A LDR-PCR approach for multiplex polymorphisms genotyping of severely degraded DNA with fragment sizes <100 bp

Development and Validation of a Forensic Multiplex System With 38 X-InDel Loci

In the present study, a novel multiplex system, AGCU X-InDel 38 kit, was designed to amplify 38 X-InDel markers and amelogenin in a single Polymerase Chain Reaction (PCR). To demonstrate the suitability and efficiency for forensic applications, a series of validation experiments were conducted, including sensitivity, species specificity, reproducibility, stability, case samples, balance of peak height, size precision, as well as allele frequency and forensic parameter analysis. The results showed that AGCU X-InDel 38 kit was capable to get full profiles even with 62.5 pg of template DNA, and full profiles can be obtained when hematin concentration ≤25 μmol/L, or hemoglobin concentration ≤50 μmol/L, showing good tolerance to six common inhibitors. Moreover, the analyzed case samples indicated that AGCU X-InDel 38 kit had better performance for degraded and trace DNA samples. The 200 unrelated males from Guangdong Han population showed that the combined PD_Male and PD_Female were both more than 0.999999999, and the combined MEC_Krüger, MEC_Kishida, and MEC_{Desmarais  Duo} were 0.999369481, 0.999999917, and 0.999941556, respectively. Robust discrimination capability of this novel multiplex system could be demonstrated through the high values of forensic parameters. In conclusion, AGCU X-InDel 38 kit is sensitive, precise, reproducible, and highly informative and could be used as a complementary tool for complex and challenging kinship cases.

Association of the cyclooxygenase-2 1759A allele with migraine in Chinese Han individuals

Cyclooxygenase-2 (COX-2) is known to be involved in the pathogenesis of migraine, and some polymorphisms are known to affect the expression of COX-2. This retrospective case-control study aimed to explore the associations between the -765 G>C (rs20417), -1759 G>A (rs3218625), and -8473 C>T (rs5275) COX-2 polymorphisms and migraine in Chinese Han individuals. One hundred and ten unrelated Han Chinese patients with migraine and 108 healthy controls were recruited between 03/2014 and 08/2016 at the First Affiliated Hospital of Nanjing Medical University and the First People's Hospital of Lianyungang City. The genotypes of all polymorphisms in controls followed the Hardy-Weinberg equilibrium (P = 0.215, P = 0.884, and P = 0.689). There were differences in the genotype and allele distributions of the COX-2-1759G>A (Gly587Arg) polymorphism between the migraine and control groups (P = 0.038 and P = 0.040, respectively). Compared with the COX-2-1759AG genotype, GG genotype carriers had an increased risk of migraine (odds ratio (OR) = 8.720, 95% confidence interval (CI): 1.072-70.960, P = 0.038). The frequency of the COX-2-1759A allele in patients with migraine was significantly lower than the controls (OR = 0.119, 95%CI: 0.015-0.957, P = 0.040). Adjusted age and sex, a statistical difference was found in the dominant model of COX-2-1759 G>A (OR = 0.118, 95% CI 0.014 to 0.962, P = 0.046). No significant difference was detected regarding the -765G>C and -8473T>C polymorphisms between the two groups. The COX-2 1759A allele might be involved in the development of migraine in Chinese Han individuals, but this will have to be confirmed in large-scale studies.

Genotyping genetic markers from LCN and degraded DNA by HRM and their application in hair shaft

Degraded and low copy number (LCN) DNA samples are common challenging materials in forensic casework because they increase the difficulty of sample processing and reduce the possibility of obtaining genetic information from DNA. High-resolution melting (HRM) curve analysis is promising for genotyping genetic markers and has been applied to the detection of LCN and degraded DNA in the field of forensic science. However, the exact assessment based on HRM at multiple genetic markers from both degraded and LCN DNA materials has not been optimized. To explore the ability of HRM to genotype LCN and degraded DNA samples, we selected three genetic markers to genotype in experimental LCN and degraded DNA and practical hair shaft materials, which are often encountered as degraded and LCN DNA in forensic medicine. The results show that DNA samples of as low as 100 pg and as short as 60 bp were successfully genotyped by the HRM assay at all three genetic markers, whereas in hair shaft DNA, two loci were accurately genotyped. The HRM assay established in this study can be applied to LCN and degraded DNA analysis in forensic casework and can act as a reference point before genotyping short tandem repeat markers. Developing the HRM strategy for genotyping DNA genetic markers enriches detectable targets in hair shaft samples and provides valuable data for further exploration.

A study of the association of rs12040273 with susceptibility and severity of coronary artery disease in a Chinese Han population

BACKGROUND

The single nucleotide polymorphism (SNP) rs12040273, a variant of UDP-N-acetylgalactosamine, polypeptide GalNAc-transferase 2, has recently been reported to be significantly associated with development of carotid artery intima-media thickness (IMT) in a Chinese population based on a genome-wide association study. Because IMT is a potent marker of coronary artery disease (CAD), the aim of this study was to evaluate the relation of rs12040273 to susceptibility and severity of CAD in a Chinese Han population.

METHODS

We performed a hospital-based case-control study. Three hundred and thirty-one individuals (199 CAD patients and 112 non-CAD controls) undergoing coronary angiography were consecutively enrolled in the study. The Gensini score results were used to assess the severity of CAD. The method of polymerase chain reaction-ligase detection reaction (PCR-LDR) was used to distinguish different genotypes at rs12040273.

RESULTS

The distribution of genotypes at rs12040273 was comparable between CAD patients and non-CAD controls (P > 0.05). The frequencies of the genotypes were also not significantly associated with the risk of CAD and its severity assessed by the Gensini score method, with the OR of 1.38 (95% CI = 0.80-2.40, P = 0.24) and 1.14 (95% CI = 0.69-1.86, P = 0.60) respectively. However, stratified analysis showed that the serum HDL-C levels of subjects with the CC genotype were significantly higher than those with CT/TT genotypes in non-CAD controls (P = 0.002).

CONCLUSION

Our results suggest that the rs12040273 variants might not be associated with the susceptibility of CAD or its severity in a Chinese Han population. Moreover, the CC genotype could be associated with elevated serum HDL-C levels.

Relevance Study on Cerebral Infarction and Resistin Gene Polymorphism in Chinese Han Population

Recent research on genome-wide associations has implicated that the serum resistin level and its gene polymorphism are associated with cerebral infarction (CI) morbidity and prognosis, and could thereby regulate CI. This study aimed to investigate the association between the resistin single nucleotide polymorphism (SNP) and the susceptibility to CI in the Chinese Han population. A total of 550 CI patients and 313 healthy controls were genotyped. Nine SNPs of the resistin gene previously shown were sequenced and assessed for an association with CI. The numbers of GG genotype carriers of rs3219175 and rs3486119 in the CI group were significantly higher than those in the control group among the middle-aged group (aged 45-65), at 76% vs 67.9% (P=0.025) and 75.5% vs 67.9% (P=0.031). rs3219175 and rs34861192 were associated with CI in the dominant and superdominant models according to the genetic model analysis (P<0.05). Meanwhile, there was strong linkage disequilibrium among the rs34124816, rs3219175, rs34861192, rs1862513, rs3745367, 180C/G and rs3745369 sites. In a haplotype analysis, the occurrence rate of the haplotype AGGCAGC was 1.97 times (P<0.05) higher in the patient group than in the control group. In addition, the numbers of GG genotype carriers of rs3219175 and rs3486119 in the middle-aged male CI patients and the middle-aged small artery occlusion (SAO) CI patients were higher than those in the control group (P<0.05). In the Chinese Han middle-aged population, the GG gene type carriers of the resistin gene sites rs3219175 and rs34861192 had a high risk for CI onset, especially in middle-aged male patients and SAO CI in all middle-aged patients.

Association of rs10811656 on 9P21.3 with the risk of coronary artery disease in a Chinese population

BACKGROUND

Genome-wide association studies have reported that the 9p21.3 locus confers risk for coronary artery disease (CAD). However, it is not known whether rs10811656 is linked with CAD in a Chinese population. Thus, the purpose of this study was to investigate the potential association between rs10811656 and the risk of CAD in a Chinese population.

METHODS

We conducted a hospital-based, case-control study with 251 CAD patients and 304 controls to examine the potential association of rs10811656 with CAD.

RESULTS

The frequencies of the TT genotypes in CAD cases were significantly different from those in controls (adjusted OR: 1.96, 95 % CI: 1.09-3.505, P = 0.024). Compared to controls, rs10811656 was significantly associated with the stable angina pectoris (adjusted OR: 1.42, 95 % CI: 1.06-1.90, P = 0.017), but not with acute coronary syndrome. There was also a highly significant association of rs10811656 with double-vessel and triple-vessel disease when patients were divided into subgroups based on the number of diseased vessels (adjusted OR: 1.68 and 1.60, 95 % CI: 1.14-2.44 and 1.10-2.33, P = 0.009 and 0.02, respectively).

CONCLUSION

Our results suggest that the rs10811656 locus might be associated with CAD in a Chinese Han population.

Enhanced discrimination of single nucleotide polymorphisms using 3' nucleotide differences in ligase detection reaction probes

The ligase detection reaction (LDR) is a highly specific genotyping method for single nucleotide variations. Although LDR typically discriminates single nucleotide polymorphism (SNP) alleles at the 3' end of so-called LDR discriminating probes, we designed probes in which the position of nucleotide differences for discrimination was shifted to the second and third nucleotides from the 3' end. Using the 3'-modified probes, we targeted SNPs of the human ABO group and investigated the specificity and efficiency of ligation by a universal LDR assay. We demonstrated that one or two nucleotide shifts of differences in discriminating probes improve the allele balance in detecting both base substitutions and short deletions. In regard to short deletions, moreover, the shifts of nucleotide differences in discriminating probes form the perfect-machted or multiple-mismatched structures (the bulge structures) in the discriminating probe-target DNA duplex and may contribute to enhance ligation efficiency.