Association study of MC1R gene polymorphisms with freckles in Chinese Han population from Chengdu / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To assess the association between single nucleotide polymorphisms (SNPs) of melanocortin-1 receptor gene (MC1R) and freckles in Chinese Han population from Chengdu.</p><p><b>METHODS</b>Twenty randomly selected samples were used to select SNPs of the MC1R gene through DNA sequencing. Pyrosequencing in combination with DNA pooling technique was used to assess allelic frequencies of the selected SNPs in 111 individuals with freckles and 124 normal controls. Representative SNPs were selected based on their functional implications and minimum allele frequency (MAF> 0.05). Genotype of the SNPs were determined with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or pyrosequencing.</p><p><b>RESULTS</b>Based on results of DNA sequencing and pyrosequencing, 4 SNPs (rs2228479, rs885479, rs33932559 and rs2228478) were selected to determine the genotype for each sample. Comparison of genotypic and allelic frequencies of the 4 SNPs with χ (2) test has found no significant difference between the two groups (P> 0.05). For rs33932559, the frequencies of T allele were respectively 90.09% and 91.94% for individuals with freckles and normal controls. For rs2228479 and rs2228478, the frequencies of G and A allele were both about 77%. For rs885479, the frequency of T allele was about 60%. None of the above 3 SNPs showed a significant difference between the two groups in terms of allelic or genotypic frequencies.</p><p><b>CONCLUSION</b>No association between the selected SNPs of MC1R gene has been found with development of freckles for the selected Chinese Han population from Chengdu.</p>

The polymorphism of ten STR loci in Chinese Han population in Chengdu / 法医学杂志

OBJECTIVE@#To obtain data of polymorphism distribution of 10 short tandem repeat (STR) D1S2145, D3S2433, D5S1507, D5S2502, D8S2319, D9S926, D16S767, D17S2181, GATA140E03, GATA196B10 in Chinese Han population in Chengdu and to evaluate their usefulness in the field of forensic science and their species specificity.@*METHODS@#DNA of 100 unrelated individuals of Chengdu Han population was extracted with Chelex method, amplified by PCR, then typed with silver staining after polyacrylamide gel electrophoresis(PAGE). Ten different animals were selected as the controls in this study for evaluating the species specificity of the ten STR loci.@*RESULTS@#In the ten STR loci of Chengdu Han population, 6, 5, 8, 5, 6, 7, 7, 5, 7 and 7 alleles were found, respectively. 17, 14, 28, 15, 16, 18, 15, 14, 19 and 21 genotypes were observed in the ten loci, respectively. The allele and genotype frequency distributions of the ten loci were detected no deviation from the Hardy-Weinberg law of equilibrium. By comparison with the data from 10 different animals, the species specificity of D3S2433, D5S1507, D5S2502, D8S2319 and GATA196B10 was good, but part of animals had amplification product at typing field of the other loci.@*CONCLUSION@#The 10 STR loci mentioned above are highly polymorphic and can be used in the forensic personal identification and paternity testing.

Multiplexed mutagenically separated PCR assay for rapid detection of SNP loci in mitochondrial DNA coding region / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To develop a multiplexed mutagenically separated PCR (MS-PCR) for single nucleotide polymorphism (SNP) loci typing in mitochondrial DNA coding regions and to study the applications in investigating the allele frequencies and haplotypes of four SNP loci in mitochondrial DNA coding regions in Chinese Chengdu Han population.</p><p><b>METHODS</b>Four SNP loci C12705T, A8701G, G8584A and C10400T, two allele specific forward primer with 4 bases different in size and a common reverse primer were designed for SNP typing. The primers simultaneously were amplified in a single tube. The genotyping of SNPs was determined by the two allele specific fragments different in size after polyacrylamide gel and silver staining.</p><p><b>RESULTS</b>The different SNP loci comprised a single band with different size respectively. Typing results were completely consistent with those by direct sequencing. The allelic frequencies of C12705T, A8701G, G8584A and C10400T were 0.3813/0.6187, 0.4813/0.5187, 0.8250/0.1750 and 0.4938/0.5062 respectively. A total of 6 different haplotypes was identified and the genetic diversity reached 0.7137.</p><p><b>CONCLUSION</b>Multiplexed MS-PCR is a simple, rapid, accurate and efficient method for SNP typing, which will be very powerful for SNPs in the database establishing of mitochondrial DNA coding regions, the testing of forensic and population genetics research.</p>

Allele frequencies and species specificity of five short tandem repeat loci of Chinese Han population in Chengdu / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To obtain the data in polymorphism distribution of the five short tandem repeat (STR) loci: D18S979, D11S2014, D18S548, D1S1667 and GATA164F07 of Chinese Han population in Chengdu, and to evaluate their usefulness in the field of species specificity in forensic science.</p><p><b>METHODS</b>PCR, polyacrylamide gel electrophoresis (PAGE) and silver staining techniques were used to analyze the DNA samples from 100 unrelated individuals of Chinese Han ethnic group in Chengdu. Twelve different animals: monkey, pig, dog, bull, goat, chicken, duck, eel, mudfish, rabbit, guinea pig and mouse were selected as controls in this study for evaluating the species specificity of the five STR loci.</p><p><b>RESULTS</b>Six alleles and twelve genotypes were observed in D18S979. Five alleles and eleven genotypes were observed in D11S2014. Five alleles and thirteen genotypes were observed in D18S548. Seven alleles and nineteen genotypes were observed in D1S1667. Six alleles and fourteen genotypes were observed in GATA164F07. The genotype distributions of the five loci were analyzed by some related software and no deviation from the Hardy-Weinberg equilibrium was observed. Evaluated by way of using different animals as controls, monkey had amplification products at the extra-typing field of D18S979, D11S2014 and D1S1667. Bull, dog and eel had amplification product at typing field of D18S979, and pig, duck, mouse and rabbit had weak product. Bull had weak product at the typing field of D18S548. Dog, goat and eel had product at the typing field of D1S1667. Dog had weak product at the typing field of GATA164F07. Mudfish, chicken and guinea pig had no amplification product at the five loci.</p><p><b>CONCLUSION</b>These data indicate that D18S979, D18S548, D1S1667 and GATA164F07 are highly polymorphic and D11S2014, D18S548 and GATA164F07 can play a key role in species identification.</p>

Polymorphisms of seven short tandem repeat loci: D1S2142, D1S3733, D2S1774, D3S2459, D21S1409, D21S1437 and D21S2055 of Chinese Han population in Chengdu / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To obtain the data in polymorphism distribution of the seven short tandem repeat (STR) loci: D1S2142, D1S3733, D2S1774, D3S2459, D21S1409, D21S1437 and D21S2055 of Chinese Han population in Chengdu, and evaluate the polymorphism data usefulness to the forensic science.</p><p><b>METHODS</b>PCR, polyacrylamide gel electrophoresis (PAGE) and silver staining techniques were used to analyze the DNA samples from unrelated individuals of Chinese Han ethnic group in Chengdu.</p><p><b>RESULTS</b>Eleven alleles and twenty-three genotypes were observed in D1S2142. Eight alleles and nineteen genotypes were observed in D1S3733. Eight alleles and fifteen genotypes were observed in D2S1774. Seven alleles and nineteen genotypes were observed in D3S2459. Six alleles and twelve genotypes were observed in D21S1409. Nine alleles and twenty-six genotypes were observed in D21S1437. Twenty alleles and seventy-seven genotypes were observed in D21S2055. The genotype distributions of the seven STR loci showed no deviation from the Hardy-Weinberg equilibrium. The parentage testing of 50 cases revealed an autosomal codominant inheritances and no mutations happened to seven STR loci.</p><p><b>CONCLUSION</b>These data indicate that D1S2142, D1S3733, D2S1774, D3S2459, D21S1409, D21S1437 and D21S2055 have good polymorphism, with high probability of exclusion and probability of discrimination power as well as being loci available as the candidate genetic markers to forensic parentage testing and personal identification.</p>

Genetic polymorphisms of fifteen short tandem repeat loci in Chengdu Han population / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To acquire the population genetic data of fifteen short tandem repeat (STR) loci in Chengdu Han population.</p><p><b>METHODS</b>A total of 210 EDTA-blood specimens were collected from the unrelated individuals in Chengdu Han population. The DNA samples were extracted with Chelex method and amplified by multiplex PCR technique. The PCR products were analyzed by an automatic genetic analyzer; the relative fragment's lengths of PCR products were calculated by gene scan analysis software and afterward genotyped by genotype software.</p><p><b>RESULTS</b>Fifteen STR loci of the 210 samples showed a successful result of genotyping. The heterozygosities of the fifteen STR loci in Chengdu Han population were found to be 0.529-0.881; the combined exclusion probability and discrimination power for the fifteen STR loci in Chengdu Han population were determined to be 0.999998 and 7.3 x 10 (-17); respectively.</p><p><b>CONCLUSION</b>The distinct genotype of fifteen STR loci and the sex of sample could be unveiled just through PCR and electrophoresis once, and a higher measured value could be obtained for both the combined discrimination power and the exclusion probability; the fifteen STR loci can meet the needs of the parentage testing and personal identification in forensic medicine.</p>

Sequence polymorphisms of the mitochondrial DNA control region in 100 Chengdu Hans in China / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To study the genetic polymorphisms of the mitochondrial DNA (mtDNA) control region in Chengdu Han population.</p><p><b>METHODS</b>Sequence polymorphisms of the mtDNA control region, hypervariable regions I and II from 100 unrelated Chinese Hans were determined by PCR and direct sequencing.</p><p><b>RESULTS</b>Sequences of 404 nucleotides for hypervariable region I and 379 nucleotides for region II were obtained. Ninety-two and fifty variable sites were revealed in region I and region II respectively as compared to the reference sequence, and a total of 97 different genetic patterns from both the regions I and II were determined. The probability of identity was estimated at 1.84% for region I, 1.94% for region II, and 1.18% for both the regions.</p><p><b>CONCLUSION</b>These results suggest that sequence polymorphism of mtDNA control region would be very useful in forensic practice as a marker for individual identification.</p>

Study on the construction of standard D12S391 allelic ladder and its genetic polymorphism in six populations / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To resolve the problem of the accuracy and standardization of short tandem repeat-polymerase chain reaction (STR-PCR) typing in forensic practice, the authors have designed a new method of producing standard D12S391 allelic ladder.</p><p><b>METHODS</b>Nine different PCR amplified D12S391 allelic fragments were isolated from the gel, eluted into the distilled water and re-amplified by PCR. The purified allelic fragments were then blunt-end subcloned individually into the pUC plasmid vectors and transfected into competent E.coli DH5 alpha(TM) cells. The sequencing results confirmed that the size and the structure of the inserts were correct. The recombinant plasmids DNA with 9 inserts were then used as templates for PCR re-amplification to generate D12S391 standard ladder.</p><p><b>RESULTS</b>With the ladder, the authors studied the genetic polymorphisms of D12S391 locus in six populations (German, Japanese and Chinese south-western Han, northern Han, Weiwu'er and Hui populations), and the respective primary data in the six populations were obtained. D12S391 locus showed high polymorphism in all six populations, and its exclusion power and discrimination power are 0.609-0.786 and 0.940-0.952 respectively.</p><p><b>CONCLUSION</b>The results demonstrate that the standard ladder generated via this method is excellent, and D12S391 locus is robust for genetic research and forensic application.</p>

Study on the construction of standard D1S549 allelic ladder via molecular cloning and its genetic polymorphism in Chinese three populations / 法医学杂志

OBJECTIVE@#To resolve the problem of the accuracy and standardization of STR-PCR typing in forensic practice, we have designed a new method to produce standard D1S549 allelic ladder.@*METHODS@#Eight different PCR amplified D1S549 allelic fragments were isolated from the gel, eluted into the distilled water and re-amplified by PCR. The purified allelic fragments were then blunt-end subcloned individually into the pUC plasmid vectors and transfected into competent E. coli DH5 alpha cells.@*RESULTS@#The sequencing results confirmed that the size and the construe of the inserts were correct. The recombinant plasmids DNA with 8 inserts were then used as templates for re-amplification to generate D1S549 standard ladder, with which the genetic polymorphisms of D1S549 locus in Chinese Han population in chengdu, Hui population in Gansu and Wei population in Xinjiang were studied.@*CONCLUSION@#The results showed that the standard ladder made via this method is excellent, and D1S549 locus is robust for genetic research and forensic application.

Study on the construction of standard D12S375 allelic ladder and its genetic polymorphism in Chinese Han, Hui and Wei populations / 中国法医学杂志

s:To resolve the problem of the accuracy and standardization of STR PCR typing in forensic science practice,we have designed a new method to produce standard D12S375 allelic ladder.Seven different PCR amplified D12S375 allelic fragments were isolated from the gel,eluted into the distilled water and reamplified by PCR.The purified allelic fragments were then blunt end subcloned individually into the pUC plasmid vectors and transfected into competent E.coli DH5? TM cells.The sequencing results confirmed that the size and the constructure of the inserts were correct.The recombinant plasmids DNA with 7 inserts were then used as templates for reamplification to generate D12S375 standard ladder, with which the genetic polymorphisms of D12S375 locus in Chinese Han population in Chengdu,Hui population in Gansu and Wei population in Xinjiang were studied.