Allelic frequencies for the HLA-DQA1, D1S80, HUMTHO1, HUMTPOX, HUMCSF1PO and HUMVWA loci in Cantabria (middle north Spain)

Allele frequencies for six DNA polymorphisms have been studied in a population sample from Cantabria (middle north Spain) using the polymerase chain reaction. The HLA-DQA1 locus was analyzed by the reverse dot-blot technique and the other five by polyacrylamide gel electrophoresis followed by silver staining. Six alleles were found for HLA-DQA1. 15 alleles for D1S80, 6 alleles for HUMTHO1 and HUMCSF1PO, 7 for HUMTPOX and 8 alleles for HUMVWA. The 21 repeat allele in HUMVWA had not previously been reported in a Spanish population. The genotype distributions met Hardy-Weinberg expectations for all the systems and some statistical parameters of forensic interest were calculated. Comparisons with other populations revealed significant differences for HLA-DQA1, HUMVWA and HUMTHO1, with interracial differences being more pronounced than between Spanish populations. The HUMVWA system showed the highest forensic efficiency of the six polymorphisms studied.     

Characterisation of variant alleles at the HumD21S11 locus implies unique Australasian genotypes and re-classification of nomenclature guidelines

Several variant alleles of the HumD21S11 locus have only been reported in Australasian population samples. Fifteen such alleles were observed in Caucasian and Australian Aborigine sub-population databases compiled from residents of the state of Western Australia. Each variant was sequenced to authenticate the allelic designation and determine the structural conformation. Nine novel structural variants are described. The structure of the repeat region of these rare alleles combined with the STR designation brings aspects of the HumD21S11 nomenclature guidelines into question, in particular the designation of common incomplete repeats (or "0.2's"). The conformation of the sequences provides evidence in support of a genetic relationship between the Australian Aborigine and the Papuan people.     

Analysis of AmpFlSTR MiniFiler™ loci and its forensic application

The allele frequencies of eight MiniFiler™ loci have been analyzed in 101 Japanese individuals living in Kanagawa with informed consent by means of ABI 310 Genetic Analyzer. A total of 7 alleles for D13S317, 8 alleles for D7S820, 11 alleles for D2S1338, 11 alleles for D21S11, 5 alleles for D16S539, 14 alleles for D18S51, 8 alleles for CSF1PO, and 13 alleles for FGA were observed. The polymorphic profiles of these MiniFiler™ loci in the present study were essentially the same as those obtained by using the AmpFlSTR^® Identifiler^® PCR Amplification kit. The combined matching probability of eight MiniFiler™ loci and cumulative probability of paternity exclusion were estimated as 1.97 × 10⁻¹⁰ and 0.9996, respectively. The MiniFiler™ kit was useful for individual identification in forensic analysis.     

A study of ten red cell enzymatic markers in the Naples' population. Report of a new GPT variant phenotype

A sample of the population of Naples has been examined for several red cell enzyme markers. About 2,000 newborn have been analyzed for ACP, GLO I, and UMPK; 1,000 of them were also analyzed for PepA and PepB, and 500 for PGM1 and PGM2. In addition about 400 school children have been typed for the PGD and PGP polymorphisms. The observed gene frequencies for the polymorphic systems are: ACPA = 0.293, ACPB = 0.667 and ACPC = 0.040; GLO1 = 0.372; GPT2 = 0.462; UMPK2 = 0.029; PGM21 = 0.279; PGDC = 0.037; PGP1 = 0.953, PGP2 = 0.038 and PGP3 = 0.009. Moreover during the screening of PepA, PepB and GPT markers, some rare alleles have been encountered, one of which, at the GPT locus, has never been reported before. We propose for it the name GPT10.     

Allele frequency distribution for 21 autosomal STR loci in Nepal

The allele frequency distributions of 21 autosomal loci contained in the AmpFlSTR Identifiler, the Powerplex 16 and the FFFL multiplex PCR kits, was studied in 953 unrelated individuals from Nepal. Several new alleles (i.e. not yet reported in the NIST Short Tandem Repeat DNA Internet DataBase [http://www.cstl.nist.gov/biotech/strbase/]) have been detected in the process.     

Sequence‐based Saudi population data for the SE33 locus

A set of 87 reference samples collected from the population of Saudi Arabia were sequenced using the ForenSeq™DNA Signature Prep Kit on a MiSeq FGx™. The FASTQ files contain the sequences of the SE33 STR, but are not reported by the ForenSeq™ Universal Analysis Software (UAS). The STRait Razor software was used to recover and to report SE33 sequence‐based data for the Saudi population. Ninety-six sequence-based alleles were recovered, most of which had previously reported motif patterns. Two unreported motif patterns found in three alleles and seven novel allele sequences were reported. We also reported a single discordance between the sequence-based data and the CE data that was due to the presence of a common TTTT deletion. SE33 had 130% more sequence-based alleles; the highest number of observed sequence variants were in alleles 27.2 and 30.2, which each had 7 sequence variants. The statistical parameters emphasize the usefulness of using the sequence-based data.     

Investigation into the usefulness of DNA profiling of earprints

DNA profiling of biological trace evidence has been used for many years. The application of this technique specifically to the DNA profiling of earprints has not to date been thoroughly investigated. This report presents the results of 60 earprints collected from three healthy adult volunteers under controlled laboratory conditions. DNA profile analysis revealed that high levels of non-donor alleles are observed when earprints are collected for DNA profiling. The source of these non-donor alleles is investigated and the impact that their presence within the profile may have on the use of this technique is discussed.     

Significant association of TH01 allele 9.3 and SIDS

Sudden infant death syndrome (SIDS) constitutes a considerable percentage of infant death of unknown etiology. Individual catecholamine response variation is suspected to play a role in SIDS. TH01 is a tetrameric short tandem repeat marker in the tyrosine hydroxylase gene, which regulates gene expression and catecholamine production with allele 9.3 exerting a particularly strong effect on noradrenaline production. We investigated in an age-controlled study the TH01 allele frequencies in 127 cases of SIDS and 406 control cases to assess whether in SIDS cases a distinct TH01 allele distribution could be determined as has been reported by a previous study. We found that genotypes containing one or two 9.3 alleles were significantly more frequent in SIDS patients (58.2%) than in control subjects (48.4%, p=0.038), whereas all other alleles were more frequent in the control subjects. Our findings support the notion that there exists a significant association between TH01 gene configuration and SIDS.     

pMCT118位点扩增片段长度多态性及其应用

本文报道了对98例中国人 pMCT118位点扩增片段长度多态性的等位基因频率调查及有关法医生物物证检验问题的研究。用多聚酶链反应、小型聚丙烯酰胺凝胶电泳和银染方法,在12h 内检测低至1ngDNA 的 pMCT118位点扩增片段长度多态性。已发现22个等位基因,大小分布在340～780bp 之间,基因频率为0.005～0.3,杂合度为79%。对6个家系22名相关个体的分析符合孟德尔定律。探讨了微量检材样品制备和对混合斑、单根毛囊、唾液等生物检材的法医应用。对20个实际案例进行了检验。     

Typing study of human semen DIA3 by isoelectric focusing--distribution in the Wuhan population, China

Human semen DIA3 typing was studied by isoelectric focusing on ultra-thin-layer polyacrylamide gel which resulted in a simpler and more definite separation of the products of DIA3 alleles than hitherto. In 198 semen samples collected from unrelated Chinese males four different phenotypes were observed. The DIA3 allele frequencies were calculated: DIA 3(1) = 0.7727, DIA 3(2) = 0.2172, DIA 3(3) = 0.0101. The results of the stability study of 12 laboratory-prepared semen stains stored at room temperature suggested that DIA3 in seminal strains is a relatively stable genetic marker. Our gene frequencies have been compared to those reported in other populations.     

Additional data on PGP genetic transmission in family groups

PGP (phosphoglycolate phosphatase, EC 3.1.3.18.) gentic studies were performed in 188 families including a total of 415 offspring in the Galician population. The results are in agreement with the formal hypothesis of three codominant alleles at an autosomal locus. No silent alleles have been observed.     

An experimental extension to the discrete Laplace method for Y-STR haplotype frequency estimation

Frequency estimation for Y-STR haplotypes is a challenging problem because limited data are available and complex dependencies exist within the data. As a result, various statistical methods have been proposed for frequency estimation. The discrete Laplace method has been recommended in some contexts by the DNA commission of the ISFG. This method is limited to haplotypes with single integer repeat alleles only at all loci. We propose a generalisation of the method that handles duplicated loci such as DYS385 and less common alleles that are not integer repeats. The extension is implemented in an experimental R package called disclapmix2.     

中国汉族人群15个STR基因座的等位基因频率调查

目的 调查10071名中国汉族无关个体15个STR基因座的等位基因的类型及其频率，并与以往相关文献报道的汉族群体资料进行统计比较。方法 应用PowerPlex~(TM)16荧光标记复合扩增系统，对10071份中国汉族无关个体的血样DNA进行15个STR基因座的复合扩增；用ABI 377或3100遗传分析仪对扩增产物进行分型，统计15个STR基因座的基因频率。结果 15个STR基因座共发现226个等位基因，频率在0.0001～0.5512；除D8S1179基因座外，其它基因座均发现稀有等位基因，数目1～7个不等，共34个。在中国汉族人群，稀有D21S11基因座的等位基因32.1和36.2，D18S51基因座的等位基因15.2和17.2，Penta E基因座的等位基因15.2、17.4、18.4、19.4、26和27，D7S820基因座的等位基因9.2、10.1、11.1和15，Penta D基因座的等位基因18、19和20，TPOX基因座的等位基因14，FGA基因座的等位基因13，以及较常见但欧洲稀有的D21S11基因座的等位基因30.3和D7S820基因座的等位基因9.1和9.2等均为首次报道。结论 大样本基因频率调查有利于观察STR基因座的稀有等位基因；本研究结果与以往相关文献报道的结果有不同程度的差异。     

Matching and partially-matching DNA profiles

The DNA profiles of two individuals can have 0, 1, or 2 pairs of alleles that are the same at each locus. These events may be called mismatches, partial matches or matches, respectively, and they have probabilities that depend on the population proportions of alleles as well as the population structure parameter theta. The observed and expected numbers of pairs of individuals with various numbers of matching or partially matching loci in FBI and Australian databases are found to be in good agreement provided theta is set equal to some small value greater than zero. The likelihood ratios for two individuals having a specified degree of relationship versus being unrelated also depend on the numbers of matching and partially matching loci, but even unrelated pairs of individuals can have likelihood ratios that support hypotheses of relatedness. Matching probabilities allow predictions to be made for the sizes of databases that are expected to contain a pair of individuals with high numbers of matching loci. It is very likely that two individuals with at least 9 matching loci among the 13 CODIS loci have already been typed.     

Genetic variation of 13 STR loci in the four endogamous tribal populations of Eastern India

We have analysed 13 autosomal STR loci in four endogamous tribal populations from two eastern states (Orissa and Nagaland) of India. The Gadaba, Kuvi Khond and Lotha Naga populations have not been analysed for microsatellite genetic variation previously. The allele frequencies for all loci are within the range observed in the geographical region and racial background, though some alleles showed greater variation. Departures from the Hardy-Weinberg equilibrium were tested by three methods and two loci (THO1 and TPOX) showed significant departures for all measures in Gadaba and Lotha Naga populations. The exclusion probability and discrimination probability were high for all analysed loci in all populations. There is no evidence for association of alleles among the STR loci studied. This allele frequency information will be useful for forensic, paternity and population genetic studies.     

Genotyping of five short tandem repeat loci via triplex and duplex PCR

We have developed a triplex PCR method for D3S1359, HumTH01 and HumTPO tetranucleotide loci and a duplex PCR method for HumFES/FPS and HumvWA31A tetranucleotide loci using high resolution polyacrylamide gel electrophoresis and silver staining. The methods were evaluated for paternity testing and individual identification and allele frequencies at these loci are reported for 189–3387 unrelated individuals in the Finnish population. The D3S1359 locus, especially, was found to be a highly informative locus. Seventeen alleles were found in the D3S1359 locus with a highest observed allele frequency of 0.199, a high exclusion power (PE) in paternity testing (0.78) and a high observed heterozygosity (0.89). The combined PE for these five loci was 0.99.     

Sequence variation in humans and other primates at six short tandem repeat loci used in forensic identity testing

A large number of alleles from the six different short tandem repeat (STR) loci FGA, D3S1358, vWA, CSF1PO, TPOX and TH01, used in human identity testing were sequenced to provide support for the robustness of fluorescent STR DNA typing by allele size. Sequence information for some of these loci (FGA, vWA, TH01) is an extension of published work, whereas no extensive sequence information is available with respect to the D3S1358, CSF1PO, and TPOX loci. Sequencing of alleles at each locus has provided quantitative data with respect to the true nucleotide length of common alleles, and of alleles that vary in length from the common alleles. All alleles that were identified as "off-ladder" alleles through fluorescent typing at these STR loci have proven to be true length variant alleles. Sequencing at the D3S1358 and CSF1PO loci allowed for the establishment of a common nomenclature for these loci. A correlation between percent stutter and the length of the core tandem repeat is demonstrated at the FGA locus. Alleles in which the core tandem repeat is interrupted by a repeat unit of different sequence have a reduced percent stutter. DNA samples from three non-human primates (chimpanzee, orangutan, and gorilla) were compared to the human sequences, and shown to differ markedly across loci with respect to their homology. The effects of primer binding site mutations on the amplification efficiency at a particular locus, and methods used to interpret amplification imbalance of heterozygous alleles at a locus is also addressed.     

Postmortem molecular screening for mutations in ryanodine receptor type 1 (RYR1) gene in psychiatric patients suspected of having died of neuroleptic malignant syndrome

Postmortem diagnosis of neuroleptic malignant syndrome (NMS) is difficult to perform, because the clinical symptoms just before death are not usually available. Malignant hyperthermia (MH) is a catastrophic, life-threatening hypermetabolic syndrome triggered by certain anesthetics. Ryanodine receptor type 1 (RYR1) gene mutations are known to be involved in susceptibility to MH. Similarities in clinical features, such as elevated body temperature, between NMS and MH have led to the suggestion that NMS is a neurogenic form of MH. In this study, we analyzed possible mutations of the RYR1 gene in 11 psychiatric patients suspected at autopsy to have died of NMS. All cases were suspected of having elevated body temperature at death, and their causes of death could not be determined by autopsy examinations. Two mutations (R4645Q and A612T) in the RYR1 gene were identified. The R4645Q mutation has previously been reported in MH patients, but five heterozygous mutations were also found in 400 Japanese control alleles. The other mutation was novel, and was not found in the same control alleles. The results of this study provide the first successful identification of RYR1 mutations in psychiatric patients suspected at autopsy of having died of NMS. However, the association between RYR1 gene mutations and cause of death in psychiatric patients suspected of dying of NMS remains unclear.     

Sequence analysis of STR polymorphisms at locus ACTBP2 in the Taiwanese population

A highly polymorphic sequence structure is reported in the human beta-actin related pseudogene 2 (ACTBP2) (SE33) locus in members of the Taiwanese Han population. A total of 100 unrelated members of the Taiwanese Han population were used in the study. Alleles that shared the same size but differ in their sequence are described to allow for inter laboratory sharing of data. PCR products amplified from this locus were separated by single-strand conformation polymorphism electrophoresis, the single-stranded DNA bands were excised from the gels, a second amplification performed, and then the PCR products were sequenced. All the alleles differed by either 2 or 4 bp. Sequence variations were observed as deletions or insertions in the repeat units AG (or AA) and AAAG. Additionally, transitions in the flanking regions were recorded. A total of 27 alleles with 71 associated genotypes were recorded if the alleles were defined by size, but 68 alleles with 88 associated genotypes were noted with the alleles were scored on the basis of sequence variation. The power of discrimination (Pd) of this single locus was 0.9874 making the human ACTBP2 a good alternative marker for individual identification and paternity testing.     

Sequence analysis of STR polymorphisms at locus ACTBP2 in the Taiwanese population

A highly polymorphic sequence structure is reported in the human beta-actin related pseudogene 2 (ACTBP2) (SE33) locus in members of the Taiwanese Han population. A total of 100 unrelated members of the Taiwanese Han population were used in the study. Alleles that shared the same size but differ in their sequence are described to allow for inter laboratory sharing of data. PCR products amplified from this locus were separated by single-strand conformation polymorphism electrophoresis, the single-stranded DNA bands were excised from the gels, a second amplification performed, and then the PCR products were sequenced. All the alleles differed by either 2 or 4 bp. Sequence variations were observed as deletions or insertions in the repeat units AG (or AA) and AAAG. Additionally, transitions in the flanking regions were recorded. A total of 27 alleles with 71 associated genotypes were recorded if the alleles were defined by size, but 68 alleles with 88 associated genotypes were noted with the alleles were scored on the basis of sequence variation. The power of discrimination (Pd) of this single locus was 0.9874 making the human ACTBP2 a good alternative marker for individual identification and paternity testing.