Genotyping of 90 autosomal SNPs based on next generation sequencing / 中国法医学杂志

Objective To investigate the genetic polymorphism of 90 autosomal SNPs in Guangdong Han population and assess their value in forensic medicine based on next generation sequencing. Methods Blood samples were collected from 100 unrelated individuals. Through using AutoMate ExpressTM Nucleic Acid Extraction System, DNA was extracted. HID-Ion AmpliSeq? Identity Panel was applied for library preparation while Ion OneTouch? 2 system (OT2) was employed for emulsion PCR (emPCR). NGS was performed on the Ion PGM? system. Sequencing results were analysed using the Torrent Suite v4.4.2 with the HID_SNP_Genotyper v4.3.1 plugin. The forensic parameters were calculated and compared with GoldeneyeTM 20A systems. Results According to the Bonferroni correction, the genotypes of 90 autosomal SNPs were in accordance with Hardy-Weinberg equilibrium and no linkage disequilibrium was observed. The average Ho of 90 autosomal SNPs was 0.423, the average DP was 0.560 and the average PIC was 0.329. The CDP (cumulative power of discrimination) of 90 autosomal SNPs system was 1-1.20×10-33, which was greater than that of 20A System. The CPEtri (cumulative excluding probability of trio paternity) was 0.999 999 911 and the CPEduo (cumulative excluding probability of duo paternity) was 0.999 882. Both of these two parameters were below that of 20A System. Conclusion It suggested that the 90 autosomal SNPs System can be applied to forensic individual discrimination and trio paternity testing independently. Besides, it is supposed to be used in the duo paternity testing as an assistant measure.

Analysis of rare alleles of D13S325 falling in the range of adjacent locus / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To analyze the rare alleles of D13S325 locus which fell in the size range of D12S391 locus with the STRtyper-10G kit.</p><p><b>METHODS</b>Genotyping results of cases with suspected rare alleles of D13S325 were verified with Sinofiler(TM) kit and a singleplex amplification system. The rare alleles were separated and sequenced.</p><p><b>RESULTS</b>Five families were detected with rare alleles of the D13S325 locus, which were misread as allele 20 of D12S391 locus. The alleles were named as 5.1 based on DNA sequences and have a frequency of 0.156 × 10(-2).</p><p><b>CONCLUSION</b>As the rare allele 5.1 of D13S325 locus with the STRtyper-10G kit is prone to be mistyped, attention should be paid in the paternity testing, personal identification and DNA database search.</p>

Strategy of Conclusion-Making for Paternity Testing with Short Tandem Repeats Genotyping / 中山大学学报(医学科学版)

[Objective] To propose a criterion for making conclusions on paternity tests based on STR genotyping. [Method] To use binomial distribution formula to calculate minimal numbers of STR loci that must be tested for different scenarios in paternity testing. [ Results ] We proposed a set of criteria for making STR paternity testing conclusions. For triplet tests, concluded "paternity positive" for the following four cases when the cumulative paternity index (PI) was greater than 10 000: 1) no inconsistent STR locus was detected in 15 loci (PE > 0.571 4/locus) or 2) only one inconsistent STR locus was detected in 19 loci or 3) only two inconsistent STR loci were detected in 28 loci or 4) only three inconsistent STR loci were detected in 35 loci; otherwise, concluded "paternity negative" when at least four inconsistent STR loci had been detected. For single parent tests, concluded "paternity non-exclusive" for the following cases when the cumulative PI was greater than 10 000: 1) no inconsistent STR locus was detected in 18 loci (PE>0.411/locus) or 2) only one inconsistent STR locus was detected in 29 loci or 3) two inconsistent STR loci were detected in 41 loci; concluded "paternity negative" when three or more inconsistent loci were detected. [Conclusion] Our experience has proven that these criteria are robust in STR paternity testing.

Genetic Polymorphism Analysis of Nine Short Tandem Repeat Loci in Han Population of Southern China / 中山大学学报(医学科学版)

[Objective] To investigate the genetic polymorphism of nine short tandem repeat (STR) loci in Han population of Southern China.[Methods] The 9 STR loci (D11S2368,D12S391,D13S325,D18S1364,D22-GATA198B05,D6S1043,D2S1772,D7S3048,D8S1132) were amplified with STR＿Typer＿10＿v1 kit for 1619 unrelated individuals of Han population in Southern China.The PCR products were analyzed with 3100 genetic analyzer and GeneMapper ID 3.1v software.The forensic efficiency parameters were calculated by PowerState V12.xls and the Hardy-Weinberg equilibrium was tested with Arlequin 3.11v software.[Results] The genetic polymorphism of 9 STR loci in Han population of Southern China was quite high.The heterozygosities (H) ranged from 0.818 to 0.879.The match probabilities (MP) ranged from 0.031 to 0.063.The powers of discrimination (PD) ranged from 0.937 to 0.970,the probabilities of exclusion (PE) ranged from 0.632 to 0.753,the polymorphism information contents (PIC) ranged from 0.80 to 0.88 and the typical paternity indices (TPI) ranged from 2.74-4.13,respectively.These data were in accord with Hardy-Weinberg equilibrium (P ＞ 0.05).[Conclusion] Nine STR loci are highly polymorphic in Chinese Han population.They are new useful tools for paternity testing,individual identification,and for the research of human genetics and anthropology.

Linkage analysis of susceptibility genes for familial schizophrenia on chromosome 1 in Chinese population / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To explore the molecular genetic relationship between chromosome 1 and susceptibility genes for familial schizophrenia in Chinese population.</p><p><b>METHODS</b>A genome scanning was conducted in 32 multiplex pedigrees from Chinese population by using 29 microsatellite markers on chromosome 1.</p><p><b>RESULTS</b>Multipoint parametric analysis detected a maximum heterogenicity Lod of 1.70 at 262.52 cM under a recessive model; multipoint non-parametric analysis detected a maximum non-parameter linkage (NPL) of 1.71 (P=0.046) at 262.52 cM, then 1.37 (P=0.086) at 149.70 cM, corresponding to marker D1S206 and D1S425 respectively.</p><p><b>CONCLUSION</b>These results give further supports to the presence of susceptibility genes on chromosome 1q for familial schizophrenia.</p>

A linkage analysis of quantitative trait loci for familial schizophrenia on chromosome 1 / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To explore the molecular genetic relationship between chromosome 1 and quantitative trait loci for familial schizophrenia.</p><p><b>METHODS</b>A series of assessment scales included positive and negative syndrome scale (PANSS), global assessment of functional scale (GAFS), premorbid schizoid and schizotypal traits scale (PSST), premorbid social adjustment scale (PSA) were applied to quantify the phenotypes of schizophrenia. Non-parametric linkage analysis of quantitative traits was conducted in 32 multiplex pedigrees with schizophrenia by using 29 microsatellite makers on chromosome 1.</p><p><b>RESULTS</b>Haseman-Elston quantitative trait analysis detected a maximum Traditional H-E Lods of 1.73 and a maximum EH H-E Lods of 1.65 of negative symptoms (PANSS-N ) at 147.64 cM, which was overlapped to the positive region of 1q21-23 in qualitative linkage analysis.</p><p><b>CONCLUSION</b>The results suggest there might be an independent quantitative trait locus of negative symptoms on 1q21-23 for familial schizophrenia.</p>

A study of genetic polymorphisms of 11 Y chromosome specific STR loci / 中国法医学杂志

Objective To study the genetic polymorphisms of 11 Y chromosome specific STR loci in Guangzhou Han population. Method The DNA extracted from blood samples of unrelated individuals in Han population living in Guangzhou were amplified by PCR. The PCR products were analyzed by using PAGE. Results 3-5 alleles were detected in 11 Y - STR loci respectively in Han population in Guangzhou. The minimum GD value was 0.3037 (DYS434), while the maximum GD value was 0.8455 (DYS390) . Conclusion The 11 Y - specific STR loci are highly polymorphic and are suitable for personal identification and paternity testing.

Study on Optimal Conditions in Arbitrarily Primed PCR Human DNA Fingerprinting / 中山大学学报(医学科学版)

【Objective】To explore the optimal conditions in fingerprinting (APHDF).【Methods】The human DNA fingerprints were detected by APHDF.A pair of short primers was used for amplification.The experimental conditions including template,Mg2+,deoxyribonucleotides,and parameters of cycle,were optimized.【Results】The template DNA should be abstracted freshly and the concentration should be ranged from 50～550 mg/L.The best concentration of Mg2+was 5.0 mmol/L.The deoxyribonucleotides concentration was optimal at 0.2 mmol/L.The PCR cycling parameters were as follows :The denaturing temperatures,annealing temperatures and extension temperatures were 94 ℃ and 90 ℃ for 30 s,43 ℃ and 48 ℃ for 40 s or 50 s,and 72 ℃ for 1 min or 80 s,respectively.【Conclusion】The optimal conditions of the experiment are obtained,with good reproducibility and high specificity.Therefore,this method can be widely applied in practice.