortium (BPC3). The 40 most significant SNPs were followed up in 4872 aggressive prostate cancer cases and 24,534 controls from the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium.
OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Odds ratios (ORs) and 95% confidence intervals (CIs) for aggressive prostate cancer were estimated.
RESULTS AND LIMITATIONS: A total of 4666 SNPs were evaluated by the BPC3. Two signals were seen in regions already reported for prostate cancer risk. rs7014346 at 8q24.21 was marginally associated with aggressive prostate cancer in the BPC3 trial (p=1.6×10(-6)), whereas after meta-analysis by PRACTICAL the summary OR was 1.21 (95% CI 1.16-1.27; p=3.22×10(-18)). rs9900242 at 17q24.3 was also marginally associated with aggressive disease in the meta-analysis (OR 0.90, 95% CI 0.86-0.94; p=2.5×10(-6)). Neither of these SNPs remained statistically significant when conditioning on correlated known prostate cancer SNPs. The meta-analysis by BPC3 and PRACTICAL identified a third promising signal, marked by rs16844874 at 2q34, independent of known prostate cancer loci (OR 1.12, 95% CI 1.06-1.19; p=4.67×10(-5)); it has been shown that SNPs correlated with this signal affect glycine concentrations. The main limitation is the heterogeneity in the definition of aggressive prostate cancer between BPC3 and PRACTICAL.
CONCLUSIONS: We did not identify new SNPs for aggressive prostate cancer. However, rs16844874 may provide preliminary genetic evidence on the role of the glycine pathway in prostate cancer etiology.
PATIENT SUMMARY: We evaluated whether genetic variants associated with several traits are linked to the risk of aggressive prostate cancer. No new such variants were identified.

Matched MeSH terms: Polymorphism, Single Nucleotide*
Fulltext Leptin and leptin receptor gene polymorphisms and their association with plasma leptin levels and obesity in a multi-ethnic Malaysian suburban population

Fan SH, Say YH

J Physiol Anthropol, 2014;33:15.
PMID: 24947733 DOI: 10.1186/1880-6805-33-15

BACKGROUND: This study was to investigate the prevalence of single nucleotide polymorphisms (SNPs) in leptin gene LEP (A19G and G2548A) and leptin receptor gene LEPR (K109R and Q223R) and their association with fasting plasma leptin level (PLL) and obesity in a Malaysian suburban population in Kampar, Perak.
METHODS: Convenience sampling was performed with informed consents, and the study sample was drawn from patients who were patrons of the Kampar Health Clinic. A total of 408 subjects (mean age, 52.4 +/- 13.7 years; 169 men, 239 women; 190 obese, 218 non-obese; 148 Malays, 177 ethnic Chinese, 83 ethnic Indians) participated. Socio-demographic data and anthropometric measurements were taken, and genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).
RESULTS: The LEP A19G, G2548A and LEPR K109R, Q223R variant allele frequencies were 0.74, 0.67 and 0.61, 0.79, respectively. The genotype and allele distributions of these gene variants were significantly different among ethnic groups, but not among body mass index (BMI) classes. Subjects with LEPR K109 and Q223 allele had significantly higher systolic blood pressure and adiposity indices after adjustment for ethnicity (higher BMI, total body and subcutaneous fat; lower skeletal muscle percentage). Subjects with LEPR 109R allele had lower PLL than their wild-type allele counterparts. The influence of LEP A19G and G2548A SNPs on blood pressures, anthropometrics, and PLL was not evident. Interestingly, synergistic effect of the LEP and LEPR SNPs was observed as subjects homozygous for all four SNPs studied exhibited significantly higher subcutaneous fat and PLL than those with other genotype combinations.
CONCLUSIONS: The LEP and LEPR SNPs in this study may not be an obesity marker among Malaysians in this population, but were associated with ethnicity. Our findings suggest that each of these SNPs contributes to minor but significant variation in obesity-related traits and in combination they display synergistic effects on subcutaneous fat and PLL.

Matched MeSH terms: Polymorphism, Single Nucleotide/genetics*
Fulltext HLA-A SNPs and amino acid variants are associated with nasopharyngeal carcinoma in Malaysian Chinese

Chin YM, Mushiroda T, Takahashi A, Kubo M, Krishnan G, Yap LF, et al.

Int J Cancer, 2015 Feb 1;136(3):678-87.
PMID: 24947555 DOI: 10.1002/ijc.29035

Nasopharyngeal carcinoma (NPC) arises from the mucosal epithelium of the nasopharynx and is constantly associated with Epstein-Barr virus type 1 (EBV-1) infection. We carried out a genome-wide association study (GWAS) of 575,247 autosomal SNPs in 184 NPC patients and 236 healthy controls of Malaysian Chinese ethnicity. Potential association signals were replicated in a separate cohort of 260 NPC patients and 245 healthy controls. We confirmed the association of HLA-A to NPC with the strongest signal detected in rs3869062 (p = 1.73 × 10(-9)). HLA-A fine mapping revealed associations in the amino acid variants as well as its corresponding SNPs in the antigen peptide binding groove (p(HLA-A-aa-site-99) = 3.79 × 10(-8), p(rs1136697) = 3.79 × 10(-8)) and T-cell receptor binding site (p(HLA-A-aa-site-145) = 1.41 × 10(-4), p(rs1059520) = 1.41 × 10(-4)) of the HLA-A. We also detected strong association signals in the 5'-UTR region with predicted active promoter states (p(rs41545520) = 7.91 × 10(-8)). SNP rs41545520 is a potential binding site for repressor ATF3, with increased binding affinity for rs41545520-G correlated with reduced HLA-A expression. Multivariate logistic regression diminished the effects of HLA-A amino acid variants and SNPs, indicating a correlation with the effects of HLA-A*11:01, and to a lesser extent HLA-A*02:07. We report the strong genetic influence of HLA-A on NPC susceptibility in the Malaysian Chinese.

Matched MeSH terms: Polymorphism, Single Nucleotide*
Fulltext Variant GADL1 and response to lithium in bipolar I disorder

Consortium on Lithium Genetics, Hou L, Heilbronner U, Rietschel M, Kato T, Kuo PH, et al.

N Engl J Med, 2014 05 08;370(19):1857-9.
PMID: 24806176 DOI: 10.1056/NEJMc1401817
Matched MeSH terms: Polymorphism, Single Nucleotide*
Fulltext Novel SNPs in heat shock protein 70 gene and their association with sperm quality traits of Boer goats and Boer crosses

Nikbin S, Panandam JM, Yaakub H, Murugaiyah M, Sazili AQ

Anim. Reprod. Sci., 2014 May;146(3-4):176-81.
PMID: 24674824 DOI: 10.1016/j.anireprosci.2014.03.001

The semen quality of bucks affects the reproduction performance of the herd and is influenced by genetic and non-genetic factors. Heat shock protein 70 (HSP70) is considered as an important gene affecting semen quality traits. The objectives of this study are to find single nucleotide polymorphisms in HSP70 coding region and their association with semen quality traits on Boer and Boer cross bucks. DNA isolated from 53 goats (36 pure South African Boer and 17 Boer crosses) was subjected to PCR amplification of the exon 1 region of the caprine HSP70 gene. Single-strand conformation polymorphism (SSCP) was used to detect polymorphisms and the variant DNA fragments were sequenced. Two synonymous SNPs (74A>C (ss836187517) and 191C>G (ss836187518)) were detected. Qualities of fresh and post-thaw semen were evaluated for sperm concentration, semen volume, sperm motility and velocity traits, live sperm percentage, and abnormal sperm rate. The C allele of ss836187517 and G allele of ss836187518 were at higher frequencies in both the breeds. The C allele of ss836187517 appeared to be the favorable allele for semen concentration, progressive motility of fresh semen, and motility and sperm lateral head displacement of post-thaw semen. A negative overdominance was observed for ss836187517 alleles on velocity traits of post-thaw semen. The C allele of ss836187518 was favorable for sperm concentration and progressive motility. Results herein suggest that the SNPs in HSP70 may affect on semen quality in tropical regions and specially on the potential of semen for freezing.

Matched MeSH terms: Polymorphism, Single Nucleotide/physiology*
Fulltext High density SNP and SSR-based genetic maps of two independent oil palm hybrids

Ting NC, Jansen J, Mayes S, Massawe F, Sambanthamurthi R, Ooi LC, et al.

BMC Genomics, 2014;15:309.
PMID: 24767304 DOI: 10.1186/1471-2164-15-309

Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.

Matched MeSH terms: Polymorphism, Single Nucleotide/genetics*
Fulltext RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case-control study

Chong ET, Lee CC, Chua KH, Chuah JA, Lee PC

BMJ Open, 2014;4(1):e004109.
PMID: 24394801 DOI: 10.1136/bmjopen-2013-004109

Our study aimed to investigate the association of CYP2E1 C-1019T RsaI and T7678A DraI polymorphisms and factors such as age, gender and ethnicity to the risk of gastrointestinal cancer (GIC) in Malaysians.

Matched MeSH terms: Polymorphism, Single Nucleotide*
Fulltext SNP array technology: an array of hope in breast cancer research

Ho CC, Mun KS, Naidu R

Malays J Pathol, 2013 Jun;35(1):33-43.
PMID: 23817393 MyJurnal

Breast cancer is the most common malignancy in women worldwide. The incidence of breast cancer in Malaysia is lower compared to international statistics, with peak occurrence in the age group between 50 to 59 years of age and mortality rates of 18.6%. Despite current diagnostic and prognostic methods, the outcome for individual subjects remain poor. This is in part due to breast cancers' wide genetic heterogeneity. Various platforms for genetics studies are now employed to determine the identity of these genetic abnormalities, including microarray methods like high density single-nucleotide-polymorphism (SNP) oligonucleotide arrays which combine the power of chromosomal comparative genomic hybridization (cCGH) and loss of heterozygosity (LOH) in the offering of higher-resolution mappings. These platforms and their applications in highlighting the genomic alteration frameworks manifested in breast carcinoma will be discussed.

Matched MeSH terms: Polymorphism, Single Nucleotide/genetics*
Fulltext MabsBase: a Mycobacterium abscessus genome and annotation database

Heydari H, Wee WY, Lokanathan N, Hari R, Mohamed Yusoff A, Beh CY, et al.

PLoS One, 2013;8(4):e62443.
PMID: 23658631 DOI: 10.1371/journal.pone.0062443

Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions, to support the expanding scientific community interested in M. abscessus research. The MabsBase is freely available at http://mabscessus.um.edu.my.

Matched MeSH terms: Polymorphism, Single Nucleotide*
Fulltext Platelet alloantigen polymorphism and migraine headaches

Bhaskar S, Abdullah JM

Neurosciences (Riyadh), 2013 Apr;18(2):185-6.
PMID: 23545624
Matched MeSH terms: Polymorphism, Single Nucleotide*
Fulltext GABRG2 rs211037 polymorphism and epilepsy: a systematic review and meta-analysis

Haerian BS, Baum L

Seizure, 2013 Jan;22(1):53-8.
PMID: 23140995 DOI: 10.1016/j.seizure.2012.10.007

PURPOSE: The gamma-aminobutyric acid A receptor, gamma 2 (GABRG2) gene encodes the GABRγ2 protein, which has been implicated in susceptibility to epilepsy. Several studies have examined a possible link between the exonic GABRG2 rs211037 locus and susceptibility to febrile seizure (FS) and idiopathic generalized epilepsy (IGE), however results have been inconclusive. We therefore performed a systematic review and meta-analysis to examine whether this polymorphism is associated with FS or IGE.
METHODS: Eight studies comprising 1871 epilepsy patients and 1387 controls, which evaluated association of the GABRG2 rs211037 polymorphism with susceptibility to epilepsy, were included in this meta-analysis. Meta-analysis was carried out separately for FS and IGE.
RESULTS: Meta-analysis showed a significant association between this polymorphism and susceptibility to FS in a codominant (TT vs. CC, OR 0.47, 95% CI 0.30-0.73, p=0.0008 and TT vs. CT, OR 0.59, 95% CI 0.42-0.83, p=0.003) and dominant (OR 0.54, 95% CI 0.39-0.75, p=0.0002) genetic models, influenced by two studies with small sample size. Neither allele nor genotype association was observed with IGE.
CONCLUSION: This study showed significant association of GABRG2 rs211037 with susceptibility to FS, caused by two studies with small sample sizes, however the possibility of false positive results due to the effect of significant studies for FS cannot be excluded. Future studies with larger sample sizes of these patients are suggested to verify the results.

Matched MeSH terms: Polymorphism, Single Nucleotide/genetics*
Mutation screening of IRF6 among families with non-syndromic oral clefts and identification of two novel variants: review of the literature

Salahshourifar I, Wan Sulaiman WA, Halim AS, Zilfalil BA

Eur J Med Genet, 2012 Jun;55(6-7):389-93.
PMID: 22440537 DOI: 10.1016/j.ejmg.2012.02.006

Non-syndromic oral clefts share the main clinical features of Van der Woude Syndrome (VWS), with the exception of the lower lip pit. Thus, about 15% of VWS cases are indistinguishable from cases with non-syndromic oral clefts. IRF6 mutations are the major cause of VWS; however, variants in this gene show strong association with non-syndromic oral clefts, with a higher increased risk among cases with cleft lip only (CLO). A total of 39 individuals, including 16 patients with CLO and 23 patients with a family history of cleft, were examined for IRF6 mutations in the present study. Seven variants, including five known (c.-75-4 A>; G, c.-73T>; C, c.459G>; T 5, c.820G>; A, and c.1060 + 37C>; T) and two novel (c.-75-23G>; C and c.1380G>; T), were found. Both novel variants were inherited from non-affected parents and we did not find also in the 120 control chromosomes. In silico analysis revealed that both c.1380G>; T and c.-75-23G>; C variants may disrupts a putative exonic splicing enhancer and intronic splicing binding site for SC35, respectively. Taken together, the presence of deleterious IRF6 variants in patients with non-syndromic oral clefts could be most likely an evidence for VWS. While, IRF6 variants could, at best, contribute to clefting as part of a complex inheritance pattern, with both additional genes and environmental factors having a role.

Matched MeSH terms: Polymorphism, Single Nucleotide*
Differences in allele frequencies of autosomal dominant hypercholesterolemia SNPs in the Malaysian population

Alex L, Chahil JK, Lye SH, Bagali P, Ler LW

J Hum Genet, 2012 Jun;57(6):358-62.
PMID: 22534770 DOI: 10.1038/jhg.2012.34

Hypercholesterolemia is caused by different interactions of lifestyle and genetic determinants. At the genetic level, it can be attributed to the interactions of multiple polymorphisms, or as in the example of familial hypercholesterolemia (FH), it can be the result of a single mutation. A large number of genetic markers, mostly single nucleotide polymorphisms (SNP) or mutations in three genes, implicated in autosomal dominant hypercholesterolemia (ADH), viz APOB (apolipoprotein B), LDLR (low density lipoprotein receptor) and PCSK9 (proprotein convertase subtilisin/kexin type-9), have been identified and characterized. However, such studies have been insufficiently undertaken specifically in Malaysia and Southeast Asia in general. The main objective of this study was to identify ADH variants, specifically ADH-causing mutations and hypercholesterolemia-associated polymorphisms in multiethnic Malaysian population. We aimed to evaluate published SNPs in ADH causing genes, in this population and to report any unusual trends. We examined a large number of selected SNPs from previous studies of APOB, LDLR, PCSK9 and other genes, in clinically diagnosed ADH patients (n=141) and healthy control subjects (n=111). Selection of SNPs was initiated by searching within genes reported to be associated with ADH from known databases. The important finding was 137 mono-allelic markers (44.1%) and 173 polymorphic markers (55.8%) in both subject groups. By comparing to publicly available data, out of the 137 mono-allelic markers, 23 markers showed significant differences in allele frequency among Malaysians, European Whites, Han Chinese, Yoruba and Gujarati Indians. Our data can serve as reference for others in related fields of study during the planning of their experiments.

Matched MeSH terms: Polymorphism, Single Nucleotide*

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